X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=27fc8697e327dd09effa82921acca97b64092a27;hb=2305d687bac5ed8a76ecb93c54c7b090a928e362;hp=993737b38cefcf8d311fe1a4aaa4cde80b42582a;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 993737b..27fc869 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,24 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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 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 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 java.util.Locale;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
 
 public class JnetAnnotationMaker
 {
@@ -33,17 +41,17 @@ public class JnetAnnotationMaker
    * adds the annotation parsed by prediction to al.
    * 
    * @param prediction
-   *                JPredFile
+   *          JPredFile
    * @param al
-   *                AlignmentI
+   *          AlignmentI
    * @param firstSeq
-   *                int the index of the sequence to attach the annotation to
-   *                (usually zero)
+   *          int the index of the sequence to attach the annotation to (usually
+   *          zero)
    * @param noMsa
-   *                boolean
+   *          boolean
    * @param delMap
-   *                mapping from columns in JPredFile prediction to residue
-   *                number in al.getSequence(firstSeq)
+   *          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
@@ -53,18 +61,19 @@ public class JnetAnnotationMaker
     // 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 width = preds[0].getLength();
     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 + ")"));
+      throw (new Exception(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;
@@ -76,106 +85,132 @@ public class JnetAnnotationMaker
       existingAnnotations = al.getAlignmentAnnotation().length;
     }
 
+    Annotation[] sol = new Annotation[al.getWidth()];
+    boolean firstsol = true;
+
     while (i < preds.length)
     {
-      String id = preds[i].getName().toUpperCase();
+      String id = preds[i].getName().toUpperCase(Locale.ROOT);
 
       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 = Float.valueOf(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 = Float.valueOf(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(),
+                    "JPred Output", annotations, 0f, 10f,
+                    AlignmentAnnotation.BAR_GRAPH);
+          }
+          else
+          {
+            annot = new AlignmentAnnotation(preds[i].getName(),
+                    "JPred 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]);
@@ -184,7 +219,23 @@ public class JnetAnnotationMaker
 
       i++;
     }
+    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();
 
     /*