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Calls Terminating in Network Operations

sd_cardI/O Operations
org.apache.tomcat.util
HttpDate.write(...) ...................... source
calls java.io.OutputStream.write(...)
org.broad.igv
DirectoryManager.canWrite(...) ........... source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.delete(...)
calls java.io.File.deleteOnExit(...)
calls java.io.File.createNewFile(...)
calls java.io.File.canWrite(...)
DirectoryManager.deleteDirectory(...) .... source -- Delete the directory and all contents recu...
calls java.io.File.getAbsolutePath(...)
DirectoryManager.getCacheDirectory(...) .. source
calls java.io.File.exists(...)
calls java.io.File.File(...)
calls java.io.File.mkdir(...)
DirectoryManager.getFastaCacheDirectory(...) source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.isDirectory(...)
calls java.io.File.mkdir(...)
DirectoryManager.getGeneListDirectory(...) source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
calls java.io.File.canRead(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.canWrite(...)
DirectoryManager.getGenomeCacheDirectory(...) source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
calls java.io.File.canRead(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.canWrite(...)
DirectoryManager.getIgvDirectory(...) .... source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
calls java.io.PrintStream.println(...)
calls java.io.File.File(...)
calls java.io.File.getParentFile(...)
calls java.io.File.canRead(...)
DirectoryManager.getIgvDirectoryOverride(...) source
calls java.io.File.File(...)
calls java.io.File.exists(...)
DirectoryManager.getLegacyIGVDirectory(...) source -- REturn the pre 2.1 release IGV directory. ...
calls java.io.File.File(...)
DirectoryManager.getLegacyPreferencesFile(...) source -- Return the pre 2.1 release properties file...
calls java.io.File.File(...)
DirectoryManager.getLogFile(...) ......... source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.createNewFile(...)
DirectoryManager.getPreferencesFile(...) . source -- Return the user preferences property file ...
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.createNewFile(...)
DirectoryManager.getSamDirectory(...) .... source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
DirectoryManager.getUserHome(...) ........ source
calls java.io.File.File(...)
DirectoryManager.initializeLog(...) ...... source
calls java.io.File.getAbsolutePath(...)
DirectoryManager.isChildOf(...) .......... source
calls java.io.File.getParentFile(...)
calls java.io.File.equals(...)
DirectoryManager.moveDirectoryContents(...) source
calls java.io.File.exists(...)
calls java.io.File.isDirectory(...)
calls java.io.File.listFiles(...)
calls java.io.File.toPath(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
DirectoryManager.moveIGVDirectory(...) ... source -- Move the "igv" directory to a new location...
calls java.io.File.equals(...)
calls java.io.File.exists(...)
calls java.io.File.getParent(...)
calls java.io.File.getAbsolutePath(...)
DirectoryManager.setIgvDirectory(...) .... source
calls java.io.File.getAbsolutePath(...)
org.broad.igv.batch
BatchRunner.isBatchFile(...) ............. source -- Returns true if this is "provably" a batch...
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
BatchRunner.run(...) ..................... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
CommandExecutor.createParents(...) ....... source
calls java.io.File.getParentFile(...)
calls java.io.File.exists(...)
calls java.io.File.mkdirs(...)
CommandExecutor.createSnapshot(...) ...... source
calls java.io.File.getAbsoluteFile(...)
calls java.io.File.getParentFile(...)
calls java.io.File.exists(...)
calls java.io.File.File(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.PrintStream.println(...)
CommandExecutor.getFile(...) ............. source
calls java.io.File.File(...)
calls java.io.File.isAbsolute(...)
CommandExecutor.goto1(...) ............... source
calls java.io.PrintStream.println(...)
CommandExecutor.loadFiles(...) ........... source -- Load files -- used by port, batch, and htt...
calls java.io.File.File(...)
calls java.io.File.exists(...)
CommandExecutor.setSnapshotDirectory(...) source -- Set a directory to deposit image snapshots
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
CommandListener.processClientSession(...) source -- Process a client session. Loop continuousl...
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.flush(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
CommandListener.sendHTTPResponse(...) .... source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
Exec.main(...) ........................... source
calls java.io.OutputStreamWriter.OutputStreamWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.flush(...)
calls java.io.OutputStream.close(...)
calls java.io.InputStream.read(...)
calls java.io.PrintStream.print(...)
TestClient.main(...) ..................... source
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.PrintStream.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
TestClient.runBatchFile(...) ............. source
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintStream.println(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
TestClient.testMultiLocus(...) ........... source
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintStream.println(...)
org.broad.igv.bbfile ......................... -- Created by IntelliJ IDEA. User: martind Da...
BBFileHeader.print(...) .................. source
calls java.io.PrintStream.println(...)
BBFileHeader.readBBFileHeader(...) ....... source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readUnsignedShort(...)
calls java.io.DataInputStream.readLong(...)
BBFileReader.readNullTerminatedString(...) source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.InputStream.read(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
BBTotalSummaryBlock.BBTotalSummaryBlock(...) source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readLong(...)
calls java.io.DataInputStream.readFloat(...)
BBZoomLevelFormat.BBZoomLevelFormat(...) . source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
BBZoomLevelHeader.print(...) ............. source
calls java.io.PrintStream.println(...)
BBZoomLevelHeader.readZoomLevelHeader(...) source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readLong(...)
BPTree.readBPTreeNode(...) ............... source
calls java.io.DataInputStream.readByte(...)
calls java.io.DataInputStream.readUnsignedShort(...)
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readLong(...)
BPTreeHeader.readHeader(...) ............. source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readLong(...)
BedFeature.print(...) .................... source
calls java.io.PrintStream.println(...)
BigBedDataBlock.BigBedDataBlock(...) ..... source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
BigBedDataBlock.getBedData(...) .......... source
calls java.io.DataInputStream.readInt(...)
BigBedDataBlock.readHighToLowString(...) . source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.FilterInputStream.read(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
BigWigSection.BigWigSection(...) ......... source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
BigWigSection.getSectionData(...) ........ source
calls java.io.DataInputStream.readFloat(...)
calls java.io.DataInputStream.readInt(...)
BigWigSectionHeader.BigWigSectionHeader(...) source
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readByte(...)
calls java.io.DataInputStream.readUnsignedShort(...)
RPTree.readRPTreeNode(...) ............... source
calls java.io.DataInputStream.readByte(...)
calls java.io.DataInputStream.readUnsignedShort(...)
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readLong(...)
RPTreeHeader.readHeader(...) ............. source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readLong(...)
ZoomDataBlock.ZoomDataBlock(...) ......... source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
ZoomDataBlock.getZoomData(...) ........... source
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readFloat(...)
org.broad.igv.bedpe
BedPEParser.parse(...) ................... source
calls java.io.BufferedReader.readLine(...)
BedPEUtils.interactionToBedPE(...) ....... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintStream.println(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
BedPEUtils.juiceboxToBedPE(...) .......... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintStream.println(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.blast
BlastParser.parse(...) ................... source -- Method description <p/> queryID,subjectID,...
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
Region.toBed(...) ........................ source
calls java.io.StringWriter.StringWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
calls java.io.StringWriter.toString(...)
org.broad.igv.data
IGVDatasetParser.scan(...) ............... source -- Scan the datafile for chromosome breaks.
calls java.io.InputStream.close(...)
ZipUtils.getCrc(...) ..................... source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.InputStream.read(...)
calls java.io.BufferedInputStream.close(...)
ZipUtils.zipDirRecursive(...) ............ source
calls java.io.File.list(...)
calls java.io.File.listFiles(...)
calls java.io.File.isDirectory(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.length(...)
calls java.io.InputStream.read(...)
calls java.io.FileInputStream.close(...)
ZipUtils.zipDirectory(...) ............... source
calls java.io.FileOutputStream.FileOutputStream(...)
org.broad.igv.data.expression
ExpressionFileParser.ExpressionFileParser(...) source
calls java.io.File.getAbsolutePath(...)
ExpressionFileParser.findHeaderLine(...) . source
calls java.io.BufferedReader.readLine(...)
ExpressionFileParser.isGCT(...) .......... source -- Test to determine if the path referes to a...
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
ExpressionFileParser.parse(...) .......... source -- Parse the file and return a Dataset
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
ExpressionFileParser.parseHeader(...) .... source
calls java.io.BufferedReader.readLine(...)
GeneToLocusHelper.loadProbeMap(...) ...... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
ProbeToLocusMap.loadMapping(...) ......... source
calls java.io.BufferedReader.readLine(...)
ProbeToLocusMap.loadMapping(...) ......... source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.InputStream.close(...)
org.broad.igv.data.seg
FreqData.dumpData(...) ................... source
calls java.io.PrintStream.println(...)
SegmentedBinaryLocalReader.readAsFloats(...) source -- Read the content of a zip entry as an arra...
calls java.io.File.File(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readFloat(...)
SegmentedBinaryLocalReader.readAsInts(...) source -- Read the contents of a zip entry as an arr...
calls java.io.File.File(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
SegmentedBinaryLocalReader.readAsStrings(...) source
calls java.io.File.File(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
SegmentedBinaryLocalReader.readChromosomeData(...) source
calls java.io.File.File(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
SegmentedChromosomeData.deserialize(...) . source -- Initialize the object by deserializing the...
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readChar(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readFloat(...)
