package jalview.io; import jalview.datamodel.*; import java.net.URL; import java.io.BufferedReader; import java.io.InputStreamReader; import java.io.FileReader; public class JnetAnnotationMaker { /** * adds the annotation parsed by prediction to al. * @param prediction JPredFile * @param al AlignmentI * @param FirstSeq int - * @param noMsa boolean */ public static void add_annotation(JPredFile prediction, AlignmentI al, int FirstSeq, boolean noMsa) throws Exception { int i = 0; SequenceI[] preds = prediction.getSeqsAsArray(); // in the future we could search for the query // sequence in the alignment before calling this function. SequenceI seqRef = al.getSequenceAt(FirstSeq); int width = preds[0].getSequence().length(); int[] gapmap = al.getSequenceAt(FirstSeq).gapMap(); if (gapmap.length != width) { throw (new Exception( "Number of residues in supposed query sequence ('" + al.getSequenceAt(FirstSeq).getName() + "'\n" + al.getSequenceAt(FirstSeq).getSequence() + ")\ndiffer from number of prediction sites in prediction (" + width + ")")); } AlignmentAnnotation annot; Annotation[] annotations = null; while (i < preds.length) { String id = preds[i].getName().toUpperCase(); if (id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED")) { annotations = new Annotation[al.getWidth()]; if (id.equals("JNETPRED") || id.equals("JNETPSSM") || id.equals("JNETFREQ") || id.equals("JNETHMM") || id.equals("JNETALIGN") || id.equals("JPRED")) { for (int j = 0; j < width; j++) { annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0); } } else if (id.equals("JNETCONF")) { for (int j = 0; j < width; j++) { float value = new Float(preds[i].getCharAt( j) + "").floatValue(); annotations[gapmap[j]] = new Annotation(preds[i].getCharAt( j) + "", "", preds[i].getCharAt(j), value); } } else { for (int j = 0; j < width; j++) { annotations[gapmap[j]] = new Annotation(preds[i].getCharAt( j) + "", "", ' ', 0); } } if (id.equals("JNETCONF")) { annot = new AlignmentAnnotation(preds[i].getName(), "JNet Output", annotations, 0f, 10f, AlignmentAnnotation.BAR_GRAPH); } else { annot = new AlignmentAnnotation(preds[i].getName(), "JNet Output", annotations); } if (seqRef != null) { annot.createSequenceMapping(seqRef, 0); seqRef.addAlignmentAnnotation(annot); } al.addAnnotation(annot); if (noMsa) { al.deleteSequence(preds[i]); } } i++; } //Hashtable scores = prediction.getScores(); /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"), "JnetpropH", "Jnet Helix Propensity", 0f,1f,1); addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"), "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1); addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"), "JnetpropC", "Jnet Coil Propensity", 0f,1f,1); */ } }