/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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 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.
-*
-* 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
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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 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.
+ *
+ * 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
*/package jalview.io;
import jalview.datamodel.*;
public class JnetAnnotationMaker
{
public static void add_annotation(JPredFile prediction, AlignmentI al,
- int firstSeq, boolean noMsa) throws Exception {
- JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, (int[]) null);
+ int firstSeq, boolean noMsa)
+ throws Exception
+ {
+ JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, (int[])null);
}
+
/**
* adds the annotation parsed by prediction to al.
* @param prediction JPredFile
SequenceI seqRef = al.getSequenceAt(firstSeq);
int width = preds[0].getSequence().length;
int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
- if ((delMap!=null && delMap.length > width) || (delMap==null && gapmap.length!=width))
+ if ( (delMap != null && delMap.length > width) ||
+ (delMap == null && gapmap.length != width))
{
throw (new Exception(
- "Number of residues in "+(delMap==null ? "" : " mapped ")+"supposed query sequence ('" +
+ "Number of residues in " + (delMap == null ? "" : " mapped ") +
+ "supposed query sequence ('" +
al.getSequenceAt(firstSeq).getName() + "'\n" +
- al.getSequenceAt(firstSeq).getSequence() +
+ al.getSequenceAt(firstSeq).getSequenceAsString() +
")\ndiffer from number of prediction sites in prediction (" + width +
")"));
}
Annotation[] annotations = null;
int existingAnnotations = 0;
- if(al.getAlignmentAnnotation()!=null)
- existingAnnotations = al.getAlignmentAnnotation().length;
-
+ if (al.getAlignmentAnnotation() != null)
+ {
+ existingAnnotations = al.getAlignmentAnnotation().length;
+ }
while (i < preds.length)
{
/* if (delMap!=null) {
for (int j=0; j<annotations.length; j++)
annotations[j] = new Annotation("","",'',0);
- }
- */
+ }
+ */
if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
id.equals("JNETFREQ") || id.equals("JNETHMM") ||
id.equals("JNETALIGN") || id.equals("JPRED"))
{
- if (delMap==null) {
+ if (delMap == null)
+ {
for (int j = 0; j < width; j++)
{
annotations[gapmap[j]] = new Annotation("", "",
preds[i].getCharAt(j), 0);
}
- } else {
+ }
+ else
+ {
for (int j = 0; j < width; j++)
{
annotations[gapmap[delMap[j]]] = new Annotation("", "",
}
else if (id.equals("JNETCONF"))
{
- if (delMap==null) {
+ if (delMap == null)
+ {
for (int j = 0; j < width; j++)
{
float value = new Float(preds[i].getCharAt(
- j) + "").floatValue();
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
- j) + "", "", preds[i].getCharAt(j),
- value);
+ j) + "").floatValue();
+ annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+ j) + "", "", preds[i].getCharAt(j),
+ value);
}
- } else {
+ }
+ else
+ {
for (int j = 0; j < width; j++)
{
float value = new Float(preds[i].getCharAt(
j) + "").floatValue();
- annotations[gapmap[delMap[j]]] = new Annotation(preds[i].getCharAt(
- j) + "", "", preds[i].getCharAt(j),
+ annotations[gapmap[delMap[j]]] = new Annotation(preds[i].
+ getCharAt(
+ j) + "", "", preds[i].getCharAt(j),
value);
- }
}
+ }
}
else
{
- if (delMap==null) {
+ if (delMap == null)
+ {
for (int j = 0; j < width; j++)
{
annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
j) + "", "", ' ', 0);
}
- } else {
+ }
+ else
+ {
for (int j = 0; j < width; j++)
{
- annotations[gapmap[delMap[j]]] = new Annotation(preds[i].getCharAt(
- j) + "", "", ' ', 0);
+ annotations[gapmap[delMap[j]]] = new Annotation(preds[i].
+ getCharAt(
+ j) + "", "", ' ', 0);
}
}
}