X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=6828202da66c0dda62cc07345543fb8f2bad629b;hb=69e8792b5f1ed2c02cff0a1ee328793ab5c0f423;hp=3feae5d740ca6f9c9eead8bd044b800ffbf957cc;hpb=4550191c87ce9e044ce35980d4c926684fe4f04a;p=jalview.git diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index 3feae5d..6828202 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -59,22 +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; @@ -98,7 +95,8 @@ 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] @@ -150,7 +148,7 @@ public class JnetAnnotationMaker { for (int j = 0; j < width; j++) { - float value = new Float(preds[i].getCharAt(j) + "") + float value = Float.valueOf(preds[i].getCharAt(j) + "") .floatValue(); annotations[gapmap[j]] = new Annotation( preds[i].getCharAt(j) + "", "", @@ -161,7 +159,7 @@ public class JnetAnnotationMaker { for (int j = 0; j < width; j++) { - float value = new Float(preds[i].getCharAt(j) + "") + float value = Float.valueOf(preds[i].getCharAt(j) + "") .floatValue(); annotations[gapmap[delMap[j]]] = new Annotation( preds[i].getCharAt(j) + "", "", @@ -222,8 +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); @@ -234,8 +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();