SegmentedChromosomeData.serialize(...) ... source -- Serialize this instance to a stream. <p/> ...
calls java.io.BufferedOutputStream.BufferedOutputStream(...)
calls java.io.DataOutputStream.DataOutputStream(...)
calls java.io.DataOutputStream.writeChars(...)
calls java.io.DataOutputStream.writeChar(...)
calls java.io.DataOutputStream.writeInt(...)
calls java.io.DataOutputStream.writeFloat(...)
calls java.io.DataOutputStream.flush(...)
org.broad.igv.feature
AbstractFeatureParser.dumpFeatures(...) .. source -- Convenience method. Write a list of featur...
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
AbstractFeatureParser.loadFeatures(...) .. source -- Load all features in this file.
calls java.io.BufferedReader.readLine(...)
AminoAcidManager.initAANameMap(...) ...... source -- Initialize table of amino acid names, for ...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
AminoAcidManager.readJSONFromStream(...) . source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
BasePairFileUtils.loadConnectTable(...) .. source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
BasePairFileUtils.loadDotBracket(...) .... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
BasePairFileUtils.loadPairingProb(...) ... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
BasePairFileUtils.writeBasePairFile(...) . source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
CytoBandFileParser.loadData(...) ......... source -- Method description
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
EmblFeatureTableParser.combineFeatureTables(...) source
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
EmblFeatureTableParser.extractGenes(...) . source -- Utility method to extract the gene records...
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
EmblFeatureTableParser.loadFeatures(...) . source -- Method description
calls java.io.BufferedReader.readLine(...)
EmblFeatureTableParser.loadTracks(...) ... source -- Method description
calls java.io.BufferedReader.close(...)
EmblFeatureTableParser.parseJoinString(...) source -- FT CDS join(complement(5000933..5001976), ...
calls java.io.BufferedReader.readLine(...)
EmblFeatureTableParser.splitByType(...) .. source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.computeBedDensity(...) .. source -- Compute feature density in units of # / wi...
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.covertProbeMapToBedFile(...) source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.createCanonicalGeneFile(...) source -- Create a "canonical" gene file from an ann...
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.createImports(...) ...... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.createTSSFile(...) ...... source -- Create a bed file of "TSS regions", define...
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.probeToBed(...) ......... source -- Utility to convert a file with the followi...
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.refgeneToBed(...) ....... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.splitEmblFileByType(...) source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.splitGffFileByType(...) . source -- Given a GFF File, creates a new GFF file f...
calls java.io.BufferedReader.readLine(...)
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.close(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintStream.println(...)
calls java.io.PrintWriter.close(...)
FeatureFileUtils.splitRepeatMasker(...) .. source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.File.File(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FeatureUtils.exportEDX(...) .............. source -- Export a gene in "edx" format LYZ hg19 12 ...
calls java.io.PrintStream.println(...)
calls java.io.PrintStream.print(...)
GFFParser.loadFeatures(...) .............. source
calls java.io.BufferedReader.readLine(...)
GFFParser.main(...) ...................... source
calls java.io.PrintStream.println(...)
ShapeFileUtils.loadShape(...) ............ source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
ShapeFileUtils.writeWigFile(...) ......... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
org.broad.igv.feature.bionano
SMAPParser.parseFeatures(...) ............ source
calls java.io.BufferedReader.readLine(...)
org.broad.igv.feature.genome
ChromSizesParser.parse(...) .............. source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
GenbankParser.readFeatures(...) .......... source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.close(...)
GenbankParser.readFeatures(...) .......... source -- FEATURES Location/Qualifiers source 1..105...
calls java.io.BufferedReader.readLine(...)
GenbankParser.readFeatures(...) .......... source
calls java.io.BufferedReader.close(...)
GenbankParser.readFeatures_(...) ......... source
calls java.io.BufferedReader.readLine(...)
GenbankParser.readLocus(...) ............. source -- Read the locus line LOCUS NT_030059 105338...
calls java.io.BufferedReader.readLine(...)
GenbankParser.readOriginSequence(...) .... source -- Read the origin section. Example... <p/> O...
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.OutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
Genome.getSpeciesForID(...) .............. source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.InputStream.close(...)
GenomeBuilderDialog.chooseArchiveFile(...) source
calls java.io.File.File(...)
GenomeBuilderPane.chrAliasButtonActionPerformed(...) source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getParentFile(...)
GenomeBuilderPane.cytobandFileButtonActionPerformed(...) source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getParentFile(...)
GenomeBuilderPane.fastaFileButtonActionPerformed(...) source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getParentFile(...)
GenomeBuilderPane.refFlatFileButtonActionPerformed(...) source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getParentFile(...)
GenomeBuilderPane.showGenomeArchiveDirectoryChooser(...) source
calls java.io.File.File(...)
calls java.io.File.getName(...)
calls java.io.File.getParentFile(...)
calls java.io.File.getAbsolutePath(...)
GenomeDescriptor.GenomeDescriptor(...) ... source
calls java.io.File.exists(...)
calls java.io.File.File(...)
GenomeImporter.createGenomeArchive(...) .. source -- Create a zip containing all the informatio...
calls java.io.File.getAbsolutePath(...)
calls java.io.File.exists(...)
calls java.io.File.isDirectory(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
calls java.io.File.getParent(...)
calls java.io.OutputStreamWriter.close(...)
calls java.io.File.delete(...)
GenomeImporter.createGenomeArchive(...) .. source
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.OutputStream.write(...)
calls java.io.File.length(...)
calls java.io.File.getName(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.InputStream.read(...)
calls java.io.BufferedInputStream.close(...)
GenomeImporter.createGenomePropertyFile(...) source -- This method creates the property.txt file ...
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.OutputStreamWriter.OutputStreamWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.File.getName(...)
calls java.io.PrintWriter.flush(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
calls java.io.PrintWriter.close(...)
GenomeImporter.getSequenceFiles(...) ..... source
calls java.io.File.listFiles(...)
calls java.io.File.getName(...)
calls java.io.File.isDirectory(...)
GenomeManager.clearGenomeCache(...) ...... source -- Delete .genome files from the cache directory
calls java.io.File.listFiles(...)
calls java.io.File.getName(...)
calls java.io.File.delete(...)
GenomeManager.defineGenome(...) .......... source -- Create a genome archive (.genome) file.
calls java.io.File.getParentFile(...)
calls java.io.File.File(...)
calls java.io.File.getAbsolutePath(...)
GenomeManager.downloadFasta(...) ......... source -- Download a fasta file and associated index...
calls java.io.File.File(...)
GenomeManager.generateGenomeList(...) .... source -- Given a directory, looks for all .genome f...
calls java.io.File.listFiles(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
GenomeManager.getArchiveFile(...) ........ source -- Returns a File of the provided genomePath....
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
calls java.io.File.File(...)
GenomeManager.getFullPath(...) ........... source
calls java.io.File.File(...)
calls java.io.File.isAbsolute(...)
calls java.io.File.getParent(...)
calls java.io.File.getCanonicalPath(...)
GenomeManager.loadChrAliases(...) ........ source
calls java.io.BufferedReader.readLine(...)
GenomeManager.loadChrAliases(...) ........ source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.close(...)
GenomeManager.loadChrAliases(...) ........ source -- Load the chromosome alias file, if any, sp...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.InputStream.close(...)
GenomeManager.loadCytobandFile(...) ...... source -- Load the cytoband file specified in the ge...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.InputStream.close(...)
GenomeManager.loadDotGenomeFile(...) ..... source -- Create a genome from a ".genome" file. In ...
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.InputStream.close(...)
GenomeManager.loadFastaFile(...) ......... source -- Create a Genome from a single fasta file.
calls java.io.File.getAbsolutePath(...)
calls java.io.IOException.IOException(...)
GenomeManager.loadGenome(...) ............ source
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
GenomeManager.loadSequenceMap(...) ....... source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.BufferedReader.close(...)
GenomeManager.parseGenomeArchiveFile(...) source -- Creates a genome descriptor.
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.FileNotFoundException.FileNotFoundException(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.FileInputStream.close(...)
GenomeManager.refreshCache(...) .......... source -- Refresh a locally cached genome if appropr...
calls java.io.File.exists(...)
calls java.io.File.lastModified(...)
GenomeManager.updateSequenceMapFile(...) . source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
GenomeUtils.exportChromSizes(...) ........ source -- Export a "chrom.sizes" file for the specif...
calls java.io.File.File(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
GenomeUtils.findNonFastas(...) ........... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintStream.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
GenomeUtils.main(...) .................... source
calls java.io.File.File(...)
GenomeUtils.mergeINCDCNames(...) ......... source -- Merge chromosome names from an NCBI assemb...
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.PrintStream.println(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
GenomeUtils.updateChromSizes(...) ........ source -- Create .chrom.sizes file for each genome f...
calls java.io.BufferedReader.readLine(...)
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.PrintStream.println(...)
calls java.io.BufferedReader.close(...)
RemoveGenomesDialog.deleteDownloadedGenomes(...) source -- Delete the specified .genome files.
calls java.io.File.delete(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
calls java.io.File.exists(...)
org.broad.igv.feature.genome.fasta
FastaBlockCompressedSequence.readFully(...) source
calls java.io.InputStream.read(...)
calls java.io.EOFException.EOFException(...)
