From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 14 Nov 2017 19:36:53 +0000 (+0000)
Subject: JAL-2831 tidies and tests
X-Git-Tag: Release_2_10_3b1~28^2~4
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=8e820dadfebf0ced59476338df0fa391590f5401

JAL-2831 tidies and tests
---

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index e463cc3..0cc8d7c 100644
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -563,7 +563,7 @@ public class ViewportRanges extends ViewportProperties
    * Calculate wrapped start residue from visible start residue
    * 
    * @param res
-   *          absolute start residue
+   *          visible start residue
    * @return left column of panel res will be located in
    */
   private int calcWrappedStartResidue(int res)
@@ -571,11 +571,6 @@ public class ViewportRanges extends ViewportProperties
     int oldStartRes = startRes;
     int width = getViewportWidth();
 
-    /*if (res >= oldStartRes && res < oldStartRes + width)
-    {
-      return false;
-    }*/
-
     boolean up = res < oldStartRes;
     int widthsToScroll = Math.abs((res - oldStartRes) / width);
     if (up)
@@ -633,15 +628,15 @@ public class ViewportRanges extends ViewportProperties
    * Set the viewport location so that a position is visible
    * 
    * @param x
-   *          column to be visible
+   *          column to be visible: absolute position in alignment
    * @param y
-   *          row to be visible
+   *          row to be visible: absolute position in alignment
    */
   public boolean setViewportLocation(int x, int y)
   {
     boolean changedLocation = false;
 
-    // convert the x,y location to absolute values
+    // convert the x,y location to visible coordinates
     int visX = al.getHiddenColumns().findColumnPosition(x);
     int visY = al.getHiddenSequences().findIndexWithoutHiddenSeqs(y);
 
@@ -660,18 +655,22 @@ public class ViewportRanges extends ViewportProperties
       else
       {
         // set the viewport x location to contain vis_x
+        int newstartres = visX;
         int width = getViewportWidth();
-        updateStartEndRes(visX, visX + width - 1);
+        if (newstartres + width - 1 > getVisibleAlignmentWidth() - 1)
+        {
+          newstartres = getVisibleAlignmentWidth() - width;
+        }
+        updateStartEndRes(newstartres, newstartres + width - 1);
 
         // set the viewport y location to contain vis_y
-        int startseq = visY;
+        int newstartseq = visY;
         int height = getViewportHeight();
-        if (startseq + height - 1 > getVisibleAlignmentHeight() - 1)
+        if (newstartseq + height - 1 > getVisibleAlignmentHeight() - 1)
         {
-          startseq = getVisibleAlignmentHeight() - height;
+          newstartseq = getVisibleAlignmentHeight() - height;
         }
-        updateStartEndSeq(startseq,
-              startseq + height - 1);
+        updateStartEndSeq(newstartseq, newstartseq + height - 1);
 
         newresseq = new int[] { startRes, startSeq };
       }
diff --git a/test/jalview/viewmodel/ViewportRangesTest.java b/test/jalview/viewmodel/ViewportRangesTest.java
index af2424d..41a313f 100644
--- a/test/jalview/viewmodel/ViewportRangesTest.java
+++ b/test/jalview/viewmodel/ViewportRangesTest.java
@@ -402,14 +402,13 @@ public class ViewportRangesTest {
     assertEquals(vr.getEndRes(), 52);
   }
 
-  // leave until JAL-2388 is merged and we can do without viewport
-  /*@Test(groups = { "Functional" })
+  @Test(groups = { "Functional" })
   public void testScrollToVisible()
   {
     ViewportRanges vr = new ViewportRanges(al);
     vr.setViewportStartAndWidth(12,5);
     vr.setViewportStartAndHeight(10,6);
-    vr.scrollToVisible(13,14)
+    vr.scrollToVisible(13, 14);
     
     // no change
     assertEquals(vr.getStartRes(), 12);
@@ -420,7 +419,15 @@ public class ViewportRangesTest {
     assertEquals(vr.getStartSeq(), 6);
     
     // test for hidden columns too
-  }*/
+    al.getHiddenColumns().hideColumns(1, 3);
+    vr.scrollToVisible(13, 3);
+    assertEquals(vr.getStartRes(), 6);
+    assertEquals(vr.getStartSeq(), 3);
+
+    vr.scrollToVisible(2, 9);
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getStartSeq(), 4);
+  }
 
   @Test(groups = { "Functional" })
   public void testEventFiring()
@@ -853,6 +860,76 @@ public class ViewportRangesTest {
     assertEquals(vr.getStartSeq(), 1);
     assertEquals(vr.getStartRes(), 43);
   }
+
+  @Test(groups = { "Functional" })
+  public void testSetViewportLocation()
+  {
+    AlignmentI al2 = gen.generate(60, 80, 1, 0, 0);
+
+    ViewportRanges vr = new ViewportRanges(al2);
+
+    // start with viewport on 5-14
+    vr.setViewportStartAndWidth(5, 10);
+    assertEquals(vr.getStartRes(), 5);
+    assertEquals(vr.getEndRes(), 14);
+
+    vr.setViewportStartAndHeight(3, 13);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+
+    // set location to (8,5) - no change
+    vr.setViewportLocation(8, 5);
+    assertEquals(vr.getStartRes(), 5);
+    assertEquals(vr.getEndRes(), 14);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+
+    // set location to (40,50) - change to top left (40,50)
+    vr.setViewportLocation(40, 50);
+    assertEquals(vr.getStartRes(), 40);
+    assertEquals(vr.getEndRes(), 49);
+    assertEquals(vr.getStartSeq(), 50);
+    assertEquals(vr.getEndSeq(), 62);
+
+    // set location past end of alignment - resets to leftmost pos
+    vr.setViewportLocation(63, 85);
+    assertEquals(vr.getStartRes(), 50);
+    assertEquals(vr.getEndRes(), 59);
+    assertEquals(vr.getStartSeq(), 67);
+    assertEquals(vr.getEndSeq(), 79);
+
+    // hide some columns
+    al2.getHiddenColumns().hideColumns(20, 50);
+    vr.setViewportLocation(55, 4);
+    assertEquals(vr.getStartRes(), 19);
+    assertEquals(vr.getEndRes(), 28);
+    assertEquals(vr.getStartSeq(), 4);
+    assertEquals(vr.getEndSeq(), 16);
+
+    // hide some sequences
+    al2.getHiddenSequences().hideSequence(al2.getSequenceAt(3));
+    al2.getHiddenSequences().hideSequence(al2.getSequenceAt(4));
+    vr.setViewportLocation(17, 5);
+    assertEquals(vr.getStartRes(), 17);
+    assertEquals(vr.getEndRes(), 26);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+
+    // set wrapped mode
+    vr.setWrappedMode(true);
+    vr.setViewportLocation(1, 8);
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getEndRes(), 9);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+
+    // try further down the alignment
+    vr.setViewportLocation(57, 5);
+    assertEquals(vr.getStartRes(), 20);
+    assertEquals(vr.getEndRes(), 29);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+  }
 }
 
 // mock listener for property change events