X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJnetAnnotationMaker.java;h=be063c882abc742295660eee09cd80c89734d651;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=577e8742652c1414e7edceedbbc0aaca94b7e460;hpb=a5481d6e853a962af603f4a21b171ba6fc9c200d;p=jalview.git

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index 577e874..be063c8 100755
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -1,20 +1,20 @@
 /*
-* 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
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.*;
@@ -22,9 +22,12 @@ 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);
+                                    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
@@ -42,14 +45,16 @@ 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].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 ('" +
+          "Number of residues in " + (delMap == null ? "" : " mapped ") +
+          "supposed query sequence ('" +
           al.getSequenceAt(firstSeq).getName() + "'\n" +
-          al.getSequenceAt(firstSeq).getSequence() +
+          al.getSequenceAt(firstSeq).getSequenceAsString() +
           ")\ndiffer from number of prediction sites in prediction (" + width +
           ")"));
     }
@@ -58,9 +63,10 @@ public class JnetAnnotationMaker
     Annotation[] annotations = null;
 
     int existingAnnotations = 0;
-    if(al.getAlignmentAnnotation()!=null)
-       existingAnnotations = al.getAlignmentAnnotation().length;
-
+    if (al.getAlignmentAnnotation() != null)
+    {
+      existingAnnotations = al.getAlignmentAnnotation().length;
+    }
 
     while (i < preds.length)
     {
@@ -73,19 +79,22 @@ public class JnetAnnotationMaker
         /*        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) {
+          if (delMap == null)
+          {
             for (int j = 0; j < width; j++)
             {
               annotations[gapmap[j]] = new Annotation("", "",
                   preds[i].getCharAt(j), 0);
             }
-          } else {
+          }
+          else
+          {
             for (int j = 0; j < width; j++)
             {
               annotations[gapmap[delMap[j]]] = new Annotation("", "",
@@ -95,39 +104,47 @@ public class JnetAnnotationMaker
         }
         else if (id.equals("JNETCONF"))
         {
-          if (delMap==null) {
+          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);
+                  j) + "").floatValue();
+              annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                  j) + "", "", preds[i].getCharAt(j),
+                  value);
             }
-          } else {
+          }
+          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),
+              annotations[gapmap[delMap[j]]] = new Annotation(preds[i].
+                  getCharAt(
+                      j) + "", "", preds[i].getCharAt(j),
                   value);
-              }
             }
+          }
         }
         else
         {
-          if (delMap==null) {
+          if (delMap == null)
+          {
             for (int j = 0; j < width; j++)
             {
               annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
                   j) + "", "", ' ', 0);
             }
-          } else {
+          }
+          else
+          {
             for (int j = 0; j < width; j++)
             {
-            annotations[gapmap[delMap[j]]] = new Annotation(preds[i].getCharAt(
-                j) + "", "", ' ', 0);            
+              annotations[gapmap[delMap[j]]] = new Annotation(preds[i].
+                  getCharAt(
+                      j) + "", "", ' ', 0);
             }
           }
         }
@@ -178,4 +195,4 @@ public class JnetAnnotationMaker
      */
 
   }
-}
\ No newline at end of file
+}