1 line
192 KiB
JSON
1 line
192 KiB
JSON
{"url": "http://mondego.ics.uci.edu/projects/SourcererCC/precision/TP-1.txt", "content": "$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/25479.java 191 202\n/home/jeff/BigCloneBench/sample/default/111615.java 181 189\n----------------------------------------\n public String visitClassType(ClassType type, Void p) {\n StringBuilder sb = new StringBuilder();\n sb.append(\"C{\");\n if (type.outerType != null) {\n sb.append(print(type.outerType));\n sb.append(\".\");\n }\n sb.append(type.name);\n if (type.typeArgs != null) sb.append(print(\"<\", type.typeArgs, \">\"));\n sb.append(\"}\");\n return sb.toString();\n }\n\n----------------------------------------\n public String visitClassSigType(ClassSigType type, Void p) {\n StringBuilder sb = new StringBuilder();\n sb.append(\"CS{\");\n if (type.typeParamTypes != null) sb.append(print(\"<\", type.typeParamTypes, \">\"));\n sb.append(print(type.superclassType));\n if (type.superinterfaceTypes != null) sb.append(print(\"i(\", type.superinterfaceTypes, \")\"));\n sb.append(\"}\");\n return sb.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1725393.java 1122 1133\n/home/jeff/BigCloneBench/sample/selected/1778922.java 1122 1133\n----------------------------------------\n protected boolean sameSenoneSequence(int[] ssid1, int[] ssid2) {\n if (ssid1.length == ssid2.length) {\n for (int i = 0; i < ssid1.length; i++) {\n if (ssid1[i] != ssid2[i]) {\n return false;\n }\n }\n return true;\n } else {\n return false;\n }\n }\n\n----------------------------------------\n protected boolean sameSenoneSequence(int[] ssid1, int[] ssid2) {\n if (ssid1.length == ssid2.length) {\n for (int i = 0; i < ssid1.length; i++) {\n if (ssid1[i] != ssid2[i]) {\n return false;\n }\n }\n return true;\n } else {\n return false;\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/1297.java 56 63\n/home/jeff/BigCloneBench/sample/default/54578.java 56 63\n----------------------------------------\n private static void add(Configuration cfg, String s) {\n int pos = s.indexOf('=');\n if (pos == -1) {\n cfg.put(s, \"\");\n } else {\n cfg.put(s.substring(0, pos), s.substring(pos + 1));\n }\n }\n\n----------------------------------------\n private static void add(Configuration cfg, String s) {\n int pos = s.indexOf('=');\n if (pos == -1) {\n cfg.put(s, \"\");\n } else {\n cfg.put(s.substring(0, pos), s.substring(pos + 1));\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2638229.java 91 96\n/home/jeff/BigCloneBench/sample/selected/2001558.java 27 32\n----------------------------------------\n public static TsHandler getInstance() {\n if (instance == null) {\n instance = new TsHandler();\n }\n return instance;\n }\n\n----------------------------------------\n public static synchronized UserService getInstance() {\n if (instance == null) {\n instance = new UserService();\n }\n return instance;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/6320.java 297 306\n/home/jeff/BigCloneBench/sample/default/19573.java 297 306\n----------------------------------------\n public void query() throws IOException, TransformerConfigurationException {\n SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance();\n Templates xslt = loadDcmDirXSL(tf);\n DirReader reader = fact.newDirReader(dirFile);\n try {\n query(\"\", 1, 0, reader.getFirstRecordBy(null, keys, ignoreCase), tf, xslt);\n } finally {\n reader.close();\n }\n }\n\n----------------------------------------\n public void query() throws IOException, TransformerConfigurationException {\n SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance();\n Templates xslt = loadDcmDirXSL(tf);\n DirReader reader = fact.newDirReader(dirFile);\n try {\n query(\"\", 1, 0, reader.getFirstRecordBy(null, keys, ignoreCase), tf, xslt);\n } finally {\n reader.close();\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/114239.java 1532 1546\n/home/jeff/BigCloneBench/sample/default/59932.java 1006 1019\n----------------------------------------\n public void test124() throws Exception {\n byte[] buffer;\n ByteArrayOutputStream stream = new ByteArrayOutputStream();\n CsvWriter writer = new CsvWriter(stream, ',', Charset.forName(\"ISO-8859-1\"));\n writer.setRecordDelimiter(';');\n writer.setUseTextQualifier(false);\n writer.setEscapeMode(CsvWriter.ESCAPE_MODE_BACKSLASH);\n writer.write(\"1;2\");\n writer.endRecord();\n writer.close();\n buffer = stream.toByteArray();\n stream.close();\n String data = Charset.forName(\"ISO-8859-1\").decode(ByteBuffer.wrap(buffer)).toString();\n Assert.assertEquals(\"1\\\\;2;\", data);\n }\n\n----------------------------------------\n public void test56() throws Exception {\n byte[] buffer;\n ByteArrayOutputStream stream = new ByteArrayOutputStream();\n CsvWriter writer = new CsvWriter(stream, '\\t', Charset.forName(\"ISO-8859-1\"));\n writer.write(\"1,2\");\n writer.write(\"3\");\n writer.write(\"blah \\\"some stuff in quotes\\\"\");\n writer.endRecord();\n writer.close();\n buffer = stream.toByteArray();\n stream.close();\n String data = Charset.forName(\"ISO-8859-1\").decode(ByteBuffer.wrap(buffer)).toString();\n Assert.assertEquals(\"1,2\\t3\\t\\\"blah \\\"\\\"some stuff in quotes\\\"\\\"\\\"\\r\\n\", data);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/67669.java 168 184\n/home/jeff/BigCloneBench/sample/default/106112.java 187 203\n----------------------------------------\n public void test5() throws Exception {\n String data = \"1\\n2\";\n CsvReader reader = CsvReader.parse(data);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"1\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"1\", reader.getRawRecord());\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"2\", reader.get(0));\n Assert.assertEquals(1L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"2\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n Assert.assertEquals(\"\", reader.getRawRecord());\n reader.close();\n }\n\n----------------------------------------\n public void test6() throws Exception {\n String data = \"1\\r\\n2\";\n CsvReader reader = CsvReader.parse(data);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"1\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"1\", reader.getRawRecord());\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"2\", reader.get(0));\n Assert.assertEquals(1L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"2\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n Assert.assertEquals(\"\", reader.getRawRecord());\n reader.close();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2202740.java 153 183\n/home/jeff/BigCloneBench/sample/selected/225359.java 151 181\n----------------------------------------\n private boolean _jspx_meth_html_005flink_005f0(PageContext _jspx_page_context) throws Throwable {\n PageContext pageContext = _jspx_page_context;\n JspWriter out = _jspx_page_context.getOut();\n org.apache.struts.taglib.html.LinkTag _jspx_th_html_005flink_005f0 = (org.apache.struts.taglib.html.LinkTag) _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.get(org.apache.struts.taglib.html.LinkTag.class);\n _jspx_th_html_005flink_005f0.setPageContext(_jspx_page_context);\n _jspx_th_html_005flink_005f0.setParent(null);\n _jspx_th_html_005flink_005f0.setStyleId(\"incluir\");\n _jspx_th_html_005flink_005f0.setHref(\"login.do\");\n int _jspx_eval_html_005flink_005f0 = _jspx_th_html_005flink_005f0.doStartTag();\n if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.SKIP_BODY) {\n if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.EVAL_BODY_INCLUDE) {\n out = _jspx_page_context.pushBody();\n _jspx_th_html_005flink_005f0.setBodyContent((javax.servlet.jsp.tagext.BodyContent) out);\n _jspx_th_html_005flink_005f0.doInitBody();\n }\n do {\n out.write(\"In\u00edcio\");\n int evalDoAfterBody = _jspx_th_html_005flink_005f0.doAfterBody();\n if (evalDoAfterBody != javax.servlet.jsp.tagext.BodyTag.EVAL_BODY_AGAIN) break;\n } while (true);\n if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.EVAL_BODY_INCLUDE) {\n out = _jspx_page_context.popBody();\n }\n }\n if (_jspx_th_html_005flink_005f0.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) {\n _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.reuse(_jspx_th_html_005flink_005f0);\n return true;\n }\n _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.reuse(_jspx_th_html_005flink_005f0);\n return false;\n }\n\n----------------------------------------\n private boolean _jspx_meth_html_005flink_005f0(PageContext _jspx_page_context) throws Throwable {\n PageContext pageContext = _jspx_page_context;\n JspWriter out = _jspx_page_context.getOut();\n org.apache.struts.taglib.html.LinkTag _jspx_th_html_005flink_005f0 = (org.apache.struts.taglib.html.LinkTag) _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.get(org.apache.struts.taglib.html.LinkTag.class);\n _jspx_th_html_005flink_005f0.setPageContext(_jspx_page_context);\n _jspx_th_html_005flink_005f0.setParent(null);\n _jspx_th_html_005flink_005f0.setStyleId(\"incluir\");\n _jspx_th_html_005flink_005f0.setHref(\"login.do\");\n int _jspx_eval_html_005flink_005f0 = _jspx_th_html_005flink_005f0.doStartTag();\n if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.SKIP_BODY) {\n if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.EVAL_BODY_INCLUDE) {\n out = _jspx_page_context.pushBody();\n _jspx_th_html_005flink_005f0.setBodyContent((javax.servlet.jsp.tagext.BodyContent) out);\n _jspx_th_html_005flink_005f0.doInitBody();\n }\n do {\n out.write(\"In\u00edcio\");\n int evalDoAfterBody = _jspx_th_html_005flink_005f0.doAfterBody();\n if (evalDoAfterBody != javax.servlet.jsp.tagext.BodyTag.EVAL_BODY_AGAIN) break;\n } while (true);\n if (_jspx_eval_html_005flink_005f0 != javax.servlet.jsp.tagext.Tag.EVAL_BODY_INCLUDE) {\n out = _jspx_page_context.popBody();\n }\n }\n if (_jspx_th_html_005flink_005f0.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) {\n _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.reuse(_jspx_th_html_005flink_005f0);\n return true;\n }\n _005fjspx_005ftagPool_005fhtml_005flink_005fstyleId_005fhref.reuse(_jspx_th_html_005flink_005f0);\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/939512.java 85 90\n/home/jeff/BigCloneBench/sample/selected/1656760.java 328 333\n----------------------------------------\n private org.omg.CORBA.portable.OutputStream _OB_att_get_MyChannel(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) {\n EventChannel _ob_r = MyChannel();\n org.omg.CORBA.portable.OutputStream out = handler.createReply();\n EventChannelHelper.write(out, _ob_r);\n return out;\n }\n\n----------------------------------------\n private org.omg.CORBA.portable.OutputStream _OB_op_remove_all_filters(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) {\n org.omg.CORBA.portable.OutputStream out = null;\n remove_all_filters();\n out = handler.createReply();\n return out;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/70505.java 524 546\n/home/jeff/BigCloneBench/sample/default/103146.java 629 646\n----------------------------------------\n private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveSeries(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeSeries(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/497716.java 267 277\n/home/jeff/BigCloneBench/sample/selected/522719.java 320 330\n----------------------------------------\n public static int nullSafeHashCode(Object[] array) {\n if (array == null) {\n return 0;\n }\n int hash = INITIAL_HASH;\n int arraySize = array.length;\n for (int i = 0; i < arraySize; i++) {\n hash = MULTIPLIER * hash + nullSafeHashCode(array[i]);\n }\n return hash;\n }\n\n----------------------------------------\n public static int nullSafeHashCode(float[] array) {\n if (array == null) {\n return 0;\n }\n int hash = INITIAL_HASH;\n int arraySize = array.length;\n for (int i = 0; i < arraySize; i++) {\n hash = MULTIPLIER * hash + hashCode(array[i]);\n }\n return hash;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1169293.java 339 364\n/home/jeff/BigCloneBench/sample/selected/69355.java 228 253\n----------------------------------------\n public boolean Great(Float x) {\n long e1 = m_E;\n long e2 = x.m_E;\n long v1 = m_Val;\n long v2 = x.m_Val;\n while (e1 != e2) {\n if (e1 > e2) {\n if (Math.abs(v1) < maxLimit) {\n v1 *= 10;\n e1--;\n } else {\n v2 /= 10;\n e2++;\n }\n } else if (e1 < e2) {\n if (Math.abs(v2) < maxLimit) {\n v2 *= 10;\n e2--;\n } else {\n v1 /= 10;\n e1++;\n }\n }\n }\n return v1 > v2;\n }\n\n----------------------------------------\n public boolean Great(Float x) {\n long e1 = m_E;\n long e2 = x.m_E;\n long v1 = m_Val;\n long v2 = x.m_Val;\n while (e1 != e2) {\n if (e1 > e2) {\n if (Math.abs(v1) < Long.MAX_VALUE / 100) {\n v1 *= 10;\n e1--;\n } else {\n v2 /= 10;\n e2++;\n }\n } else if (e1 < e2) {\n if (Math.abs(v2) < Long.MAX_VALUE / 100) {\n v2 *= 10;\n e2--;\n } else {\n v1 /= 10;\n e1++;\n }\n }\n }\n return v1 > v2;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2576682.java 8 39\n/home/jeff/BigCloneBench/sample/selected/871670.java 12 42\n----------------------------------------\n public boolean download(String address, String localFileName) {\n OutputStream out = null;\n URLConnection conn = null;\n InputStream in = null;\n try {\n URL url = new URL(address);\n out = new BufferedOutputStream(new FileOutputStream(localFileName));\n conn = url.openConnection();\n in = conn.getInputStream();\n byte[] buffer = new byte[1024];\n int numRead;\n long numWritten = 0;\n while ((numRead = in.read(buffer)) != -1) {\n out.write(buffer, 0, numRead);\n numWritten += numRead;\n }\n return true;\n } catch (Exception exception) {\n exception.printStackTrace();\n } finally {\n try {\n if (in != null) {\n in.close();\n }\n if (out != null) {\n out.close();\n }\n } catch (IOException ioe) {\n }\n }\n return false;\n }\n\n----------------------------------------\n public static void download(String address, String localFileName) {\n OutputStream out = null;\n URLConnection conn = null;\n InputStream in = null;\n try {\n URL url = new URL(address);\n out = new BufferedOutputStream(new FileOutputStream(localFileName));\n conn = url.openConnection();\n in = conn.getInputStream();\n byte[] buffer = new byte[1024];\n int numRead;\n long numWritten = 0;\n while ((numRead = in.read(buffer)) != -1) {\n out.write(buffer, 0, numRead);\n numWritten += numRead;\n }\n System.out.println(localFileName + \"\\t\" + numWritten);\n } catch (Exception exception) {\n exception.printStackTrace();\n } finally {\n try {\n if (in != null) {\n in.close();\n }\n if (out != null) {\n out.close();\n }\n } catch (IOException ioe) {\n }\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/124923.java 1041 1055\n/home/jeff/BigCloneBench/sample/default/102869.java 1138 1153\n----------------------------------------\n public void test58() throws Exception {\n byte[] buffer;\n ByteArrayOutputStream stream = new ByteArrayOutputStream();\n CsvWriter writer = new CsvWriter(stream, '\\t', Charset.forName(\"ISO-8859-1\"));\n writer.write(\"data\\r\\nmore data\");\n writer.write(\" 3\\t\", false);\n writer.write(\" 3\\t\");\n writer.write(\" 3\\t\", true);\n writer.endRecord();\n writer.close();\n buffer = stream.toByteArray();\n stream.close();\n String data = Charset.forName(\"ISO-8859-1\").decode(ByteBuffer.wrap(buffer)).toString();\n Assert.assertEquals(\"\\\"data\\r\\nmore data\\\"\\t3\\t3\\t\\\" 3\\t\\\"\\r\\n\", data);\n }\n\n----------------------------------------\n public void test74() throws Exception {\n byte[] buffer;\n ByteArrayOutputStream stream = new ByteArrayOutputStream();\n CsvWriter writer = new CsvWriter(stream, ',', Charset.forName(\"ISO-8859-1\"));\n writer.setEscapeMode(CsvWriter.ESCAPE_MODE_BACKSLASH);\n writer.setUseTextQualifier(false);\n writer.write(\"1,2\");\n writer.write(\"3\");\n writer.write(\"blah \\\"some stuff in quotes\\\"\");\n writer.endRecord();\n writer.close();\n buffer = stream.toByteArray();\n stream.close();\n String data = Charset.forName(\"ISO-8859-1\").decode(ByteBuffer.wrap(buffer)).toString();\n Assert.assertEquals(\"1\\\\,2,3,blah \\\"some stuff in quotes\\\"\\r\\n\", data);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/73115.java 