-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-import java.net.URL;\r
-import java.io.BufferedReader;\r
-import java.io.InputStreamReader;\r
-import java.io.FileReader;\r
-\r
-\r
-public class JnetAnnotationMaker\r
-{\r
- /**\r
- * adds the annotation parsed by prediction to al.\r
- * @param prediction JPredFile\r
- * @param al AlignmentI\r
- * @param FirstSeq int -\r
- * @param noMsa boolean\r
- */\r
- public static void add_annotation(JPredFile prediction, AlignmentI al,\r
- int FirstSeq, boolean noMsa)\r
- throws Exception\r
- {\r
- int i = 0;\r
- SequenceI[] preds = prediction.getSeqsAsArray();\r
- // in the future we could search for the query\r
- // sequence in the alignment before calling this function.\r
- SequenceI seqRef = al.getSequenceAt(FirstSeq);\r
- int width = preds[0].getSequence().length();\r
- int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
- if (gapmap.length != width)\r
- {\r
- throw (new Exception(\r
- "Number of residues in supposed query sequence ('" +\r
- al.getSequenceAt(FirstSeq).getName() + "'\n" +\r
- al.getSequenceAt(FirstSeq).getSequence() +\r
- ")\ndiffer from number of prediction sites in prediction (" + width +\r
- ")"));\r
- }\r
-\r
- AlignmentAnnotation annot;\r
- Annotation[] annotations = null;\r
-\r
- while (i < preds.length)\r
- {\r
- String id = preds[i].getName().toUpperCase();\r
-\r
- if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
- id.startsWith("JPRED"))\r
- {\r
- annotations = new Annotation[al.getWidth()];\r
-\r
- if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||\r
- id.equals("JNETFREQ") || id.equals("JNETHMM") ||\r
- id.equals("JNETALIGN") || id.equals("JPRED"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- annotations[gapmap[j]] = new Annotation("", "",\r
- preds[i].getCharAt(j), 0);\r
- }\r
- }\r
- else if (id.equals("JNETCONF"))\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- float value = Float.parseFloat(preds[i].getCharAt(\r
- j) + "");\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
- j) + "", "", preds[i].getCharAt(j),\r
- value);\r
- }\r
- }\r
- else\r
- {\r
- for (int j = 0; j < width; j++)\r
- {\r
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
- j) + "", "", ' ', 0);\r
- }\r
- }\r
-\r
- if (id.equals("JNETCONF"))\r
- {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output", annotations, 0f,\r
- 10f,\r
- AlignmentAnnotation.BAR_GRAPH);\r
- }\r
- else\r
- {\r
- annot = new AlignmentAnnotation(preds[i].getName(),\r
- "JNet Output", annotations);\r
- }\r
-\r
- if (seqRef != null)\r
- {\r
- annot.createSequenceMapping(seqRef, 0);\r
- seqRef.addAlignmentAnnotation(annot);\r
- }\r
-\r
- al.addAnnotation(annot);\r
-\r
- if (noMsa)\r
- {\r
- al.deleteSequence(preds[i]);\r
- }\r
- }\r
-\r
- i++;\r
- }\r
-\r
- //Hashtable scores = prediction.getScores();\r
-\r
- /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),\r
- "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),\r
- "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
-\r
- addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),\r
- "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
- */\r
-\r
- }\r
-}\r
+/*
+ * 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);
+ }
+
+ /**
+ * adds the annotation parsed by prediction to al.
+ * @param prediction JPredFile
+ * @param al AlignmentI
+ * @param firstSeq int -
+ * @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 i = 0;
+ SequenceI[] preds = prediction.getSeqsAsArray();
+ // 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[] 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 +
+ ")"));
+ }
+
+ AlignmentAnnotation annot;
+ Annotation[] annotations = null;
+
+ int existingAnnotations = 0;
+ if (al.getAlignmentAnnotation() != null)
+ {
+ existingAnnotations = al.getAlignmentAnnotation().length;
+ }
+
+ 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 (delMap == null)
+ {
+ 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);
+ }
+ }
+ }
+ else if (id.equals("JNETCONF"))
+ {
+ 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
+ {
+ 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
+ {
+ if (delMap == null)
+ {
+ 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);
+ }
+
+ 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);
+ */
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff