Merge branch 'bug/JAL-2421overviewboxflicker' into

features/JAL-2388OverviewWindow

Conflicts:
	src/jalview/gui/AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 3e24b94..146df38 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -91,9 +91,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  int hextent = 0;
+  private int hextent = 0;
 
-  int vextent = 0;
+  private int vextent = 0;
 
   /*
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
@@ -688,7 +688,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void setScrollValues(int x, int y)
   {
-    // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
     if (av == null || av.getAlignment() == null)
     {
       return;
@@ -698,6 +697,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (av.hasHiddenColumns())
     {
+      // reset the width to exclude hidden columns
       width = av.getColumnSelection().findColumnPosition(width);
     }
 
@@ -734,6 +734,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       x = 0;
     }
 
+
+    // update endRes after x has (possibly) been adjusted
     av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
             .getCharWidth())) - 1);
 

diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
new file mode 100644 (file)
index 0000000..f3b6876
--- /dev/null
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -0,0 +1,217 @@
+/*
+ * 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.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class AlignmentPanelTest
+{
+  SequenceI seq1 = new Sequence(
+          "Seq1",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq2 = new Sequence(
+          "Seq2",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq3 = new Sequence(
+          "Seq3",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq4 = new Sequence(
+          "Seq4",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq5 = new Sequence(
+          "Seq5",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq6 = new Sequence(
+          "Seq6",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq7 = new Sequence(
+          "Seq7",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq8 = new Sequence(
+          "Seq8",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq9 = new Sequence(
+          "Seq9",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq10 = new Sequence(
+          "Seq10",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq11 = new Sequence(
+          "Seq11",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq12 = new Sequence(
+          "Seq12",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq13 = new Sequence(
+          "Seq13",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq14 = new Sequence(
+          "Seq14",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq15 = new Sequence(
+          "Seq15",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq16 = new Sequence(
+          "Seq16",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq17 = new Sequence(
+          "Seq17",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq18 = new Sequence(
+          "Seq18",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq19 = new Sequence(
+          "Seq19",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq20 = new Sequence(
+          "Seq20",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq21 = new Sequence(
+          "Seq21",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq22 = new Sequence(
+          "Seq22",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq23 = new Sequence(
+          "Seq23",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  AlignFrame af;
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Jalview.main(new String[] { "-nonews", "-props",
+        "test/jalview/testProps.jvprops" });
+
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+            DataSourceType.FILE);
+
+    /*
+     * wait for Consensus thread to complete
+     */
+    synchronized (this)
+    {
+      while (af.getViewport().getConsensusSeq() == null)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
+  }
+
+
+  /**
+   * Test side effect that end residue is set correctly by setScrollValues, with
+   * or without hidden columns
+   */
+  @Test(groups = "Functional")
+  public void TestSetScrollValues()
+  {
+    int oldres = af.getViewport().getEndRes();
+    af.alignPanel.setScrollValues(-1, 5);
+
+    // setting -ve x value does not change residue
+    assertEquals(af.getViewport().getEndRes(), oldres);
+
+    af.alignPanel.setScrollValues(0, 5);
+
+    // setting 0 as x value does not change residue
+    assertEquals(af.getViewport().getEndRes(), oldres);
+
+    af.alignPanel.setScrollValues(5, 5);
+    // setting x value to 5 extends endRes by 5 residues
+    assertEquals(af.getViewport().getEndRes(), oldres + 5);
+
+    // scroll to position after hidden columns sets endres to oldres (width) +
+    // position
+    int scrollpos = 60;
+    af.getViewport().hideColumns(30, 50);
+    af.alignPanel.setScrollValues(scrollpos, 5);
+    assertEquals(af.getViewport().getEndRes(), oldres + scrollpos);
+
+    // scroll to position within hidden columns, still sets endres to oldres +
+    // position
+    // not sure if this is actually correct behaviour but this is what Jalview
+    // currently does
+    scrollpos = 40;
+    af.getViewport().showAllHiddenColumns();
+    af.getViewport().hideColumns(30, 50);
+    af.alignPanel.setScrollValues(scrollpos, 5);
+    assertEquals(af.getViewport().getEndRes(), oldres + scrollpos);
+
+    // scroll to position within <width> distance of the end of the alignment
+    // endRes should be set to width of alignment - 1
+    scrollpos = 130;
+    af.getViewport().showAllHiddenColumns();
+    af.alignPanel.setScrollValues(scrollpos, 5);
+    assertEquals(af.getViewport().getEndRes(), af.getViewport()
+            .getAlignment().getWidth() - 1);
+
+    // now hide some columns, and scroll to position within <width>
+    // distance of the end of the alignment
+    // endRes should be set to width of alignment - 1 - the number of hidden
+    // columns
+    af.getViewport().hideColumns(30, 50);
+    af.alignPanel.setScrollValues(scrollpos, 5);
+    assertEquals(af.getViewport().getEndRes(), af.getViewport()
+            .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
+                                                  // columns
+  }
+}