X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMapping.java;h=b6b4c966c65967dae3a53037b59bc50f6407cd7f;hb=28a00b99bbd8f25fd894d5941149f2e1a45ed0f2;hp=e54b53ec1e9917a8da23c3aa789903c99743105e;hpb=385e63c78d289d4beae9c1ad2b187c0ea311ffbc;p=jalview.git

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index e54b53e..b6b4c96 100644
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 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.datamodel;
 
 import java.util.Vector;
@@ -219,6 +236,11 @@ public class Mapping
       if (map != null)
       {
         int[] frange = map.locateInFrom(f.getBegin(), f.getEnd());
+        if (frange == null)
+        {
+          // JBPNote - this isprobably not the right thing to doJBPHack
+          return null;
+        }
         SequenceFeature[] vf = new SequenceFeature[frange.length / 2];
         for (int i = 0, v = 0; i < frange.length; i += 2, v++)
         {
@@ -226,7 +248,7 @@ public class Mapping
           vf[v].setBegin(frange[i]);
           vf[v].setEnd(frange[i + 1]);
           if (frange.length > 2)
-            vf[v].setDescription(f.getDescription() + "\nPart " + v);
+            vf[v].setDescription(f.getDescription() + "\nPart " + (v + 1));
         }
         return vf;
       }
@@ -342,7 +364,8 @@ public class Mapping
       for (int vc = 0; vc < viscontigs.length; vc += 2)
       {
         // find a mapped range in this visible region
-        int[] mpr = locateMappedRange(1+viscontigs[vc], viscontigs[vc + 1]-1);
+        int[] mpr = locateMappedRange(1 + viscontigs[vc],
+                viscontigs[vc + 1] - 1);
         if (mpr != null)
         {
           for (int m = 0; m < mpr.length; m += 2)
@@ -358,49 +381,58 @@ public class Mapping
           }
         }
       }
-      int[] from = new int[fromRange.size()*2];
-      int[] to = new int[toRange.size()*2];
+      int[] from = new int[fromRange.size() * 2];
+      int[] to = new int[toRange.size() * 2];
       int[] r;
-      for (int f=0,fSize=fromRange.size(); f<fSize; f++)
+      for (int f = 0, fSize = fromRange.size(); f < fSize; f++)
       {
         r = (int[]) fromRange.elementAt(f);
-        from[f*2] = r[0];
-        from[f*2+1] = r[1];
+        from[f * 2] = r[0];
+        from[f * 2 + 1] = r[1];
       }
-      for (int f=0,fSize=toRange.size(); f<fSize; f++)
+      for (int f = 0, fSize = toRange.size(); f < fSize; f++)
       {
         r = (int[]) toRange.elementAt(f);
-        to[f*2] = r[0];
-        to[f*2+1] = r[1];
+        to[f * 2] = r[0];
+        to[f * 2 + 1] = r[1];
       }
-      copy.setMap(new MapList(from, to, map.getFromRatio(), map.getToRatio()));
+      copy.setMap(new MapList(from, to, map.getFromRatio(), map
+              .getToRatio()));
     }
     return copy;
   }
+
   public static void main(String[] args)
   {
     /**
-     * trite test of the intersectVisContigs method
-     * for a simple DNA -> Protein exon map and a range of visContigs
+     * trite test of the intersectVisContigs method for a simple DNA -> Protein
+     * exon map and a range of visContigs
      */
-    MapList fk = new MapList(new int[] { 1,6,8,13,15,23}, new int[] { 1,7}, 3, 1);
+    MapList fk = new MapList(new int[]
+    { 1, 6, 8, 13, 15, 23 }, new int[]
+    { 1, 7 }, 3, 1);
     Mapping m = new Mapping(fk);
-    Mapping m_1 = m.intersectVisContigs(new int[] {fk.getFromLowest(), fk.getFromHighest()});
-    Mapping m_2 = m.intersectVisContigs(new int[] {1,7,11,20});
-    System.out.println(""+m_1.map.getFromRanges());
-    
-    
+    Mapping m_1 = m.intersectVisContigs(new int[]
+    { fk.getFromLowest(), fk.getFromHighest() });
+    Mapping m_2 = m.intersectVisContigs(new int[]
+    { 1, 7, 11, 20 });
+    System.out.println("" + m_1.map.getFromRanges());
+
   }
+
   /**
    * get the sequence being mapped to - if any
+   * 
    * @return null or a dataset sequence
    */
   public SequenceI getTo()
   {
     return to;
   }
+
   /**
    * set the dataset sequence being mapped to if any
+   * 
    * @param tto
    */
   public void setTo(SequenceI tto)
@@ -408,7 +440,9 @@ public class Mapping
     to = tto;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see java.lang.Object#finalize()
    */
   protected void finalize() throws Throwable
@@ -417,5 +451,5 @@ public class Mapping
     to = null;
     super.finalize();
   }
-  
+
 }