X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=51924549b03f599083103edc656b34438ceb7db8;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=993737b38cefcf8d311fe1a4aaa4cde80b42582a;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 993737b..5192454 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,24 +1,30 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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
{
@@ -33,17 +39,17 @@ public class JnetAnnotationMaker
* adds the annotation parsed by prediction to al.
*
* @param prediction
- * JPredFile
+ * JPredFile
* @param al
- * AlignmentI
+ * AlignmentI
* @param firstSeq
- * int the index of the sequence to attach the annotation to
- * (usually zero)
+ * int the index of the sequence to attach the annotation to (usually
+ * zero)
* @param noMsa
- * boolean
+ * boolean
* @param delMap
- * mapping from columns in JPredFile prediction to residue
- * number in al.getSequence(firstSeq)
+ * mapping from columns in JPredFile prediction to residue number in
+ * al.getSequence(firstSeq)
*/
public static void add_annotation(JPredFile prediction, AlignmentI al,
int firstSeq, boolean noMsa, int[] delMap) throws Exception
@@ -58,13 +64,17 @@ public class JnetAnnotationMaker
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;
@@ -76,6 +86,9 @@ 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();
@@ -83,99 +96,121 @@ 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();
/*