From 607cd66d3ccb056b773d9c32271ebf08e06a451c Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 30 May 2017 19:28:42 +0100
Subject: [PATCH] JAL-2573 Fixes for alignment < viewport width, and similarly
 height

---
 src/jalview/gui/AlignmentPanel.java            |    3 ++-
 src/jalview/viewmodel/ViewportRanges.java      |   18 ++++++++++----
 test/jalview/viewmodel/ViewportRangesTest.java |   30 +++++++++++++++++-------
 3 files changed, 37 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ce9e989..395f6b3 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -416,7 +416,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       if (centre)
       {
-        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
+                - 1;
         start = Math.max(start - offset, 0);
         end = end + offset - 1;
       }
diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 56c1d39..743d212 100644
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -139,6 +139,10 @@ public class ViewportRanges extends ViewportProperties
     {
       endRes = 0;
     }
+    else if (end > getVisibleAlignmentWidth() - 1)
+    {
+      endRes = getVisibleAlignmentWidth() - 1;
+    }
     else
     {
       endRes = end;
@@ -326,9 +330,12 @@ public class ViewportRanges extends ViewportProperties
     {
       vpstart = 0;
     }
-    else if (vpstart + w - 1 > getVisibleAlignmentWidth() - 1)
+    else if ((w <= getVisibleAlignmentWidth())
+            && (vpstart + w - 1 > getVisibleAlignmentWidth() - 1))
+    // viewport width is less than the full alignment and we are running off the
+    // RHS edge
     {
-      vpstart = getVisibleAlignmentWidth() - 1;
+      vpstart = getVisibleAlignmentWidth() - w;
     }
     setStartEndRes(vpstart, vpstart + w - 1);
   }
@@ -350,7 +357,10 @@ public class ViewportRanges extends ViewportProperties
     {
       vpstart = 0;
     }
-    else if (vpstart + h - 1 > getVisibleAlignmentHeight() - 1)
+    else if ((h <= getVisibleAlignmentHeight())
+            && (vpstart + h - 1 > getVisibleAlignmentHeight() - 1))
+    // viewport height is less than the full alignment and we are running off
+    // the bottom
     {
       vpstart = getVisibleAlignmentHeight() - h;
     }
@@ -429,7 +439,7 @@ public class ViewportRanges extends ViewportProperties
     }
     else
     {
-      if (endRes > getVisibleAlignmentWidth() - 1)
+      if (endRes >= getVisibleAlignmentWidth() - 1)
       {
         return false;
       }
diff --git a/test/jalview/viewmodel/ViewportRangesTest.java b/test/jalview/viewmodel/ViewportRangesTest.java
index 9c0d41b..80bd4db 100644
--- a/test/jalview/viewmodel/ViewportRangesTest.java
+++ b/test/jalview/viewmodel/ViewportRangesTest.java
@@ -23,6 +23,8 @@ public class ViewportRangesTest {
 
   AlignmentI al = gen.generate(20, 30, 1, 5, 5);
 
+  AlignmentI smallAl = gen.generate(7, 2, 2, 5, 5);
+
   @BeforeMethod
   public void cleanUp()
   {
@@ -126,7 +128,11 @@ public class ViewportRangesTest {
     assertEquals(vr.getEndRes(), 19);
 
     vr.setStartEndRes(al.getWidth(), al.getWidth());
-    assertEquals(vr.getEndRes(), al.getWidth());
+    assertEquals(vr.getEndRes(), al.getWidth() - 1);
+
+    ViewportRanges vrsmall = new ViewportRanges(smallAl);
+    vrsmall.setStartEndRes(al.getWidth(), al.getWidth());
+    assertEquals(vrsmall.getEndRes(), 6);
   }
 
   @Test(groups = { "Functional" })
@@ -196,7 +202,13 @@ public class ViewportRangesTest {
     // reset out of bounds start values to within bounds
     vr.setViewportStartAndWidth(35, 5);
     assertEquals(vr.getViewportWidth(), 5);
-    assertEquals(vr.getStartRes(), 20);
+    assertEquals(vr.getStartRes(), 16);
+
+    // small alignment doesn't get bounds reset
+    ViewportRanges vrsmall = new ViewportRanges(smallAl);
+    vrsmall.setViewportStartAndWidth(0, 63);
+    assertEquals(vrsmall.getViewportWidth(), 7);
+    assertEquals(vrsmall.getStartRes(), 0);
   }
 
   @Test(groups = { "Functional" })
@@ -283,12 +295,12 @@ public class ViewportRangesTest {
     vr.scrollRight(false);
     assertEquals(vr.getStartRes(), 0);
 
-    vr.setViewportStartAndWidth(19, 5);
+    vr.setViewportStartAndWidth(15, 5);
     vr.scrollRight(true);
-    assertEquals(vr.getStartRes(), 20);
+    assertEquals(vr.getStartRes(), 16);
     // can't scroll right past end
     vr.scrollRight(true);
-    assertEquals(vr.getStartRes(), 20);
+    assertEquals(vr.getStartRes(), 16);
   }
 
   @Test(groups = { "Functional" })
@@ -298,7 +310,7 @@ public class ViewportRangesTest {
 
     // hide last 2 columns
     HiddenColumns cols = new HiddenColumns();
-    cols.hideColumns(18, 19);
+    cols.hideColumns(19, 20);
     al.setHiddenColumns(cols);
 
     vr.setViewportStartAndWidth(1, 5);
@@ -308,12 +320,12 @@ public class ViewportRangesTest {
     vr.scrollRight(false);
     assertEquals(vr.getStartRes(), 0);
 
-    vr.setViewportStartAndWidth(19, 5);
+    vr.setViewportStartAndWidth(13, 5);
     vr.scrollRight(true);
-    assertEquals(vr.getStartRes(), 18);
+    assertEquals(vr.getStartRes(), 14);
     // can't scroll right past last visible col
     vr.scrollRight(true);
-    assertEquals(vr.getStartRes(), 18);
+    assertEquals(vr.getStartRes(), 14);
   }
 
   @Test(groups = { "Functional" })
-- 
1.7.10.2