From 6fb07f0a97888d9590b4fa7b9993955e30080782 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 3 Oct 2017 09:26:35 +0100
Subject: [PATCH] Added checks for X mouse coordinate being >= 0 and a test
 for JAL-2750

---
 src/jalview/datamodel/SequenceGroup.java       |   43 +++++++-----------------
 src/jalview/gui/ScalePanel.java                |    4 ++-
 test/jalview/gui/ValidColumnSelectionTest.java |   35 ++++++++++++++++++-
 3 files changed, 49 insertions(+), 33 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 20b23a9..221b031 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -102,7 +102,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   public ResidueShaderI cs;
 
   // start column (base 0)
-  int startRes = 0;
+  private int startRes = 0;
 
   // end column (base 0)
   int endRes = 0;
@@ -184,19 +184,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.displayText = displayText;
     this.colourText = colourText;
     this.cs = new ResidueShader(scheme);
-    
-    if (start > 0) // sanity check for negative start column positions
-    {
-      startRes = start;
-    }
-    else
-    {
-      jalview.bin.Cache.log.warn(
-              "Negative start column index detected, resetting to default index: "
-                      + startRes);
-      // start = startRes;
-    }
-    
+    startRes = start;
     endRes = end;
     recalcConservation();
   }
@@ -221,19 +209,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       displayText = seqsel.displayText;
       colourText = seqsel.colourText;
       
-      if (seqsel.startRes > 0) // sanity check for negative start column
-                               // positions
-      {
-        startRes = seqsel.startRes;
-      }
-      else
-      {
-        jalview.bin.Cache.log.warn(
-                "Negative start column index detected, resetting to default index: "
-                        + startRes);
-        // seqsel.startRes = startRes;
-      }
-  
+      startRes = seqsel.startRes;
       endRes = seqsel.endRes;
       cs = new ResidueShader((ResidueShader) seqsel.cs);
       if (seqsel.description != null)
@@ -778,11 +754,16 @@ public class SequenceGroup implements AnnotatedCollectionI
    * 
    * @param i
    */
-  public void setStartRes(int i)
+  public void setStartRes(int newStart)
   {
-    int before = startRes;
-    startRes = i;
-    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+   newStart= Math.max(0,newStart); // sanity check for negative start column positions
+   int before = startRes;
+   startRes = newStart;
+
+   changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+    
+
+
   }
 
   /**
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 1db4051..ef2392c 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -275,7 +275,9 @@ public class ScalePanel extends JPanel
   {
     mouseDragging = false;
 
-    int res = (evt.getX() / av.getCharWidth())
+    int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+
+    int res = (xCords / av.getCharWidth())
             + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
diff --git a/test/jalview/gui/ValidColumnSelectionTest.java b/test/jalview/gui/ValidColumnSelectionTest.java
index 81d35f2..c65f236 100644
--- a/test/jalview/gui/ValidColumnSelectionTest.java
+++ b/test/jalview/gui/ValidColumnSelectionTest.java
@@ -1,5 +1,15 @@
 package jalview.gui;
 
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.awt.event.MouseEvent;
+
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -13,8 +23,31 @@ public class ValidColumnSelectionTest
   }
 
   @Test(groups = "Functional")
-  public void testColumnSelection()
+  public void testPreventNegativeStartColumn()
   {
+    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.mousePressed(mouse);
+    scalePanel.mouseDragged(mouse);
+    mouse = new MouseEvent(scalePanel, 0, 1, 0, -30, 0, 1, false);
+    scalePanel.mouseReleased(mouse);
+
+    SequenceGroup sg = scalePanel.av.getSelectionGroup();
+    int startCol = sg.getStartRes();
+
+    assertTrue(startCol >= 0);
+
 
   }
 
-- 
1.7.10.2