FastaBlockCompressedSequence.readGziMappings(...) source
calls java.io.BufferedInputStream.BufferedInputStream(...)
FastaIndex.parseIndexFile(...) ........... source -- Parse the contents of an index file <p/> E...
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
FastaIndexedSequence.getSequence(...) .... source -- Return the sequence for the query interval...
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
FastaSequenceParser.parseFasta(...) ...... source -- Read an entire fasta file, which might be ...
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
calls java.io.ByteArrayOutputStream.reset(...)
calls java.io.OutputStream.write(...)
calls java.io.BufferedReader.close(...)
FastaUtils.createIndexFile(...) .......... source -- Creates an index for the provided fasta fi...
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.BufferedWriter.close(...)
FastaUtils.regularizeFastaFile(...) ...... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
FastaUtils.writeLine(...) ................ source
calls java.io.Writer.write(...)
org.broad.igv.feature.sprite
ClusterParser.parse(...) ................. source
calls java.io.BufferedReader.readLine(...)
org.broad.igv.feature.tribble
CodecFactory.getVCFCodec(...) ............ source -- Return the appropriate VCFCodec based on t...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
EMBLTableCodec.EmblTableIterator.EmblTableIterator(...) source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
EMBLTableCodec.EmblTableIterator.close(...) source
calls java.io.BufferedReader.close(...)
EMBLTableCodec.EmblTableIterator.next(...) source
calls java.io.BufferedReader.readLine(...)
EMBLTableCodec.EmblTableIterator.parseJoinString(...) source -- FT CDS join(complement(5000933..5001976), ...
calls java.io.BufferedReader.readLine(...)
MUTCodec.isMutationAnnotationFile(...) ... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.goby ........................... -- This package provides Goby support for IGV.
GobyAlignmentQueryReader.GobyAlignmentQueryReader(...) source -- Construct a query reader for this filename...
calls java.io.PrintStream.println(...)
GobyCountArchiveDataSource.GobyCountArchiveDataSource(...) source
calls java.io.File.getPath(...)
org.broad.igv.google
Ga4ghAPIHelper.doPost(...) ............... source
calls java.io.OutputStream.write(...)
calls java.io.OutputStream.close(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
Ga4ghAPIHelper.getErrorMessage(...) ...... source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
GoogleUtils.main(...) .................... source
calls java.io.PrintStream.println(...)
OAuthProvider.OAuthProvider(...) ......... source
calls java.io.IOException.IOException(...)
OAuthProvider.findUrlsInSessionFile(...) . source -- Generate a set of all urls in the session ...
calls java.io.File.File(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
OAuthUtils.fetchOauthProperties(...) ..... source
calls java.io.File.File(...)
calls java.io.File.exists(...)
org.broad.igv.gwas
EqtlPreprocessor.main(...) ............... source
calls java.io.File.listFiles(...)
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
EqtlPreprocessor.process(...) ............ source
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintStream.println(...)
calls java.io.FileOutputStream.close(...)
calls java.io.BufferedReader.close(...)
EqtlPreprocessor.write(...) .............. source
calls java.io.OutputStream.write(...)
EqtlPreprocessor.writeIndexPosition(...) . source
calls java.io.RandomAccessFile.RandomAccessFile(...)
calls java.io.RandomAccessFile.getChannel(...)
calls java.io.RandomAccessFile.write(...)
calls java.io.RandomAccessFile.close(...)
GWASParser.main(...) ..................... source
calls java.io.PrintStream.println(...)
GWASParser.parse(...) .................... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.lists
GeneListEditDialog.parseBed(...) ......... source
calls java.io.StringReader.StringReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
GeneListManager.deleteGroup(...) ......... source
calls java.io.File.exists(...)
calls java.io.File.delete(...)
GeneListManager.deleteList(...) .......... source -- Return true if a group was also removed.
calls java.io.File.exists(...)
calls java.io.File.delete(...)
GeneListManager.exportGMT(...) ........... source -- #name=Example gene lists Proneural dev gen...
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
GeneListManager.importFile(...) .......... source
calls java.io.File.getPath(...)
calls java.io.File.getName(...)
calls java.io.File.getParentFile(...)
calls java.io.File.equals(...)
calls java.io.File.File(...)
GeneListManager.loadBEDFile(...) ......... source
calls java.io.File.File(...)
calls java.io.File.getName(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
GeneListManager.loadDefaultLists(...) .... source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.close(...)
GeneListManager.loadGMTFile(...) ......... source
calls java.io.BufferedReader.close(...)
GeneListManager.loadGMTFile(...) ......... source
calls java.io.BufferedReader.readLine(...)
GeneListManager.loadGRPFile(...) ......... source
calls java.io.File.File(...)
calls java.io.File.getName(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
GeneListManager.loadUserLists(...) ....... source
calls java.io.File.exists(...)
calls java.io.File.listFiles(...)
calls java.io.File.getPath(...)
GeneListManager.saveGeneList(...) ........ source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
calls java.io.File.getAbsolutePath(...)
GeneListManagerUI.exportButtonActionPerformed(...) source -- Export the selected group to a GMT file
calls java.io.File.File(...)
org.broad.igv.maf
MAFIndex.loadIndex(...) .................. source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
MAFIndex.writeIndex(...) ................. source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
MAFListReader.loadDictionaryFile(...) .... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
MAFListReader.loadSpeciesNames(...) ...... source -- Load a file containing species IDs and names.
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.InputStream.close(...)
MAFParser.loadAlignments(...) ............ source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
MAFParser.parseBlock(...) ................ source -- Parse an alignment block.
calls java.io.BufferedReader.readLine(...)
MAFParser.parseHeader(...) ............... source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
MAFTileCodec.decode(...) ................. source
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readUTF(...)
MAFTileCodec.encode(...) ................. source -- Serialize an MATile to a stream
calls java.io.DataOutputStream.writeInt(...)
calls java.io.DataOutputStream.writeUTF(...)
calls java.io.DataOutputStream.flush(...)
MAFUtils.createTestFile(...) ............. source -- Create a test file by keeping a sampling o...
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
MAFtoSAM.addHeaderAndSort(...) ........... source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.flush(...)
calls java.io.PrintWriter.close(...)
MAFtoSAM.convert(...) .................... source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.flush(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
calls java.io.File.deleteOnExit(...)
MAFtoSAM.outputHeader(...) ............... source
calls java.io.PrintWriter.println(...)
MAFtoSAM.parseBlock(...) ................. source
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintStream.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
org.broad.igv.prefs
IGVPreferences.getDefineGenomeInputDirectory(...) source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
IGVPreferences.getLastExportedRegionDirectory(...) source
calls java.io.File.File(...)
IGVPreferences.getLastGenomeImportDirectory(...) source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
IGVPreferences.getLastSnapshotDirectory(...) source
calls java.io.File.File(...)
IGVPreferences.getLastTrackDirectory(...) source
calls java.io.File.File(...)
IGVPreferences.print(...) ................ source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
IGVPreferences.setDefineGenomeInputDirectory(...) source
calls java.io.File.getAbsolutePath(...)
IGVPreferences.setLastExportedRegionDirectory(...) source
calls java.io.File.getAbsolutePath(...)
IGVPreferences.setLastGenomeImportDirectory(...) source
calls java.io.File.getAbsolutePath(...)
IGVPreferences.setLastSnapshotDirectory(...) source
calls java.io.File.getAbsolutePath(...)
IGVPreferences.setLastTrackDirectory(...) source
calls java.io.File.isDirectory(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getParent(...)
PreferencesEditor.init(...) .............. source
calls java.io.File.getAbsolutePath(...)
PreferencesManager.load(...) ............. source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
PreferencesManager.loadDefaults23(...) ... source -- Load defaults form version 2.3. Catch any ...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
PreferencesManager.loadPreferenceList(...) source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
PreferencesManager.loadUserPreferences(...) source
calls java.io.File.getAbsolutePath(...)
PreferencesManager.storePreferences(...) . source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.flush(...)
calls java.io.PrintWriter.close(...)
calls java.io.OutputStreamWriter.close(...)
org.broad.igv.repeats
RepeatMaskSplitter.closeWriters(...) ..... source
calls java.io.PrintWriter.close(...)
RepeatMaskSplitter.main(...) ............. source
calls java.io.File.File(...)
RepeatMaskSplitter.split(...) ............ source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.File.getParentFile(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.File.File(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
org.broad.igv.sam
AlignmentTileLoader.receiveEvent(...) .... source
calls java.io.PrintStream.println(...)
HaplotypeUtils.V.add(...) ................ source
calls java.io.PrintStream.println(...)
HaplotypeUtils.V.distance(...) ........... source
calls java.io.PrintStream.println(...)
HaplotypeUtils.V.distance(...) ........... source
calls java.io.PrintStream.println(...)
HaplotypeUtils.V.updateLabel(...) ........ source
calls java.io.PrintStream.println(...)
SAMWriter.writeAlignmentFilePicard(...) .. source -- Use Picard to write alignment subset, as r...
calls java.io.File.File(...)
org.broad.igv.sam.cram
ReferenceDiskCache.checkCacheSize(...) ... source
calls java.io.File.exists(...)
calls java.io.File.listFiles(...)
calls java.io.File.delete(...)
calls java.io.File.length(...)