121 131\n/home/jeff/BigCloneBench/sample/default/73188.java 121 131\n----------------------------------------\n Converter(SkinProperty[] allProps, Hashtable romizedProps) {\n this.allProps = new Hashtable();\n for (int i = 0; i < allProps.length; ++i) {\n SkinProperty p = allProps[i];\n this.allProps.put(p.name, p);\n }\n this.allPropsArray = allProps;\n this.romizedProps = romizedProps;\n this.missingProps = new Vector();\n this.unknownProps = new Vector();\n }\n\n----------------------------------------\n Converter(SkinProperty[] allProps, Hashtable romizedProps) {\n this.allProps = new Hashtable();\n for (int i = 0; i < allProps.length; ++i) {\n SkinProperty p = allProps[i];\n this.allProps.put(p.name, p);\n }\n this.allPropsArray = allProps;\n this.romizedProps = romizedProps;\n this.missingProps = new Vector();\n this.unknownProps = new Vector();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/57136.java 215 226\n/home/jeff/BigCloneBench/sample/default/73101.java 200 214\n----------------------------------------\n public void execute(String[] args, int offset) throws InterruptedException, IOException, GeneralSecurityException {\n switch(mode) {\n case ECHO:\n echo();\n break;\n case SEND:\n send(args, offset);\n break;\n default:\n throw new RuntimeException(\"Illegal mode: \" + mode);\n }\n }\n\n----------------------------------------\n public void execute(String[] args, int offset) throws InterruptedException, IOException, GeneralSecurityException {\n switch(mode) {\n case ECHO:\n echo();\n break;\n case SEND:\n send(args, offset);\n break;\n case POLL:\n poll();\n break;\n default:\n throw new RuntimeException(\"Illegal mode: \" + mode);\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/6937.java 509 520\n/home/jeff/BigCloneBench/sample/default/132787.java 509 520\n----------------------------------------\n private void doRemove(DirWriter w, int[] counter, boolean delFiles) throws IOException {\n for (DirRecord rec = w.getFirstRecord(true); rec != null; rec = rec.getNextSibling(true)) {\n if (patientIDs.contains(rec.getDataset().getString(Tags.PatientID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n counter[1] += w.remove(rec);\n } else if (doRemoveStudy(w, rec, counter, delFiles)) {\n counter[1] += w.remove(rec);\n }\n }\n }\n\n----------------------------------------\n private void doRemove(DirWriter w, int[] counter, boolean delFiles) throws IOException {\n for (DirRecord rec = w.getFirstRecord(true); rec != null; rec = rec.getNextSibling(true)) {\n if (patientIDs.contains(rec.getDataset().getString(Tags.PatientID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n counter[1] += w.remove(rec);\n } else if (doRemoveStudy(w, rec, counter, delFiles)) {\n counter[1] += w.remove(rec);\n }\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/51387.java 43 52\n/home/jeff/BigCloneBench/sample/default/122700.java 43 52\n----------------------------------------\n public void testCommas() {\n String sequence = \"1,2,3,4,5\";\n assertEquals(sequence, sequenceUsingDo(1, 5));\n assertEquals(sequence, sequenceUsingFor(1, 5));\n assertEquals(sequence, sequenceUsingWhile(1, 5));\n sequence = \"8\";\n assertEquals(sequence, sequenceUsingDo(8, 8));\n assertEquals(sequence, sequenceUsingFor(8, 8));\n assertEquals(sequence, sequenceUsingWhile(8, 8));\n }\n\n----------------------------------------\n public void testCommas() {\n String sequence = \"1,2,3,4,5\";\n assertEquals(sequence, sequenceUsingDo(1, 5));\n assertEquals(sequence, sequenceUsingFor(1, 5));\n assertEquals(sequence, sequenceUsingWhile(1, 5));\n sequence = \"8\";\n assertEquals(sequence, sequenceUsingDo(8, 8));\n assertEquals(sequence, sequenceUsingFor(8, 8));\n assertEquals(sequence, sequenceUsingWhile(8, 8));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/18466.java 401 406\n/home/jeff/BigCloneBench/sample/default/33571.java 379 384\n----------------------------------------\n private void doOverwrite(Dataset ds) {\n for (Iterator it = overwrite.iterator(); it.hasNext(); ) {\n DcmElement el = (DcmElement) it.next();\n ds.putXX(el.tag(), el.vr(), el.getByteBuffer());\n }\n }\n\n----------------------------------------\n private void doOverwrite(Dataset ds) {\n for (Iterator it = overwrite.iterator(); it.hasNext(); ) {\n DcmElement el = (DcmElement) it.next();\n ds.putXX(el.tag(), el.vr(), el.getByteBuffer());\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/10101.java 640 645\n/home/jeff/BigCloneBench/sample/default/41669.java 519 524\n----------------------------------------\n public String _getFileNameRoot() {\n if (0 < writer__iFileNameRoots.length) {\n return writer__iFileNameRoots[writer__iCurrentFileIndex];\n }\n return \"\";\n }\n\n----------------------------------------\n public String _getFileNameRoot() {\n if (0 < writer__iFileNameRoots.length) {\n return writer__iFileNameRoots[writer__iCurrentFileIndex];\n }\n return \"\";\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2213635.java 61 66\n/home/jeff/BigCloneBench/sample/selected/1138251.java 45 50\n----------------------------------------\n private org.omg.CORBA.portable.OutputStream _OB_att_get_MyAdmin(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) {\n SupplierAdmin _ob_r = MyAdmin();\n org.omg.CORBA.portable.OutputStream out = handler.createReply();\n SupplierAdminHelper.write(out, _ob_r);\n return out;\n }\n\n----------------------------------------\n private org.omg.CORBA.portable.OutputStream _OB_att_get_supports_dynamic_properties(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) {\n boolean _ob_r = supports_dynamic_properties();\n org.omg.CORBA.portable.OutputStream out = handler.createReply();\n out.write_boolean(_ob_r);\n return out;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/124021.java 8 31\n/home/jeff/BigCloneBench/sample/default/50984.java 14 37\n----------------------------------------\n public static void doVersionCheck(View view) {\n view.showWaitCursor();\n try {\n URL url = new URL(jEdit.getProperty(\"version-check.url\"));\n InputStream in = url.openStream();\n BufferedReader bin = new BufferedReader(new InputStreamReader(in));\n String line;\n String version = null;\n String build = null;\n while ((line = bin.readLine()) != null) {\n if (line.startsWith(\".version\")) version = line.substring(8).trim(); else if (line.startsWith(\".build\")) build = line.substring(6).trim();\n }\n bin.close();\n if (version != null && build != null) {\n if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else {\n GUIUtilities.message(view, \"version-check\" + \".up-to-date\", new String[0]);\n }\n }\n } catch (IOException e) {\n String[] args = { jEdit.getProperty(\"version-check.url\"), e.toString() };\n GUIUtilities.error(view, \"read-error\", args);\n }\n view.hideWaitCursor();\n }\n\n----------------------------------------\n public static void doVersionCheck(View view) {\n view.showWaitCursor();\n try {\n URL url = new URL(jEdit.getProperty(\"version-check.url\"));\n InputStream in = url.openStream();\n BufferedReader bin = new BufferedReader(new InputStreamReader(in));\n String line;\n String version = null;\n String build = null;\n while ((line = bin.readLine()) != null) {\n if (line.startsWith(\".version\")) version = line.substring(8).trim(); else if (line.startsWith(\".build\")) build = line.substring(6).trim();\n }\n bin.close();\n if (version != null && build != null) {\n if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else {\n GUIUtilities.message(view, \"version-check\" + \".up-to-date\", new String[0]);\n }\n }\n } catch (IOException e) {\n String[] args = { jEdit.getProperty(\"version-check.url\"), e.toString() };\n GUIUtilities.error(view, \"read-error\", args);\n }\n view.hideWaitCursor();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/238734.java 462 477\n/home/jeff/BigCloneBench/sample/selected/967656.java 308 324\n----------------------------------------\n private boolean _jspx_meth_html_005fhidden_005f3(javax.servlet.jsp.tagext.JspTag _jspx_th_html_005fform_005f0, PageContext _jspx_page_context) throws Throwable {\n PageContext pageContext = _jspx_page_context;\n JspWriter out = _jspx_page_context.getOut();\n org.apache.struts.taglib.html.HiddenTag _jspx_th_html_005fhidden_005f3 = (org.apache.struts.taglib.html.HiddenTag) _005fjspx_005ftagPool_005fhtml_005fhidden_005fstyleId_005fproperty_005fnobody.get(org.apache.struts.taglib.html.HiddenTag.class);\n _jspx_th_html_005fhidden_005f3.setPageContext(_jspx_page_context);\n _jspx_th_html_005fhidden_005f3.setParent((javax.servlet.jsp.tagext.Tag) _jspx_th_html_005fform_005f0);\n _jspx_th_html_005fhidden_005f3.setProperty(\"idProcedimento\");\n _jspx_th_html_005fhidden_005f3.setStyleId(\"idProcedimento\");\n int _jspx_eval_html_005fhidden_005f3 = _jspx_th_html_005fhidden_005f3.doStartTag();\n if (_jspx_th_html_005fhidden_005f3.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) {\n _005fjspx_005ftagPool_005fhtml_005fhidden_005fstyleId_005fproperty_005fnobody.reuse(_jspx_th_html_005fhidden_005f3);\n return true;\n }\n _005fjspx_005ftagPool_005fhtml_005fhidden_005fstyleId_005fproperty_005fnobody.reuse(_jspx_th_html_005fhidden_005f3);\n return false;\n }\n\n----------------------------------------\n private boolean _jspx_meth_html_005ftext_005f2(javax.servlet.jsp.tagext.JspTag _jspx_th_html_005fform_005f0, PageContext _jspx_page_context) throws Throwable {\n PageContext pageContext = _jspx_page_context;\n JspWriter out = _jspx_page_context.getOut();\n org.apache.struts.taglib.html.TextTag _jspx_th_html_005ftext_005f2 = (org.apache.struts.taglib.html.TextTag) _005fjspx_005ftagPool_005fhtml_005ftext_005fstyleId_005fsize_005fproperty_005fnobody.get(org.apache.struts.taglib.html.TextTag.class);\n _jspx_th_html_005ftext_005f2.setPageContext(_jspx_page_context);\n _jspx_th_html_005ftext_005f2.setParent((javax.servlet.jsp.tagext.Tag) _jspx_th_html_005fform_005f0);\n _jspx_th_html_005ftext_005f2.setProperty(\"paciente\");\n _jspx_th_html_005ftext_005f2.setStyleId(\"paciente\");\n _jspx_th_html_005ftext_005f2.setSize(\"50\");\n int _jspx_eval_html_005ftext_005f2 = _jspx_th_html_005ftext_005f2.doStartTag();\n if (_jspx_th_html_005ftext_005f2.doEndTag() == javax.servlet.jsp.tagext.Tag.SKIP_PAGE) {\n _005fjspx_005ftagPool_005fhtml_005ftext_005fstyleId_005fsize_005fproperty_005fnobody.reuse(_jspx_th_html_005ftext_005f2);\n return true;\n }\n _005fjspx_005ftagPool_005fhtml_005ftext_005fstyleId_005fsize_005fproperty_005fnobody.reuse(_jspx_th_html_005ftext_005f2);\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/682167.java 160 192\n/home/jeff/BigCloneBench/sample/selected/682167.java 194 226\n----------------------------------------\n public static String stripTags(String in, boolean stripBRTag) {\n if (in == null) return null;\n char ch;\n int i = 0;\n int last = 0;\n char[] input = in.toCharArray();\n int len = input.length;\n StringBuilder out = new StringBuilder((int) (len * 1.3));\n for (; i < len; i++) {\n ch = input[i];\n if (ch > '>') {\n } else if (ch == '<') {\n if (!stripBRTag && i + 3 < len && input[i + 1] == 'b' && input[i + 2] == 'r' && input[i + 3] == '>') {\n i += 3;\n continue;\n }\n if (i > last) {\n if (last > 0) out.append(\" \");\n out.append(input, last, i - last);\n }\n last = i + 1;\n } else if (ch == '>') {\n last = i + 1;\n }\n }\n if (last == 0) {\n return in;\n }\n if (i > last) {\n out.append(input, last, i - last);\n }\n return out.toString();\n }\n\n----------------------------------------\n public static String escapeHTMLTags(String in) {\n if (in == null) return null;\n char ch;\n int i = 0;\n int last = 0;\n char[] input = in.toCharArray();\n int len = input.length;\n StringBuilder out = new StringBuilder((int) (len * 1.3));\n for (; i < len; i++) {\n ch = input[i];\n if (ch > '>') {\n } else if (ch == '<') {\n if (i > last) out.append(input, last, i - last);\n last = i + 1;\n out.append(LT_ENCODE);\n } else if (ch == '>') {\n if (i > last) out.append(input, last, i - last);\n last = i + 1;\n out.append(GT_ENCODE);\n } else if (ch == '\"') {\n if (i > last) out.append(input, last, i - last);\n last = i + 1;\n out.append(QUOTE_ENCODE);\n }\n }\n if (last == 0) {\n return in;\n }\n if (i > last) {\n out.append(input, last, i - last);\n }\n return out.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/24546.java 667 685\n/home/jeff/BigCloneBench/sample/default/94821.java 662 680\n----------------------------------------\n private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n File file = w.getRefFile(rec.getRefFileIDs());\n if (!file.exists()) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n File file = w.getRefFile(rec.getRefFileIDs());\n if (!file.exists()) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/31509.java 253 269\n/home/jeff/BigCloneBench/sample/default/111936.java 231 247\n----------------------------------------\n public void echo() throws InterruptedException, IOException, GeneralSecurityException {\n long t1 = System.currentTimeMillis();\n int count = 0;\n for (int i = 0; i < repeatWhole; ++i) {\n ActiveAssociation active = openAssoc();\n if (active != null) {\n if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) {\n log.error(messages.getString(\"noPCEcho\"));\n } else for (int j = 0; j < repeatSingle; ++j, ++count) {\n active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null);\n }\n active.release(true);\n }\n }\n long dt = System.currentTimeMillis() - t1;\n log.info(MessageFormat.format(messages.getString(\"echoDone\"), new Object[] { new Integer(count), new Long(dt) }));\n }\n\n----------------------------------------\n public void echo() throws InterruptedException, IOException, GeneralSecurityException {\n long t1 = System.currentTimeMillis();\n int count = 0;\n for (int i = 0; i < repeatWhole; ++i) {\n ActiveAssociation active = openAssoc();\n if (active != null) {\n if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) {\n log.error(messages.getString(\"noPCEcho\"));\n } else for (int j = 0; j < repeatSingle; ++j, ++count) {\n active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null);\n }\n active.release(true);\n }\n }\n long dt = System.currentTimeMillis() - t1;\n log.info(MessageFormat.format(messages.getString(\"echoDone\"), new Object[] { new Integer(count), new Long(dt) }));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2252238.java 13 21\n/home/jeff/BigCloneBench/sample/selected/2507460.java 331 342\n----------------------------------------\n public static void pump(InputStream in, OutputStream out) throws IOException {\n byte[] buffer = new byte[1];\n int bytes_read = 0;\n while (bytes_read != -1) {\n bytes_read = in.read(buffer);\n if (bytes_read == -1) break;\n out.write(buffer, 0, bytes_read);\n }\n }\n\n----------------------------------------\n public static void copy(InputStream in, OutputStream out) throws IOException {\n synchronized (in) {\n synchronized (out) {\n byte[] buffer = new byte[256];\n while (true) {\n int bytesRead = in.read(buffer);\n if (bytesRead == -1) break;\n out.write(buffer, 0, bytesRead);\n }\n }\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/293134.java 72 80\n/home/jeff/BigCloneBench/sample/selected/2727194.java 76 84\n----------------------------------------\n public static String getExtension(File f) {\n String ext = null;\n String s = f.getName();\n int i = s.lastIndexOf('.');\n if (i > 0 && i < s.length() - 1) {\n ext = s.substring(i + 1).toLowerCase();\n }\n return ext;\n }\n\n----------------------------------------\n public static String getExtension(File f) {\n String ext = null;\n String s = f.getName();\n int i = s.lastIndexOf('.');\n if (i > 0 && i < s.length() - 1) {\n ext = s.substring(i + 1).toLowerCase();\n }\n return ext;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/97360.java 548 570\n/home/jeff/BigCloneBench/sample/default/35432.java 648 665\n----------------------------------------\n private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveInstances(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeInstances(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/129715.java 548 570\n/home/jeff/BigCloneBench/sample/default/106446.java 522 544\n----------------------------------------\n