refactored hidden regions methods and made an AlignmentView preserve

[jalview.git] / src / jalview / datamodel / CigarArray.java

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index b8cdf52..33e91a8 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -118,7 +118,7 @@ public class CigarArray extends CigarBase
    * applyDeletions\r
    * edits underlying refCigars to propagate deleted regions, and removes deletion\r
    * operations from CigarArray operation list.\r
-   * @return int[] position where deletion occured in cigarArray or null if none occured\r
+   * @return int[] position after deletion occured and range of deletion in cigarArray or null if none occured\r
    */\r
   public int[] applyDeletions()\r
   {\r
@@ -127,31 +127,45 @@ public class CigarArray extends CigarBase
       return null;\r
     int cursor=0; // range counter for deletions\r
     int vcursor=0; // visible column index\r
-    for (int i=0; i<length; i++) {\r
+    int offset=0; // shift in visible column index as deletions are made\r
+    int i=0;\r
+    while (i<length) {\r
       if (operation[i]!=D) {\r
         if (operation[i]==M)\r
           cursor+=range[i];\r
-        vcursor+=range[i];\r
+        vcursor+=range[i++];\r
       }\r
       else\r
       {\r
         if (delpos==null)\r
           delpos=new java.util.Vector();\r
         int delstart=cursor, delend=cursor+range[i]-1; // inclusive\r
-        delpos.addElement(new Integer(vcursor-1)); // index of left hand column of hidden region boundary\r
+        delpos.addElement(new int[] { vcursor+offset, range[i]}); // index of right hand column after hidden region boundary\r
+        offset+=range[i]-1; // shift in visible column coordinates\r
         System.arraycopy(operation, i+1, operation, i, length-i);\r
         System.arraycopy(range, i+1, range, i, length-i);\r
         length--;\r
+        /*        int dmax=0;\r
+         for (int s=0; s<refCigars.length; s++) {\r
+           int d = refCigars[s].deleteRange(delstart, delend);\r
+           if (d>dmax)\r
+             dmax=d;\r
+         }\r
+         offset+=dmax; // shift in visible column coordinates\r
+         */\r
         for (int s=0; s<refCigars.length; s++) {\r
-          refCigars[s].deleteRange(delstart, delend);\r
+          int d = refCigars[s].deleteRange(delstart, delend);\r
         }\r
+\r
       }\r
     }\r
     if (delpos!=null)\r
     {\r
-      int[] pos=new int[delpos.size()];\r
+      int[] pos=new int[delpos.size()*2];\r
       for (int k = 0, l = delpos.size(); k < l; k++) {\r
-        pos[k] = ((Integer) delpos.elementAt(k)).intValue();\r
+        int[] dr = ((int[]) delpos.elementAt(k));\r
+        pos[k*2] = dr[0];\r
+        pos[k*2+1] = dr[1];\r
         delpos.setElementAt(null,k);\r
       }\r
       delpos=null;\r