EditCommand implemented

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

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 1f91e26..d3b56be 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -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
@@ -375,7 +395,9 @@ public class IdCanvas extends JPanel
       Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
                            av.getFont().getSize());\r
 \r
-      if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
+\r
+      if (av.alignment.getSequenceAt(i)!=null\r
+          && av.alignment.getSequenceAt(i).getHiddenSequences() != null)\r
         gg.setFont(bold);\r
       else\r
         gg.setFont(italic);\r