public BinaryClusterScore(){ writer = new PsimiTabWriter(PsimiTabVersion.v2_5); }
public void saveScoreInMitab(String fileName) throws IOException { PsimiTabWriter writer = new PsimiTabWriter(); File file = new File(fileName); BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(file)); try{ Map<Integer, EncoreInteraction> interactionMapping = getInteractionMapping(); Encore2Binary iConverter = new Encore2Binary(getMappingIdDbNames()); for(Integer mappingId:interactionMapping.keySet()){ EncoreInteraction eI = interactionMapping.get(mappingId); BinaryInteraction bI = iConverter.getBinaryInteraction(eI); writer.write(bI, bufferedWriter); } } finally { bufferedWriter.close(); } }
PsimiTabWriter writer = new psidev.psi.mi.tab.PsimiTabWriter(); writer.write(interactions, new File("C:\\psimitab.csv"));
@Override public void saveResultsInMitab(String fileName) throws IOException { PsimiTabWriter writer = new PsimiTabWriter(); File file = new File(fileName); BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(file)); try{ Map<Integer, EncoreInteraction> interactionMapping = getInteractionMapping(); Encore2Binary iConverter = new Encore2Binary(getMappingIdDbNames()); for(Integer mappingId:interactionMapping.keySet()){ EncoreInteraction eI = interactionMapping.get(mappingId); BinaryInteraction bI = iConverter.getBinaryInteractionForScoring(eI); writer.write(bI, bufferedWriter); } } finally { bufferedWriter.close(); } }
@Override public void saveResultsInMitab(String fileName) throws IOException { PsimiTabWriter writer = new PsimiTabWriter(); File file = new File(fileName); BufferedWriter bufferedWriter = new BufferedWriter(new FileWriter(file)); try{ Map<Integer, EncoreInteraction> interactionMapping = getInteractionMapping(); Encore2Binary iConverter = new Encore2Binary(getMappingIdDbNames()); for(Integer mappingId:interactionMapping.keySet()){ EncoreInteraction eI = interactionMapping.get(mappingId); BinaryInteraction bI = iConverter.getBinaryInteraction(eI); writer.write(bI, bufferedWriter); } } finally { bufferedWriter.close(); } }
PsimiTabWriter writer = new PsimiTabWriter(); FileWriter fileWriter = new FileWriter(output); writer.writeMitabHeader(fileWriter);
/** * 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(); } }
PsimiTabWriter writer = new PsimiTabWriter(); writer.write(interactions, outputFile);
PsimiTabWriter fileWriter = new PsimiTabWriter();
public IntActClusterScore(){ super(); setMappingIdDbNames("uniprotkb,intact"); writer = new PsimiTabWriter(PsimiTabVersion.v2_5); // we want direct interaction = 5 setDirectInteractionWeight_5(); // we want method weights with PCA = 1.5 //initializeMethodWeights_PCA_1_5(); initializeMethodWeights(); setPublicationWeight(0.0f); this.miscore = new UnNormalizedMIScore(); }