X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=dabd8ca219b6a3a2ea40e2dae2df0e903ed56470;hb=ad5029edaf36ceaafb4e269f2e00b0e1e0d7ffc4;hp=9a397d7597c3c02c1c799c89362d79825b12cf20;hpb=a665055e234b20c818820bddedf203b7fd138252;p=jalview.git
diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 9a397d7..dabd8ca 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,123 +1,203 @@
-package jalview.io;
-
-import jalview.datamodel.*;
-import java.net.URL;
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
-import java.io.FileReader;
-
-
-public class JnetAnnotationMaker
-{
- /**
- * adds the annotation parsed by prediction to al.
- * @param prediction JPredFile
- * @param al AlignmentI
- * @param FirstSeq int -
- * @param noMsa boolean
- */
- public static void add_annotation(JPredFile prediction, AlignmentI al,
- int FirstSeq, boolean noMsa)
- 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 (gapmap.length != width)
- {
- throw (new Exception(
- "Number of residues in supposed query sequence ('" +
- al.getSequenceAt(FirstSeq).getName() + "'\n" +
- al.getSequenceAt(FirstSeq).getSequence() +
- ")\ndiffer from number of prediction sites in prediction (" + width +
- ")"));
- }
-
- AlignmentAnnotation annot;
- Annotation[] annotations = null;
-
- 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 (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++)
- {
- annotations[gapmap[j]] = new Annotation("", "",
- preds[i].getCharAt(j), 0);
- }
- }
- else if (id.equals("JNETCONF"))
- {
- for (int j = 0; j < width; j++)
- {
- float value = Float.parseFloat(preds[i].getCharAt(
- j) + "");
- annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
- j) + "", "", preds[i].getCharAt(j),
- value);
- }
- }
- else
- {
- for (int j = 0; j < width; j++)
- {
- annotations[gapmap[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, 0);
- seqRef.addAlignmentAnnotation(annot);
- }
-
- al.addAnnotation(annot);
-
- 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);
- */
-
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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 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 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