showqual, showcons never used

[jalview.git] / src / jalview / gui / IdCanvas.java

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 30152cc..84f18ba 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -53,7 +53,7 @@ public class IdCanvas extends JPanel
     {\r
         setLayout(new BorderLayout());\r
         this.av = av;\r
-        PaintRefresher.Register(this, av.alignment);\r
+        PaintRefresher.Register(this, av.getSequenceSetId());\r
     }\r
 \r
     /**\r
@@ -331,12 +331,32 @@ public class IdCanvas extends JPanel
 \r
     void drawMarker(int i, int starty, int yoffset)\r
     {\r
-      int hiddenIndex = av.adjustForHiddenSeqs(i);\r
-      int lastIndex = av.adjustForHiddenSeqs(i - 1);\r
-      int nextIndex = av.adjustForHiddenSeqs(i + 1);\r
+\r
+      SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;\r
+      //Use this method here instead of calling hiddenSeq adjust\r
+      //3 times.\r
+      int hSize = hseqs.length;\r
+\r
+      int hiddenIndex = i;\r
+      int lastIndex = i - 1;\r
+      int nextIndex = i + 1;\r
+\r
+      for(int j=0; j<hSize; j++)\r
+      {\r
+        if (hseqs[j] != null)\r
+        {\r
+          if(j-1<hiddenIndex)\r
+            hiddenIndex++;\r
+          if(j-1<lastIndex)\r
+            lastIndex++;\r
+          if(j-1<nextIndex)\r
+            nextIndex++;\r
+        }\r
+      }\r
 \r
       boolean below = (hiddenIndex > lastIndex + 1);\r
-      boolean above = (nextIndex>hiddenIndex+1);\r
+      boolean above = (nextIndex > hiddenIndex+1);\r
+\r
 \r
         gg.setColor(Color.blue);\r
         if(below)\r