From 86c5dd9042f68b78a4ff6d732cc8700b74042c7c Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 8 Jun 2017 09:26:59 +0100
Subject: [PATCH] JAL-2526 setStatusMessage avoid redundant findPosition from
 SearchResults

---
 src/jalview/gui/SeqPanel.java |   53 +++++++++++++++++++++++++++++------------
 1 file changed, 38 insertions(+), 15 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 8e65840..5634ead 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -868,19 +868,48 @@ public class SeqPanel extends JPanel implements MouseListener,
    *          aligned sequence object
    * @param column
    *          alignment column
-   * @param seq
+   * @param seqIndex
    *          index of sequence in alignment
    * @return sequence position of residue at column, or adjacent residue if at a
    *         gap
    */
-  int setStatusMessage(SequenceI sequence, final int column, int seq)
+  int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
+  {
+    char sequenceChar = sequence.getCharAt(column);
+    int pos = sequence.findPosition(column);
+    setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+
+    return pos;
+  }
+
+  /**
+   * Builds the status message for the current cursor location and writes it to
+   * the status bar, for example
+   * 
+   * <pre>
+   * Sequence 3 ID: FER1_SOLLC
+   * Sequence 5 ID: FER1_PEA Residue: THR (4)
+   * Sequence 5 ID: FER1_PEA Residue: B (3)
+   * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+   * </pre>
+   * 
+   * @param sequence
+   * @param seqIndex
+   *          sequence position in the alignment (1..)
+   * @param sequenceChar
+   *          the character under the cursor
+   * @param residuePos
+   *          the sequence residue position (if not over a gap)
+   */
+  protected void setStatusMessage(SequenceI sequence, int seqIndex,
+          char sequenceChar, int residuePos)
   {
     StringBuilder text = new StringBuilder(32);
 
     /*
      * Sequence number (if known), and sequence name.
      */
-    String seqno = seq == -1 ? "" : " " + (seq + 1);
+    String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
     text.append("Sequence").append(seqno).append(" ID: ")
             .append(sequence.getName());
 
@@ -889,13 +918,12 @@ public class SeqPanel extends JPanel implements MouseListener,
     /*
      * Try to translate the display character to residue name (null for gap).
      */
-    final String displayChar = String.valueOf(sequence.getCharAt(column));
-    boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
-    int pos = sequence.findPosition(column);
+    boolean isGapped = Comparison.isGap(sequenceChar);
 
     if (!isGapped)
     {
       boolean nucleotide = av.getAlignment().isNucleotide();
+      String displayChar = String.valueOf(sequenceChar);
       if (nucleotide)
       {
         residue = ResidueProperties.nucleotideName.get(displayChar);
@@ -909,11 +937,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
               .append(": ").append(residue == null ? displayChar : residue);
 
-      text.append(" (").append(Integer.toString(pos)).append(")");
+      text.append(" (").append(Integer.toString(residuePos)).append(")");
     }
     ap.alignFrame.statusBar.setText(text.toString());
-
-    return pos;
   }
 
   /**
@@ -941,12 +967,9 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       if (seq == ds)
       {
-        /*
-         * Convert position in sequence (base 1) to sequence character array
-         * index (base 0)
-         */
-        int start = m.getStart() - m.getSequence().getStart();
-        setStatusMessage(seq, start, sequenceIndex);
+        int start = m.getStart();
+        setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
+                start);
         return;
       }
     }
-- 
1.7.10.2