private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveInstances(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveSeries(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/12172.java 64 71\n/home/jeff/BigCloneBench/sample/default/91574.java 54 62\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingDo(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n do {\n if (i > start) builder.append(',');\n builder.append(i);\n } while (++i <= stop);\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/45886.java 73 82\n/home/jeff/BigCloneBench/sample/default/120094.java 64 71\n----------------------------------------\n String sequenceUsingWhile(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n while (i <= stop) {\n if (i > start) builder.append(',');\n builder.append(i);\n i++;\n }\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1059992.java 1101 1112\n/home/jeff/BigCloneBench/sample/selected/1521582.java 1122 1133\n----------------------------------------\n protected boolean sameSenoneSequence(int[] ssid1, int[] ssid2) {\n if (ssid1.length == ssid2.length) {\n for (int i = 0; i < ssid1.length; i++) {\n if (ssid1[i] != ssid2[i]) {\n return false;\n }\n }\n return true;\n } else {\n return false;\n }\n }\n\n----------------------------------------\n protected boolean sameSenoneSequence(int[] ssid1, int[] ssid2) {\n if (ssid1.length == ssid2.length) {\n for (int i = 0; i < ssid1.length; i++) {\n if (ssid1[i] != ssid2[i]) {\n return false;\n }\n }\n return true;\n } else {\n return false;\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/34946.java 185 192\n/home/jeff/BigCloneBench/sample/selected/2634974.java 247 258\n----------------------------------------\n public int indexOf(Object elem) {\n if (elem == null) {\n for (int i = 0; i < size; i++) if (elementData[i] == null) return i;\n } else {\n for (int i = 0; i < size; i++) if (elem.equals(elementData[i])) return i;\n }\n return -1;\n }\n\n----------------------------------------\n public int lastIndexOf(Object o) {\n if (o == null) {\n for (int i = size - 1; i >= 0; i--) {\n if (array[i] == null) return (i);\n }\n } else {\n for (int i = size - 1; i >= 0; i--) {\n if (o.equals(array[i])) return (i);\n }\n }\n return (-1);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/10254.java 64 71\n/home/jeff/BigCloneBench/sample/default/121888.java 64 71\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/113632.java 27 46\n/home/jeff/BigCloneBench/sample/default/44695.java 27 46\n----------------------------------------\n private static void readAndRewrite(File inFile, File outFile) throws IOException {\n ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile)));\n DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis);\n Dataset ds = DcmObjectFactory.getInstance().newDataset();\n dcmParser.setDcmHandler(ds.getDcmHandler());\n dcmParser.parseDcmFile(null, Tags.PixelData);\n PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR());\n System.out.println(\"reading \" + inFile + \"...\");\n pdReader.readPixelData(false);\n ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile)));\n DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;\n ds.writeDataset(out, dcmEncParam);\n ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength());\n System.out.println(\"writing \" + outFile + \"...\");\n PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR());\n pdWriter.writePixelData();\n out.flush();\n out.close();\n System.out.println(\"done!\");\n }\n\n----------------------------------------\n private static void readAndRewrite(File inFile, File outFile) throws IOException {\n ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile)));\n DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis);\n Dataset ds = DcmObjectFactory.getInstance().newDataset();\n dcmParser.setDcmHandler(ds.getDcmHandler());\n dcmParser.parseDcmFile(null, Tags.PixelData);\n PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR());\n System.out.println(\"reading \" + inFile + \"...\");\n pdReader.readPixelData(false);\n ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile)));\n DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;\n ds.writeDataset(out, dcmEncParam);\n ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength());\n System.out.println(\"writing \" + outFile + \"...\");\n PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR());\n pdWriter.writePixelData();\n out.flush();\n out.close();\n System.out.println(\"done!\");\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/28532.java 369 379\n/home/jeff/BigCloneBench/sample/default/119807.java 546 557\n----------------------------------------\n public void test18() throws Exception {\n String data = \"1\\r\";\n CsvReader reader = CsvReader.parse(data);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"1\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"1\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n public void test29() throws Exception {\n String data = \"\\\"double\\\\\\\"\\\\\\\"double quotes\\\"\";\n CsvReader reader = CsvReader.parse(data);\n reader.setEscapeMode(CsvReader.ESCAPE_MODE_BACKSLASH);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"double\\\"\\\"double quotes\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"\\\"double\\\\\\\"\\\\\\\"double quotes\\\"\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/16641.java 308 322\n/home/jeff/BigCloneBench/sample/default/98990.java 308 322\n----------------------------------------\n private int query(String prefix, int no, int level, DirRecord dr, SAXTransformerFactory tf, Templates xslt) throws IOException, TransformerConfigurationException {\n int count = 1;\n for (; dr != null; dr = dr.getNextSiblingBy(null, keys, ignoreCase)) {\n if (level >= qrLevel) {\n Dataset ds = dr.getDataset();\n String prompt = POS_FORMAT.format(ds.getItemOffset()) + prefix + count + \" [\" + dr.getType() + \"] #\" + no;\n ds.writeDataset(getTransformerHandler(tf, xslt, prompt), dict);\n ++no;\n } else {\n no = query(prefix + count + '.', no, level + 1, dr.getFirstChildBy(null, keys, ignoreCase), tf, xslt);\n }\n ++count;\n }\n return no;\n }\n\n----------------------------------------\n private int query(String prefix, int no, int level, DirRecord dr, SAXTransformerFactory tf, Templates xslt) throws IOException, TransformerConfigurationException {\n int count = 1;\n for (; dr != null; dr = dr.getNextSiblingBy(null, keys, ignoreCase)) {\n if (level >= qrLevel) {\n Dataset ds = dr.getDataset();\n String prompt = POS_FORMAT.format(ds.getItemOffset()) + prefix + count + \" [\" + dr.getType() + \"] #\" + no;\n ds.writeDataset(getTransformerHandler(tf, xslt, prompt), dict);\n ++no;\n } else {\n no = query(prefix + count + '.', no, level + 1, dr.getFirstChildBy(null, keys, ignoreCase), tf, xslt);\n }\n ++count;\n }\n return no;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/97360.java 650 667\n/home/jeff/BigCloneBench/sample/default/35432.java 648 665\n----------------------------------------\n private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeInstances(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeInstances(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/243138.java 383 414\n/home/jeff/BigCloneBench/sample/selected/342350.java 314 335\n----------------------------------------\n private void drawAnchorBox(Graphics2D g2) {\n Rectangle r = getAnchorRect();\n int x = r.x;\n int y = r.y;\n int width = r.x + r.width - 6;\n int height = r.y + r.height - 6;\n int centerx = (x + width) / 2;\n int centery = (y + height) / 2;\n Vector<Point> selPts = new Vector<Point>();\n selPts.add(new Point(centerx, centery));\n VGArrow vgArrow = (VGArrow) refBase;\n int quart = vgArrow.getArrowHeadQuarter();\n if (quart == 0 | quart == 4) {\n selPts.add(new Point(x, y));\n selPts.add(new Point(width, height));\n } else if (quart == 2 | quart == 6) {\n selPts.add(new Point(x, height));\n selPts.add(new Point(width, y));\n }\n if (quart == 1 | quart == 5) {\n selPts.add(new Point(x, height / 2));\n selPts.add(new Point(width, height / 2));\n }\n if (quart == 3 | quart == 7) {\n selPts.add(new Point(width / 2, 0));\n selPts.add(new Point(width / 2, height));\n }\n g2.setColor(Color.green);\n for (Point kPkt : selPts) {\n g2.fillRect(kPkt.x, kPkt.y, 6, 6);\n }\n }\n\n----------------------------------------\n private void drawAnchorBox(Graphics2D g2) {\n Rectangle r = getAnchorRect();\n int x = r.x;\n int y = r.y;\n int width = r.x + r.width - 6;\n int height = r.y + r.height - 6;\n int centerx = (x + width) / 2;\n int centery = (y + height) / 2;\n Vector<Point> selPts = new Vector<Point>();\n selPts.add(new Point(x, y));\n selPts.add(new Point(x, height));\n selPts.add(new Point(width, y));\n selPts.add(new Point(width, height));\n selPts.add(new Point(centerx, y));\n selPts.add(new Point(centerx, height));\n selPts.add(new Point(x, centery));\n selPts.add(new Point(width, centery));\n g2.setColor(Color.green);\n for (Point kPkt : selPts) {\n g2.fillRect(kPkt.x, kPkt.y, 6, 6);\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/113166.java 126 138\n/home/jeff/BigCloneBench/sample/default/76337.java 126 138\n----------------------------------------\n public void testCasting() {\n List students = new ArrayList();\n students.add(new Student(\"a\"));\n students.add(new Student(\"b\"));\n List names = new ArrayList();\n Iterator it = students.iterator();\n while (it.hasNext()) {\n Student student = (Student) it.next();\n names.add(student.getLastName());\n }\n assertEquals(\"a\", names.get(0));\n assertEquals(\"b\", names.get(1));\n }\n\n----------------------------------------\n public void testCasting() {\n List students = new ArrayList();\n students.add(new Student(\"a\"));\n students.add(new Student(\"b\"));\n List names = new ArrayList();\n Iterator it = students.iterator();\n while (it.hasNext()) {\n Student student = (Student) it.next();\n names.add(student.getLastName());\n }\n assertEquals(\"a\", names.get(0));\n assertEquals(\"b\", names.get(1));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/26122.java 620 625\n/home/jeff/BigCloneBench/sample/default/118575.java 579 584\n----------------------------------------\n public void _setFileNameSuffix(String rSuffix) {\n if (null == rSuffix) {\n return;\n }\n writer__iFileNameSuffix = rSuffix;\n }\n\n----------------------------------------\n public void _setFileNameSuffix(String rSuffix) {\n if (null == rSuffix) {\n return;\n }\n writer__iFileNameSuffix = rSuffix;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/47314.java 148 158\n/home/jeff/BigCloneBench/sample/selected/1366120.java 119 129\n----------------------------------------\n public int compare(int row1, int row2) {\n compares++;\n for (int level = 0; level < sortingColumns.size(); level++) {\n int column = sortingColumns.elementAt(level);\n int result = compareRowsByColumn(row1, row2, column);\n if (result != 0) {\n return ascending ? result : -result;\n }\n }\n return 0;\n }\n\n----------------------------------------\n public int compare(int row1, int row2) {\n compares++;\n for (int level = 0; level < sortingColumns.size(); level++) {\n Integer column = (Integer) sortingColumns.elementAt(level);\n int result = compareRowsByColumn(row1, row2, column.intValue());\n if (result != 0) {\n return ascending ? result : -result;\n }\n }\n return 0;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/76273.java 159 173\n/home/jeff/BigCloneBench/sample/default/11030.java 159 173\n----------------------------------------\n public void testPartialDimensions() {\n final int rows = 3;\n int[][] matrix = new int[rows][];\n matrix[0] = new int[] { 0 };\n matrix[1] = new int[] { 1, 2 };\n matrix[2] = new int[] { 3, 4, 5 };\n assertEquals(1, matrix[1][0]);\n assertEquals(5, matrix[2][2]);\n int[][] matrix2 = { { 0 }, { 1, 2 }, { 3, 4, 5 } };\n assertEquals(1, matrix2[1][0]);\n assertEquals(5, matrix2[2][2]);\n int[] z1 = { 3, 4, 5 };\n int[] z2 = { 3, 4, 5 };\n assertTrue(Arrays.equals(z1, z2));\n }\n\n----------------------------------------\n public void testPartialDimensions() {\n final int rows = 3;\n int[][] matrix = new int[rows][];\n matrix[0] = new int[] { 0 };\n matrix[1] = new int[] { 1, 2 };\n matrix[2] = new int[] { 3, 4, 5 };\n assertEquals(1, matrix[1][0]);\n assertEquals(5, matrix[2][2]);\n int[][] matrix2 = { { 0 }, { 1, 2 }, { 3, 4, 5 } };\n assertEquals(1, matrix2[1][0]);\n assertEquals(5, matrix2[2][2]);\n int[] z1 = { 3, 4, 5 };\n int[] z2 = { 3, 4, 5 };\n assertTrue(Arrays.equals(z1, z2));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/497716.java 752 771\n/home/jeff/BigCloneBench/sample/selected/1782576.java 705 724\n----------------------------------------\n public static String nullSafeToString(long[] array) {\n if (array == null) {\n return NULL_STRING;\n }\n int length = array.length;\n if (length == 0) {\n return EMPTY_ARRAY;\n }\n StringBuilder sb = new StringBuilder();\n for (int i = 0; i < length; i++) {\n if (i == 0) {\n sb.append(ARRAY_START);\n } else {\n sb.append(ARRAY_ELEMENT_SEPARATOR);\n }\n sb.append(array[i]);\n }\n sb.append(ARRAY_END);\n return sb.toString();\n }\n\n----------------------------------------\n public static String nullSafeToString(int[] array) {\n if (array == null) {\n return NULL_STRING;\n }\n int length = array.length;\n if (length == 0) {\n return EMPTY_ARRAY;\n }\n StringBuffer buffer = new StringBuffer();\n for (int i = 0; i < length; i++) {\n if (i == 0) {\n buffer.append(ARRAY_START);\n } else {\n buffer.append(ARRAY_ELEMENT_SEPARATOR);\n }\n buffer.append(array[i]);\n }\n buffer.append(ARRAY_END);\n return buffer.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/8509.java 231 247\n/home/jeff/BigCloneBench/sample/default/128156.java 231 247\n----------------------------------------\n public void echo() throws InterruptedException, IOException, GeneralSecurityException {\n long t1 = System.currentTimeMillis();\n int count = 0;\n for (int i = 0; i < repeatWhole; ++i) {\n ActiveAssociation active = openAssoc();\n if (active != null) {\n if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) {\n log.error(messages.getString(\"noPCEcho\"));\n } else for (int j = 0; j < repeatSingle; ++j, ++count) {\n active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null);\n }\n active.release(true);\n }\n }\n long dt = System.currentTimeMillis() - t1;\n log.info(MessageFormat.format(messages.getString(\"echoDone\"), new Object[] { new Integer(count), new Long(dt) }));\n }\n\n----------------------------------------\n public void echo() throws InterruptedException, IOException, GeneralSecurityException {\n long t1 = System.currentTimeMillis();\n int count = 0;\n for (int i = 0; i < repeatWhole; ++i) {\n ActiveAssociation active = openAssoc();\n if (active != null) {\n if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) {\n log.error(messages.getString(\"noPCEcho\"));\n } else for (int j = 0; j < repeatSingle; ++j, ++count) {\n active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null);\n }\n active.release(true);\n }\n }\n long dt = System.currentTimeMillis() - t1;\n log.info(MessageFormat.format(messages.getString(\"echoDone\"), new Object[] { new Integer(count), new Long(dt) }));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/114239.java 334 353\n/home/jeff/BigCloneBench/sample/default/73729.java 1684 1702\n----------------------------------------\n public void test16() throws Exception {\n String data = \"\\r\\r\\n1\\r\";\n CsvReader reader = CsvReader.parse(data);\n reader.setDelimiter('\\r');\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"\", reader.get(0));\n Assert.assertEquals(\"\", reader.get(1));\n Assert.assertEquals(\"\", reader.get(2));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(3, reader.getColumnCount());\n Assert.assertEquals(\"\\r\\r\", reader.getRawRecord());\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"1\", reader.get(0));\n Assert.assertEquals(\"\", reader.get(1));\n Assert.assertEquals(1L, reader.getCurrentRecord());\n Assert.assertEquals(2, reader.getColumnCount());\n Assert.assertEquals(\"1\\r\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n public void