X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=c9f1fcf7defd1489d50188909e1b785a63f154af;hb=9f118a08c0f093fb30a51a2459e2609b3c959614;hp=a6779a6e998f61a67d1ad7e32d8f87cf8b6a8e74;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java index a6779a6..c9f1fcf 100755 --- a/src/jalview/io/JnetAnnotationMaker.java +++ b/src/jalview/io/JnetAnnotationMaker.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -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] @@ -192,13 +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) @@ -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();