JAL-2571 Corrected alignment width/height checks to visible only

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 1daaf43..a98b10e 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -170,7 +170,13 @@ public class HiddenSequences
   public List<SequenceI> showAll(
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> revealedSeqs = new ArrayList<>();
+
+    if (hiddenSequences == null)
+    {
+      return revealedSeqs;
+    }
+
     for (int i = 0; i < hiddenSequences.length; i++)
     {
       if (hiddenSequences[i] != null)
@@ -199,7 +205,7 @@ public class HiddenSequences
   public List<SequenceI> showSequence(int alignmentIndex,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
+    List<SequenceI> revealedSeqs = new ArrayList<>();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
     if (repSequence != null && hiddenRepSequences != null
             && hiddenRepSequences.containsKey(repSequence))

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 0878cbb..012ac94 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -393,8 +393,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY,
-              av);
+      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
     }
     setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index da39e36..56c1d39 100644 (file)
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -20,7 +20,6 @@
  */
 package jalview.viewmodel;
 
-import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 
@@ -122,9 +121,9 @@ public class ViewportRanges extends ViewportProperties
   public void setStartEndRes(int start, int end)
   {
     int oldstartres = this.startRes;
-    if (start > al.getWidth() - 1)
+    if (start > getVisibleAlignmentWidth() - 1)
     {
-      startRes = al.getWidth() - 1;
+      startRes = getVisibleAlignmentWidth() - 1;
     }
     else if (start < 0)
     {
@@ -164,9 +163,9 @@ public class ViewportRanges extends ViewportProperties
   {
     int startres = res;
     int width = getViewportWidth();
-    if (startres + width - 1 > al.getWidth() - 1)
+    if (startres + width - 1 > getVisibleAlignmentWidth() - 1)
     {
-      startres = al.getWidth() - width;
+      startres = getVisibleAlignmentWidth() - width;
     }
     setStartEndRes(startres - width + 1, startres);
   }
@@ -183,9 +182,9 @@ public class ViewportRanges extends ViewportProperties
   {
     int startseq = seq;
     int height = getViewportHeight();
-    if (startseq + height - 1 > al.getHeight() - 1)
+    if (startseq + height - 1 > getVisibleAlignmentHeight() - 1)
     {
-      startseq = al.getHeight() - height;
+      startseq = getVisibleAlignmentHeight() - height;
     }
     setStartEndSeq(startseq, startseq + height - 1);
   }
@@ -203,9 +202,9 @@ public class ViewportRanges extends ViewportProperties
   public void setStartEndSeq(int start, int end)
   {
     int oldstartseq = this.startSeq;
-    if (start > al.getHeight() - 1)
+    if (start > getVisibleAlignmentHeight() - 1)
     {
-      startSeq = al.getHeight() - 1;
+      startSeq = getVisibleAlignmentHeight() - 1;
     }
     else if (start < 0)
     {
@@ -217,9 +216,9 @@ public class ViewportRanges extends ViewportProperties
     }
 
     int oldendseq = this.endSeq;
-    if (end >= al.getHeight())
+    if (end >= getVisibleAlignmentHeight())
     {
-      endSeq = al.getHeight() - 1;
+      endSeq = getVisibleAlignmentHeight() - 1;
     }
     else if (end < 0)
     {
@@ -327,9 +326,9 @@ public class ViewportRanges extends ViewportProperties
     {
       vpstart = 0;
     }
-    else if (vpstart + w - 1 > al.getWidth() - 1)
+    else if (vpstart + w - 1 > getVisibleAlignmentWidth() - 1)
     {
-      vpstart = al.getWidth() - 1;
+      vpstart = getVisibleAlignmentWidth() - 1;
     }
     setStartEndRes(vpstart, vpstart + w - 1);
   }
@@ -351,9 +350,9 @@ public class ViewportRanges extends ViewportProperties
     {
       vpstart = 0;
     }
-    else if (vpstart + h - 1 > al.getHeight() - 1)
+    else if (vpstart + h - 1 > getVisibleAlignmentHeight() - 1)
     {
-      vpstart = al.getHeight() - h;
+      vpstart = getVisibleAlignmentHeight() - h;
     }
     setStartEndSeq(vpstart, vpstart + h - 1);
   }
@@ -399,7 +398,7 @@ public class ViewportRanges extends ViewportProperties
     }
     else
     {
-      if (endSeq >= al.getHeight() - 1)
+      if (endSeq >= getVisibleAlignmentHeight() - 1)
       {
         return false;
       }
@@ -430,7 +429,7 @@ public class ViewportRanges extends ViewportProperties
     }
     else
     {
-      if (endRes > al.getWidth() - 1)
+      if (endRes > getVisibleAlignmentWidth() - 1)
       {
         return false;
       }
@@ -463,11 +462,8 @@ public class ViewportRanges extends ViewportProperties
    *          x position in alignment
    * @param y
    *          y position in alignment
-   * @param av
-   *          viewport to be visible in. Here until hidden columns JAL-2388
-   *          merged, then use alignment to get hidden cols
    */
-  public void scrollToVisible(int x, int y, AlignViewportI av)
+  public void scrollToVisible(int x, int y)
   {
     while (y < startSeq)
     {

diff --git a/test/jalview/viewmodel/ViewportRangesTest.java b/test/jalview/viewmodel/ViewportRangesTest.java
index 3cd2096..9c0d41b 100644 (file)
--- a/test/jalview/viewmodel/ViewportRangesTest.java
+++ b/test/jalview/viewmodel/ViewportRangesTest.java
@@ -5,12 +5,16 @@ import static org.testng.Assert.assertTrue;
 
 import jalview.analysis.AlignmentGenerator;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenSequences;
 
 import java.beans.PropertyChangeEvent;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class ViewportRangesTest {
@@ -19,6 +23,14 @@ public class ViewportRangesTest {
 
