X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=9cc7b4a35ff054f5a6a3a48728216f0eaa197105;hb=1c251a57c7b2fb70dabceb480d0170363357558f;hp=b4e0d71b6db75a7789228d74ad392a17a1c390b7;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index b4e0d71..9cc7b4a 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -68,10 +68,49 @@ 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
    * 
    * @return String
    */
+  @Override
   public String getSequenceString(char GapChar)
   {
     return (length == 0) ? "" : (String) getSequenceAndDeletions(
@@ -455,18 +494,18 @@ public class SeqCigar extends CigarSimple
   /**
    * create an alignment from the given array of cigar sequences and gap
    * character, and marking the given segments as visible in the given
-   * columselection.
+   * hiddenColumns.
    * 
    * @param alseqs
    * @param gapCharacter
-   * @param colsel
-   *          - columnSelection where hidden regions are marked
+   * @param hidden
+   *          - hiddenColumns where hidden regions are marked
    * @param segments
    *          - visible regions of alignment
    * @return SequenceI[]
    */
   public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
-          char gapCharacter, ColumnSelection colsel, int[] segments)
+          char gapCharacter, HiddenColumns hidden, int[] segments)
   {
     SequenceI[] seqs = new SequenceI[alseqs.length];
     StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
@@ -538,7 +577,7 @@ public class SeqCigar extends CigarSimple
           if (segments == null)
           {
             // add a hidden column for this deletion
-            colsel.hideColumns(inspos, inspos + insert.length - 1);
+            hidden.hideColumns(inspos, inspos + insert.length - 1);
           }
         }
       }
@@ -559,7 +598,7 @@ public class SeqCigar extends CigarSimple
       {
         // int start=shifts.shift(segments[i]-1)+1;
         // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
-        colsel.hideColumns(segments[i + 1], segments[i + 1]
+        hidden.hideColumns(segments[i + 1], segments[i + 1]
                 + segments[i + 2] - 1);
       }
     }