X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=a6779a6e998f61a67d1ad7e32d8f87cf8b6a8e74;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=60fb601def8aeaa90d5a052c55c2f01b5346fcaf;hpb=51eebe77f74dda2f4ff336dfe0fea0ed68b86e5b;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 60fb601..a6779a6 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,145 +1,254 @@
-/*
-* 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.*;
-
-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;
-
-    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 (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, 1, false);
-          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);
-     */
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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);
+  }
+
+  /**
+   * 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(
+              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;
+    }
+
+    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("JNETSOL"))
+        {
+          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)
+            {
+              sol[sposw] = new Annotation(0f);
+            }
+            if (preds[i].getCharAt(spos) == 'B'
+                    && (sol[sposw].value == 0f || sol[sposw].value < amnt))
+            {
+              sol[sposw].value = amnt;
+            }
+          }
+          firstsol = false;
+        }
+        else
+        {
+          // 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)
+            {
+              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++;
+    }
+    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);
+     */
+
+  }
+}