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); } } }
protected BinaryInteraction toBinaryInteraction(Object doc) throws PsimiTabException { BinaryInteraction binaryInteraction = mitabReader.readLine(toMitabLine(doc)); return binaryInteraction; }
/** * 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 boolean hasNext() { try { if (interactionStreamReader != null && lineConsummed) { String line = interactionStreamReader.readLine(); nextLine = line != null ? mReader.readLine(line) : null; if (nextLine == null) { closeStreamReader(); interactionStreamReader = null; } else { lineIndex++; lineConsummed = false; } } } catch (Exception e) { closeStreamReader(); throw new RuntimeException("Error while reading the file.", e); } return (nextLine != null); }
public PsimiTabIterator(Reader psiMiTabInteractionsReader) { boolean isHeader = true; if (psiMiTabInteractionsReader == null) { throw new IllegalArgumentException("You must give a non null input stream."); } if (psiMiTabInteractionsReader instanceof BufferedReader) { this.interactionStreamReader = (BufferedReader) psiMiTabInteractionsReader; } else { this.interactionStreamReader = new BufferedReader(psiMiTabInteractionsReader); } this.mReader = new PsimiTabReader(); try { do { String firstLine = interactionStreamReader.readLine(); if(firstLine == null){ nextLine = null; isHeader = false; } else if (!firstLine.isEmpty() && !firstLine.startsWith("#")) { //This line is not a comment, we read nextLine = mReader.readLine(firstLine); lineIndex++; isHeader = false; } } while (isHeader); } catch (Exception e) { closeStreamReader(); throw new RuntimeException("Error while reading the header line.", e); } }
public List<BinaryInteraction> getInteractions(String query, int firstResult, int maxNumberOfResults) throws IOException { List<BinaryInteraction> results = new ArrayList<BinaryInteraction>(Math.min(2048, maxNumberOfResults)); String url = service.getRestUrl(); PsicquicSimpleClient client = new PsicquicSimpleClient(url); InputStream is = client.getByQuery(query, PsicquicSimpleClient.MITAB25, firstResult, maxNumberOfResults); PsimiTabReader tabReader = new PsimiTabReader(); BufferedReader in = new BufferedReader(new InputStreamReader(is)); String str; while ((str = in.readLine()) != null) { BinaryInteraction interaction = null; try { interaction = tabReader.readLine(str); } catch (PsimiTabException e) { throw new IOException("Impossible to read the mitab line", e); } results.add(interaction); } in.close(); return results; } }
/** * @deprecated Use addBinaryInteractionToIndex(IndexWriter, BinaryInteraction) method instead */ @Deprecated public void addLineToIndex(IndexWriter indexWriter, String line) throws IOException, MitabLineException { try { addBinaryInteractionToIndex(indexWriter, documentBuilder.getMitabReader().readLine(line)); } catch (PsimiTabException e) { throw new MitabLineException(e); } }