JAL-2075 findPosition for SeqCigar (with test)

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

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 31957d7..98b0de5 100644 (file)
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -68,6 +68,43 @@ public class SeqCigar extends CigarSimple
   }
 
   /**
+   * 
+   * @param column
+   * @return position in sequence for column (or -1 if no match state exists)
+   */
+  public int findPosition(int column)
+  {
+    int w = 0, ew, p = refseq.findPosition(start);
+    if (column < 0)
+    {
+      return -1;
+    }
+    if (range != null)
+    {
+      for (int i = 0; i < length; i++)
+      {
+        if (operation[i] == M || operation[i] == D)
+        {
+          p += range[i];
+        }
+        if (operation[i] == M || operation[i] == I)
+        {
+          ew = w + range[i];
+          if (column < ew)
+          {
+            if (operation[i] == I)
+            {
+              return -1;
+            }
+            return p - (ew - column);
+          }
+          w = ew;
+        }
+      }
+    }
+    return -1;
+  }
+
   /**
    * Returns sequence as a string with cigar operations applied to it
    *