ReferenceDiskCache.deleteCache(...) ...... source
calls java.io.File.File(...)
calls java.io.File.delete(...)
ReferenceDiskCache.getCacheDirectory(...) source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
ReferenceDiskCache.readSequence(...) ..... source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.FileInputStream.close(...)
ReferenceDiskCache.saveSequence(...) ..... source
calls java.io.File.File(...)
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.OutputStream.write(...)
calls java.io.File.delete(...)
calls java.io.FileOutputStream.close(...)
org.broad.igv.sam.lite
BAMIndex.loadIndex(...) .................. source
calls java.io.BufferedInputStream.BufferedInputStream(...)
BAMReader.readString(...) ................ source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.EOFException.EOFException(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
BGUnzip.blockUnzip(...) .................. source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
org.broad.igv.sam.reader
AlignmentIndexer.createSamIndex(...) ..... source
calls java.io.File.getParent(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
AlignmentIndexer.createSamIndex(...) ..... source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.File.length(...)
calls java.io.PrintStream.println(...)
calls java.io.FileInputStream.close(...)
calls java.io.File.getName(...)
AlignmentIndexer.getInstance(...) ........ source
calls java.io.File.getName(...)
AlignmentIndexer.updateProgress(...) ..... source
calls java.io.PrintStream.println(...)
AlignmentReaderFactory.getBamListReader(...) source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
BAMReader.getSamReader(...) .............. source
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.File.File(...)
CGIAlignmentReader.getSequenceNames(...) . source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.InputStream.close(...)
CGIAlignmentReader.loadHeader(...) ....... source -- Try to load header, if there are any error...
calls java.io.InputStream.close(...)
CGIAlignmentReader.main(...) ............. source
calls java.io.PrintStream.println(...)
DotAlignedCodec.decode(...) .............. source
calls java.io.DataInputStream.readUTF(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readBoolean(...)
DotAlignedCodec.encode(...) .............. source
calls java.io.DataOutputStream.writeUTF(...)
calls java.io.DataOutputStream.writeInt(...)
calls java.io.DataOutputStream.writeBoolean(...)
DotAlignedCodec.setInputStream(...) ...... source
calls java.io.DataInputStream.DataInputStream(...)
DotAlignedCodec.setOutputStream(...) ..... source
calls java.io.DataOutputStream.DataOutputStream(...)
DotAlignedIndexer.DotAlignedIndexer(...) . source
calls java.io.File.getName(...)
DotAlignedParser.createAlignment(...) .... source
calls java.io.PrintStream.println(...)
FeatureIndex.FeatureIndex(...) ........... source
calls java.io.File.getAbsolutePath(...)
FeatureIndex.FeatureIndex(...) ........... source
calls java.io.InputStream.close(...)
FeatureIndex.read(...) ................... source -- Read the index. Translate the chromosome n...
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readUTF(...)
calls java.io.DataInputStream.readLong(...)
FeatureIndex.store(...) .................. source -- Store a SamIndex to a File.
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.BufferedOutputStream.BufferedOutputStream(...)
calls java.io.DataOutputStream.DataOutputStream(...)
calls java.io.DataOutputStream.writeInt(...)
calls java.io.DataOutputStream.writeUTF(...)
calls java.io.DataOutputStream.writeLong(...)
calls java.io.FilterOutputStream.close(...)
GeraldReader.GeraldReader(...) ........... source
calls java.io.FileInputStream.FileInputStream(...)
GeraldReader.close(...) .................. source
calls java.io.FileInputStream.close(...)
GeraldReader.GeraldIterator.close(...) ... source
calls java.io.FileInputStream.close(...)
GeraldReader.GeraldQueryIterator.seekToStart(...) source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.FileInputStream.getChannel(...)
SamUtils.createIndexFor(...) ............. source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
SamUtils.getIndexFor(...) ................ source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.lastModified(...)
SamUtils.getUserIdxFile(...) ............. source
calls java.io.File.getName(...)
calls java.io.File.getParent(...)
calls java.io.File.File(...)
org.broad.igv.sashimi
SashimiPlot.JunctionTrackMouseAdapter.ActionListenerAnonymous.actionPerformed(...) source
calls java.io.File.File(...)
org.broad.igv.session
History.printStack(...) .................. source
calls java.io.PrintStream.println(...)
IndexAwareSessionReader.loadSession(...) . source -- Load an inex aware session from the given ...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
SessionWriter.saveSession(...) ........... source -- Method description
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.OutputStreamWriter.OutputStreamWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.Writer.write(...)
calls java.io.Writer.close(...)
SessionWriter.writePanels(...) ........... source
calls java.io.File.getAbsolutePath(...)
SessionWriter.writeResources(...) ........ source
calls java.io.File.getAbsolutePath(...)
UCSCSessionReader.loadSession(...) ....... source -- Load a UCSC session from the given stream.
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
org.broad.igv.tdf
BufferedByteWriter.BufferedByteWriter(...) source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
BufferedByteWriter.bytesWritten(...) ..... source
calls java.io.ByteArrayOutputStream.size(...)
BufferedByteWriter.getBytes(...) ......... source
calls java.io.ByteArrayOutputStream.toByteArray(...)
BufferedByteWriter.put(...) .............. source -- Writes the specified byte to this buffered...
calls java.io.ByteArrayOutputStream.write(...)
BufferedByteWriter.put(...) .............. source -- Writes <code>len</code> bytes from the spe...
calls java.io.ByteArrayOutputStream.write(...)
BufferedByteWriter.put(...) .............. source
calls java.io.OutputStream.write(...)
BufferedByteWriter.putInt(...) ........... source
calls java.io.ByteArrayOutputStream.write(...)
BufferedByteWriter.putLong(...) .......... source -- Writes a <code>long</code> to the underlyi...
calls java.io.ByteArrayOutputStream.write(...)
BufferedByteWriter.putNullTerminatedString(...) source
calls java.io.OutputStream.write(...)
calls java.io.ByteArrayOutputStream.write(...)
BufferedByteWriter.putShort(...) ......... source
calls java.io.ByteArrayOutputStream.write(...)
TDFReader.dumpIndex(...) ................. source -- Print index entries (for debugging)
calls java.io.PrintStream.println(...)
TDFUtils.dumpAllTiles(...) ............... source
calls java.io.PrintStream.println(...)
TDFUtils.dumpDatasets(...) ............... source
calls java.io.PrintStream.println(...)
calls java.io.PrintStream.print(...)
TDFUtils.dumpRange(...) .................. source
calls java.io.PrintStream.println(...)
calls java.io.PrintStream.print(...)
TDFUtils.dumpRootAttributes(...) ......... source
calls java.io.PrintStream.println(...)
TDFUtils.dumpSummary(...) ................ source
calls java.io.PrintStream.println(...)
calls java.io.PrintStream.print(...)
TDFUtils.dumpTile(...) ................... source
calls java.io.PrintStream.println(...)
TDFUtils.dumpTileData(...) ............... source
calls java.io.PrintStream.print(...)
calls java.io.PrintStream.println(...)
TDFUtils.tdfToBedgraph(...) .............. source
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.BufferedOutputStream.BufferedOutputStream(...)
calls java.io.PrintStream.PrintStream(...)
calls java.io.PrintStream.println(...)
calls java.io.PrintStream.close(...)
TDFWriter.TDFWriter(...) ................. source
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.BufferedOutputStream.BufferedOutputStream(...)
TDFWriter.closeFile(...) ................. source -- Write out the group and dataset index and ...
calls java.io.OutputStream.close(...)
TDFWriter.write(...) ..................... source
calls java.io.OutputStream.write(...)
TDFWriter.writeIndexPosition(...) ........ source
calls java.io.RandomAccessFile.RandomAccessFile(...)
calls java.io.RandomAccessFile.getChannel(...)
calls java.io.RandomAccessFile.write(...)
calls java.io.RandomAccessFile.close(...)
TDFWriter.writeInt(...) .................. source
calls java.io.OutputStream.write(...)
TDFWriter.writeTile(...) ................. source
calls java.io.PrintStream.println(...)
org.broad.igv.tools
CommandLineStatusMonitor.incrementPercentComplete(...) source
calls java.io.PrintStream.println(...)
CommandLineStatusMonitor.setPercentComplete(...) source
calls java.io.PrintStream.println(...)
calls java.io.PrintStream.print(...)
CoverageCounter.WigWriter.WigWriter(...) . source
calls java.io.FileWriter.FileWriter(...)
calls java.io.OutputStreamWriter.OutputStreamWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
CoverageCounter.WigWriter.addData(...) ... source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
CoverageCounter.WigWriter.close(...) ..... source
calls java.io.PrintWriter.close(...)
CoverageCounter.WigWriter.outputColumnLabelLine(...) source -- If column labels non-standard we output wh...
calls java.io.PrintWriter.println(...)
CoverageCounter.WigWriter.outputStepLine(...) source
calls java.io.PrintWriter.println(...)
CoverageCounter.WigWriter.outputTrackLine(...) source
calls java.io.PrintWriter.println(...)
IgvTools.GFFToBed(...) ................... source
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.PrintStream.PrintStream(...)
calls java.io.PrintStream.print(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintStream.flush(...)
calls java.io.PrintStream.close(...)
