X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=d5593e38ba1c92de0b224433949d3effa987c042;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=07a0068d2f17bd110164cd91c1e20d50fb6d4793;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 07a0068..d5593e3 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,41 +1,58 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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.*;
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+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 {
-    JnetAnnotationMaker.add_annotation(prediction, al, firstSeq, noMsa, (int[]) null);
+          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)
+   * 
+   * @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();
@@ -44,118 +61,156 @@ public class JnetAnnotationMaker
     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).getSequence() +
-          ")\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;
     Annotation[] annotations = null;
 
     int existingAnnotations = 0;
-    if(al.getAlignmentAnnotation()!=null)
-       existingAnnotations = al.getAlignmentAnnotation().length;
+    if (al.getAlignmentAnnotation() != null)
+    {
+      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) {
-            for (int j = 0; j < width; j++)
+          float amnt = (id.endsWith("25") ? 3f : id.endsWith("5") ? 6f : 9f);
+          for (int spos = 0; spos < width; spos++)
+          {
+            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) {
-            for (int j = 0; j < width; j++)
+          // 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"))
+          {
+            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) {
-            for (int j = 0; j < width; j++)
+          }
+          else if (id.equals("JNETCONF"))
+          {
+            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++)
+            else
             {
-            annotations[gapmap[delMap[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
+          {
+            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);
-        }
+          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]);
@@ -164,17 +219,35 @@ public class JnetAnnotationMaker
 
       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);
      */
 
   }