Examples of BlastParser

Examples of org.broad.igv.synteny.BlastParser

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    }


    private void loadSyntentyMapping(ResourceLocator locator, List<Track> newTracks) {

        List<BlastMapping> mappings = (new BlastParser()).parse(locator.getPath());
        List<htsjdk.tribble.Feature> features = new ArrayList<htsjdk.tribble.Feature>(mappings.size());
        features.addAll(mappings);

        Genome genome = GenomeManager.getInstance().getCurrentGenome();
        FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
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Examples of versusSNP.blast.BlastParser

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        JOptionPane.showMessageDialog(null, UICaption.dialog_error_path_empty, UICaption.dialog_caption_error, JOptionPane.ERROR_MESSAGE);
        loopAlignmentLoader(dialog);
      }
      document.setQueryGenome(dialog.getId1());
      document.setSubjectGenome(dialog.getId2());
      new Thread(new BlastParser(dialog.getPath(), document)).start();
    }
  }
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Examples of versusSNP.blast.BlastParser

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      new ORFFile().readFile(args[1] + ".txt", genome2);
      genome2.sortOrfList();
      FastaFile fastaFile2 = new FastaFile();
      fastaFile2.readFile(args[1] + ".fasta", genome2);
      genome2.attachSequences(fastaFile2.getSequences());
      BlastParser parser = new BlastParser();
      parser.parse(args[0] + "-" + args[1]);
      genome1.attachBlastSets(parser.getBlastList(), genome2, true);
      genome1.printSNPSummary(genome2);
    } else {
      new VersusSNP().setVisible(true);
    }
  }
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