X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureRenderer.java;h=e80d01a3c039d4fce9446a3a043b4b893414afe8;hb=b14411143cbfb4d311f68b3d3b73a645bf8200e8;hp=6e38f1b9eabfb7788d78e4ecba5547283e7b7224;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 6e38f1b..e80d01a 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -1,16 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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.gui;
 
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.*;
 import java.util.*;
 
-public class FeatureRenderer implements RendererI
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class FeatureRenderer
 {
   AlignViewport av;
-
   SequenceGroup currentSequenceGroup = null;
-  SequenceGroup [] allGroups = null;
+  SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
 
@@ -19,53 +37,72 @@ public class FeatureRenderer implements RendererI
     this.av = av;
   }
 
-
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
+  public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
+                           int start, int end, int x1, int y1, int width,
+                           int height)
   {
     Vector features = seq.getSequenceFeatures();
     Enumeration e = features.elements();
-    while( e.hasMoreElements() )
+
+    while (e.hasMoreElements())
     {
-      SequenceFeature sf = (SequenceFeature)e.nextElement();
-      int fstart = seq.findIndex(sf.getStart())-1;
-      int fend = seq.findIndex(sf.getEnd())-1;
+      SequenceFeature sf = (SequenceFeature) e.nextElement();
+
+      if (sf.getStart() > seq.getEnd())
+      {
+        continue;
+      }
+
+      int fstart = seq.findIndex(sf.getStart()) - 1;
+      int fend = seq.findIndex(sf.getEnd()) - 1;
 
-      if(    (fstart>=start&&fstart<=end) || (fend>=start&&fend<=end))
+      if ( ( (fstart <= end) && (fend >= start)))
       {
-        if(fstart==fend)
+        if (fstart < 0)
+        { // fix for if the feature we have starts before the sequence start,
+          fstart = 0; // but the feature end is still valid!!
+        }
+
+        if (fstart == fend)
         {
           g.setColor(Color.red);
-          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
+          g.fillRoundRect( (fstart - start) * width, y1, width,
+                          height, 4, 4);
           g.setColor(Color.white);
 
           char s = seq.getSequence().charAt(fstart);
           FontMetrics fm = g.getFontMetrics();
-          int charOffset =  (width - fm.charWidth(s))/2;
-          int pady = height/5;
-          g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);
-
+          int charOffset = (width - fm.charWidth(s)) / 2;
+          int pady = height / 5;
+          g.drawString(String.valueOf(s),
+                       charOffset + x1 + (width * (fstart - start)),
+                       (y1 + height) - pady);
         }
         else
         {
           for (int i = fstart; i <= fend; i++)
           {
+            char s = seq.getSequence().charAt(i);
+
+            if (jalview.util.Comparison.isGap(s))
+            {
+              continue;
+            }
+
             g.setColor(Color.blue);
-            g.fillRect( (i-start) * width, y1, width, height);
+            g.fillRect( (i - start) * width, y1, width, height);
 
             g.setColor(Color.white);
-            char s = seq.getSequence().charAt(i);
+
             FontMetrics fm = g.getFontMetrics();
             int charOffset = (width - fm.charWidth(s)) / 2;
             int pady = height / 5;
             g.drawString(String.valueOf(s),
-                         charOffset + x1 + width * (i-start),
-                         y1 + height - pady);
-
+                         charOffset + x1 + (width * (i - start)),
+                         (y1 + height) - pady);
           }
         }
       }
-
     }
-   }
-
+  }
 }