X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceCursor.java;h=24752bf4b1c2a9e94947bc2537e2f3e0b2cc81b0;hb=a3ca1aac6c00fc2240fa21be9df43adcc1b964ff;hp=f439ee162ab4caca69c5b13199fd5a6e7a0dc20b;hpb=70a93ebbabd80e25c60a0e6444013ed4260b09a5;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceCursor.java b/src/jalview/datamodel/SequenceCursor.java
index f439ee1..24752bf 100644
--- a/src/jalview/datamodel/SequenceCursor.java
+++ b/src/jalview/datamodel/SequenceCursor.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 /**
@@ -22,6 +42,16 @@ public class SequenceCursor
   public final int columnPosition;
 
   /**
+   * column position (1...) of first residue in the sequence, or 0 if undefined
+   */
+  public final int firstColumnPosition;
+
+  /**
+   * column position (1...) of last residue in the sequence, or 0 if undefined
+   */
+  public final int lastColumnPosition;
+
+  /**
    * a token which may be used to check whether this cursor is still valid for
    * its sequence (allowing it to be ignored if the sequence has changed)
    */
@@ -42,9 +72,36 @@ public class SequenceCursor
    */
   public SequenceCursor(SequenceI seq, int resPos, int column, int tok)
   {
+    this(seq, resPos, column, 0, 0, tok);
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param seq
+   *          sequence this cursor applies to
+   * @param resPos
+   *          residue position in sequence (start..)
+   * @param column
+   *          column position in alignment (1..)
+   * @param firstResCol
+   *          column position of the first residue in the sequence (1..), or 0
+   *          if not known
+   * @param lastResCol
+   *          column position of the last residue in the sequence (1..), or 0 if
+   *          not known
+   * @param tok
+   *          a token that may be validated by the sequence to check the cursor
+   *          is not stale
+   */
+  public SequenceCursor(SequenceI seq, int resPos, int column, int firstResCol,
+          int lastResCol, int tok)
+  {
     sequence = seq;
     residuePosition = resPos;
     columnPosition = column;
+    firstColumnPosition = firstResCol;
+    lastColumnPosition = lastResCol;
     token = tok;
   }
 
@@ -80,7 +137,9 @@ public class SequenceCursor
   @Override
   public String toString()
   {
-    return (sequence == null ? "" : sequence.getName()) + ":Pos"
-            + residuePosition + ":Col" + columnPosition + ":tok" + token;
+    String name = sequence == null ? "" : sequence.getName();
+    return String.format("%s:Pos%d:Col%d:startCol%d:endCol%d:tok%d", name,
+            residuePosition, columnPosition, firstColumnPosition,
+            lastColumnPosition, token);
   }
 }