   AlignmentI al = gen.generate(20, 30, 1, 5, 5);
 
+  @BeforeMethod
+  public void cleanUp()
+  {
+    ColumnSelection sel = new ColumnSelection();
+    al.getHiddenColumns().revealAllHiddenColumns(sel);
+    al.getHiddenSequences().showAll(null);
+  }
+
   @Test(groups = { "Functional" })
   public void testViewportRanges() 
   {
@@ -213,7 +225,7 @@ public class ViewportRangesTest {
     vr.pageDown();
 
     // pagedown to bottom does not go beyond end, and height stays same
-    assertEquals(vr.getStartSeq(), 23);
+    assertEquals(vr.getStartSeq(), 24);
     assertEquals(vr.getViewportHeight(), 6);
   }
 
@@ -228,6 +240,30 @@ public class ViewportRangesTest {
     vr.scrollUp(true);
     assertEquals(vr.getStartSeq(), 0);
 
+    vr.setViewportStartAndHeight(24, 5);
+    vr.scrollUp(false);
+    assertEquals(vr.getStartSeq(), 25);
+    // can't scroll beyond bottom
+    vr.scrollUp(false);
+    assertEquals(vr.getStartSeq(), 25);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testScrollUpWithHidden()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+
+    // hide last sequence
+    HiddenSequences hidden = new HiddenSequences(al);
+    hidden.hideSequence(al.getSequenceAt(29));
+
+    vr.setViewportStartAndHeight(1, 5);
+    vr.scrollUp(true);
+    assertEquals(vr.getStartSeq(), 0);
+    // can't scroll above top
+    vr.scrollUp(true);
+    assertEquals(vr.getStartSeq(), 0);
+
     vr.setViewportStartAndHeight(23, 5);
     vr.scrollUp(false);
     assertEquals(vr.getStartSeq(), 24);
@@ -256,6 +292,31 @@ public class ViewportRangesTest {
   }
 
   @Test(groups = { "Functional" })
+  public void testScrollRightWithHidden()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+
+    // hide last 2 columns
+    HiddenColumns cols = new HiddenColumns();
+    cols.hideColumns(18, 19);
+    al.setHiddenColumns(cols);
+
+    vr.setViewportStartAndWidth(1, 5);
+    vr.scrollRight(false);
+    assertEquals(vr.getStartRes(), 0);
+    // can't scroll left past start
+    vr.scrollRight(false);
+    assertEquals(vr.getStartRes(), 0);
+
+    vr.setViewportStartAndWidth(19, 5);
+    vr.scrollRight(true);
+    assertEquals(vr.getStartRes(), 18);
+    // can't scroll right past last visible col
+    vr.scrollRight(true);
+    assertEquals(vr.getStartRes(), 18);
+  }
+
+  @Test(groups = { "Functional" })
   public void testScrollToWrappedVisible()
   {
     ViewportRanges vr = new ViewportRanges(al);
@@ -296,7 +357,7 @@ public class ViewportRangesTest {
   {
     ViewportRanges vr = new ViewportRanges(al);
     MockPropChangeListener l = new MockPropChangeListener(vr);
-    List<String> emptylist = new ArrayList<String>();
+    List<String> emptylist = new ArrayList<>();
 
     vr.setViewportWidth(5);
     vr.setViewportHeight(5);
@@ -425,11 +486,10 @@ public class ViewportRangesTest {
     assertTrue(l.verify(1, Arrays.asList("startres")));
     l.reset();
 
-    // TODO test scrollToVisibble once hidden columns JAL-2388 merged in
-    // to avoid somersaults with align viewport
-    /*vr.scrollToVisible(10, 10);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
-    l.reset();*/
+    vr.scrollToVisible(10, 10);
+    assertTrue(l.verify(4,
+            Arrays.asList("startseq", "startseq", "startseq", "startseq")));
+    l.reset();
 
     vr.scrollToWrappedVisible(5);
     assertTrue(l.verify(1, Arrays.asList("startres")));
@@ -442,9 +502,9 @@ class MockPropChangeListener implements ViewportListenerI
 {
   private int firecount = 0;
 
-  private List<String> events = new ArrayList<String>();
+  private List<String> events = new ArrayList<>();
 
-  private List<Integer> newvalues = new ArrayList<Integer>();
+  private List<Integer> newvalues = new ArrayList<>();
 
   public MockPropChangeListener(ViewportRanges vr)
   {