test138() throws Exception {\n CsvReader reader = CsvReader.parse(\"1;; ;1\");\n reader.setRecordDelimiter(';');\n Assert.assertTrue(reader.getSkipEmptyRecords());\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"1\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"\", reader.get(0));\n Assert.assertEquals(1L, reader.getCurrentRecord());\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"1\", reader.get(0));\n Assert.assertEquals(2L, reader.getCurrentRecord());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/453804.java 146 151\n/home/jeff/BigCloneBench/sample/selected/615198.java 132 137\n----------------------------------------\n protected IDocumentProvider getDocumentProvider(IEditorInput input) {\n if (input instanceof IFileEditorInput || input instanceof URIEditorInput) {\n return edu.toronto.cs.openome_model.diagram.part.Openome_modelDiagramEditorPlugin.getInstance().getDocumentProvider();\n }\n return super.getDocumentProvider(input);\n }\n\n----------------------------------------\n protected IDocumentProvider getDocumentProvider(IEditorInput input) {\n if (input instanceof IFileEditorInput || input instanceof URIEditorInput) {\n return FilesystemDiagramEditorPlugin.getInstance().getDocumentProvider();\n }\n return super.getDocumentProvider(input);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1030949.java 677 687\n/home/jeff/BigCloneBench/sample/selected/900584.java 673 682\n----------------------------------------\n public Matrix arrayTimes(Matrix B) {\n checkMatrixDimensions(B);\n Matrix X = new Matrix(m, n);\n double[][] C = X.getArray();\n for (int i = 0; i < m; i++) {\n for (int j = 0; j < n; j++) {\n C[i][j] = A[i][j] * B.A[i][j];\n }\n }\n return X;\n }\n\n----------------------------------------\n public Matrix times(double s) {\n Matrix X = new Matrix(m, n);\n double[][] C = X.getArray();\n for (int i = 0; i < m; i++) {\n for (int j = 0; j < n; j++) {\n C[i][j] = s * A[i][j];\n }\n }\n return X;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2242014.java 269 292\n/home/jeff/BigCloneBench/sample/selected/2095100.java 334 357\n----------------------------------------\n private String decodePercent(String str) throws InterruptedException {\n try {\n StringBuffer sb = new StringBuffer();\n for (int i = 0; i < str.length(); i++) {\n char c = str.charAt(i);\n switch(c) {\n case '+':\n sb.append(' ');\n break;\n case '%':\n sb.append((char) Integer.parseInt(str.substring(i + 1, i + 3), 16));\n i += 2;\n break;\n default:\n sb.append(c);\n break;\n }\n }\n return new String(sb.toString().getBytes());\n } catch (Exception e) {\n sendError(HTTP_BADREQUEST, \"BAD REQUEST: Bad percent-encoding.\");\n return null;\n }\n }\n\n----------------------------------------\n private String decodePercent(String str) throws InterruptedException {\n try {\n StringBuffer sb = new StringBuffer();\n for (int i = 0; i < str.length(); i++) {\n char c = str.charAt(i);\n switch(c) {\n case '+':\n sb.append(' ');\n break;\n case '%':\n sb.append((char) Integer.parseInt(str.substring(i + 1, i + 3), 16));\n i += 2;\n break;\n default:\n sb.append(c);\n break;\n }\n }\n return new String(sb.toString().getBytes());\n } catch (Exception e) {\n sendError(HTTP_BADREQUEST, \"BAD REQUEST: Bad percent-encoding.\");\n return null;\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2666453.java 788 820\n/home/jeff/BigCloneBench/sample/selected/2666453.java 1017 1050\n----------------------------------------\n public void cosRegisterPeer(java.lang.String peerName, tcg.syscontrol.cos.ICosProcessManager p_peerManager) throws tcg.syscontrol.cos.CosFailedToRegisterException {\n while (true) {\n if (!this._is_local()) {\n org.omg.CORBA.portable.InputStream _is = null;\n try {\n org.omg.CORBA.portable.OutputStream _os = _request(\"cosRegisterPeer\", true);\n _os.write_string(peerName);\n tcg.syscontrol.cos.ICosProcessManagerHelper.write(_os, p_peerManager);\n _is = _invoke(_os);\n return;\n } catch (org.omg.CORBA.portable.RemarshalException _rx) {\n } catch (org.omg.CORBA.portable.ApplicationException _ax) {\n String _id = _ax.getId();\n if (_id.equals(\"IDL:tcg/syscontrol/cos/CosFailedToRegisterException:1.0\")) {\n throw tcg.syscontrol.cos.CosFailedToRegisterExceptionHelper.read(_ax.getInputStream());\n }\n throw new RuntimeException(\"Unexpected exception \" + _id);\n } finally {\n this._releaseReply(_is);\n }\n } else {\n org.omg.CORBA.portable.ServantObject _so = _servant_preinvoke(\"cosRegisterPeer\", _opsClass);\n if (_so == null) throw new org.omg.CORBA.UNKNOWN(\"local invocations not supported!\");\n ICosProcessManagerOperations _localServant = (ICosProcessManagerOperations) _so.servant;\n try {\n _localServant.cosRegisterPeer(peerName, p_peerManager);\n } finally {\n _servant_postinvoke(_so);\n }\n return;\n }\n }\n }\n\n----------------------------------------\n public tcg.syscontrol.cos.ICosManagedProcess cosGetActiveManagedProcess(short index) throws tcg.syscontrol.cos.CosIndexOutOfBoundException {\n while (true) {\n if (!this._is_local()) {\n org.omg.CORBA.portable.InputStream _is = null;\n try {\n org.omg.CORBA.portable.OutputStream _os = _request(\"cosGetActiveManagedProcess\", true);\n _os.write_ushort(index);\n _is = _invoke(_os);\n tcg.syscontrol.cos.ICosManagedProcess _result = tcg.syscontrol.cos.ICosManagedProcessHelper.read(_is);\n return _result;\n } catch (org.omg.CORBA.portable.RemarshalException _rx) {\n } catch (org.omg.CORBA.portable.ApplicationException _ax) {\n String _id = _ax.getId();\n if (_id.equals(\"IDL:tcg/syscontrol/cos/CosIndexOutOfBoundException:1.0\")) {\n throw tcg.syscontrol.cos.CosIndexOutOfBoundExceptionHelper.read(_ax.getInputStream());\n }\n throw new RuntimeException(\"Unexpected exception \" + _id);\n } finally {\n this._releaseReply(_is);\n }\n } else {\n org.omg.CORBA.portable.ServantObject _so = _servant_preinvoke(\"cosGetActiveManagedProcess\", _opsClass);\n if (_so == null) throw new org.omg.CORBA.UNKNOWN(\"local invocations not supported!\");\n ICosProcessManagerOperations _localServant = (ICosProcessManagerOperations) _so.servant;\n tcg.syscontrol.cos.ICosManagedProcess _result;\n try {\n _result = _localServant.cosGetActiveManagedProcess(index);\n } finally {\n _servant_postinvoke(_so);\n }\n return _result;\n }\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/120462.java 150 156\n/home/jeff/BigCloneBench/sample/default/118160.java 150 156\n----------------------------------------\n private static int toTag(String tagStr) {\n try {\n return (int) Long.parseLong(tagStr, 16);\n } catch (NumberFormatException e) {\n return Tags.forName(tagStr);\n }\n }\n\n----------------------------------------\n private static int toTag(String tagStr) {\n try {\n return (int) Long.parseLong(tagStr, 16);\n } catch (NumberFormatException e) {\n return Tags.forName(tagStr);\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/50297.java 30 44\n/home/jeff/BigCloneBench/sample/default/83276.java 30 44\n----------------------------------------\n public Configuration(URL url) {\n InputStream in = null;\n try {\n load(in = url.openStream());\n } catch (Exception e) {\n throw new RuntimeException(\"Could not load configuration from \" + url, e);\n } finally {\n if (in != null) {\n try {\n in.close();\n } catch (IOException ignore) {\n }\n }\n }\n }\n\n----------------------------------------\n public Configuration(URL url) {\n InputStream in = null;\n try {\n load(in = url.openStream());\n } catch (Exception e) {\n throw new RuntimeException(\"Could not load configuration from \" + url, e);\n } finally {\n if (in != null) {\n try {\n in.close();\n } catch (IOException ignore) {\n }\n }\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/45048.java 253 269\n/home/jeff/BigCloneBench/sample/default/57136.java 243 259\n----------------------------------------\n public void echo() throws InterruptedException, IOException, GeneralSecurityException {\n long t1 = System.currentTimeMillis();\n int count = 0;\n for (int i = 0; i < repeatWhole; ++i) {\n ActiveAssociation active = openAssoc();\n if (active != null) {\n if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) {\n log.error(messages.getString(\"noPCEcho\"));\n } else for (int j = 0; j < repeatSingle; ++j, ++count) {\n active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null);\n }\n active.release(true);\n }\n }\n long dt = System.currentTimeMillis() - t1;\n log.info(MessageFormat.format(messages.getString(\"echoDone\"), new Object[] { new Integer(count), new Long(dt) }));\n }\n\n----------------------------------------\n public void echo() throws InterruptedException, IOException, GeneralSecurityException {\n long t1 = System.currentTimeMillis();\n int count = 0;\n for (int i = 0; i < repeatWhole; ++i) {\n ActiveAssociation active = openAssoc();\n if (active != null) {\n if (active.getAssociation().getAcceptedTransferSyntaxUID(PCID_ECHO) == null) {\n log.error(messages.getString(\"noPCEcho\"));\n } else for (int j = 0; j < repeatSingle; ++j, ++count) {\n active.invoke(aFact.newDimse(PCID_ECHO, oFact.newCommand().initCEchoRQ(j)), null);\n }\n active.release(true);\n }\n }\n long dt = System.currentTimeMillis() - t1;\n log.info(MessageFormat.format(messages.getString(\"echoDone\"), new Object[] { new Integer(count), new Long(dt) }));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/44659.java 54 62\n/home/jeff/BigCloneBench/sample/default/112296.java 54 62\n----------------------------------------\n String sequenceUsingDo(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n do {\n if (i > start) builder.append(',');\n builder.append(i);\n } while (++i <= stop);\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingDo(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n do {\n if (i > start) builder.append(',');\n builder.append(i);\n } while (++i <= stop);\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/41662.java 113 124\n/home/jeff/BigCloneBench/sample/default/56904.java 113 124\n----------------------------------------\n private boolean found(List<List<String>> table, String target) {\n boolean found = false;\n search: for (List<String> row : table) {\n for (String value : row) {\n if (value.equals(target)) {\n found = true;\n break search;\n }\n }\n }\n return found;\n }\n\n----------------------------------------\n private boolean found(List<List<String>> table, String target) {\n boolean found = false;\n search: for (List<String> row : table) {\n for (String value : row) {\n if (value.equals(target)) {\n found = true;\n break search;\n }\n }\n }\n return found;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/79086.java 705 713\n/home/jeff/BigCloneBench/sample/default/81123.java 707 715\n----------------------------------------\n private static void exit(String prompt, boolean error) {\n if (prompt != null) {\n System.err.println(prompt);\n }\n if (error) {\n System.err.println(messages.getString(\"try\"));\n }\n System.exit(1);\n }\n\n----------------------------------------\n private static void exit(String prompt, boolean error) {\n if (prompt != null) {\n System.err.println(prompt);\n }\n if (error) {\n System.err.println(messages.getString(\"try\"));\n }\n System.exit(1);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/82401.java 83 91\n/home/jeff/BigCloneBench/sample/default/8578.java 83 91\n----------------------------------------\n public static boolean url(String url, String pkglisturl, DocErrorReporter reporter) {\n String errMsg = composeExternPackageList(url, pkglisturl);\n if (errMsg != null) {\n reporter.printError(errMsg);\n return false;\n } else {\n return true;\n }\n }\n\n----------------------------------------\n public static boolean url(String url, String pkglisturl, DocErrorReporter reporter) {\n String errMsg = composeExternPackageList(url, pkglisturl);\n if (errMsg != null) {\n reporter.printError(errMsg);\n return false;\n } else {\n return true;\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/44026.java 667 685\n/home/jeff/BigCloneBench/sample/default/134647.java 667 685\n----------------------------------------\n private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n File file = w.getRefFile(rec.getRefFileIDs());\n if (!file.exists()) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n File file = w.getRefFile(rec.getRefFileIDs());\n if (!file.exists()) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/80510.java 264 274\n/home/jeff/BigCloneBench/sample/default/106112.java 264 274\n----------------------------------------\n public void test11() throws Exception {\n String data = \"\\\"July 4th, 2005\\\"\";\n CsvReader reader = CsvReader.parse(data);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"July 4th, 2005\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"\\\"July 4th, 2005\\\"\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n public void test11() throws Exception {\n String data = \"\\\"July 4th, 2005\\\"\";\n CsvReader reader = CsvReader.parse(data);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"July 4th, 2005\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"\\\"July 4th, 2005\\\"\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/79290.java 300 338\n/home/jeff/BigCloneBench/sample/default/112571.java 309 347\n----------------------------------------\n private boolean sendFile(ActiveAssociation active, File file) throws InterruptedException, IOException {\n InputStream in = null;\n DcmParser parser = null;\n Dataset ds = null;\n try {\n try {\n in = new BufferedInputStream(new FileInputStream(file));\n parser = pFact.newDcmParser(in);\n FileFormat format = parser.detectFileFormat();\n if (format != null) {\n ds = oFact.newDataset();\n parser.setDcmHandler(ds.getDcmHandler());\n parser.parseDcmFile(format, Tags.PixelData);\n if (parser.getReadTag() == Tags.PixelData) {\n if (parser.getStreamPosition() + parser.getReadLength() > file.length()) {\n throw new EOFException(\"Pixel Data Length: \" + parser.getReadLength() + \" exceeds file length: \" + file.length());\n }\n }\n log.info(MessageFormat.format(messages.getString(\"readDone\"), new Object[] { file }));\n } else {\n log.error(MessageFormat.format(messages.getString(\"failformat\"), new Object[] { file }));\n return false;\n }\n } catch (IOException e) {\n log.error(MessageFormat.format(messages.getString(\"failread\"), new Object[] { file, e }));\n return false;\n }\n sendDataset(active, file, parser, ds);\n return true;\n } finally {\n if (in != null) {\n try {\n in.close();\n } catch (IOException ignore) {\n }\n ;\n }\n }\n }\n\n----------------------------------------\n private boolean sendFile(ActiveAssociation active, File file, Dataset mergeDataset) throws InterruptedException, IOException {\n InputStream in = null;\n DcmParser parser = null;\n Dataset ds = null;\n try {\n try {\n in = new BufferedInputStream(new FileInputStream(file));\n parser = pFact.newDcmParser(in);\n try {\n FileFormat format = parser.detectFileFormat();\n ds = oFact.newDataset();\n parser.setDcmHandler(ds.getDcmHandler());\n parser.parseDcmFile(format, Tags.PixelData);\n if (parser.getReadTag() == Tags.PixelData) {\n if (parser.getStreamPosition() + parser.getReadLength() > file.length()) {\n throw new EOFException(\"Pixel Data Length: \" + parser.getReadLength() + \" exceeds file length: \" + file.length());\n }\n }\n log.info(MessageFormat.format(messages.getString(\"readDone\"), new Object[] { file }));\n } catch (DcmParseException e) {\n log.error(MessageFormat.format(messages.getString(\"failformat\"), new Object[] { file }));\n return false;\n }\n } catch (IOException e) {\n log.error(MessageFormat.format(messages.getString(\"failread\"), new Object[] { file, e }));\n return false;\n }\n sendDataset(active, file, parser, merge(ds, mergeDataset));\n return true;\n } finally {\n if (in != null) {\n try {\n in.close();\n } catch (IOException ignore) {\n }\n ;\n }\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/76273.java 64 71\n/home/jeff/BigCloneBench/sample/default/115412.java 54 62\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingDo(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n do {\n if (i > start) builder.append(',');\n builder.append(i);\n } while (++i <= stop);\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/103762.java 546 568\n/home/jeff/BigCloneBench/sample/default/67675.java 548 570\n----------------------------------------\n private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveInstances(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveInstances(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/330378.java 1030 1046\n/home/jeff/BigCloneBench/sample/selected/2198965.java 1131 1147\n----------------------------------------\n public void test_18_119_writeObject() {\n Object objToSave = null;\n Object objLoaded;\n try {\n objToSave = Locale.CHINESE;\n if (DEBUG) System.out.println(\"Obj = \" + objToSave);\n objLoaded = dumpAndReload(objToSave);\n assertTrue(MSG_TEST_FAILED + objToSave, Locale.CHINESE.equals(objLoaded));\n } catch (IOException e) {\n fail(\"IOException serializing \" + objToSave + \" : \" + e.getMessage());\n } catch (ClassNotFoundException e) {\n fail(\"ClassNotFoundException reading Object type : \" + e.getMessage());\n } catch (Error err) {\n System.out.println(\"Error when obj = \" + objToSave);\n throw err;\n }\n }\n\n----------------------------------------\n public void test_18_38_writeObject() {\n Object objToSave = null;\n try {\n java.io.IOException ex = new java.io.NotActiveException(FOO);\n objToSave = ex;\n if (DEBUG) System.out.println(\"Obj = \" + objToSave);\n dumpAndReload(objToSave);\n assertTrue(MSG_TEST_FAILED + objToSave, true);\n } catch (IOException e) {\n fail(\"IOException serializing \" + objToSave + \" : \" + e.getMessage());\n } catch (ClassNotFoundException e) {\n fail(\"ClassNotFoundException reading Object type : \" + e.getMessage());\n } catch (Error err) {\n System.out.println(\"Error when obj = \" + objToSave);\n throw err;\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/74326.java 73 85\n/home/jeff/BigCloneBench/sample/default/99553.java 73 85\n----------------------------------------\n private static void encapsulate(Configuration cfg, File pdfFile, File dcmFile) throws IOException {\n final DcmObjectFactory df = DcmObjectFactory.getInstance();\n Dataset ds = df.newDataset();\n for (Iterator it = cfg.entrySet().iterator(); it.hasNext(); ) {\n Map.Entry e = (Map.Entry) it.next();\n put(ds, toTags(StringUtils.split((String) e.getKey(), '/')), (String) e.getValue());\n }\n addUIDs(ds);\n addContentDateTime(ds);\n ds.setFileMetaInfo(df.newFileMetaInfo(ds, UIDs.ExplicitVRLittleEndian));\n write(pdfFile, dcmFile, ds);\n System.out.println(\"Encapsulate \" + pdfFile + \" into \" + dcmFile);\n }\n\n----------------------------------------\n private static void encapsulate(Configuration cfg, File pdfFile, File dcmFile) throws IOException {\n final DcmObjectFactory df = DcmObjectFactory.getInstance();\n Dataset ds = df.newDataset();\n for (Iterator it = cfg.entrySet().iterator(); it.hasNext(); ) {\n Map.Entry e = (Map.Entry) it.next();\n put(ds, toTags(StringUtils.split((String) e.getKey(), '/')), (String) e.getValue());\n }\n addUIDs(ds);\n addContentDateTime(ds);\n ds.setFileMetaInfo(df.newFileMetaInfo(ds, UIDs.ExplicitVRLittleEndian));\n write(pdfFile, dcmFile, ds);\n System.out.println(\"Encapsulate \" + pdfFile + \" into \" + dcmFile);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/45206.java 54 62\n/home/jeff/BigCloneBench/sample/default/113986.java 54 62\n----------------------------------------\n String sequenceUsingDo(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n do {\n if (i > start) builder.append(',');\n builder.append(i);\n } while (++i <= stop);\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingDo(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n do {\n if (i > start) builder.append(',');\n builder.append(i);\n } while (++i <= stop);\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/139001.java 29 43\n/home/jeff/BigCloneBench/sample/selected/2515946.java 30 44\n----------------------------------------\n static void setChannel(Channel ch, int val) {\n try {\n if (!ch.isConnected()) {\n ch.requestConnection();\n }\n ch.putVal(val);\n Thread.sleep(CaMonitorScalar.caputExtraTimeOut);\n } catch (ConnectionException e) {\n e.printStackTrace();\n } catch (PutException e) {\n e.printStackTrace();\n } catch (InterruptedException e) {\n e.printStackTrace();\n }\n }\n\n----------------------------------------\n static void setChannel(Channel ch, double val) {\n try {\n if (!ch.isConnected()) {\n ch.requestConnection();\n }\n ch.putVal(val);\n Thread.sleep(CaMonitorIntArray.caputExtraTimeOut);\n } catch (ConnectionException e) {\n e.printStackTrace();\n } catch (PutException e) {\n e.printStackTrace();\n } catch (InterruptedException e) {\n e.printStackTrace();\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/47340.java 19 34\n/home/jeff/BigCloneBench/sample/default/78023.java 19 34\n----------------------------------------\n public void testPalindrome() {\n assertFalse(isPalindrome(\"abcdef\"));\n assertFalse(isPalindrome(\"abccda\"));\n assertTrue(isPalindrome(\"abccba\"));\n assertFalse(isPalindrome(\"abcxba\"));\n assertTrue(isPalindrome(\"a\"));\n assertTrue(isPalindrome(\"aa\"));\n assertFalse(isPalindrome(\"ab\"));\n assertTrue(isPalindrome(\"\"));\n assertTrue(isPalindrome(\"aaa\"));\n assertTrue(isPalindrome(\"aba\"));\n assertTrue(isPalindrome(\"abbba\"));\n assertTrue(isPalindrome(\"abba\"));\n assertFalse(isPalindrome(\"abbaa\"));\n assertFalse(isPalindrome(\"abcda\"));\n }\n\n----------------------------------------\n public void testPalindrome() {\n assertFalse(isPalindrome(\"abcdef\"));\n assertFalse(isPalindrome(\"abccda\"));\n assertTrue(isPalindrome(\"abccba\"));\n assertFalse(isPalindrome(\"abcxba\"));\n assertTrue(isPalindrome(\"a\"));\n assertTrue(isPalindrome(\"aa\"));\n assertFalse(isPalindrome(\"ab\"));\n assertTrue(isPalindrome(\"\"));\n assertTrue(isPalindrome(\"aaa\"));\n assertTrue(isPalindrome(\"aba\"));\n assertTrue(isPalindrome(\"abbba\"));\n assertTrue(isPalindrome(\"abba\"));\n assertFalse(isPalindrome(\"abbaa\"));\n assertFalse(isPalindrome(\"abcda\"));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/107391.java 125 141\n/home/jeff/BigCloneBench/sample/default/121997.java 125 141\n----------------------------------------\n public void run() {\n int exitCode = -99;\n boolean exited = false;\n do {\n try {\n exitCode = tac.exitValue();\n exited = true;\n } catch (IllegalThreadStateException e) {\n System.out.println(\"still alive!\");\n try {\n Thread.sleep(1000);\n } catch (Exception ee) {\n }\n }\n } while (!exited);\n System.out.println(\"exitValue(): Process exited with code \" + exitCode);\n }\n\n----------------------------------------\n public void run() {\n int exitCode = -99;\n boolean exited = false;\n do {\n try {\n exitCode = tac.exitValue();\n exited = true;\n } catch (IllegalThreadStateException e) {\n System.out.println(\"still alive!\");\n try {\n Thread.sleep(1000);\n } catch (Exception ee) {\n }\n }\n } while (!exited);\n System.out.println(\"exitValue(): Process exited with code \" + exitCode);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/106446.java 546 568\n/home/jeff/BigCloneBench/sample/default/53104.java 570 590\n----------------------------------------\n private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveInstances(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doRemoveInstances(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (sopInstUIDs.contains(rec.getRefSOPInstanceUID()) || matchFileIDs(rec.getRefFileIDs())) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/100859.java 19 34\n/home/jeff/BigCloneBench/sample/default/16496.java 19 34\n----------------------------------------\n public void testPalindrome() {\n assertFalse(isPalindrome(\"abcdef\"));\n assertFalse(isPalindrome(\"abccda\"));\n assertTrue(isPalindrome(\"abccba\"));\n assertFalse(isPalindrome(\"abcxba\"));\n assertTrue(isPalindrome(\"a\"));\n assertTrue(isPalindrome(\"aa\"));\n assertFalse(isPalindrome(\"ab\"));\n assertTrue(isPalindrome(\"\"));\n assertTrue(isPalindrome(\"aaa\"));\n assertTrue(isPalindrome(\"aba\"));\n assertTrue(isPalindrome(\"abbba\"));\n assertTrue(isPalindrome(\"abba\"));\n assertFalse(isPalindrome(\"abbaa\"));\n assertFalse(isPalindrome(\"abcda\"));\n }\n\n----------------------------------------\n public void testPalindrome() {\n assertFalse(isPalindrome(\"abcdef\"));\n assertFalse(isPalindrome(\"abccda\"));\n assertTrue(isPalindrome(\"abccba\"));\n assertFalse(isPalindrome(\"abcxba\"));\n assertTrue(isPalindrome(\"a\"));\n assertTrue(isPalindrome(\"aa\"));\n assertFalse(isPalindrome(\"ab\"));\n assertTrue(isPalindrome(\"\"));\n assertTrue(isPalindrome(\"aaa\"));\n assertTrue(isPalindrome(\"aba\"));\n assertTrue(isPalindrome(\"abbba\"));\n assertTrue(isPalindrome(\"abba\"));\n assertFalse(isPalindrome(\"abbaa\"));\n assertFalse(isPalindrome(\"abcda\"));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/112239.java 414 423\n/home/jeff/BigCloneBench/sample/default/54915.java 506 515\n----------------------------------------\n public void addTCP(final short port) {\n Thread t;\n t = new Thread(new Runnable() {\n\n public void run() {\n serveTCP(port);\n }\n });\n t.start();\n }\n\n----------------------------------------\n public void addTCP(final InetAddress addr, final short port) {\n Thread t;\n t = new Thread(new Runnable() {\n\n public void run() {\n serveTCP(addr, port);\n }\n });\n t.start();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/14709.java 517 539\n/home/jeff/BigCloneBench/sample/default/115118.java 546 568\n----------------------------------------\n private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveSeries(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doRemoveSeries(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (seriesUIDs.contains(rec.getDataset().getString(Tags.SeriesInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveInstances(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/15109.java 90 172\n/home/jeff/BigCloneBench/sample/default/33993.java 90 172\n----------------------------------------\n public void convert(File src, File dest) throws IOException {\n InputStream in = new BufferedInputStream(new FileInputStream(src));\n DcmParser p = pfact.newDcmParser(in);\n Dataset ds = fact.newDataset();\n p.setDcmHandler(ds.getDcmHandler());\n try {\n FileFormat format = p.detectFileFormat();\n if (format != FileFormat.ACRNEMA_STREAM) {\n System.out.println(\"\\n\" + src + \": not an ACRNEMA stream!\");\n return;\n }\n p.parseDcmFile(format, Tags.PixelData);\n if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) {\n System.out.println(\"\\n\" + src + \": contains UIDs!\" + \" => probable already DICOM - do not convert\");\n return;\n }\n boolean hasPixelData = p.getReadTag() == Tags.PixelData;\n boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12;\n int pxlen = p.getReadLength();\n if (hasPixelData) {\n if (inflate) {\n ds.putUS(Tags.BitsAllocated, 16);\n pxlen = pxlen * 4 / 3;\n }\n if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) {\n System.out.println(\"\\n\" + src + \": mismatch pixel data length!\" + \" => do not convert\");\n return;\n }\n }\n ds.putUI(Tags.StudyInstanceUID, uid(studyUID));\n ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID));\n ds.putUI(Tags.SOPInstanceUID, uid(instUID));\n ds.putUI(Tags.SOPClassUID, classUID);\n if (!ds.contains(Tags.NumberOfSamples)) {\n ds.putUS(Tags.NumberOfSamples, 1);\n }\n if (!ds.contains(Tags.PhotometricInterpretation)) {\n ds.putCS(Tags.PhotometricInterpretation, \"MONOCHROME2\");\n }\n if (fmi) {\n ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian));\n }\n OutputStream out = new BufferedOutputStream(new FileOutputStream(dest));\n try {\n } finally {\n ds.writeFile(out, encodeParam());\n if (hasPixelData) {\n if (!skipGroupLen) {\n out.write(PXDATA_GROUPLEN);\n int grlen = pxlen + 8;\n out.write((byte) grlen);\n out.write((byte) (grlen >> 8));\n out.write((byte) (grlen >> 16));\n out.write((byte) (grlen >> 24));\n }\n out.write(PXDATA_TAG);\n out.write((byte) pxlen);\n out.write((byte) (pxlen >> 8));\n out.write((byte) (pxlen >> 16));\n out.write((byte) (pxlen >> 24));\n }\n if (inflate) {\n int b2, b3;\n for (; pxlen > 0; pxlen -= 3) {\n out.write(in.read());\n b2 = in.read();\n b3 = in.read();\n out.write(b2 & 0x0f);\n out.write(b2 >> 4 | ((b3 & 0x0f) << 4));\n out.write(b3 >> 4);\n }\n } else {\n for (; pxlen > 0; --pxlen) {\n out.write(in.read());\n }\n }\n out.close();\n }\n System.out.print('.');\n } finally {\n in.close();\n }\n }\n\n----------------------------------------\n public void convert(File src, File dest) throws IOException {\n InputStream in = new BufferedInputStream(new FileInputStream(src));\n DcmParser p = pfact.newDcmParser(in);\n Dataset ds = fact.newDataset();\n p.setDcmHandler(ds.getDcmHandler());\n try {\n FileFormat format = p.detectFileFormat();\n if (format != FileFormat.ACRNEMA_STREAM) {\n System.out.println(\"\\n\" + src + \": not an ACRNEMA stream!\");\n return;\n }\n p.parseDcmFile(format, Tags.PixelData);\n if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) {\n System.out.println(\"\\n\" + src + \": contains UIDs!\" + \" => probable already DICOM - do not convert\");\n return;\n }\n boolean hasPixelData = p.getReadTag() == Tags.PixelData;\n boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12;\n int pxlen = p.getReadLength();\n if (hasPixelData) {\n if (inflate) {\n ds.putUS(Tags.BitsAllocated, 16);\n pxlen = pxlen * 4 / 3;\n }\n if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) {\n System.out.println(\"\\n\" + src + \": mismatch pixel data length!\" + \" => do not convert\");\n return;\n }\n }\n ds.putUI(Tags.StudyInstanceUID, uid(studyUID));\n ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID));\n ds.putUI(Tags.SOPInstanceUID, uid(instUID));\n ds.putUI(Tags.SOPClassUID, classUID);\n if (!ds.contains(Tags.NumberOfSamples)) {\n ds.putUS(Tags.NumberOfSamples, 1);\n }\n if (!ds.contains(Tags.PhotometricInterpretation)) {\n ds.putCS(Tags.PhotometricInterpretation, \"MONOCHROME2\");\n }\n if (fmi) {\n ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian));\n }\n OutputStream out = new BufferedOutputStream(new FileOutputStream(dest));\n try {\n } finally {\n ds.writeFile(out, encodeParam());\n if (hasPixelData) {\n if (!skipGroupLen) {\n out.write(PXDATA_GROUPLEN);\n int grlen = pxlen + 8;\n out.write((byte) grlen);\n out.write((byte) (grlen >> 8));\n out.write((byte) (grlen >> 16));\n out.write((byte) (grlen >> 24));\n }\n out.write(PXDATA_TAG);\n out.write((byte) pxlen);\n out.write((byte) (pxlen >> 8));\n out.write((byte) (pxlen >> 16));\n out.write((byte) (pxlen >> 24));\n }\n if (inflate) {\n int b2, b3;\n for (; pxlen > 0; pxlen -= 3) {\n out.write(in.read());\n b2 = in.read();\n b3 = in.read();\n out.write(b2 & 0x0f);\n out.write(b2 >> 4 | ((b3 & 0x0f) << 4));\n out.write(b3 >> 4);\n }\n } else {\n for (; pxlen > 0; --pxlen) {\n out.write(in.read());\n }\n }\n out.close();\n }\n System.out.print('.');\n } finally {\n in.close();\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/401339.java 136 142\n/home/jeff/BigCloneBench/sample/selected/615198.java 132 137\n----------------------------------------\n protected void setDocumentProvider(IEditorInput input) {\n if (input instanceof IFileEditorInput || input instanceof URIEditorInput) {\n setDocumentProvider(FilesystemDiagramEditorPlugin.getInstance().getDocumentProvider());\n } else {\n super.setDocumentProvider(input);\n }\n }\n\n----------------------------------------\n protected IDocumentProvider getDocumentProvider(IEditorInput input) {\n if (input instanceof IFileEditorInput || input instanceof URIEditorInput) {\n return FilesystemDiagramEditorPlugin.getInstance().getDocumentProvider();\n }\n return super.getDocumentProvider(input);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/23336.java 194 203\n/home/jeff/BigCloneBench/sample/default/123780.java 194 203\n----------------------------------------\n public void testRetroCollections() {\n {\n List names = new Vector();\n Map dictionary = new Hashtable();\n }\n {\n List<String> names = new Vector<String>();\n Map<String, String> dictionary = new Hashtable<String, String>();\n }\n }\n\n----------------------------------------\n public void testRetroCollections() {\n {\n List names = new Vector();\n Map dictionary = new Hashtable();\n }\n {\n List<String> names = new Vector<String>();\n Map<String, String> dictionary = new Hashtable<String, String>();\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/93534.java 210 223\n/home/jeff/BigCloneBench/sample/default/10394.java 216 229\n----------------------------------------\n private ActiveAssociation openAssoc() throws IOException, GeneralSecurityException {\n Association assoc = aFact.newRequestor(newSocket(url.getHost(), url.getPort()));\n assoc.setAcTimeout(acTimeout);\n assoc.setDimseTimeout(dimseTimeout);\n assoc.setSoCloseDelay(soCloseDelay);\n assoc.setPackPDVs(packPDVs);\n PDU assocAC = assoc.connect(assocRQ);\n if (!