JAL-2526 cache first/last residue column positions in cursor

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

diff --git a/src/jalview/datamodel/SequenceCursor.java b/src/jalview/datamodel/SequenceCursor.java
index f439ee1..b5929bf 100644 (file)
--- a/src/jalview/datamodel/SequenceCursor.java
+++ b/src/jalview/datamodel/SequenceCursor.java
@@ -22,6 +22,16 @@ 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 +52,36 @@ 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 +117,9 @@ 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);
   }
 }