src/jalview/io/AnnotationUtil.java

   1 package jalview.io;
   2
   3 import jalview.analysis.AAFrequency;
   4 import jalview.analysis.Conservation;
   5 import jalview.datamodel.AlignmentAnnotation;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.datamodel.Annotation;
   8 import jalview.datamodel.ProfilesI;
   9 import jalview.datamodel.SequenceI;
  10
  11 public class AnnotationUtil
  12 {
  13
  14   public static AlignmentAnnotation getConsensusAnnotationFromFile(
  15           String file)
  16   {
  17     AlignmentI alignment = readAlignmentFile(file);
  18     // AlignFrame af = new AlignFrame(alignment, 5, 5);
  19     // af.setVisible(false);
  20     // AlignmentAnnotation consensus = af.getViewport()
  21     // .getAlignmentConsensusAnnotation();
  22     // af.dispose();
  23     // System.out.println(consensus);
  24
  25     SequenceI[] alignmentSeqs = alignment.getSequencesArray();
  26     int width = alignment.getWidth();
  27     long nseq = alignmentSeqs.length;
  28     boolean ignoreGapsConsensus = true;
  29     boolean showSequenceLogo = false;
  30
  31     AlignmentAnnotation consensusAnnotation = new AlignmentAnnotation(
  32             "Consensus",
  33             "PID", new Annotation[1], 0f, 100f,
  34             AlignmentAnnotation.BAR_GRAPH);
  35     consensusAnnotation.hasText = true;
  36     consensusAnnotation.autoCalculated = true;
  37
  38     alignment.addAnnotation(consensusAnnotation);
  39     ProfilesI hconsensus = AAFrequency.calculate(alignmentSeqs, width, 0,
  40             width,
  41             true);
  42
  43     AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
  44             hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
  45             ignoreGapsConsensus, showSequenceLogo, nseq);
  46
  47     System.out.println(">>>>> Consensus Annotation : "
  48             + consensusAnnotation);
  49     return consensusAnnotation;
  50   }
  51
  52   public static AlignmentAnnotation getConservationAnnotationFromFile(
  53           String file, SequenceI seqRef)
  54   {
  55     AlignmentAnnotation conservationAnnotation = null;
  56     int foundAnnotCount = seqRef.getAnnotation().length;
  57     if (seqRef != null && foundAnnotCount < 3)
  58     {
  59       AlignmentI alignment = readAlignmentFile("/Users/tcnofoegbu/Desktop/query.jal");
  60       // AlignmentI alignment = readAlignmentFile(file);
  61       // ColumnSelection cs = new ColumnSelection();
  62       // SequenceI querySeq = alignment.getSequenceAt(0);
  63       // cs.hideInsertionsFor(querySeq);
  64       // AlignViewport av = new AlignViewport(alignment);
  65       // av.setColumnSelection(cs);
  66       //
  67       // alignment = av.getAlignment();
  68       int alWidth = alignment.getWidth();
  69       int ConsPercGaps = 25;
  70
  71       AlignmentAnnotation quality = new AlignmentAnnotation("Quality",
  72               "Alignment Quality based on Blosum62 scores",
  73               new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
  74       quality.hasText = true;
  75       quality.autoCalculated = true;
  76
  77       conservationAnnotation = new AlignmentAnnotation("Conservation",
  78               "PID", new Annotation[1], 0f, 100f,
  79               AlignmentAnnotation.BAR_GRAPH);
  80       conservationAnnotation.hasText = true;
  81       conservationAnnotation.autoCalculated = true;
  82       alignment.addAnnotation(conservationAnnotation);
  83       Conservation cons = Conservation.calculateConservation("All",
  84               alignment.getSequences(), 0, alWidth - 1, false,
  85               ConsPercGaps, quality != null);
  86       cons.completeAnnotations(conservationAnnotation, quality, 0, alWidth);
  87       System.out.println(">>>");
  88
  89       conservationAnnotation.createSequenceMapping(seqRef, 1, true);
  90       seqRef.addAlignmentAnnotation(conservationAnnotation);
  91
  92       // conservationAnnotation.createSequenceMapping(
  93       // seqRef.getDatasetSequence(), 1, true);
  94       // seqRef.getDatasetSequence().addAlignmentAnnotation(
  95       // conservationAnnotation);
  96     }
  97
  98     return conservationAnnotation;
  99   }
 100
 101   private static AlignmentI readAlignmentFile(String f)
 102   {
 103     System.out.println("Reading file: " + f);
 104     try
 105     {
 106       FormatAdapter rf = new FormatAdapter();
 107       DataSourceType protocol = AppletFormatAdapter.checkProtocol(f);
 108       AlignmentI al = rf.readFile(f, protocol,
 109               new IdentifyFile().identify(f, protocol));
 110       return al;
 111     } catch (Exception e)
 112     {
 113       e.printStackTrace();
 114     }
 115     return null;
 116   }
 117
 118   public static void main(String[] args)
 119   {
 120     // getConservationAnnotationFromFile("http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/cd1b897af035cdf5/query.jal");
 121     getConsensusAnnotationFromFile("http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/cd1b897af035cdf5/query.jal");
 122   }
 123
 124 }