From 999f2dccf898ff34d180a3fef7fae8b80e8d2fcf Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 20 Mar 2019 12:25:31 +0000
Subject: [PATCH] JAL-3212 unit test and fix for Scale Panel bug

---
 src/jalview/gui/ScalePanel.java      |    5 +--
 test/jalview/gui/ScalePanelTest.java |   66 +++++++++++++++++++++++++++++-----
 2 files changed, 61 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index b95c569..b392c8f 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -279,14 +279,15 @@ public class ScalePanel extends JPanel
     ap.getSeqPanel().stopScrolling();
 
     int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+    ViewportRanges ranges = av.getRanges();
     int res = (xCords / av.getCharWidth())
-            + av.getRanges().getStartRes();
+            + ranges.getStartRes();
+    res = Math.min(res, ranges.getEndRes());
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
               .visibleToAbsoluteColumn(res);
     }
-    res = Math.min(res, av.getRanges().getEndRes());
     res = Math.max(0, res);
 
     if (!stretchingGroup)
diff --git a/test/jalview/gui/ScalePanelTest.java b/test/jalview/gui/ScalePanelTest.java
index 91b541c..0ec1c1f 100644
--- a/test/jalview/gui/ScalePanelTest.java
+++ b/test/jalview/gui/ScalePanelTest.java
@@ -1,12 +1,18 @@
 package jalview.gui;
 
+import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.event.MouseEvent;
 
@@ -28,16 +34,12 @@ public class ScalePanelTest
     SequenceI seq1 = new Sequence("Seq1", "MATRESS");
     SequenceI seq2 = new Sequence("Seq2", "MADNESS");
     AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
-    
+
     AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
             al.getHeight());
-    ScalePanel scalePanel = new ScalePanel(
-            alignFrame.getViewport(), alignFrame.alignPanel
-    );
-    
-    MouseEvent mouse = new MouseEvent(
-            scalePanel, 0, 1, 0, 4, 0, 1, false
-    );
+    ScalePanel scalePanel = alignFrame.alignPanel.getScalePanel();
+
+    MouseEvent mouse = new MouseEvent(scalePanel, 0, 1, 0, 4, 0, 1, false);
     scalePanel.mousePressed(mouse);
     scalePanel.mouseDragged(mouse);
 
@@ -51,8 +53,56 @@ public class ScalePanelTest
     int startCol = sg.getStartRes();
 
     assertTrue(startCol >= 0);
+  }
 
+  /**
+   * Test for JAL-3212
+   */
+  @Test(groups = "Functional")
+  public void testSelectColumns_withHidden()
+  {
+    String seq1 = ">Seq1\nANTOFAGASTAVALPARAISOMONTEVIDEOANTANANARIVO";
+    AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(seq1,
+            DataSourceType.PASTE);
+    ScalePanel scalePanel = alignFrame.alignPanel.getScalePanel();
 
+    /*
+     * hide columns 1-20 (of 43); then 'drag' to select columns 30-31;
+     * 31 is 51 in absolute columns but bug JAL-3212 reduces it to
+     * endRes which is 22
+     */
+    AlignViewport viewport = alignFrame.getViewport();
+    ViewportRanges ranges = viewport.getRanges();
+    assertEquals(ranges.getStartRes(), 0);
+    assertEquals(ranges.getEndRes(), 42);
+    viewport.hideColumns(0, 19);
+    alignFrame.alignPanel.updateLayout();
+    assertEquals(ranges.getStartRes(), 0);
+    assertEquals(ranges.getEndRes(), 22);
+    
+    int cw = viewport.getCharWidth();
+    int xPos = 9 * cw + 2;
+    MouseEvent mouse = new MouseEvent(scalePanel, 0, 1, 0, xPos, 0, 1,
+            false);
+    scalePanel.mousePressed(mouse);
+    scalePanel.mouseDragged(mouse);
+    xPos += cw;
+    mouse = new MouseEvent(scalePanel, 0, 1, 0, xPos, 0, 1, false);
+    scalePanel.mouseReleased(mouse);
+
+    SequenceGroup sg = scalePanel.av.getSelectionGroup();
+    assertEquals(sg.getStartRes(), 29);
+    assertEquals(sg.getEndRes(), 30);
+  }
+
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    /*
+     * use read-only test properties file
+     */
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Jalview.main(new String[] { "-nonews" });
   }
 
 }
-- 
1.7.10.2