From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 27 May 2017 11:41:43 +0000 (+0100)
Subject: Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
X-Git-Tag: Release_2_10_2~3^2~68
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2bb31b63e0da18f05ac45fa105cf724b3927bc60;hp=29c1b348223da118a14845f9aeb2fe9e34612a32;p=jalview.git

Merge branch 'task/JAL-2562_SequenceI.findPosition' into develop
---

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/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 92f797f..e81553b 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -189,12 +189,13 @@ public interface SequenceI extends ASequenceI
   public int findIndex(int pos);
 
   /**
-   * Returns the sequence position for an alignment position
+   * Returns the sequence position for an alignment position.
    * 
    * @param i
    *          column index in alignment (from 0..<length)
    * 
-   * @return residue number for residue (left of and) nearest ith column
+   * @return TODO: JAL-2562 - residue number for residue (left of and) nearest
+   *         ith column
    */
   public int findPosition(int i);
 
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);
+  }
+}