(assocAC instanceof AAssociateAC)) {\n return null;\n }\n ActiveAssociation retval = aFact.newActiveAssociation(assoc, null);\n retval.start();\n return retval;\n }\n\n----------------------------------------\n private ActiveAssociation openAssoc() throws IOException, GeneralSecurityException {\n Association assoc = aFact.newRequestor(newSocket(url.getHost(), url.getPort()));\n assoc.setAcTimeout(acTimeout);\n assoc.setDimseTimeout(dimseTimeout);\n assoc.setSoCloseDelay(soCloseDelay);\n assoc.setPackPDVs(packPDVs);\n PDU assocAC = assoc.connect(assocRQ);\n if (!(assocAC instanceof AAssociateAC)) {\n return null;\n }\n ActiveAssociation retval = aFact.newActiveAssociation(assoc, null);\n retval.start();\n return retval;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2696114.java 459 471\n/home/jeff/BigCloneBench/sample/selected/825557.java 664 676\n----------------------------------------\n public static int[] split(String s, String delimiter, int x) {\n String[] array = split(s, delimiter);\n int[] newArray = new int[array.length];\n for (int i = 0; i < array.length; i++) {\n int value = x;\n try {\n value = Integer.parseInt(array[i]);\n } catch (Exception e) {\n }\n newArray[i] = value;\n }\n return newArray;\n }\n\n----------------------------------------\n public static long[] split(String s, String delimiter, long x) {\n String[] array = split(s, delimiter);\n long[] newArray = new long[array.length];\n for (int i = 0; i < array.length; i++) {\n long value = x;\n try {\n value = Long.parseLong(array[i]);\n } catch (Exception e) {\n }\n newArray[i] = value;\n }\n return newArray;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/939512.java 127 132\n/home/jeff/BigCloneBench/sample/selected/459626.java 80 85\n----------------------------------------\n private org.omg.CORBA.portable.OutputStream _OB_att_get_push_suppliers(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) {\n int[] _ob_r = push_suppliers();\n org.omg.CORBA.portable.OutputStream out = handler.createReply();\n ProxyIDSeqHelper.write(out, _ob_r);\n return out;\n }\n\n----------------------------------------\n private org.omg.CORBA.portable.OutputStream _OB_att_get_default_consumer_admin(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) {\n TypedConsumerAdmin _ob_r = default_consumer_admin();\n org.omg.CORBA.portable.OutputStream out = handler.createReply();\n TypedConsumerAdminHelper.write(out, _ob_r);\n return out;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/62853.java 970 989\n/home/jeff/BigCloneBench/sample/default/11754.java 970 989\n----------------------------------------\n public void test54() throws Exception {\n byte[] buffer;\n ByteArrayOutputStream stream = new ByteArrayOutputStream();\n CsvWriter writer = new CsvWriter(stream, ',', Charset.forName(\"ISO-8859-1\"));\n writer.write(\"1,2\");\n writer.write(\"3\");\n writer.write(\"blah \\\"some stuff in quotes\\\"\");\n writer.endRecord();\n Assert.assertFalse(writer.getForceQualifier());\n writer.setForceQualifier(true);\n Assert.assertTrue(writer.getForceQualifier());\n writer.write(\"1,2\");\n writer.write(\"3\");\n writer.write(\"blah \\\"some stuff in quotes\\\"\");\n writer.close();\n buffer = stream.toByteArray();\n stream.close();\n String data = Charset.forName(\"ISO-8859-1\").decode(ByteBuffer.wrap(buffer)).toString();\n Assert.assertEquals(\"\\\"1,2\\\",3,\\\"blah \\\"\\\"some stuff in quotes\\\"\\\"\\\"\\r\\n\\\"1,2\\\",\\\"3\\\",\\\"blah \\\"\\\"some stuff in quotes\\\"\\\"\\\"\", data);\n }\n\n----------------------------------------\n public void test54() throws Exception {\n byte[] buffer;\n ByteArrayOutputStream stream = new ByteArrayOutputStream();\n CsvWriter writer = new CsvWriter(stream, ',', Charset.forName(\"ISO-8859-1\"));\n writer.write(\"1,2\");\n writer.write(\"3\");\n writer.write(\"blah \\\"some stuff in quotes\\\"\");\n writer.endRecord();\n Assert.assertFalse(writer.getForceQualifier());\n writer.setForceQualifier(true);\n Assert.assertTrue(writer.getForceQualifier());\n writer.write(\"1,2\");\n writer.write(\"3\");\n writer.write(\"blah \\\"some stuff in quotes\\\"\");\n writer.close();\n buffer = stream.toByteArray();\n stream.close();\n String data = Charset.forName(\"ISO-8859-1\").decode(ByteBuffer.wrap(buffer)).toString();\n Assert.assertEquals(\"\\\"1,2\\\",3,\\\"blah \\\"\\\"some stuff in quotes\\\"\\\"\\\"\\r\\n\\\"1,2\\\",\\\"3\\\",\\\"blah \\\"\\\"some stuff in quotes\\\"\\\"\\\"\", data);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/93572.java 64 71\n/home/jeff/BigCloneBench/sample/default/66539.java 64 71\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1017245.java 479 487\n/home/jeff/BigCloneBench/sample/selected/211182.java 440 450\n----------------------------------------\n public double normF() {\n double f = 0;\n for (int i = 0; i < m; i++) {\n for (int j = 0; j < n; j++) {\n f = Maths.hypot(f, A[i][j]);\n }\n }\n return f;\n }\n\n----------------------------------------\n public double norm1() {\n double f = 0;\n for (int j = 0; j < n; j++) {\n double s = 0;\n for (int i = 0; i < m; i++) {\n s += Math.abs(A[i][j]);\n }\n f = Math.max(f, s);\n }\n return f;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/478993.java 259 273\n/home/jeff/BigCloneBench/sample/selected/1726071.java 257 271\n----------------------------------------\n public static View findView(DiagramEditPart diagramEditPart, EObject targetElement, LazyElement2ViewMap lazyElement2ViewMap) {\n boolean hasStructuralURI = false;\n if (targetElement.eResource() instanceof XMLResource) {\n hasStructuralURI = ((XMLResource) targetElement.eResource()).getID(targetElement) == null;\n }\n View view = null;\n if (hasStructuralURI && !lazyElement2ViewMap.getElement2ViewMap().isEmpty()) {\n view = (View) lazyElement2ViewMap.getElement2ViewMap().get(targetElement);\n } else if (findElementsInDiagramByID(diagramEditPart, targetElement, lazyElement2ViewMap.editPartTmpHolder) > 0) {\n EditPart editPart = (EditPart) lazyElement2ViewMap.editPartTmpHolder.get(0);\n lazyElement2ViewMap.editPartTmpHolder.clear();\n view = editPart.getModel() instanceof View ? (View) editPart.getModel() : null;\n }\n return (view == null) ? diagramEditPart.getDiagramView() : view;\n }\n\n----------------------------------------\n public static View findView(org.eclipse.gmf.runtime.diagram.ui.editparts.DiagramEditPart diagramEditPart, EObject targetElement, LazyElement2ViewMap lazyElement2ViewMap) {\n boolean hasStructuralURI = false;\n if (targetElement.eResource() instanceof XMLResource) {\n hasStructuralURI = ((XMLResource) targetElement.eResource()).getID(targetElement) == null;\n }\n View view = null;\n if (hasStructuralURI && !lazyElement2ViewMap.getElement2ViewMap().isEmpty()) {\n view = (View) lazyElement2ViewMap.getElement2ViewMap().get(targetElement);\n } else if (findElementsInDiagramByID(diagramEditPart, targetElement, lazyElement2ViewMap.editPartTmpHolder) > 0) {\n EditPart editPart = (EditPart) lazyElement2ViewMap.editPartTmpHolder.get(0);\n lazyElement2ViewMap.editPartTmpHolder.clear();\n view = editPart.getModel() instanceof View ? (View) editPart.getModel() : null;\n }\n return (view == null) ? diagramEditPart.getDiagramView() : view;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/21403.java 175 180\n/home/jeff/BigCloneBench/sample/default/130398.java 175 180\n----------------------------------------\n public void testArrayEquality() {\n int[] a = { 1, 2, 3 };\n int[] b = { 1, 2, 3 };\n assertFalse(a.equals(b));\n assertFalse(a == b);\n }\n\n----------------------------------------\n public void testArrayEquality() {\n int[] a = { 1, 2, 3 };\n int[] b = { 1, 2, 3 };\n assertFalse(a.equals(b));\n assertFalse(a == b);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/22303.java 955 967\n/home/jeff/BigCloneBench/sample/default/73729.java 762 773\n----------------------------------------\n public void test52() throws Exception {\n String data = \"\\\\xfa\\\\u0afa\\\\xFA\\\\u0AFA\";\n CsvReader reader = CsvReader.parse(data);\n reader.setUseTextQualifier(false);\n reader.setEscapeMode(CsvReader.ESCAPE_MODE_BACKSLASH);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"\u00fa\u0afa\u00fa\u0afa\", reader.get(0));\n Assert.assertEquals(\"\\\\xfa\\\\u0afa\\\\xFA\\\\u0AFA\", reader.getRawRecord());\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n public void test41() throws Exception {\n String data = \"double\\\\\\\\\\\\\\\\double backslash\";\n CsvReader reader = CsvReader.parse(data);\n reader.setUseTextQualifier(false);\n reader.setEscapeMode(CsvReader.ESCAPE_MODE_BACKSLASH);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"double\\\\\\\\double backslash\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/14709.java 517 539\n/home/jeff/BigCloneBench/sample/default/129715.java 650 667\n----------------------------------------\n private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveSeries(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeInstances(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/849450.java 189 197\n/home/jeff/BigCloneBench/sample/selected/361180.java 604 613\n----------------------------------------\n public double[][] getArrayCopy() {\n double[][] C = new double[m][n];\n for (int i = 0; i < m; i++) {\n for (int j = 0; j < n; j++) {\n C[i][j] = A[i][j];\n }\n }\n return C;\n }\n\n----------------------------------------\n public Matrix uminus() {\n Matrix X = new Matrix(m, n);\n double[][] C = X.getArray();\n for (int i = 0; i < m; i++) {\n for (int j = 0; j < n; j++) {\n C[i][j] = -A[i][j];\n }\n }\n return X;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/682654.java 133 139\n/home/jeff/BigCloneBench/sample/selected/69006.java 142 147\n----------------------------------------\n public void cancel() {\n try {\n transport.close();\n } catch (Exception e) {\n return;\n }\n }\n\n----------------------------------------\n public void finalize() {\n try {\n close();\n } catch (Exception e) {\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/98684.java 522 544\n/home/jeff/BigCloneBench/sample/default/63015.java 631 648\n----------------------------------------\n private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveSeries(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeSeries(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/45886.java 73 82\n/home/jeff/BigCloneBench/sample/default/56146.java 54 62\n----------------------------------------\n String sequenceUsingWhile(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n while (i <= stop) {\n if (i > start) builder.append(',');\n builder.append(i);\n i++;\n }\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingDo(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n do {\n if (i > start) builder.append(',');\n builder.append(i);\n } while (++i <= stop);\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2290446.java 189 194\n/home/jeff/BigCloneBench/sample/selected/2356990.java 59 64\n----------------------------------------\n private org.omg.CORBA.portable.OutputStream _OB_att_get_max_link_follow_policy(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) {\n FollowOption _ob_r = max_link_follow_policy();\n org.omg.CORBA.portable.OutputStream out = handler.createReply();\n FollowOptionHelper.write(out, _ob_r);\n return out;\n }\n\n----------------------------------------\n private org.omg.CORBA.portable.OutputStream _OB_att_get_def_follow_policy(org.omg.CORBA.portable.InputStream in, org.omg.CORBA.portable.ResponseHandler handler) {\n FollowOption _ob_r = def_follow_policy();\n org.omg.CORBA.portable.OutputStream out = handler.createReply();\n FollowOptionHelper.write(out, _ob_r);\n return out;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/72479.java 179 257\n/home/jeff/BigCloneBench/sample/default/22797.java 179 257\n----------------------------------------\n void calculateDiscoveryRates(int nBioReps, CombinationPair nullhyp) {\n if (proteinList == null) return;\n this.overallFilterPassCount = new double[this.GStatisticCutoffs.size()][this.PValueCutoffs.size()];\n this.nullhypothesisFilterPassCount = new double[this.GStatisticCutoffs.size()][this.PValueCutoffs.size()];\n this.nullhypothesisFilterPassProteins = new Vector<Vector<Vector<Protein>>>();\n for (int gi = 0; gi < this.GStatisticCutoffs.size(); gi++) {\n this.nullhypothesisFilterPassProteins.add(new Vector<Vector<Protein>>());\n for (int pi = 0; pi < this.PValueCutoffs.size(); pi++) {\n this.nullhypothesisFilterPassProteins.elementAt(gi).add(new Vector<Protein>());\n this.overallFilterPassCount[gi][pi] = 0;\n this.nullhypothesisFilterPassCount[gi][pi] = 0;\n }\n }\n CombinationGenerator combos = new CombinationGenerator(nBioReps);\n int[] groupsCount = new int[nBioReps];\n BitSet[] selections = new BitSet[nBioReps];\n double selectionRate = (double) this.nMaxPermutations / combos.getTotal().doubleValue();\n if (selectionRate < 1.0) {\n System.out.println(\"Randomly sampling \" + Math.round(combos.getTotal().doubleValue() * selectionRate) + \" (\" + (int) Math.ceil(selectionRate * 100.0) + \"%) of \" + combos.getTotal().intValue() + \" data permutations...\");\n } else {\n System.out.println(\"Processing \" + combos.getTotal().intValue() + \" data permutations...\");\n }\n for (int order = 0; order < nBioReps; order++) {\n int orderSize = combos.getOrderSize(order);\n selections[order] = new BitSet(orderSize);\n if (selectionRate < 1.0) {\n Random r = new Random(orderSize);\n int nSelect = 1 + (int) ((double) orderSize * selectionRate);\n nSelect = Math.min(nSelect, orderSize);\n for (int i = nSelect; i > 0; ) {\n int slot = r.nextInt(orderSize);\n if (!selections[order].get(slot)) {\n selections[order].set(slot);\n i--;\n }\n }\n } else {\n selections[order].set(0, orderSize);\n }\n }\n double progress = 0;\n int last_pct = 0;\n while (combos.hasMore()) {\n CombinationPair pair = combos.getNext();\n int order = pair.getOrder();\n int pctdone = (int) (100.0 * ++progress / combos.getTotal().doubleValue());\n if (pctdone != last_pct) {\n last_pct = pctdone;\n System.out.print(((last_pct % 5) == 0) ? (last_pct + \"%\") : \".\");\n }\n if (selections[order].get(groupsCount[order]++)) {\n this.nPermutationsTried++;\n boolean bNullHyp = pair.equals(nullhyp);\n for (Protein prot : this.proteinList) {\n ProteinPermutation perm = prot.doPermutation(pair);\n if (bNullHyp) {\n prot.nullHypothesis = perm;\n }\n for (int gi = 0; gi < GStatisticCutoffs.size(); gi++) {\n if (perm.getGStatistic() >= GStatisticCutoffs.get(gi)) {\n for (int pi = PValueCutoffs.size(); pi-- > 0; ) {\n if (perm.getPValue() <= PValueCutoffs.get(pi)) {\n this.overallFilterPassCount[gi][pi]++;\n if (bNullHyp) {\n this.nullhypothesisFilterPassCount[gi][pi]++;\n this.nullhypothesisFilterPassProteins.elementAt(gi).elementAt(pi).add(prot);\n }\n } else {\n break;\n }\n }\n } else {\n break;\n }\n }\n }\n }\n }\n }\n\n----------------------------------------\n void calculateDiscoveryRates(int nBioReps, CombinationPair nullhyp) {\n if (proteinList == null) return;\n this.overallFilterPassCount = new double[this.GStatisticCutoffs.size()][this.PValueCutoffs.size()];\n this.nullhypothesisFilterPassCount = new double[this.GStatisticCutoffs.size()][this.PValueCutoffs.size()];\n this.nullhypothesisFilterPassProteins = new Vector<Vector<Vector<Protein>>>();\n for (int gi = 0; gi < this.GStatisticCutoffs.size(); gi++) {\n this.nullhypothesisFilterPassProteins.add(new Vector<Vector<Protein>>());\n for (int pi = 0; pi < this.PValueCutoffs.size(); pi++) {\n this.nullhypothesisFilterPassProteins.elementAt(gi).add(new Vector<Protein>());\n this.overallFilterPassCount[gi][pi] = 0;\n this.nullhypothesisFilterPassCount[gi][pi] = 0;\n }\n }\n CombinationGenerator combos = new CombinationGenerator(nBioReps);\n int[] groupsCount = new int[nBioReps];\n BitSet[] selections = new BitSet[nBioReps];\n double selectionRate = (double) this.nMaxPermutations / combos.getTotal().doubleValue();\n if (selectionRate < 1.0) {\n System.out.println(\"Randomly sampling \" + Math.round(combos.getTotal().doubleValue() * selectionRate) + \" (\" + (int) Math.ceil(selectionRate * 100.0) + \"%) of \" + combos.getTotal().intValue() + \" data permutations...