From 1ae70c4324da0e26611bb2a9272dfacb92b6c234 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 27 May 2017 12:32:09 +0100
Subject: [PATCH] JAL-2526 test and documentation for SeqPanel.setStatus
 behaviour  needed to fix bug noted on JAL-2491 where
 mouseover at gap highlights position for sequence to right
 of gap in complementary view.

---
 src/jalview/appletgui/SeqPanel.java |   10 +++---
 src/jalview/gui/SeqPanel.java       |    2 +-
 test/jalview/gui/SeqPanelTest.java  |   66 +++++++++++++++++++++++++++++++++++
 3 files changed, 72 insertions(+), 6 deletions(-)
 create mode 100644 test/jalview/gui/SeqPanelTest.java

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index d46cc34..f58f420 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -412,13 +412,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    * 
    * @param sequence
    *          aligned sequence object
-   * @param res
+   * @param column
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of res in sequence
+   * @return position of column in sequence or -1 if at gap
    */
-  void setStatusMessage(SequenceI sequence, int res, int seq)
+  void setStatusMessage(SequenceI sequence, int column, int seq)
   {
     // TODO remove duplication of identical gui method
     StringBuilder text = new StringBuilder(32);
@@ -429,7 +429,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     /*
      * Try to translate the display character to residue name (null for gap).
      */
-    final String displayChar = String.valueOf(sequence.getCharAt(res));
+    final String displayChar = String.valueOf(sequence.getCharAt(column));
     if (av.getAlignment().isNucleotide())
     {
       residue = ResidueProperties.nucleotideName.get(displayChar);
@@ -452,7 +452,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     int pos = -1;
     if (residue != null)
     {
-      pos = sequence.findPosition(res);
+      pos = sequence.findPosition(column);
       text.append(" (").append(Integer.toString(pos)).append(")");
     }
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 7dfac5e..a435fee 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -869,7 +869,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of res in sequence
+   * @return position of column in sequence or -1 if at a gap
    */
   int setStatusMessage(SequenceI sequence, final int column, int seq)
   {
diff --git a/test/jalview/gui/SeqPanelTest.java b/test/jalview/gui/SeqPanelTest.java
new file mode 100644
index 0000000..488570a
--- /dev/null
+++ b/test/jalview/gui/SeqPanelTest.java
@@ -0,0 +1,66 @@
+/*
+ * 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.gui;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class SeqPanelTest
+{
+  AlignFrame af;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+  @Test(groups = "Functional")
+  public void testSetStatusReturnsPosOrMinusOne()
+  {
+    SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
+    SequenceI seq2 = new Sequence("Seq2", "AB--EFGHIJ");
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
+            al.getHeight());
+    AlignmentI visAl = alignFrame.getViewport().getAlignment();
+    assertEquals(
+            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
+                    visAl.getSequenceAt(1), 1, 1), 2);
+    assertEquals(
+            
+            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
+                    visAl.getSequenceAt(1), 2, 1), -1);
+    assertEquals(
+            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
+                    visAl.getSequenceAt(1), 3, 1), -1);
+    assertEquals(
+            alignFrame.alignPanel.getSeqPanel().setStatusMessage(
+                    visAl.getSequenceAt(1), 4, 1), 3);
+  }
+}
-- 
1.7.10.2