IgvTools.createTribbleIndex(...) ......... source -- Create a tribble style index.
calls java.io.File.File(...)
calls java.io.File.getAbsolutePath(...)
IgvTools.doCount(...) .................... source -- Compute coverage or density of an alignmen...
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.delete(...)
calls java.io.PrintStream.flush(...)
IgvTools.doGCTtoIGV(...) ................. source
calls java.io.File.getAbsolutePath(...)
calls java.io.PrintStream.println(...)
calls java.io.File.File(...)
calls java.io.File.exists(...)
IgvTools.doIndex(...) .................... source -- Create an index for an alignment or featur...
calls java.io.File.getParent(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.exists(...)
calls java.io.File.delete(...)
calls java.io.PrintStream.flush(...)
IgvTools.doSort(...) ..................... source
calls java.io.PrintStream.println(...)
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.delete(...)
calls java.io.PrintStream.flush(...)
IgvTools.estimateLineCount(...) .......... source -- Estimage the number of lines in the given ...
calls java.io.File.isDirectory(...)
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.File.getParent(...)
calls java.io.File.File(...)
calls java.io.PrintStream.println(...)
calls java.io.BufferedReader.close(...)
IgvTools.getFilesFromDirOrList(...) ...... source -- Return either (a) the children files in a ...
calls java.io.File.isDirectory(...)
calls java.io.File.listFiles(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.File.getParentFile(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.BufferedReader.close(...)
IgvTools.getSampleNames(...) ............. source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
IgvTools.indexBAM(...) ................... source
calls java.io.File.File(...)
IgvTools.loadGenome(...) ................. source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
IgvTools.main(...) ....................... source -- Main method. Used to run igvtools from the...
calls java.io.PrintStream.println(...)
IgvTools.run(...) ........................ source
calls java.io.PrintStream.println(...)
calls java.io.File.isDirectory(...)
calls java.io.File.isFile(...)
calls java.io.File.File(...)
IgvTools.sumWigs(...) .................... source
calls java.io.File.File(...)
IgvTools.toTDF(...) ...................... source
calls java.io.File.exists(...)
calls java.io.File.isDirectory(...)
calls java.io.File.File(...)
calls java.io.File.mkdir(...)
calls java.io.File.getName(...)
calls java.io.File.deleteOnExit(...)
calls java.io.File.delete(...)
calls java.io.PrintStream.flush(...)
IgvTools.writeTribbleIndex(...) .......... source
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.BufferedOutputStream.BufferedOutputStream(...)
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.delete(...)
IgvTools.Comparator<File>Anonymous.compare(...) source
calls java.io.File.getName(...)
IgvToolsGui.redirectSystemStreams(...) ... source
calls java.io.PrintStream.PrintStream(...)
IgvToolsGui.validateFields(...) .......... source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.getParentFile(...)
calls java.io.File.getParent(...)
ListAccumulator.getValue(...) ............ source
calls java.io.PrintStream.println(...)
ListAccumulator.setValue(...) ............ source
calls java.io.PrintStream.println(...)
PairedEndStats.main(...) ................. source
calls java.io.PrintStream.println(...)
PairedUtils.extractInteractions(...) ..... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
PairedUtils.extractUnexpectedPairs(...) .. source
calls java.io.File.File(...)
calls java.io.File.getName(...)
calls java.io.PrintStream.println(...)
PairedUtils.getOrientation(...) .......... source
calls java.io.PrintStream.println(...)
Preprocessor.preprocess(...) ............. source
calls java.io.File.getAbsolutePath(...)
RepeatMaskSplitter.closeWriters(...) ..... source
calls java.io.PrintWriter.close(...)
RepeatMaskSplitter.main(...) ............. source
calls java.io.File.File(...)
RepeatMaskSplitter.split(...) ............ source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.File.getParentFile(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.File.File(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
TestFileGenerator.generateTestFile(...) .. source
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
TestFileGenerator.getExpressionProbes(...) source
calls java.io.FileInputStream.FileInputStream(...)
TestFileGenerator.writeHeader(...) ....... source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
UCSCUtils.convertWIBFile(...) ............ source -- 0 bin smallint(5) unsigned not null, # bin...
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.FileInputStream.getChannel(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.DataInputStream.readFully(...)
calls java.io.BufferedReader.close(...)
calls java.io.FileInputStream.close(...)
calls java.io.PrintWriter.close(...)
UCSCUtils.main(...) ...................... source
calls java.io.PrintStream.println(...)
calls java.io.File.File(...)
WigSummer.sumWigs(...) ................... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.tools.converters
BamToBed.convert(...) .................... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
CLWtoSAM.convert(...) .................... source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.flush(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
CLWtoSAM.outputSamRecord(...) ............ source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
ExpressionFormatter.convert(...) ......... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
ExpressionFormatter.getType(...) ......... source
calls java.io.File.getName(...)
ExpressionFormatter.main(...) ............ source
calls java.io.PrintStream.println(...)
calls java.io.File.File(...)
GCTtoIGVConverter.convert(...) ........... source -- Parse the file and output in ".igv" format
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
GFFtoBed.convert(...) .................... source
calls java.io.File.getPath(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
GFFtoBed.main(...) ....................... source
calls java.io.File.File(...)
IlluminaToCN.convertFile(...) ............ source -- Converts an illumina aCGH file to multiple...
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
MFastaToSAM.convert(...) ................. source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.flush(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
MFastaToSAM.outputSamRecord(...) ......... source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
MageTabToIGVConverter.convert(...) ....... source -- Parse the file and output in ".igv" format
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintStream.println(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
WigToBed.WigToBed(...) ................... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
WigToBed.parsingComplete(...) ............ source
calls java.io.PrintWriter.close(...)
WigToBed.writeCurrentFeature(...) ........ source
calls java.io.PrintWriter.println(...)
org.broad.igv.tools.parsers
ToolsWiggleParser.parse(...) ............. source -- Parse Wiggle file into the DataConsumer
calls java.io.File.File(...)
calls java.io.File.getParent(...)
calls java.io.File.getAbsolutePath(...)
ToolsWiggleParser.parseEwigList(...) ..... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.tools.sort
AsciiSorter.AsciiSorter(...) ............. source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
AsciiSorter.run(...) ..................... source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.OutputStreamWriter.OutputStreamWriter(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.FileInputStream.close(...)
calls java.io.PrintWriter.close(...)
BAMSorter.run(...) ....................... source
calls java.io.PrintStream.println(...)
BedSorter.BedSorter(...) ................. source
calls java.io.File.getName(...)
BedSorter.writeHeader(...) ............... source
calls java.io.PrintWriter.println(...)
CNSorter.getIGVParser(...) ............... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
CNSorter.getParser(...) .................. source
calls java.io.File.getName(...)
CNSorter.writeHeader(...) ................ source
calls java.io.PrintWriter.println(...)
EQTLSorter.writeHeader(...) .............. source
calls java.io.PrintWriter.println(...)
GFFSorter.writeHeader(...) ............... source
calls java.io.PrintWriter.println(...)
GWASSorter.findColumns(...) .............. source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
GWASSorter.writeHeader(...) .............. source
calls java.io.PrintWriter.println(...)
GenericSorter.writeHeader(...) ........... source
calls java.io.PrintWriter.println(...)
InteractionSorter.writeHeader(...) ....... source
calls java.io.PrintWriter.println(...)
MUTSorter.MUTSorter(...) ................. source
calls java.io.File.getAbsolutePath(...)
MUTSorter.writeHeader(...) ............... source
calls java.io.PrintWriter.println(...)
Parser.readNextRecord(...) ............... source
calls java.io.PrintStream.println(...)
RefgeneSorter.writeHeader(...) ........... source
calls java.io.PrintWriter.println(...)
SAMSorter.writeHeader(...) ............... source
calls java.io.PrintWriter.println(...)
SortableRecordCodec.decode(...) .......... source
calls java.io.DataInputStream.readUTF(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.DataInputStream.readFully(...)
SortableRecordCodec.encode(...) .......... source
calls java.io.DataOutputStream.writeUTF(...)
calls java.io.DataOutputStream.writeInt(...)
calls java.io.DataOutputStream.write(...)
SortableRecordCodec.setInputStream(...) .. source
calls java.io.DataInputStream.DataInputStream(...)
SortableRecordCodec.setOutputStream(...) . source
calls java.io.DataOutputStream.DataOutputStream(...)
SorterFactory.getSorter(...) ............. source
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
VCFSorter.writeHeader(...) ............... source
calls java.io.PrintWriter.println(...)
org.broad.igv.tools.ui
CoverageGui.inputButtonActionPerformed(...) source
calls java.io.File.getAbsolutePath(...)
CoverageGui.outputButtonActionPerformed(...) source
calls java.io.File.getAbsolutePath(...)
CoverageGui.redirectSystemStreams(...) ... source
calls java.io.PrintStream.PrintStream(...)
org.broad.igv.track
CombinedDataSourceDialog.helpButtonActionPerformed(...) source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
FeatureDirSource.FeatureDirSource(...) ... source
calls java.io.InputStream.close(...)
FeatureDirSource.getFeatures(...) ........ source
calls java.io.BufferedReader.close(...)
FeatureDirSource.setRootDir(...) ......... source
calls java.io.File.File(...)
calls java.io.File.getParent(...)
