X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=98b0de5f39a8aac0fe1083e2e902e156b36ad0d0;hb=ccc31f21ed36c2e43b5a1b450846284151c680bb;hp=09b2e89eceb926fd363218b55e732e0ef380e9aa;hpb=960206d9ae05d85b42552025c3dec4b5f7b14c15;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 09b2e89..98b0de5 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -20,14 +20,14 @@
  */
 package jalview.datamodel;
 
-import java.util.Enumeration;
-import java.util.Hashtable;
-
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
 import jalview.util.MessageManager;
 import jalview.util.ShiftList;
 
+import java.util.Enumeration;
+import java.util.Hashtable;
+
 public class SeqCigar extends CigarSimple
 {
   /**
@@ -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(
@@ -95,7 +134,9 @@ public class SeqCigar extends CigarSimple
             refseq.getSequenceAsString(start, end), GapChar);
     if (edit_result == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
     }
     int bounds[] = (int[]) edit_result[1];
     seq = new Sequence(refseq.getName(), (String) edit_result[0],
@@ -143,11 +184,15 @@ public class SeqCigar extends CigarSimple
     boolean hasgaps = false;
     if (seq == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_set_seq_null"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_set_seq_null"));
     }
     if (_s < 0)
     {
-      throw new Error(MessageManager.formatMessage("error.implementation_error_s", new String[]{Integer.valueOf(_s).toString()}));
+      throw new Error(MessageManager.formatMessage(
+              "error.implementation_error_s", new String[] { Integer
+                      .valueOf(_s).toString() }));
     }
     String seq_string = seq.getSequenceAsString();
     if (_e == 0 || _e < _s || _e > seq_string.length())
@@ -213,7 +258,9 @@ public class SeqCigar extends CigarSimple
     // Check offsets
     if (end > ds.getLength())
     {
-      throw new Error(MessageManager.getString("error.implementation_error_seqcigar_possible"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_seqcigar_possible"));
       // end = ds.getLength();
     }
 
@@ -237,11 +284,14 @@ public class SeqCigar extends CigarSimple
     super();
     if (seq == null)
     {
-      throw new Error(MessageManager.getString("error.implmentation_bug_seq_null"));
+      throw new Error(
+              MessageManager.getString("error.implmentation_bug_seq_null"));
     }
     if (operation.length != range.length)
     {
-      throw new Error(MessageManager.getString("error.implementation_bug_cigar_operation_list_range_list"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_bug_cigar_operation_list_range_list"));
     }
 
     if (operation != null)
@@ -251,14 +301,22 @@ public class SeqCigar extends CigarSimple
 
       if (_setSeq(seq, false, 0, 0))
       {
-        throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+        throw new Error(
+                MessageManager
+                        .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
       }
       for (int i = this.length, j = 0; j < operation.length; i++, j++)
       {
         char op = operation[j];
         if (op != M && op != I && op != D)
         {
-          throw new Error(MessageManager.formatMessage("error.implementation_bug_cigar_operation", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(op).toString(),Integer.valueOf(M).toString(),Integer.valueOf(I).toString(),Integer.valueOf(D).toString()}));
+          throw new Error(MessageManager.formatMessage(
+                  "error.implementation_bug_cigar_operation", new String[] {
+                      Integer.valueOf(j).toString(),
+                      Integer.valueOf(op).toString(),
+                      Integer.valueOf(M).toString(),
+                      Integer.valueOf(I).toString(),
+                      Integer.valueOf(D).toString() }));
         }
         this.operation[i] = op;
         this.range[i] = range[j];
@@ -272,7 +330,9 @@ public class SeqCigar extends CigarSimple
       this.length = 0;
       if (_setSeq(seq, false, 0, 0))
       {
-        throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+        throw new Error(
+                MessageManager
+                        .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
       }
     }
   }
@@ -379,7 +439,9 @@ public class SeqCigar extends CigarSimple
     super();
     if (seq == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_for_new_cigar"));
     }
     _setSeq(seq, false, 0, 0);
     // there is still work to do
@@ -401,7 +463,9 @@ public class SeqCigar extends CigarSimple
     super();
     if (seq == null)
     {
-      throw new Error(MessageManager.getString("error.implementation_error_for_new_cigar"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_for_new_cigar"));
     }
     _setSeq(seq, false, start, end + 1);
     // there is still work to do
@@ -456,7 +520,9 @@ public class SeqCigar extends CigarSimple
       // endcol}, hidden regions {{start, end, col}})
       if (gs_regions[i] == null)
       {
-        throw new Error(MessageManager.formatMessage("error.implementation_error_cigar_seq_no_operations", new String[]{Integer.valueOf(i).toString()}));
+        throw new Error(MessageManager.formatMessage(
+                "error.implementation_error_cigar_seq_no_operations",
+                new String[] { Integer.valueOf(i).toString() }));
       }
       g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
       // visible