From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 24 Apr 2017 11:19:41 +0000 (+0100)
Subject: JAL-2424 final contig now an inclusive range
X-Git-Tag: Release_2_10_2~3^2~114^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=refs%2Fheads%2Fbug%2FJAL-2424getVisibleContigs

JAL-2424 final contig now an inclusive range
---

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 9db9f38..1e34036 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -970,14 +970,14 @@ public class AlignmentView
       if (start < fwidth)
       {
         viscontigs[nvis] = start;
-        viscontigs[nvis + 1] = fwidth; // end is inclusive
+        viscontigs[nvis + 1] = fwidth - 1; // end is inclusive
         nvis += 2;
       }
       return viscontigs;
     }
     else
     {
-      return new int[] { 0, width };
+      return new int[] { 0, width - 1 };
     }
   }
 
diff --git a/test/jalview/datamodel/AlignmentViewTest.java b/test/jalview/datamodel/AlignmentViewTest.java
index 594d6e6..b201c7e 100644
--- a/test/jalview/datamodel/AlignmentViewTest.java
+++ b/test/jalview/datamodel/AlignmentViewTest.java
@@ -22,7 +22,11 @@ package jalview.datamodel;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -50,4 +54,69 @@ public class AlignmentViewTest
     assertEquals(av.getVisibleAlignment('$').getSequenceAt(0)
             .getSequenceAsString(), "A$$CDE");
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetVisibleContigs()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">s1\n0123456789\n", DataSourceType.PASTE);
+    AlignViewport av = af.getViewport();
+    AlignmentView view = av.getAlignmentView(true);
+
+    /*
+     * verify getVisibleContigs returns inclusive [start, end] ranges
+     * 
+     * no columns hidden
+     */
+    int[] contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 0, 9 });
+
+    /*
+     * hide 3 internal columns
+     */
+    av.hideColumns(5, 7);
+    // the old AlignmentView is now stale!
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 0, 9 });
+    // get a fresh AlignmentView
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 0, 4, 8, 9 });
+
+    // hide first 2 columns
+    av.hideColumns(0, 1);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 2, 4, 8, 9 });
+
+    // hide last column
+    av.hideColumns(9, 9);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 2, 4, 8, 8 });
+
+    // unhide columns 5-7
+    av.showColumn(5);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 2, 8 });
+
+    // hide columns 2-7
+    av.hideColumns(2, 7);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 8, 8 });
+
+    // hide column 8
+    av.hideColumns(8, 8);
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] {});
+
+    // unhide all
+    av.showAllHiddenColumns();
+    view = av.getAlignmentView(true);
+    contigs = view.getVisibleContigs();
+    assertEquals(contigs, new int[] { 0, 9 });
+  }
 }