MutationTrack.getOMAText(...) ............ source
calls java.io.StringReader.StringReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
TestUtils.createFeatureTestFile(...) ..... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
TrackMenuUtils.exportTrackNames(...) ..... source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
TrackMenuUtils.exportVisibleAlignments(...) source
calls java.io.File.File(...)
TrackMenuUtils.exportVisibleFeatures(...) source -- Write features in {@code track} found in {...
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.flush(...)
calls java.io.PrintWriter.close(...)
TribbleFeatureSource.createIndex(...) .... source -- Present a dialog for the user to create an...
calls java.io.File.File(...)
calls java.io.File.getAbsolutePath(...)
TribbleListFeatureSource.getFeatures(...) source
calls java.io.IOException.IOException(...)
TribbleListFeatureSource.init(...) ....... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.ui
DesktopIntegration.verifyJavaPlatform(...) source
calls java.io.PrintStream.println(...)
IGV.createSnapshot(...) .................. source
calls java.io.File.getAbsolutePath(...)
IGV.createSnapshotNonInteractive(...) .... source -- Create a snapshot image of {@code target} ...
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
IGV.defineGenome(...) .................... source
calls java.io.File.getAbsolutePath(...)
IGV.doRestoreSession(...) ................ source -- Restore a session from a local file, and o...
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
IGV.loadResources(...) ................... source -- Load resources into IGV. Tracks are added ...
calls java.io.File.File(...)
calls java.io.File.exists(...)
IGV.restoreSessionSynchronous(...) ....... source -- Load a session file in the current thread....
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.InputStream.close(...)
IGV.saveImage(...) ....................... source
calls java.io.File.File(...)
IGV.selectSnapshotFile(...) .............. source
calls java.io.File.getParentFile(...)
IGV.StartupRunnable.run(...) ............. source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
Main.setIgvDirectory(...) ................ source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.mkdir(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.isDirectory(...)
calls java.io.File.canWrite(...)
Main.IGVArgs.parseArgs(...) .............. source -- Parse arguments. All arguments are optiona...
calls java.io.PrintStream.println(...)
calls java.io.File.File(...)
calls java.io.File.exists(...)
Main.IGVArgs.printHelp(...) .............. source
calls java.io.PrintStream.println(...)
ReadmeParser.getDocForCommand(...) ....... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
ReadmeParser.getReader(...) .............. source -- Get reader for the given path. To get comp...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
ResourceFileBuilder.createSampleInfoFiles(...) source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.File.getName(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
ResourceFileBuilder.doEpigenetics(...) ... source
calls java.io.File.getName(...)
ResourceFileBuilder.lookForChildren(...) . source
calls java.io.File.isDirectory(...)
calls java.io.File.listFiles(...)
calls java.io.File.getCanonicalPath(...)
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.PrintStream.println(...)
ResourceFileBuilder.outputResources(...) . source
calls java.io.PrintStream.println(...)
calls java.io.File.getCanonicalPath(...)
ResourceFileBuilder.process(...) ......... source -- Method description
calls java.io.File.listFiles(...)
calls java.io.StringWriter.StringWriter(...)
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.Writer.write(...)
calls java.io.OutputStreamWriter.close(...)
ShutdownThread.writeRegionsOfInterestFile(...) source
calls java.io.File.createNewFile(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
TooltipTextFrame.omaTest(...) ............ source
calls java.io.StringReader.StringReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
TooltipTextFrame.MyTransferHandler.createTransferable(...) source
calls java.io.StringReader.StringReader(...)
org.broad.igv.ui.action
ExportRegionsMenuAction.exportRegionsOfInterest(...) source
calls java.io.File.File(...)
ExportRegionsMenuAction.writeRegionsOfInterestFile(...) source
calls java.io.File.createNewFile(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
ExportTrackNamesMenuAction.actionPerformed(...) source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
ImportRegionsMenuAction.readRegionsOfInterestFile(...) source
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
LoadFilesMenuAction.loadFiles(...) ....... source
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
LoadFromServerAction.getNodeURLs(...) .... source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.InputStream.close(...)
LoadFromServerAction.getResourceUrls(...) source -- Returns the complete list of URLs from the...
calls java.io.BufferedReader.readLine(...)
LoadFromServerAction.readXMLDocument(...) source
calls java.io.InputStream.close(...)
LoadFromURLMenuAction.ping(...) .......... source
calls java.io.InputStream.read(...)
calls java.io.InputStream.close(...)
OpenSessionMenuAction.actionPerformed(...) source
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getParentFile(...)
OpenSessionMenuAction.doRestoreSession(...) source
calls java.io.File.File(...)
ReloadTracksMenuAction.actionPerformed(...) source -- Method description
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
RunScriptMenuAction.actionPerformed(...) . source
calls java.io.File.isFile(...)
calls java.io.File.getPath(...)
RunScriptMenuAction.chooseScriptFile(...) source
calls java.io.File.getParentFile(...)
SaveSessionMenuAction.actionPerformed(...) source -- Method description
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
calls java.io.File.getParentFile(...)
calls java.io.File.getName(...)
SaveSessionMenuAction.saveSession(...) ... source -- Saves current IGV session to {@code target...
calls java.io.File.getAbsolutePath(...)
SearchCommand.showSearchResult(...) ...... source
calls java.io.PrintStream.println(...)
org.broad.igv.ui.color
ColorUtilities.loadPalettes(...) ......... source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
PaletteToolFrame.saveItemActionPerformed(...) source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
org.broad.igv.ui.commandbar
GenomeListManager.buildItemFromPath(...) . source -- Build a GenomeListItem from a path to a fa...
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.getName(...)
GenomeListManager.clearUserDefinedGenomes(...) source -- Added for unit tests
calls java.io.File.File(...)
calls java.io.File.delete(...)
GenomeListManager.exportUserDefinedGenomeList(...) source -- Export the user-define genome property file.
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
calls java.io.File.delete(...)
GenomeListManager.getCachedGenomeArchiveList(...) source -- Gets a list of all the locally cached geno...
calls java.io.File.exists(...)
calls java.io.File.listFiles(...)
calls java.io.File.isDirectory(...)
calls java.io.File.getName(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.lastModified(...)
calls java.io.File.delete(...)
calls java.io.FileInputStream.close(...)
GenomeListManager.getServerGenomeMap(...) source -- Gets a list of all the server genome archi...
calls java.io.File.File(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
calls java.io.InputStream.close(...)
GenomeListManager.getUserDefinedGenomeMap(...) source -- Gets a list of all the user-defined genome...
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.ui.filefilters
AlignmentFileFilter.accept(...) .......... source
calls java.io.File.getName(...)
CoverageFileFilter.accept(...) ........... source
calls java.io.File.getName(...)
org.broad.igv.ui.panel
DataPanel.debugDump(...) ................. source -- Do not remove - Used for debugging only
calls java.io.PrintStream.println(...)
DataPanelContainer.FileDropTargetListener.drop(...) source
calls java.io.File.getAbsolutePath(...)
HeaderPanel.getTransferData(...) ......... source -- <p>One of three methods defined by the Tra...
calls java.io.PrintStream.println(...)
HeaderPanel.getTransferDataFlavors(...) .. source -- <p>One of three methods defined by the Tra...
calls java.io.PrintStream.println(...)
HeaderPanel.isDataFlavorSupported(...) ... source -- <p>One of three methods defined by the Tra...
calls java.io.PrintStream.println(...)
RegionNavigatorDialog.SearchFieldDocumentListener.changedUpdate(...) source
calls java.io.PrintStream.println(...)
org.broad.igv.ui.svg
SVGGraphics.applyTransform(...) .......... source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
SVGGraphics.drawLine(...) ................ source
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
SVGGraphics.drawPolygon(...) ............. source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
SVGGraphics.drawRect(...) ................ source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
SVGGraphics.drawString(...) .............. source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
SVGGraphics.fillPolygon(...) ............. source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
SVGGraphics.fillRect(...) ................ source
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
SVGGraphics.setClip(...) ................. source
calls java.io.PrintWriter.println(...)
SVGGraphics.translate(...) ............... source
calls java.io.PrintStream.println(...)
SVGTest.test1(...) ....................... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
org.broad.igv.ui.util ........................ -- SnapshotUtilities.java <p> Created on Nove...
FileDialogUtils.chooseFile(...) .......... source
calls java.io.File.getParentFile(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
FileDialogUtils.chooseNative(...) ........ source
calls java.io.File.File(...)
FileDialogUtils.fixMacExtension(...) ..... source -- Fix for bug in MacOS "native" dialog. If h...
calls java.io.File.getName(...)
FontChooser2.ActionListenerAnonymous.actionPerformed(...) source
calls java.io.PrintStream.println(...)
IndexCreatorDialog.IndexCreatorDialog(...) source -- Creates new form IndexCreatorDialog
calls java.io.File.getAbsolutePath(...)
IndexCreatorDialog.determineFileType(...) source
calls java.io.File.getName(...)
calls java.io.File.getPath(...)
IndexCreatorDialog.TribbleIndexWorker.doInBackground(...) source
calls java.io.File.getAbsolutePath(...)
ReorderableJList.main(...) ............... source
calls java.io.PrintStream.println(...)
SnapshotFileChooser.SnapshotFileFilter.accept(...) source
calls java.io.File.isDirectory(...)
calls java.io.File.getName(...)