\");\n } else {\n System.out.println(\"Processing \" + combos.getTotal().intValue() + \" data permutations...\");\n }\n for (int order = 0; order < nBioReps; order++) {\n int orderSize = combos.getOrderSize(order);\n selections[order] = new BitSet(orderSize);\n if (selectionRate < 1.0) {\n Random r = new Random(orderSize);\n int nSelect = 1 + (int) ((double) orderSize * selectionRate);\n nSelect = Math.min(nSelect, orderSize);\n for (int i = nSelect; i > 0; ) {\n int slot = r.nextInt(orderSize);\n if (!selections[order].get(slot)) {\n selections[order].set(slot);\n i--;\n }\n }\n } else {\n selections[order].set(0, orderSize);\n }\n }\n double progress = 0;\n int last_pct = 0;\n while (combos.hasMore()) {\n CombinationPair pair = combos.getNext();\n int order = pair.getOrder();\n int pctdone = (int) (100.0 * ++progress / combos.getTotal().doubleValue());\n if (pctdone != last_pct) {\n last_pct = pctdone;\n System.out.print(((last_pct % 5) == 0) ? (last_pct + \"%\") : \".\");\n }\n if (selections[order].get(groupsCount[order]++)) {\n this.nPermutationsTried++;\n boolean bNullHyp = pair.equals(nullhyp);\n for (Protein prot : this.proteinList) {\n ProteinPermutation perm = prot.doPermutation(pair);\n if (bNullHyp) {\n prot.nullHypothesis = perm;\n }\n for (int gi = 0; gi < GStatisticCutoffs.size(); gi++) {\n if (perm.getGStatistic() >= GStatisticCutoffs.get(gi)) {\n for (int pi = PValueCutoffs.size(); pi-- > 0; ) {\n if (perm.getPValue() <= PValueCutoffs.get(pi)) {\n this.overallFilterPassCount[gi][pi]++;\n if (bNullHyp) {\n this.nullhypothesisFilterPassCount[gi][pi]++;\n this.nullhypothesisFilterPassProteins.elementAt(gi).elementAt(pi).add(prot);\n }\n } else {\n break;\n }\n }\n } else {\n break;\n }\n }\n }\n }\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/35053.java 629 646\n/home/jeff/BigCloneBench/sample/default/103146.java 667 685\n----------------------------------------\n private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeSeries(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeInstances(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n File file = w.getRefFile(rec.getRefFileIDs());\n if (!file.exists()) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/98981.java 522 544\n/home/jeff/BigCloneBench/sample/default/98684.java 570 590\n----------------------------------------\n private boolean doRemoveStudy(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (studyUIDs.contains(rec.getDataset().getString(Tags.StudyInstanceUID))) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else if (doRemoveSeries(w, rec, counter, delFiles)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doRemoveInstances(DirWriter w, DirRecord parent, int[] counter, boolean delFiles) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (sopInstUIDs.contains(rec.getRefSOPInstanceUID()) || matchFileIDs(rec.getRefFileIDs())) {\n if (delFiles) {\n deleteRefFiles(w, rec, counter);\n }\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[1] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1913823.java 76 92\n/home/jeff/BigCloneBench/sample/selected/2503307.java 133 148\n----------------------------------------\n protected byte[] padBuffer() {\n int n = (int) (count % BLOCK_SIZE);\n int padding = (n < 112) ? (112 - n) : (240 - n);\n byte[] result = new byte[padding + 16];\n result[0] = (byte) 0x80;\n long bits = count << 3;\n padding += 8;\n result[padding++] = (byte) (bits >>> 56);\n result[padding++] = (byte) (bits >>> 48);\n result[padding++] = (byte) (bits >>> 40);\n result[padding++] = (byte) (bits >>> 32);\n result[padding++] = (byte) (bits >>> 24);\n result[padding++] = (byte) (bits >>> 16);\n result[padding++] = (byte) (bits >>> 8);\n result[padding] = (byte) bits;\n return result;\n }\n\n----------------------------------------\n protected byte[] padBuffer() {\n int n = (int) (count % BLOCK_SIZE);\n int padding = (n < 56) ? (56 - n) : (120 - n);\n byte[] result = new byte[padding + 8];\n result[0] = (byte) 0x80;\n long bits = count << 3;\n result[padding++] = (byte) bits;\n result[padding++] = (byte) (bits >>> 8);\n result[padding++] = (byte) (bits >>> 16);\n result[padding++] = (byte) (bits >>> 24);\n result[padding++] = (byte) (bits >>> 32);\n result[padding++] = (byte) (bits >>> 40);\n result[padding++] = (byte) (bits >>> 48);\n result[padding] = (byte) (bits >>> 56);\n return result;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2372569.java 604 623\n/home/jeff/BigCloneBench/sample/selected/2701118.java 665 684\n----------------------------------------\n public static String nullSafeToString(char[] array) {\n if (array == null) {\n return NULL_STRING;\n }\n int length = array.length;\n if (length == 0) {\n return EMPTY_ARRAY;\n }\n StringBuffer buffer = new StringBuffer();\n for (int i = 0; i < length; i++) {\n if (i == 0) {\n buffer.append(ARRAY_START);\n } else {\n buffer.append(ARRAY_ELEMENT_SEPARATOR);\n }\n buffer.append(\"'\").append(array[i]).append(\"'\");\n }\n buffer.append(ARRAY_END);\n return buffer.toString();\n }\n\n----------------------------------------\n public static String nullSafeToString(float[] array) {\n if (array == null) {\n return NULL_STRING;\n }\n int length = array.length;\n if (length == 0) {\n return EMPTY_ARRAY;\n }\n StringBuffer buffer = new StringBuffer();\n for (int i = 0; i < length; i++) {\n if (i == 0) {\n buffer.append(ARRAY_START);\n } else {\n buffer.append(ARRAY_ELEMENT_SEPARATOR);\n }\n buffer.append(array[i]);\n }\n buffer.append(ARRAY_END);\n return buffer.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/44157.java 113 124\n/home/jeff/BigCloneBench/sample/default/86457.java 113 124\n----------------------------------------\n private boolean found(List<List<String>> table, String target) {\n boolean found = false;\n search: for (List<String> row : table) {\n for (String value : row) {\n if (value.equals(target)) {\n found = true;\n break search;\n }\n }\n }\n return found;\n }\n\n----------------------------------------\n private boolean found(List<List<String>> table, String target) {\n boolean found = false;\n search: for (List<String> row : table) {\n for (String value : row) {\n if (value.equals(target)) {\n found = true;\n break search;\n }\n }\n }\n return found;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1700428.java 102 110\n/home/jeff/BigCloneBench/sample/selected/74985.java 238 246\n----------------------------------------\n public static Properties getUrlAsProperties(String urlString) throws IOException {\n Properties props = new Properties();\n InputStream in = null;\n String propfile = urlString;\n in = getUrlAsStream(propfile);\n props.load(in);\n in.close();\n return props;\n }\n\n----------------------------------------\n public static Properties getUrlAsProperties(String urlString) throws IOException {\n Properties props = new Properties();\n InputStream in = null;\n String propfile = urlString;\n in = getUrlAsStream(propfile);\n props.load(in);\n in.close();\n return props;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1827694.java 50 58\n/home/jeff/BigCloneBench/sample/selected/1827694.java 74 82\n----------------------------------------\n public static final String toString(short[] array) {\n if (array == null) return \"null\";\n StringBuffer sb = new StringBuffer(128).append('[');\n for (int j = 0; j < array.length; ++j) {\n sb.append(array[j]);\n if (j != array.length - 1) sb.append(\", \");\n }\n return sb.append(']').toString();\n }\n\n----------------------------------------\n public static final String toString(char[] array) {\n if (array == null) return \"null\";\n StringBuffer sb = new StringBuffer(128).append('[');\n for (int j = 0; j < array.length; ++j) {\n sb.append(array[j]);\n if (j != array.length - 1) sb.append(\", \");\n }\n return sb.append(']').toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/132039.java 573 587\n/home/jeff/BigCloneBench/sample/default/68839.java 573 587\n----------------------------------------\n private void initTLS(Configuration cfg) {\n try {\n cipherSuites = url.getCipherSuites();\n if (cipherSuites == null) {\n return;\n }\n tls = SSLContextAdapter.getInstance();\n char[] keypasswd = cfg.getProperty(\"tls-key-passwd\", \"passwd\").toCharArray();\n tls.setKey(tls.loadKeyStore(DcmSnd.class.getResource(cfg.getProperty(\"tls-key\", \"identity.p12\")), keypasswd), keypasswd);\n tls.setTrust(tls.loadKeyStore(DcmSnd.class.getResource(cfg.getProperty(\"tls-cacerts\", \"cacerts.jks\")), cfg.getProperty(\"tls-cacerts-passwd\", \"passwd\").toCharArray()));\n tls.init();\n } catch (Exception ex) {\n throw new RuntimeException(\"Could not initalize TLS configuration: \", ex);\n }\n }\n\n----------------------------------------\n private void initTLS(Configuration cfg) {\n try {\n cipherSuites = url.getCipherSuites();\n if (cipherSuites == null) {\n return;\n }\n tls = SSLContextAdapter.getInstance();\n char[] keypasswd = cfg.getProperty(\"tls-key-passwd\", \"passwd\").toCharArray();\n tls.setKey(tls.loadKeyStore(DcmSnd.class.getResource(cfg.getProperty(\"tls-key\", \"identity.p12\")), keypasswd), keypasswd);\n tls.setTrust(tls.loadKeyStore(DcmSnd.class.getResource(cfg.getProperty(\"tls-cacerts\", \"cacerts.jks\")), cfg.getProperty(\"tls-cacerts-passwd\", \"passwd\").toCharArray()));\n tls.init();\n } catch (Exception ex) {\n throw new RuntimeException(\"Could not initalize TLS configuration: \", ex);\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/467737.java 139 148\n/home/jeff/BigCloneBench/sample/selected/467737.java 206 216\n----------------------------------------\n public String getTextValue(String parentTag, String elementName) {\n Document rootDom = this.getDom();\n NodeList nl = rootDom.getElementsByTagName(parentTag);\n Element ele = null;\n if (nl != null && nl.getLength() > 0) {\n ele = (Element) nl.item(0);\n return getTextValue(ele, elementName);\n }\n return null;\n }\n\n----------------------------------------\n public ArrayList getElementsUnderSpecifiedElement(String elementName) {\n ArrayList resultList = new ArrayList();\n Document rootDom = this.getDom();\n NodeList nl = rootDom.getElementsByTagName(elementName);\n Element ele = null;\n if (nl != null && nl.getLength() > 0) {\n ele = (Element) nl.item(0);\n return getElementsUnderSpecifiedElement(ele);\n }\n return resultList;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/70505.java 631 648\n/home/jeff/BigCloneBench/sample/default/90537.java 631 648\n----------------------------------------\n private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeSeries(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeSeries(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/73729.java 133 146\n/home/jeff/BigCloneBench/sample/default/73729.java 356 366\n----------------------------------------\n public void test3() throws Exception {\n String data = \",\";\n CsvReader reader = CsvReader.parse(data);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"\", reader.get(0));\n Assert.assertEquals(\"\", reader.get(1));\n Assert.assertEquals(',', reader.getDelimiter());\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(2, reader.getColumnCount());\n Assert.assertEquals(\",\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n Assert.assertEquals(\"\", reader.getRawRecord());\n reader.close();\n }\n\n----------------------------------------\n public void test17() throws Exception {\n String data = \"\\\"double\\\"\\\"\\\"\\\"double quotes\\\"\";\n CsvReader reader = CsvReader.parse(data);\n Assert.assertTrue(reader.readRecord());\n Assert.assertEquals(\"double\\\"\\\"double quotes\", reader.get(0));\n Assert.assertEquals(0L, reader.getCurrentRecord());\n Assert.assertEquals(1, reader.getColumnCount());\n Assert.assertEquals(\"\\\"double\\\"\\\"\\\"\\\"double quotes\\\"\", reader.getRawRecord());\n Assert.assertFalse(reader.readRecord());\n reader.close();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/104630.java 43 52\n/home/jeff/BigCloneBench/sample/default/103574.java 43 52\n----------------------------------------\n public void testCommas() {\n String sequence = \"1,2,3,4,5\";\n assertEquals(sequence, sequenceUsingDo(1, 5));\n assertEquals(sequence, sequenceUsingFor(1, 5));\n assertEquals(sequence, sequenceUsingWhile(1, 5));\n sequence = \"8\";\n assertEquals(sequence, sequenceUsingDo(8, 8));\n assertEquals(sequence, sequenceUsingFor(8, 8));\n assertEquals(sequence, sequenceUsingWhile(8, 8));\n }\n\n----------------------------------------\n public void testCommas() {\n String sequence = \"1,2,3,4,5\";\n assertEquals(sequence, sequenceUsingDo(1, 5));\n assertEquals(sequence, sequenceUsingFor(1, 5));\n assertEquals(sequence, sequenceUsingWhile(1, 5));\n sequence = \"8\";\n assertEquals(sequence, sequenceUsingDo(8, 8));\n assertEquals(sequence, sequenceUsingFor(8, 8));\n assertEquals(sequence, sequenceUsingWhile(8, 8));\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1017245.java 357 367\n/home/jeff/BigCloneBench/sample/selected/1017245.java 375 385\n----------------------------------------\n public void setMatrix(int i0, int i1, int j0, int j1, Matrix X) {\n try {\n for (int i = i0; i <= i1; i++) {\n for (int j = j0; j <= j1; j++) {\n A[i][j] = X.get(i - i0, j - j0);\n }\n }\n } catch (ArrayIndexOutOfBoundsException e) {\n throw new ArrayIndexOutOfBoundsException(\"Submatrix indices\");\n }\n }\n\n----------------------------------------\n public void setMatrix(int[] r, int[] c, Matrix X) {\n try {\n for (int i = 0; i < r.length; i++) {\n for (int j = 0; j < c.length; j++) {\n A[r[i]][c[j]] = X.get(i, j);\n }\n }\n } catch (ArrayIndexOutOfBoundsException e) {\n throw new ArrayIndexOutOfBoundsException(\"Submatrix indices\");\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/40097.java 64 71\n/home/jeff/BigCloneBench/sample/default/57783.java 54 62\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingDo(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n do {\n if (i > start) builder.append(',');\n builder.append(i);\n } while (++i <= stop);\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/76192.java 687 703\n/home/jeff/BigCloneBench/sample/default/95647.java 687 703\n----------------------------------------\n private static Properties loadConfig() {\n InputStream in = DcmDir.class.getResourceAsStream(\"dcmdir.cfg\");\n try {\n Properties retval = new Properties();\n retval.load(in);\n return retval;\n } catch (Exception e) {\n throw new RuntimeException(\"Could not read dcmdir.cfg\", e);\n } finally {\n if (in != null) {\n try {\n in.close();\n } catch (IOException ignore) {\n }\n }\n }\n }\n\n----------------------------------------\n private static Properties loadConfig() {\n InputStream in = DcmDir.class.getResourceAsStream(\"dcmdir.cfg\");\n try {\n Properties retval = new Properties();\n retval.load(in);\n return retval;\n } catch (Exception e) {\n throw new RuntimeException(\"Could not read dcmdir.cfg\", e);\n } finally {\n if (in != null) {\n try {\n in.close();\n } catch (IOException ignore) {\n }\n }\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/115118.java 260 270\n/home/jeff/BigCloneBench/sample/default/3389.java 260 270\n----------------------------------------\n public void list() throws IOException, TransformerConfigurationException {\n SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance();\n Templates xslt = loadDcmDirXSL(tf);\n DirReader reader = fact.newDirReader(dirFile);\n reader.getFileSetInfo().writeFile2(getTransformerHandler(tf, xslt, FILE_SET_INFO), dict, null, 128, null);\n try {\n list(\"\", reader.getFirstRecord(onlyInUse), tf, xslt);\n } finally {\n reader.close();\n }\n }\n\n----------------------------------------\n public void list() throws IOException, TransformerConfigurationException {\n SAXTransformerFactory tf = (SAXTransformerFactory) TransformerFactory.newInstance();\n Templates xslt = loadDcmDirXSL(tf);\n DirReader reader = fact.newDirReader(dirFile);\n reader.getFileSetInfo().writeFile2(getTransformerHandler(tf, xslt, FILE_SET_INFO), dict, null, 128, null);\n try {\n list(\"\", reader.getFirstRecord(onlyInUse), tf, xslt);\n } finally {\n reader.close();\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/70505.java 631 648\n/home/jeff/BigCloneBench/sample/default/6937.java 648 665\n----------------------------------------\n private boolean doPurgeStudy(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeSeries(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n private boolean doPurgeSeries(DirWriter w, DirRecord parent, int[] counter) throws IOException {\n boolean matchAll = true;\n LinkedList toRemove = new LinkedList();\n for (DirRecord rec = parent.getFirstChild(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeInstances(w, rec, counter)) {\n toRemove.add(rec);\n } else {\n matchAll = false;\n }\n }\n if (matchAll) {\n return true;\n }\n for (Iterator it = toRemove.iterator(); it.hasNext(); ) {\n counter[0] += w.remove((DirRecord) it.next());\n }\n return false;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/10720.java 325 337\n/home/jeff/BigCloneBench/sample/default/6871.java 325 337\n----------------------------------------\n int getTemplateCommand(String line) {\n int startMatch = line.indexOf(templateMarker) + templateMarker.length() + 1;\n if (DEBUG) System.out.println(\"getting template command :\" + line.substring(startMatch));\n for (int i = 0; i < commands.length; ++i) {\n String current = commands[i];\n if (line.regionMatches(startMatch, current, 0, current.length())) {\n params = line.substring(startMatch + current.length());\n if (DEBUG) System.out.println(\"command is \" + commands[i] + \". params =\" + params);\n return i;\n }\n }\n return INVALID_COMMAND;\n }\n\n----------------------------------------\n int getTemplateCommand(String line) {\n int startMatch = line.indexOf(templateMarker) + templateMarker.length() + 1;\n if (DEBUG) System.out.println(\"getting template command :\" + line.substring(startMatch));\n for (int i = 0; i < commands.length; ++i) {\n String current = commands[i];\n if (line.regionMatches(startMatch, current, 0, current.length())) {\n params = line.substring(startMatch + current.length());\n if (DEBUG) System.out.println(\"command is \" + commands[i] + \". params =\" + params);\n return i;\n }\n }\n return INVALID_COMMAND;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2465371.java 1418 1456\n/home/jeff/BigCloneBench/sample/selected/2465371.java 1504 1542\n----------------------------------------\n private static void sort1(byte x[], int off, int len) {\n if (len < 7) {\n for (int i = off; i < len + off; i++) for (int j = i; j > off && x[j - 1] > x[j]; j--) swap(x, j, j - 1);\n return;\n }\n int m = off + len / 2;\n if (len > 7) {\n int l = off;\n int n = off + len - 1;\n if (len > 40) {\n int s = len / 8;\n l = med3(x, l, l + s, l + 2 * s);\n m = med3(x, m - s, m, m + s);\n n = med3(x, n - 2 * s, n - s, n);\n }\n m = med3(x, l, m, n);\n }\n byte v = x[m];\n int a = off, b = a, c = off + len - 1, d = c;\n while (true) {\n while (b <= c && x[b] <= v) {\n if (x[b] == v) swap(x, a++, b);\n b++;\n }\n while (c >= b && x[c] >= v) {\n if (x[c] == v) swap(x, c, d--);\n c--;\n }\n if (b > c) break;\n swap(x, b++, c--);\n }\n int s, n = off + len;\n s = Math.min(a - off, b - a);\n vecswap(x, off, b - s, s);\n s = Math.min(d - c, n - d - 1);\n vecswap(x, b, n - s, s);\n if ((s = b - a) > 1) sort1(x, off, s);\n if ((s = d - c) > 1) sort1(x, n - s, s);\n }\n\n----------------------------------------\n private static void sort1(double x[], int off, int len) {\n if (len < 7) {\n for (int i = off; i < len + off; i++) for (int j = i; j > off && x[j - 1] > x[j]; j--) swap(x, j, j - 1);\n return;\n }\n int m = off + len / 2;\n if (len > 7) {\n int l = off;\n int n = off + len - 1;\n if (len > 40) {\n int s = len / 8;\n l = med3(x, l, l + s, l + 2 * s);\n m = med3(x, m - s, m, m + s);\n n = med3(x, n - 2 * s, n - s, n);\n }\n m = med3(x, l, m, n);\n }\n double v = x[m];\n int a = off, b = a, c = off + len - 1, d = c;\n while (true) {\n while (b <= c && x[b] <= v) {\n if (x[b] == v) swap(x, a++, b);\n b++;\n }\n while (c >= b && x[c] >= v) {\n if (x[c] == v) swap(x, c, d--);\n c--;\n }\n if (b > c) break;\n swap(x, b++, c--);\n }\n int s, n = off + len;\n s = Math.min(a - off, b - a);\n vecswap(x, off, b - s, s);\n s = Math.min(d - c, n - d - 1);\n vecswap(x, b, n - s, s);\n if ((s = b - a) > 1) sort1(x, off, s);\n if ((s = d - c) > 1) sort1(x, n - s, s);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/676014.java 55 67\n/home/jeff/BigCloneBench/sample/selected/2242458.java 241 253\n----------------------------------------\n public IStructuredSelection findSelection(IEditorInput anInput) {\n IDiagramDocument document = SiseorDiagramEditorPlugin.getInstance().getDocumentProvider().getDiagramDocument(anInput);\n if (document == null) {\n return StructuredSelection.EMPTY;\n }\n Diagram diagram = document.getDiagram();\n IFile file = WorkspaceSynchronizer.getFile(diagram.eResource());\n if (file != null) {\n SiseorNavigatorItem item = new SiseorNavigatorItem(diagram, file, false);\n return new StructuredSelection(item);\n }\n return StructuredSelection.EMPTY;\n }\n\n----------------------------------------\n private ISelection getNavigatorSelection() {\n IDiagramDocument document = getDiagramDocument();\n if (document == null) {\n return StructuredSelection.EMPTY;\n }\n Diagram diagram = document.getDiagram();\n IFile file = WorkspaceSynchronizer.getFile(diagram.eResource());\n if (file != null) {\n PlwebNavigatorItem item = new PlwebNavigatorItem(diagram, file, false);\n return new StructuredSelection(item);\n }\n return StructuredSelection.EMPTY;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/41265.java 243 252\n/home/jeff/BigCloneBench/sample/default/21681.java 243 252\n----------------------------------------\n private TransformerHandler getTransformerHandler(SAXTransformerFactory tf, Templates tpl, String dsprompt) throws TransformerConfigurationException, IOException {\n TransformerHandler th = tf.newTransformerHandler(tpl);\n th.setResult(new StreamResult(System.out));\n Transformer t = th.getTransformer();\n t.setParameter(\"maxlen\", maxlen);\n t.setParameter(\"vallen\", vallen);\n t.setParameter(\"vallen\", vallen);\n t.setParameter(\"dsprompt\", dsprompt);\n return th;\n }\n\n----------------------------------------\n private TransformerHandler getTransformerHandler(SAXTransformerFactory tf, Templates tpl, String dsprompt) throws TransformerConfigurationException, IOException {\n TransformerHandler th = tf.newTransformerHandler(tpl);\n th.setResult(new StreamResult(System.out));\n Transformer t = th.getTransformer();\n t.setParameter(\"maxlen\", maxlen);\n t.setParameter(\"vallen\", vallen);\n t.setParameter(\"vallen\", vallen);\n t.setParameter(\"dsprompt\", dsprompt);\n return th;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2096828.java 349 359\n/home/jeff/BigCloneBench/sample/selected/2069719.java 366 376\n----------------------------------------\n public static int nullSafeHashCode(byte[] array) {\n if (array == null) {\n return 0;\n }\n int hash = INITIAL_HASH;\n int arraySize = array.length;\n for (int i = 0; i < arraySize; i++) {\n hash = MULTIPLIER * hash + array[i];\n }\n return hash;\n }\n\n----------------------------------------\n public static int nullSafeHashCode(long[] array) {\n if (array == null) {\n return 0;\n }\n int hash = INITIAL_HASH;\n int arraySize = array.length;\n for (int i = 0; i < arraySize; i++) {\n hash = MULTIPLIER * hash + hashCode(array[i]);\n }\n return hash;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/3389.java 621 629\n/home/jeff/BigCloneBench/sample/default/87896.java 619 627\n----------------------------------------\n private int doPurge(DirWriter w) throws IOException {\n int[] counter = { 0 };\n for (DirRecord rec = w.getFirstRecord(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeStudy(w, rec, counter)) {\n counter[0] += w.remove(rec);\n }\n }\n return counter[0];\n }\n\n----------------------------------------\n private int doPurge(DirWriter w) throws IOException {\n int[] counter = { 0 };\n for (DirRecord rec = w.getFirstRecord(true); rec != null; rec = rec.getNextSibling(true)) {\n if (doPurgeStudy(w, rec, counter)) {\n counter[0] += w.remove(rec);\n }\n }\n return counter[0];\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/345560.java 608 619\n/home/jeff/BigCloneBench/sample/selected/345560.java 627 638\n----------------------------------------\n private void sampleJComboBoxActionPerformed(java.awt.event.ActionEvent evt) {\n if (sampleJComboBox.getSelectedIndex() == 0) {\n editSampleJButton.setEnabled(false);\n } else if (sampleJComboBox.getSelectedIndex() == sampleJComboBox.getItemCount() - 1) {\n editSampleJButton.setEnabled(false);\n sampleJComboBox.setSelectedIndex(0);\n new NewSampleDialog(this, true);\n } else {\n editSampleJButton.setEnabled(true);\n }\n validateInput();\n }\n\n----------------------------------------\n private void protocolJComboBoxActionPerformed(java.awt.event.ActionEvent evt) {\n if (protocolJComboBox.getSelectedIndex() == 0) {\n editProtocolJButton.setEnabled(false);\n } else if (protocolJComboBox.getSelectedIndex() == protocolJComboBox.getItemCount() - 1) {\n editProtocolJButton.setEnabled(false);\n protocolJComboBox.setSelectedIndex(0);\n new NewProtocolDialog(this, true);\n } else {\n editProtocolJButton.setEnabled(true);\n }\n validateInput();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2181514.java 120 131\n/home/jeff/BigCloneBench/sample/selected/699527.java 23 34\n----------------------------------------\n public static void copyFile(File in, File out, boolean append) throws IOException {\n FileChannel inChannel = new FileInputStream(in).getChannel();\n FileChannel outChannel = new FileOutputStream(out, append).getChannel();\n try {\n inChannel.transferTo(0, inChannel.size(), outChannel);\n } catch (IOException e) {\n throw e;\n } finally {\n if (inChannel != null) inChannel.close();\n if (outChannel != null) outChannel.close();\n }\n }\n\n----------------------------------------\n public static void copyFile(File in, File out) throws IOException {\n FileChannel inChannel = new FileInputStream(in).getChannel();\n FileChannel outChannel = new FileOutputStream(out).getChannel();\n try {\n inChannel.transferTo(0, inChannel.size(), outChannel);\n } catch (IOException e) {\n throw e;\n } finally {\n if (inChannel != null) inChannel.close();\n if (outChannel != null) outChannel.close();\n }\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/85301.java 73 82\n/home/jeff/BigCloneBench/sample/default/72306.java 64 71\n----------------------------------------\n String sequenceUsingWhile(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n int i = start;\n while (i <= stop) {\n if (i > start) builder.append(',');\n builder.append(i);\n i++;\n }\n return builder.toString();\n }\n\n----------------------------------------\n String sequenceUsingFor(int start, int stop) {\n StringBuilder builder = new StringBuilder();\n for (int i = start; i <= stop; i++) {\n if (i > start) builder.append(',');\n builder.append(i);\n }\n return builder.toString();\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/default/110979.java 50 61\n/home/jeff/BigCloneBench/sample/default/87351.java 50 61\n----------------------------------------\n public List tokenize(String s, List result) {\n StringTokenizer stk = new StringTokenizer(s, \", \");\n while (stk.hasMoreTokens()) {\n String tk = stk.nextToken();\n if (tk.startsWith(\"$\")) {\n tokenize(getProperty(tk.substring(1), \"\"), result);\n } else {\n result.add(tk);\n }\n }\n return result;\n }\n\n----------------------------------------\n public List tokenize(String s, List result) {\n StringTokenizer stk = new StringTokenizer(s, \", \");\n while (stk.hasMoreTokens()) {\n String tk = stk.nextToken();\n if (tk.startsWith(\"$\")) {\n tokenize(getProperty(tk.substring(1), \"\"), result);\n } else {\n result.add(tk);\n }\n }\n return result;\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/1882693.java 962 973\n/home/jeff/BigCloneBench/sample/selected/2215261.java 963 974\n----------------------------------------\n public InputStream(java.io.InputStream in, int options) {\n super(in);\n this.breakLines = (options & DONT_BREAK_LINES) != DONT_BREAK_LINES;\n this.encode = (options & ENCODE) == ENCODE;\n this.bufferLength = encode ? 4 : 3;\n this.buffer = new byte[bufferLength];\n this.position = -1;\n this.lineLength = 0;\n this.options = options;\n this.alphabet = getAlphabet(options);\n this.decodabet = getDecodabet(options);\n }\n\n----------------------------------------\n public InputStream(java.io.InputStream in, int options) {\n super(in);\n this.breakLines = (options & DONT_BREAK_LINES) != DONT_BREAK_LINES;\n this.encode = (options & ENCODE) == ENCODE;\n this.bufferLength = encode ? 4 : 3;\n this.buffer = new byte[bufferLength];\n this.position = -1;\n this.lineLength = 0;\n this.options = options;\n this.alphabet = getAlphabet(options);\n this.decodabet = getDecodabet(options);\n }\n\n----------------------------------------\n$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$\n/home/jeff/BigCloneBench/sample/selected/2530759.java 352 367\n/home/jeff/BigCloneBench/sample/selected/472295.java 343 357\n----------------------------------------\n public void newProperties(PropertySheet ps) throws PropertyException {\n logger = ps.getLogger();\n propsFile = ps.getString(PROP_PROPERTIES_FILE, PROP_PROPERTIES_FILE_DEFAULT);\n logMath = (LogMath) ps.getComponent(PROP_LOG_MATH, LogMath.class);\n unitManager = (UnitManager) ps.getComponent(PROP_UNIT_MANAGER, UnitManager.class);\n binary = ps.getBoolean(PROP_IS_BINARY, getIsBinaryDefault());\n sparseForm = ps.getBoolean(PROP_SPARSE_FORM, getSparseFormDefault());\n vectorLength = ps.getInt(PROP_VECTOR_LENGTH, getVectorLengthDefault());\n model = ps.getString(PROP_MODEL, getModelDefault());\n dataDir = ps.getString(PROP_DATA_LOCATION, getDataLocationDefault()) + \"/\";\n distFloor = ps.getFloat(PROP_MC_FLOOR, PROP_MC_FLOOR_DEFAULT);\n mixtureWeightFloor = ps.getFloat(PROP_MW_FLOOR, PROP_MW_FLOOR_DEFAULT);\n varianceFloor = ps.getFloat(PROP_VARIANCE_FLOOR, PROP_VARIANCE_FLOOR_DEFAULT);\n useCDUnits = ps.getBoolean(PROP_USE_CD_UNITS, PROP_USE_CD_UNITS_DEFAULT);\n fileNameClasseMllr = ps.getString(\"classeMllr\", \"\");\n }\n\n----------------------------------------\n public void newProperties(PropertySheet ps) throws PropertyException {\n logger = ps.getLogger();\n propsFile = ps.getString(PROP_PROPERTIES_FILE, PROP_PROPERTIES_FILE_DEFAULT);\n logMath = (LogMath) ps.getComponent(PROP_LOG_MATH, LogMath.class);\n unitManager = (UnitManager) ps.getComponent(PROP_UNIT_MANAGER, UnitManager.class);\n binary = ps.getBoolean(PROP_IS_BINARY, getIsBinaryDefault());\n sparseForm = ps.getBoolean(PROP_SPARSE_FORM, getSparseFormDefault());\n vectorLength = ps.getInt(PROP_VECTOR_LENGTH, getVectorLengthDefault());\n model = ps.getString(PROP_MODEL, getModelDefault());\n dataDir = ps.getString(PROP_DATA_LOCATION, getDataLocationDefault()) + \"/\";\n distFloor = ps.getFloat(PROP_MC_FLOOR, PROP_MC_FLOOR_DEFAULT);\n mixtureWeightFloor = ps.getFloat(PROP_MW_FLOOR, PROP_MW_FLOOR_DEFAULT);\n varianceFloor = ps.getFloat(PROP_VARIANCE_FLOOR, PROP_VARIANCE_FLOOR_DEFAULT);\n useCDUnits = ps.getBoolean(PROP_USE_CD_UNITS, PROP_USE_CD_UNITS_DEFAULT);\n }\n\n----------------------------------------\n", "encoding": "utf-8"} |