public void write(Collection<BinaryInteraction> interactions, Writer writer) throws IOException { for (BinaryInteraction interaction : interactions) { write(interaction, writer); } }
public IntactSolrSearchResult(SolrDocumentList results, String [] fieldNames, List<FacetField> facetFields){ super(results, fieldNames, facetFields); mitabReader = new PsimiTabReader(); }
public BinaryClusterScore(){ writer = new PsimiTabWriter(PsimiTabVersion.v2_5); }
public void setBinaryInteractionIterator(InputStream inputStream, boolean hasHeader) throws ClusterServiceException { if ( inputStream != null ) { final PsimiTabReader reader = new PsimiTabReader( ); try { this.binaryInteractionIterator = reader.iterate( inputStream ); } catch ( Exception e ) { throw new ClusterServiceException( "An error occured while read MITAB data", e ); } } }
public BinaryInteraction mapLine(String line, int lineNumber) throws Exception { try { return psimitabReader.readLine(line); } catch (Exception e) { throw new Exception("Problem converting to binary interaction line "+lineNumber+": "+line); } } }
public Iterator<BinaryInteraction> getBinaryInteractionIterator() throws PsimiTabException, IOException { return mitabReader.iterate(getMitab()); } }
public void handleError(String message, Throwable e) throws PsimiTabException { throw new PsimiTabException(message, e); }
public BinaryInteraction next() { if (nextLine == null && !hasNext()) { throw new NoSuchElementException(); } BinaryInteraction interaction = nextLine; interactionsProcessedCount++; lineConsummed = true; nextLine = null; return interaction; }
public Iterator<BinaryInteraction> iterate(Reader reader) throws IOException { final BufferedReader bufferedReader = new BufferedReader(reader); return new PsimiTabIterator(bufferedReader); }
public ClusteredMitabFilter(InteractionExporter exporter, String mitab){ super(exporter, mitab); this.mitabReader = new PsimiTabReader(); }
public void setBinaryInteractionIterator(Reader r, boolean hasHeader) throws ClusterServiceException { if ( r != null ) { final PsimiTabReader reader = new PsimiTabReader( ); try { this.binaryInteractionIterator = reader.iterate( r ); } catch ( Exception e ) { throw new ClusterServiceException( "An error occured while read MITAB data", e ); } } }
/** * Creates a BinaryInteraction from a lucene document * * @param doc the Document to use * @return the binary interaction * @throws psidev.psi.mi.tab.converter.txt2tab.MitabLineException * thrown if there are syntax or other problems parsing the document/line */ public T createData( Document doc ) throws PsimiTabException { String line = createPsimiTabLine( doc ); return ( T ) this.mitabReader.readLine(line); }
public IntactSolrSearchResult(SolrDocumentList results, String [] fieldNames){ super(results, fieldNames); this.mitabReader = new PsimiTabReader(); }
protected BinaryInteraction toBinaryInteraction(Object doc) throws PsimiTabException { BinaryInteraction binaryInteraction = mitabReader.readLine(toMitabLine(doc)); return binaryInteraction; }
public NonClusteredMitabFilter(InteractionExporter exporter){ super(exporter); this.mitabReader = new PsimiTabReader(); }
public ClusteredMitabFilter(InteractionExporter exporter){ super(exporter); this.mitabReader = new PsimiTabReader(); }
public NonClusteredMitabFilter(InteractionExporter exporter, String mitab){ super(exporter, mitab); this.mitabReader = new PsimiTabReader(); }
public MitabLineMapper() { this.psimitabReader = new PsimiTabReader(); }
public void setComplexProperties(String complexProperties) throws IOException { this.complexProperties = complexProperties; initialiseMapOfPsicquicClients(); this.reader = new PsimiTabReader(); } }
protected AbstractInteractionDocumentBuilder( ColumnBasedDocumentDefinition documentDefinition ) { this.documentDefinition = documentDefinition; this.rowReader = new DefaultRowReader(this.documentDefinition); this.mitabReader = new PsimiTabReader(); }