SnapshotFileChooser.PropertyChangeListenerAnonymous.propertyChange(...) source
calls java.io.File.getName(...)
calls java.io.File.File(...)
SnapshotUtilities.exportScreenShotBufferedImage(...) source -- Export the specified {@code target} compon...
calls java.io.File.getAbsolutePath(...)
SnapshotUtilities.exportScreenshotEpsGraphics(...) source
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.OutputStream.flush(...)
calls java.io.FileOutputStream.close(...)
SnapshotUtilities.exportScreenshotSVG(...) source
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.OutputStreamWriter.OutputStreamWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.Writer.close(...)
SnapshotUtilities.fixFileExt(...) ........ source -- Add a file extension to the file if it doe...
calls java.io.File.getName(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
TracingRepaintManager.addDirtyRegion(...) source
calls java.io.PrintStream.println(...)
org.broad.igv.ui.util.download
Downloader.main(...) ..................... source
calls java.io.File.File(...)
Downloader.run(...) ...................... source
calls java.io.RandomAccessFile.RandomAccessFile(...)
calls java.io.RandomAccessFile.seek(...)
calls java.io.InputStream.read(...)
calls java.io.RandomAccessFile.write(...)
calls java.io.RandomAccessFile.close(...)
calls java.io.InputStream.close(...)
calls java.io.File.delete(...)
calls java.io.File.File(...)
calls java.io.File.toPath(...)
org.broad.igv.util
AsciiEcho.main(...) ...................... source
calls java.io.InputStream.read(...)
calls java.io.PrintStream.println(...)
BrowserLauncher.openURL_old(...) ......... source
calls java.io.File.exists(...)
calls java.io.File.File(...)
calls java.io.IOException.IOException(...)
ByteConverter.convertBytesToFloats(...) .. source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.FilterInputStream.available(...)
calls java.io.DataInputStream.readFloat(...)
calls java.io.FilterInputStream.close(...)
ByteConverter.convertBytesToInts(...) .... source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.FilterInputStream.available(...)
calls java.io.DataInputStream.readInt(...)
calls java.io.FilterInputStream.close(...)
ByteConverter.convertBytesToLongs(...) ... source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.FilterInputStream.available(...)
calls java.io.DataInputStream.readLong(...)
calls java.io.FilterInputStream.close(...)
ByteConverter.convertBytesToStrings(...) . source -- Read an array of strings from the data str...
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
calls java.io.DataInputStream.DataInputStream(...)
calls java.io.FilterInputStream.available(...)
calls java.io.DataInputStream.read(...)
CompressionUtils.compress(...) ........... source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
CompressionUtils.compress(...) ........... source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.close(...)
calls java.io.PrintStream.println(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
CompressionUtils.decompress(...) ......... source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.close(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
CompressionUtils.ungzipFile(...) ......... source -- Copy data from srcPath to destPath, ungzip...
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.InputStream.read(...)
calls java.io.OutputStream.write(...)
calls java.io.OutputStream.flush(...)
calls java.io.InputStream.close(...)
calls java.io.OutputStream.close(...)
DumpHttpHeaders.dumpFields(...) .......... source
calls java.io.PrintStream.println(...)
calls java.io.PrintStream.print(...)
FileUtils.canWriteTo(...) ................ source
calls java.io.File.createNewFile(...)
calls java.io.File.delete(...)
FileUtils.cleanup(...) ................... source
calls java.io.File.exists(...)
calls java.io.File.isDirectory(...)
calls java.io.File.listFiles(...)
calls java.io.File.delete(...)
calls java.io.File.getName(...)
calls java.io.File.getParentFile(...)
calls java.io.File.File(...)
calls java.io.File.renameTo(...)
FileUtils.copyFile(...) .................. source -- Copy a file from one location to another, ...
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.InputStream.read(...)
calls java.io.OutputStream.write(...)
calls java.io.File.delete(...)
calls java.io.File.getAbsoluteFile(...)
calls java.io.InputStream.close(...)
calls java.io.OutputStream.flush(...)
calls java.io.OutputStream.close(...)
FileUtils.deleteDir(...) ................. source -- Delete a directory and all subdirectories
calls java.io.File.isDirectory(...)
calls java.io.File.list(...)
calls java.io.File.File(...)
calls java.io.File.delete(...)
FileUtils.findExecutableOnPath(...) ...... source -- Checks the system path for the provided ex...
calls java.io.File.File(...)
calls java.io.File.isFile(...)
calls java.io.File.getAbsolutePath(...)
FileUtils.getAbsolutePath(...) ........... source -- Returns an absolute path from the parent d...
calls java.io.File.isAbsolute(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.File(...)
calls java.io.File.isDirectory(...)
calls java.io.File.getParentFile(...)
calls java.io.File.getCanonicalPath(...)
FileUtils.getContents(...) ............... source -- Read and return the file contents as a string
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
FileUtils.getFirstLine(...) .............. source -- Return the first line not starting with co...
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
FileUtils.getInstallDirectory(...) ....... source
calls java.io.File.File(...)
calls java.io.File.isDirectory(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getParentFile(...)
FileUtils.getLength(...) ................. source -- Return the length of the file, which might...
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.isFile(...)
calls java.io.File.length(...)
FileUtils.getRelativePath(...) ........... source -- Get the relative path from one file to ano...
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.isFile(...)
FileUtils.isTabDelimited(...) ............ source -- Test to see if the first non-comment line ...
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
FileUtils.readFully(...) ................. source
calls java.io.File.File(...)
calls java.io.File.length(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.InputStream.read(...)
calls java.io.InputStream.close(...)
FileUtils.resourceExists(...) ............ source
calls java.io.File.File(...)
calls java.io.File.exists(...)
FileUtils.FileFilterAnonymous.accept(...) source
calls java.io.File.getName(...)
HttpUtils.createGenomeSpaceDirectory(...) source
calls java.io.BufferedOutputStream.BufferedOutputStream(...)
calls java.io.OutputStream.write(...)
calls java.io.OutputStream.close(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.InputStream.close(...)
calls java.io.IOException.IOException(...)
HttpUtils.doPost(...) .................... source
calls java.io.OutputStream.write(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.Reader.read(...)
calls java.io.Reader.close(...)
HttpUtils.downloadFile(...) .............. source
calls java.io.File.getName(...)
HttpUtils.getContentsAsGzippedString(...) source
calls java.io.InputStream.close(...)
HttpUtils.getContentsAsJSON(...) ......... source
calls java.io.InputStream.close(...)
HttpUtils.getContentsAsString(...) ....... source
calls java.io.InputStream.close(...)
HttpUtils.openConnection(...) ............ source -- The "real" connection method
calls java.io.IOException.IOException(...)
calls java.io.FileNotFoundException.FileNotFoundException(...)
HttpUtils.readErrorStream(...) ........... source
calls java.io.InputStream.close(...)
HttpUtils.readFully(...) ................. source -- Useful helper function
calls java.io.InputStream.read(...)
calls java.io.EOFException.EOFException(...)
HttpUtils.remoteIsNewer(...) ............. source -- Compare a local and remote resource, retur...
calls java.io.File.exists(...)
calls java.io.File.lastModified(...)
HttpUtils.uploadGenomeSpaceFile(...) ..... source
calls java.io.BufferedOutputStream.BufferedOutputStream(...)
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.BufferedInputStream.read(...)
calls java.io.OutputStream.write(...)
calls java.io.OutputStream.close(...)
calls java.io.File.getName(...)
calls java.io.IOException.IOException(...)
IlluminaUtils.createProbeMappingFile(...) source
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.File.listFiles(...)
calls java.io.File.getName(...)
calls java.io.PrintStream.println(...)
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
IlluminaUtils.main(...) .................. source
calls java.io.File.File(...)
IntervalTree.Node.store(...) ............. source
calls java.io.DataOutputStream.writeInt(...)
JavaAgent.getObjectSizeRecursive(...) .... source
calls java.io.PrintStream.println(...)
LittleEndianInputStream.readUShort(...) .. source
calls java.io.EOFException.EOFException(...)
MD5Checksum.createChecksum(...) .......... source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.InputStream.read(...)
calls java.io.InputStream.close(...)
MD5Checksum.getMD5Checksum(...) .......... source
calls java.io.File.File(...)
calls java.io.File.isFile(...)
MacroSnapshotAction.setOutputDirectory(...) source
calls java.io.File.File(...)
calls java.io.File.exists(...)
OneKGUtils.createResourceXMLs(...) ....... source -- Input files contain lines of the form <p/>...
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintStream.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
ParsingUtils.fileExists(...) ............. source
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.isFile(...)
ParsingUtils.getContentLength(...) ....... source
calls java.io.InputStream.available(...)
calls java.io.File.File(...)
calls java.io.File.length(...)
ParsingUtils.getLastModified(...) ........ source -- Returns the number of milliseconds since J...
calls java.io.File.File(...)
calls java.io.File.exists(...)
calls java.io.File.lastModified(...)
ParsingUtils.loadMap(...) ................ source -- Load a text file of format {@code key}= {@...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
ParsingUtils.loadRegions(...) ............ source -- Method description
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
ParsingUtils.openBufferedReader(...) ..... source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
ParsingUtils.openBufferedReader(...) ..... source -- Open a BufferedReader on the path, which m...
