/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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
{
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;
existingAnnotations = al.getAlignmentAnnotation().length;
}
+ Annotation[] sol = new Annotation[al.getWidth()];
+ boolean firstsol = true;
+
while (i < preds.length)
{
String id = preds[i].getName().toUpperCase();
if (id.startsWith("LUPAS") || id.startsWith("JNET")
|| id.startsWith("JPRED"))
{
- annotations = new Annotation[al.getWidth()];
- /*
- * 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 (id.startsWith("JNETSOL"))
{
- if (delMap == null)
+ float amnt = (id.endsWith("25") ? 3f : id.endsWith("5") ? 6f : 9f);
+ for (int spos = 0; spos < width; spos++)
{
- for (int j = 0; j < width; j++)
+ int sposw = (delMap == null) ? gapmap[spos]
+ : gapmap[delMap[spos]];
+ if (firstsol)
{
- annotations[gapmap[j]] = new Annotation("", "",
- preds[i].getCharAt(j), 0);
+ sol[sposw] = new Annotation(0f);
}
- }
- else
- {
- for (int j = 0; j < width; j++)
+ if (preds[i].getCharAt(spos) == 'B'
+ && (sol[sposw].value == 0f || sol[sposw].value < amnt))
{
- annotations[gapmap[delMap[j]]] = new Annotation("", "",
- preds[i].getCharAt(j), 0);
+ sol[sposw].value = amnt;
}
}
+ firstsol = false;
}
- else if (id.equals("JNETCONF"))
+ else
{
- if (delMap == null)
+ // some other kind of annotation
+ annotations = new Annotation[al.getWidth()];
+ /*
+ * 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"))
{
- for (int j = 0; j < width; j++)
+ if (delMap == null)
{
- float value = new Float(preds[i].getCharAt(j) + "")
- .floatValue();
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)
- + "", "", preds[i].getCharAt(j), value);
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[j]] = new Annotation("", "",
+ preds[i].getCharAt(j), 0);
+ }
}
- }
- else
- {
- for (int j = 0; j < width; j++)
+ else
{
- float value = new Float(preds[i].getCharAt(j) + "")
- .floatValue();
- annotations[gapmap[delMap[j]]] = new Annotation(
- preds[i].getCharAt(j) + "", "",
- preds[i].getCharAt(j), value);
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[delMap[j]]] = new Annotation("", "",
+ preds[i].getCharAt(j), 0);
+ }
}
}
- }
- else
- {
- if (delMap == null)
+ else if (id.equals("JNETCONF"))
{
- for (int j = 0; j < width; j++)
+ if (delMap == null)
{
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)
- + "", "", ' ', 0);
+ 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);
+ }
+ }
+ 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), value);
+ }
}
}
else
{
- for (int j = 0; j < width; j++)
+ if (delMap == null)
{
- annotations[gapmap[delMap[j]]] = new Annotation(
- preds[i].getCharAt(j) + "", "", ' ', 0);
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[j]] = new Annotation(
+ preds[i].getCharAt(j) + "", "", ' ', 0);
+ }
+ }
+ else
+ {
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[delMap[j]]] = new Annotation(
+ preds[i].getCharAt(j) + "", "", ' ', 0);
+ }
}
}
- }
-
- if (id.equals("JNETCONF"))
- {
- annot = new AlignmentAnnotation(preds[i].getName(),
- "JNet Output", annotations, 0f, 10f,
- AlignmentAnnotation.BAR_GRAPH);
- }
- else
- {
- annot = new AlignmentAnnotation(preds[i].getName(),
- "JNet Output", annotations);
- }
- if (seqRef != null)
- {
- annot.createSequenceMapping(seqRef, 1, true);
- seqRef.addAlignmentAnnotation(annot);
- }
+ if (id.equals("JNETCONF"))
+ {
+ annot = new AlignmentAnnotation(preds[i].getName(),
+ "JNet Output", annotations, 0f, 10f,
+ AlignmentAnnotation.BAR_GRAPH);
+ }
+ else
+ {
+ annot = new AlignmentAnnotation(preds[i].getName(),
+ "JNet Output", annotations);
+ }
- al.addAnnotation(annot);
- al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
- - existingAnnotations - 1);
+ if (seqRef != null)
+ {
+ annot.createSequenceMapping(seqRef, 1, true);
+ seqRef.addAlignmentAnnotation(annot);
+ }
+ al.addAnnotation(annot);
+ al.setAnnotationIndex(annot, al.getAlignmentAnnotation().length
+ - existingAnnotations - 1);
+ }
if (noMsa)
{
al.deleteSequence(preds[i]);
i++;
}
+ if (!firstsol)
+ {
+ // add the solvent accessibility
+ annot = new AlignmentAnnotation(
+ "Jnet Burial",
+ "<html>Prediction of Solvent Accessibility<br/>levels are<ul><li>0 - Exposed</li><li>3 - 25% or more S.A. accessible</li><li>6 - 5% or more S.A. accessible</li><li>9 - Buried (<5% exposed)</li></ul>",
+ 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();
/*
git://source.jalview.org / jalview.git / blobdiff