X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=27fc8697e327dd09effa82921acca97b64092a27;hb=efff0826d9368314db6215e90a856059b86dbea8;hp=2a8a00ffbe3873507e8daa3e3cbce0e311e9113c;hpb=ff450fad8709ae81919af7a15ea382af7292794c;p=jalview.git diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index 2a8a00f..27fc869 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -20,6 +20,8 @@ */ package jalview.io; +import java.util.Locale; + import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; @@ -64,17 +66,14 @@ public class JnetAnnotationMaker 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; @@ -91,14 +90,15 @@ public class JnetAnnotationMaker while (i < preds.length) { - String id = preds[i].getName().toUpperCase(); + String id = preds[i].getName().toUpperCase(Locale.ROOT); if (id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED")) { 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 +150,7 @@ 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 +161,7 @@ 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 +222,7 @@ 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 +233,8 @@ 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();