X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=7c6c61d52695868c491b5831ec646377e4b578cd;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=60c0a68837dbef4083371d65332450d3d63c5498;hpb=2bb1ec443f93d558beeca5174023e2b9833243fc;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 60c0a68..7c6c61d 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,125 +1,200 @@
-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();
-    // 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 (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 = 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++)
-          {
-            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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+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<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);
+     */
+
+  }
+}