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
ParsingUtils.openInputStreamGZ(...) ...... source -- Open an InputStream on the resource. Wrap ...
calls java.io.File.File(...)
calls java.io.FileInputStream.FileInputStream(...)
ParsingUtils.readContentsFromStream(...) . source
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.BufferedInputStream.read(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
ResourceLocator.getFileName(...) ......... source
calls java.io.File.File(...)
calls java.io.File.getName(...)
ResourceLocator.getTrackName(...) ........ source
calls java.io.File.File(...)
calls java.io.File.getName(...)
RuntimeUtils.executeShellCommand(...) .... source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.StringWriter.StringWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
calls java.io.StringWriter.toString(...)
calls java.io.InputStream.close(...)
calls java.io.OutputStream.close(...)
RuntimeUtils.filesToURLs(...) ............ source -- Converts input files to file URLs
calls java.io.File.getAbsolutePath(...)
RuntimeUtils.getPluginJars(...) .......... source -- Return an array of jar files in the plugin...
calls java.io.File.File(...)
calls java.io.File.listFiles(...)
RuntimeUtils.loadLibrary(...) ............ source
calls java.io.File.toURI(...)
RuntimeUtils.startErrorReadingThread(...) source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
RuntimeUtils.ThreadAnonymous.run(...) .... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
S3Presigner.NullSdkHttpClient.ExecutableHttpRequestAnonymous.call(...) source
calls java.io.ByteArrayInputStream.ByteArrayInputStream(...)
SequenceGC.CalculatePercent(...) ......... source
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.read(...)
calls java.io.BufferedReader.close(...)
SequenceGC.ProcessPath(...) .............. source
calls java.io.File.getAbsolutePath(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.File.isDirectory(...)
calls java.io.File.File(...)
calls java.io.File.listFiles(...)
calls java.io.File.isFile(...)
calls java.io.File.getName(...)
calls java.io.PrintWriter.close(...)
SequenceGC.main(...) ..................... source
calls java.io.PrintStream.println(...)
SequenceGC.printUsage(...) ............... source
calls java.io.PrintStream.println(...)
StringUtils.readString(...) .............. source
calls java.io.ByteArrayOutputStream.ByteArrayOutputStream(...)
calls java.io.ByteArrayOutputStream.write(...)
calls java.io.ByteArrayOutputStream.toByteArray(...)
TutorialUtils.extractAlignments(...) ..... source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
TutorialUtils.extractFasta(...) .......... source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
TutorialUtils.extractFeatures(...) ....... source
calls java.io.File.File(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
TutorialUtils.loadFeatures(...) .......... source
calls java.io.BufferedReader.readLine(...)
TutorialUtils.parseRegions(...) .......... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
TutorialUtils.sampleVCF(...) ............. source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
TutorialUtils.sliceFasta(...) ............ source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
TutorialUtils.sliceVCF(...) .............. source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
calls java.io.BufferedReader.close(...)
URLDownloader.doDownload(...) ............ source
calls java.io.File.getAbsolutePath(...)
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.InputStream.read(...)
calls java.io.OutputStream.write(...)
calls java.io.InputStream.close(...)
calls java.io.File.delete(...)
calls java.io.OutputStream.flush(...)
calls java.io.OutputStream.close(...)
calls java.io.File.length(...)
UnzipGenomes.main(...) ................... source
calls java.io.File.File(...)
calls java.io.File.listFiles(...)
calls java.io.File.getName(...)
calls java.io.File.mkdir(...)
UnzipGenomes.unzip(...) .................. source
calls java.io.FileInputStream.FileInputStream(...)
calls java.io.BufferedInputStream.BufferedInputStream(...)
calls java.io.File.File(...)
UnzipGenomes.unzip(...) .................. source
calls java.io.File.getAbsolutePath(...)
calls java.io.PrintStream.println(...)
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.InputStream.read(...)
calls java.io.FileOutputStream.write(...)
calls java.io.FileOutputStream.close(...)
Utilities.changeFileExtension(...) ....... source -- Changes a files extension.
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
Utilities.getString(...) ................. source
calls java.io.StringWriter.StringWriter(...)
ZipArchiveWrapper.ZipArchiveWrapper(...) . source
calls java.io.FileNotFoundException.FileNotFoundException(...)
calls java.io.File.toURI(...)
ZipArchiveWrapper.ZipIterator.close(...) . source
calls java.io.File.getAbsolutePath(...)
org.broad.igv.util.blat
BlatClient.Usage(...) .................... source
calls java.io.PrintStream.println(...)
BlatClient.blat(...) ..................... source
calls java.io.PrintStream.println(...)
BlatClient.parseResult(...) .............. source -- Return the parsed results as an array of P...
calls java.io.StringReader.StringReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintStream.println(...)
BlatTableModel.save(...) ................. source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
org.broad.igv.util.collections
LRUCache.main(...) ....................... source -- Test for memory leaks
calls java.io.PrintStream.println(...)
SortingCollection.newInstance(...) ....... source -- Syntactic sugar around the ctor, to save s...
calls java.io.File.File(...)
SortingCollection.spillToDisk(...) ....... source -- Sort the records in memory, write them to ...
calls java.io.FileOutputStream.FileOutputStream(...)
calls java.io.OutputStream.flush(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.OutputStream.close(...)
SortingCollection.FileRecordIterator.FileRecordIterator(...) source
calls java.io.FileInputStream.FileInputStream(...)
org.broad.igv.util.converters
DensitiesToBedGraph.convert(...) ......... source
calls java.io.File.getAbsolutePath(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
DensitiesToBedGraph.convertAll(...) ...... source
calls java.io.File.listFiles(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
DensitiesToBedGraph.main(...) ............ source
calls java.io.File.File(...)
TarjeiToBedgraph.convert(...) ............ source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
TarjeiToBedgraph.main(...) ............... source
calls java.io.File.File(...)
calls java.io.File.listFiles(...)
calls java.io.File.getName(...)
calls java.io.File.exists(...)
calls java.io.File.getAbsolutePath(...)
org.broad.igv.util.encode
EncodeFileBrowser.getEncodeFileRecords(...) source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.InputStream.close(...)
EncodeFileRecord.getTrackName(...) ....... source -- Return a friendly name for the track. Unfo...
calls java.io.File.File(...)
calls java.io.File.getName(...)
UCSCEncodeUtils.outputRecords(...) ....... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.print(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)
UCSCEncodeUtils.parseFilesDotTxt(...) .... source
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
UCSCEncodeUtils.parseTableFile(...) ...... source
calls java.io.BufferedReader.readLine(...)
UCSCEncodeUtils.updateEncodeTableFile(...) source
calls java.io.BufferedReader.readLine(...)
calls java.io.PrintStream.println(...)
org.broad.igv.util.index
IntervalTree.Node.store(...) ............. source
calls java.io.DataOutputStream.writeInt(...)
org.broad.igv.util.stats
Distribution.print(...) .................. source
calls java.io.PrintWriter.println(...)
KaplanMeierEstimator.main(...) ........... source
calls java.io.PrintStream.println(...)
org.broad.igv.util.stream
IGVSeekableBufferedStream.reset(...) ..... source
calls java.io.IOException.IOException(...)
IGVSeekableFTPStream.read(...) ........... source
calls java.io.InputStream.read(...)
IGVSeekableHTTPStream._read(...) ......... source
calls java.io.InputStream.read(...)
calls java.io.InputStream.close(...)
IGVSeekableHTTPStream.main(...) .......... source
calls java.io.PrintStream.println(...)
IGVSeekableStreamFactory.getStreamFor(...) source
calls java.io.File.File(...)
SeekableServiceStream.read(...) .......... source
calls java.io.InputStream.read(...)
calls java.io.InputStream.close(...)
SeekableSplitStream.parseDescriptors(...) source
calls java.io.InputStreamReader.InputStreamReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.File.getName(...)
calls java.io.File.File(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.variant
VariantTrack.loadAlignmentMappings(...) .. source
calls java.io.BufferedReader.readLine(...)
calls java.io.File.File(...)
calls java.io.File.getAbsolutePath(...)
calls java.io.BufferedReader.close(...)
org.broad.igv.variant.New
VariantCodec.parseHeader(...) ............ source
calls java.io.BufferedReader.readLine(...)
org.broad.igv.variant.util
AutismUtils.createLoadXML(...) ........... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.File.File(...)
calls java.io.File.getName(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
AutismUtils.createSampleMap(...) ......... source
calls java.io.FileReader.FileReader(...)
calls java.io.BufferedReader.BufferedReader(...)
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.BufferedReader.readLine(...)
calls java.io.File.File(...)
calls java.io.File.getName(...)
calls java.io.PrintWriter.println(...)
calls java.io.BufferedReader.close(...)
calls java.io.PrintWriter.close(...)
PedigreeUtils.parseTrioFile(...) ......... source -- Parses a pedigree file containing trios of...
calls java.io.BufferedReader.readLine(...)
calls java.io.BufferedReader.close(...)
VCFtoBed.convert(...) .................... source
calls java.io.FileWriter.FileWriter(...)
calls java.io.BufferedWriter.BufferedWriter(...)
calls java.io.PrintWriter.PrintWriter(...)
calls java.io.PrintWriter.println(...)
calls java.io.PrintWriter.close(...)