/*
- * 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
+ * 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.
- *
- * 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 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 <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
{
public static void add_annotation(JPredFile prediction, AlignmentI al,
- int firstSeq, boolean noMsa)
- throws Exception
+ int firstSeq, boolean noMsa) throws Exception
{
- JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, (int[])null);
+ JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa,
+ (int[]) null);
}
/**
* adds the annotation parsed by prediction to al.
- * @param prediction JPredFile
- * @param al AlignmentI
- * @param firstSeq int the index of the sequence to attach the annotation to (usually zero)
- * @param noMsa boolean
- * @param delMap mapping from columns in JPredFile prediction to residue number in al.getSequence(firstSeq)
+ *
+ * @param prediction
+ * JPredFile
+ * @param al
+ * AlignmentI
+ * @param firstSeq
+ * int the index of the sequence to attach the annotation to (usually
+ * zero)
+ * @param noMsa
+ * boolean
+ * @param delMap
+ * 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
+ int firstSeq, boolean noMsa, int[] delMap) throws Exception
{
int i = 0;
SequenceI[] preds = prediction.getSeqsAsArray();
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 ('" +
- al.getSequenceAt(firstSeq).getName() + "'\n" +
- al.getSequenceAt(firstSeq).getSequenceAsString() +
- ")\ndiffer from number of prediction sites in prediction (" + width +
- ")"));
+ 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"))
+ 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)
+ {
+ 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
{
- 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[delMap[j]]] = new Annotation(
+ preds[i].getCharAt(j) + "", "",
+ preds[i].getCharAt(j), value);
+ }
}
}
else
{
- for (int j = 0; j < width; j++)
+ if (delMap == null)
+ {
+ for (int j = 0; j < width; j++)
+ {
+ annotations[gapmap[j]] = new Annotation(
+ preds[i].getCharAt(j) + "", "", ' ', 0);
+ }
+ }
+ else
{
- annotations[gapmap[delMap[j]]] = new Annotation(preds[i].
- getCharAt(
- j) + "", "", ' ', 0);
+ 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++;
}
-
- //Hashtable scores = prediction.getScores();
-
- /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),
- "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
-
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),
- "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
-
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),
- "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
+ 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();
+
+ /*
+ * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),
+ * "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
+ *
+ * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),
+ * "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
+ *
+ * addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),
+ * "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
*/
}
git://source.jalview.org / jalview.git / blobdiff