X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=c9f1fcf7defd1489d50188909e1b785a63f154af;hb=f3d0dc3395aff566e8005e6a6a9a13bf795c14a4;hp=c5320f1f7594457bb4e3fa9906b765464d1af43e;hpb=8002d3a28b1e21a9d89a24e4c81cf9397ecea0db;p=jalview.git diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index c5320f1..c9f1fcf 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -59,23 +59,19 @@ public class JnetAnnotationMaker // 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 width = preds[0].getLength(); int[] gapmap = al.getSequenceAt(firstSeq).gapMap(); if ((delMap != null && delMap.length > width) || (delMap == null && gapmap.length != width)) { - throw (new Exception( - MessageManager - .formatMessage( - "exception.number_of_residues_in_query_sequence_differ_from_prediction", - new String[] - { - (delMap == null ? "" : MessageManager - .getString("label.mapped")), - al.getSequenceAt(firstSeq).getName(), - al.getSequenceAt(firstSeq) - .getSequenceAsString(), - Integer.valueOf(width).toString() }))); + throw (new Exception(MessageManager.formatMessage( + "exception.number_of_residues_in_query_sequence_differ_from_prediction", + new String[] + { (delMap == null ? "" + : MessageManager.getString("label.mapped")), + al.getSequenceAt(firstSeq).getName(), + al.getSequenceAt(firstSeq).getSequenceAsString(), + Integer.valueOf(width).toString() }))); } AlignmentAnnotation annot; @@ -99,17 +95,18 @@ public class JnetAnnotationMaker { if (id.startsWith("JNETSOL")) { - float amnt = (id.endsWith("25") ? 3f : id.endsWith("5") ? 6f : 9f); + float amnt = (id.endsWith("25") ? 3f + : id.endsWith("5") ? 6f : 9f); for (int spos = 0; spos < width; spos++) { int sposw = (delMap == null) ? gapmap[spos] - : delMap[gapmap[spos]]; + : gapmap[delMap[spos]]; if (firstsol) { sol[sposw] = new Annotation(0f); } if (preds[i].getCharAt(spos) == 'B' - && (sol[spos].value == 0f || sol[spos].value < amnt)) + && (sol[sposw].value == 0f || sol[sposw].value < amnt)) { sol[sposw].value = amnt; } @@ -193,13 +190,13 @@ public class JnetAnnotationMaker if (id.equals("JNETCONF")) { annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", annotations, 0f, 10f, + "JPred Output", annotations, 0f, 10f, AlignmentAnnotation.BAR_GRAPH); } else { annot = new AlignmentAnnotation(preds[i].getName(), - "JNet Output", annotations); + "JPred Output", annotations); } if (seqRef != null) @@ -223,8 +220,7 @@ public class JnetAnnotationMaker if (!firstsol) { // add the solvent accessibility - annot = new AlignmentAnnotation( - "Jnet Burial", + annot = new AlignmentAnnotation("Jnet Burial", "Prediction of Solvent Accessibility
levels are", sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH); @@ -235,8 +231,8 @@ public class JnetAnnotationMaker seqRef.addAlignmentAnnotation(annot); } al.addAnnotation(annot); - al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length - - existingAnnotations - 1); + al.setAnnotationIndex(annot, + al.getAlignmentAnnotation().length - existingAnnotations - 1); } // Hashtable scores = prediction.getScores();