recover original data for tree and pca as alignment view.

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

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 447b4d0..8961425 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -24,7 +24,6 @@ public class CigarArray extends CigarBase
   {
     return seqcigararray;
   }
-
   /**
    * Apply CIGAR operations to several cigars in parallel
    * will throw an error if any of cigar are actually CigarArrays.
@@ -109,9 +108,67 @@ public class CigarArray extends CigarBase
    * Combines the CigarArray cigar operations with the operations in each
    * reference cigar - creating a new reference cigar
    * @return Cigar[]
-   */
+
   public CigarBase[] getEditedCigars() {
 
     return new CigarBase[] {};
   }
+*/
+  /**
+   * applyDeletions
+   * edits underlying refCigars to propagate deleted regions, and removes deletion
+   * operations from CigarArray operation list.
+   * @return int[] position where deletion occured in cigarArray or null if none occured
+   */
+  public int[] applyDeletions()
+  {
+    java.util.Vector delpos=null;
+    if (length==0)
+      return null;
+    int cursor=0; // range counter for deletions
+    int vcursor=0; // visible column index
+    for (int i=0; i<length; i++) {
+      if (operation[i]!=D) {
+        if (operation[i]==M)
+          cursor+=range[i];
+        vcursor+=range[i];
+      }
+      else
+      {
+        if (delpos==null)
+          delpos=new java.util.Vector();
+        int delstart=cursor, delend=cursor+range[i]-1; // inclusive
+        delpos.add(new Integer(vcursor-1)); // index of left hand column of hidden region boundary
+        System.arraycopy(operation, i+1, operation, i, length-i);
+        System.arraycopy(range, i+1, range, i, length-i);
+        length--;
+        for (int s=0; s<refCigars.length; s++) {
+          refCigars[s].deleteRange(delstart, delend);
+        }
+      }
+    }
+    if (delpos!=null)
+    {
+      int[] pos=new int[delpos.size()];
+      for (int k = 0, l = delpos.size(); k < l; k++) {
+        pos[k] = ((Integer) delpos.get(k)).intValue();
+        delpos.set(k,null);
+      }
+      delpos=null;
+      return pos;
+    }
+    return null;
+  }
+  /**
+   *
+   * @return SeqCigar[] or null if CigarArray is not a SeqCigarArray (ie it does not resolve to set of seqCigars)
+   */
+  public SeqCigar[] getSeqCigarArray() {
+    if (!isSeqCigarArray())
+      return null;
+    SeqCigar[] sa = new SeqCigar[refCigars.length];
+    for (int i=0; i<refCigars.length; i++)
+      sa[i] = (SeqCigar) refCigars[i];
+    return sa;
+  }
 }