public void writeMitabHeader(PrintStream ps) throws IOException { BufferedWriter bufferedWriter = null; try { bufferedWriter = new BufferedWriter(new OutputStreamWriter(ps)); writeMitabHeader(bufferedWriter); } finally { // You only need to close the outermost stream class because the close() // call is automatically trickled through all the chained classes if (bufferedWriter != null) { bufferedWriter.close(); } } }
public void writeMitabHeader(OutputStream os) throws IOException { BufferedWriter bufferedWriter = null; try { bufferedWriter = new BufferedWriter(new OutputStreamWriter(os)); writeMitabHeader(bufferedWriter); } finally { // You only need to close the outermost stream class because the close() // call is automatically trickled through all the chained classes if (bufferedWriter != null) { bufferedWriter.close(); } } }
public void writeMitabHeader(File file) throws IOException { BufferedWriter bufferedWriter = null; try { bufferedWriter = new BufferedWriter(new FileWriter(file, true)); writeMitabHeader(bufferedWriter); } finally { // You only need to close the outermost stream class because the close() // call is automatically trickled through all the chained classes if (bufferedWriter != null) { bufferedWriter.close(); } } }
PsimiTabWriter writer = new PsimiTabWriter(); FileWriter fileWriter = new FileWriter(output); writer.writeMitabHeader(fileWriter); writer.write(allClustered, fileWriter); } else {
/** * Save clustered results including scores in mitab files * @param interactionClusterScore */ private void saveMitabOutputFile(InteractionClusterScore interactionClusterScore) throws IOException, PsimiTabException { /* Retrieve results */ Map<Integer, EncoreInteraction> interactionMapping = interactionClusterScore.getInteractionMapping(); PsimiTabWriter writer = new PsimiTabWriter(PsimiTabVersion.v2_5); BufferedWriter outputWriter = new BufferedWriter(new FileWriter(mitabOutputFile)); try{ if (header){ writer.writeMitabHeader(outputWriter); } Encore2Binary iConverter = new Encore2Binary(interactionClusterScore.getMappingIdDbNames()); for(Integer mappingId:interactionMapping.keySet()){ EncoreInteraction eI = interactionMapping.get(mappingId); BinaryInteraction bI = iConverter.getBinaryInteractionForScoring(eI); writer.write(bI, outputWriter); } } finally { outputWriter.close(); } }