JAL-3099 use Alignment.getVisibleWidth() where wanted

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 83d8ade..e9081b0 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -669,14 +669,9 @@ public class AlignmentPanel extends Panel
     }
     else
     {
-      int width = av.getAlignment().getWidth();
+      int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns())
-      {
-        width = av.getAlignment().getHiddenColumns()
-                .absoluteToVisibleColumn(width);
-      }
       if (x < 0)
       {
         x = 0;

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 296f898..ef80616 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -280,15 +280,9 @@ public class IdCanvas extends Panel implements ViewportListenerI
   protected void drawIdsWrapped(int starty, final boolean doHiddenCheck,
           boolean hiddenRows)
   {
-    int maxwidth = av.getAlignment().getWidth();
+    int maxwidth = av.getAlignment().getVisibleWidth();
     int alheight = av.getAlignment().getHeight();
 
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
-
     int annotationHeight = 0;
     AnnotationLabels labels = null;
 

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 35d73de..96eb6b9 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -136,13 +136,6 @@ public class SeqCanvas extends Panel implements ViewportListenerI
               .visibleToAbsoluteColumn(endx);
     }
 
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
-
     // WEST SCALE
     for (int i = 0; i < av.getAlignment().getHeight(); i++)
     {
@@ -450,13 +443,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     int endx;
     int ypos = hgap;
   
-    int maxwidth = av.getAlignment().getWidth();
-  
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
   
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
     {
@@ -565,7 +552,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
       int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+      VisibleContigsIterator regions = hidden
               .getVisContigsIterator(startRes, endRes + 1, true);
 
       while (regions.hasNext())

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 2c5684a..d8f1629 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -667,16 +667,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      int width = av.getAlignment().getWidth();
+      int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns())
-      {
-        // reset the width to exclude hidden columns
-        width = av.getAlignment().getHiddenColumns()
-                .absoluteToVisibleColumn(width);
-      }
-
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
       vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
@@ -1002,7 +995,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
 
-    int alignmentWidth = av.getAlignment().getWidth();
+    int alignmentWidth = av.getAlignment().getVisibleWidth();
     int pagesWide = (alignmentWidth / totalRes) + 1;
 
     final int startRes = (pi % pagesWide) * totalRes;
@@ -1168,12 +1161,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int idWidth = getVisibleIdWidth(false);
 
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     int resWidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(pwidth - idWidth);
@@ -1360,12 +1348,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public AlignmentDimension getAlignmentDimension()
   {
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
             + getScalePanel().getHeight();

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index cd7b0b7..9ff0652 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -374,15 +374,9 @@ public class IdCanvas extends JPanel implements ViewportListenerI
    */
   protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
   {
-    int maxwidth = av.getAlignment().getWidth();
+    int maxwidth = av.getAlignment().getVisibleWidth();
     int alheight = av.getAlignment().getHeight();
 
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
-
     int annotationHeight = 0;
 
     if (av.isShowAnnotation())

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 8f315bd..ce7b63b 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -954,13 +954,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int startx = startRes;
     int endx;
     int ypos = hgap; // vertical offset
-    int maxwidth = av.getAlignment().getWidth();
-
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     // chop the wrapped alignment extent up into panel-sized blocks and treat
     // each block as if it were a block from an unwrapped alignment

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 691e492..6f817bb 100644 (file)
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -97,7 +97,7 @@ public class ViewportRanges extends ViewportProperties
    */
   public int getVisibleAlignmentWidth()
   {
-    return al.getWidth() - al.getHiddenColumns().getSize();
+    return al.getVisibleWidth();
   }
 
   /**

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 1d1ebd6..5e400c0 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1484,4 +1484,34 @@ public class AlignmentTest
     assertEquals(".JKLMNO", seq2.getSequenceAsString());
     assertEquals(".PQR...", seq3.getSequenceAsString());
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getWidth());
+
+    // width includes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(9, a.getWidth());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetVisibleWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getVisibleWidth());
+
+    // width excludes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(5, a.getVisibleWidth());
+  }
 }