Local adjustForhiddenSeqs routine

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 013c7a1..dd057a3 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -295,12 +295,32 @@ public class IdCanvas
 \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
+    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
     boolean below = (hiddenIndex > lastIndex + 1);\r
-    boolean above = (nextIndex>hiddenIndex+1);\r
+    boolean above = (nextIndex > hiddenIndex + 1);\r
+\r
+\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
       gg.setColor(Color.blue);\r
       if(below)\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 1f91e26..84f18ba 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