X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=6828202da66c0dda62cc07345543fb8f2bad629b;hb=efb5cfa00ee832a62dfdf59f5fb847a0e16424d9;hp=11f05b79a6164e7e7481c38b2bfcc42297d1f18e;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 11f05b7..6828202 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,23 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
public class JnetAnnotationMaker
{
@@ -52,18 +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("Number of residues in "
- + (delMap == null ? "" : " mapped ")
- + "supposed query sequence ('"
- + al.getSequenceAt(firstSeq).getName() + "'\n"
- + al.getSequenceAt(firstSeq).getSequenceAsString()
- + ")\ndiffer from number of prediction sites in prediction ("
- + 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() })));
}
AlignmentAnnotation annot;
@@ -75,6 +83,9 @@ public class JnetAnnotationMaker
existingAnnotations = al.getAlignmentAnnotation().length;
}
+ Annotation[] sol = new Annotation[al.getWidth()];
+ boolean firstsol = true;
+
while (i < preds.length)
{
String id = preds[i].getName().toUpperCase();
@@ -82,98 +93,122 @@ public class JnetAnnotationMaker
if (id.startsWith("LUPAS") || id.startsWith("JNET")
|| id.startsWith("JPRED"))
{
- annotations = new Annotation[al.getWidth()];
- /*
- * if (delMap!=null) { for (int j=0; jPrediction of Solvent Accessibility
levels are- 0 - Exposed
- 3 - 25% or more S.A. accessible
- 6 - 5% or more S.A. accessible
- 9 - Buried (<5% exposed)
",
+ sol, 0f, 9f, AlignmentAnnotation.BAR_GRAPH);
+ annot.validateRangeAndDisplay();
+ if (seqRef != null)
+ {
+ annot.createSequenceMapping(seqRef, 1, true);
+ seqRef.addAlignmentAnnotation(annot);
+ }
+ al.addAnnotation(annot);
+ al.setAnnotationIndex(annot,
+ al.getAlignmentAnnotation().length - existingAnnotations - 1);
+ }
// Hashtable scores = prediction.getScores();
/*