From da144cfa9b7997a6e8dd04ef10d55bcea3b02c71 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 12 Oct 2006 13:21:41 +0000
Subject: [PATCH] Local adjustForhiddenSeqs routine

---
 src/jalview/appletgui/IdCanvas.java |   28 ++++++++++++++++++++++++----
 src/jalview/gui/IdCanvas.java       |   28 ++++++++++++++++++++++++----
 2 files changed, 48 insertions(+), 8 deletions(-)

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 013c7a1..dd057a3 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -295,12 +295,32 @@ public class IdCanvas
 
   void drawMarker(int i, int starty, int yoffset)
   {
-    int hiddenIndex = av.adjustForHiddenSeqs(i);
-    int lastIndex = av.adjustForHiddenSeqs(i - 1);
-    int nextIndex = av.adjustForHiddenSeqs(i + 1);
+    SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+    //Use this method here instead of calling hiddenSeq adjust
+    //3 times.
+    int hSize = hseqs.length;
+
+    int hiddenIndex = i;
+    int lastIndex = i - 1;
+    int nextIndex = i + 1;
 
     boolean below = (hiddenIndex > lastIndex + 1);
-    boolean above = (nextIndex>hiddenIndex+1);
+    boolean above = (nextIndex > hiddenIndex + 1);
+
+
+
+    for(int j=0; j<hSize; j++)
+    {
+      if (hseqs[j] != null)
+      {
+        if(j-1<hiddenIndex)
+          hiddenIndex++;
+        if(j-1<lastIndex)
+          lastIndex++;
+        if(j-1<nextIndex)
+          nextIndex++;
+      }
+      }
 
       gg.setColor(Color.blue);
       if(below)
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 1f91e26..84f18ba 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -331,12 +331,32 @@ public class IdCanvas extends JPanel
 
     void drawMarker(int i, int starty, int yoffset)
     {
-      int hiddenIndex = av.adjustForHiddenSeqs(i);
-      int lastIndex = av.adjustForHiddenSeqs(i - 1);
-      int nextIndex = av.adjustForHiddenSeqs(i + 1);
+
+      SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+      //Use this method here instead of calling hiddenSeq adjust
+      //3 times.
+      int hSize = hseqs.length;
+
+      int hiddenIndex = i;
+      int lastIndex = i - 1;
+      int nextIndex = i + 1;
+
+      for(int j=0; j<hSize; j++)
+      {
+        if (hseqs[j] != null)
+        {
+          if(j-1<hiddenIndex)
+            hiddenIndex++;
+          if(j-1<lastIndex)
+            lastIndex++;
+          if(j-1<nextIndex)
+            nextIndex++;
+        }
+      }
 
       boolean below = (hiddenIndex > lastIndex + 1);
-      boolean above = (nextIndex>hiddenIndex+1);
+      boolean above = (nextIndex > hiddenIndex+1);
+
 
         gg.setColor(Color.blue);
         if(below)
-- 
1.7.10.2