JAL-2446 merged to spike branch

[jalview.git] / src / jalview / gui / SeqCanvas.java

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d015292..0e5e1b8 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -21,11 +21,14 @@
 package jalview.gui;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BasicStroke;
 import java.awt.BorderLayout;
@@ -36,6 +39,7 @@ import java.awt.Graphics2D;
 import java.awt.RenderingHints;
 import java.awt.Shape;
 import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
 import java.util.List;
 
 import javax.swing.JComponent;
@@ -46,7 +50,7 @@ import javax.swing.JComponent;
  * @author $author$
  * @version $Revision$
  */
-public class SeqCanvas extends JComponent
+public class SeqCanvas extends JComponent implements ViewportListenerI
 {
   final FeatureRenderer fr;
 
@@ -87,6 +91,8 @@ public class SeqCanvas extends JComponent
     setLayout(new BorderLayout());
     PaintRefresher.Register(this, av.getSequenceSetId());
     setBackground(Color.white);
+
+    av.getRanges().addPropertyChangeListener(this);
   }
 
   public SequenceRenderer getSequenceRenderer()
@@ -164,14 +170,17 @@ public class SeqCanvas extends JComponent
 
     if (av.hasHiddenColumns())
     {
-      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
-      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+      startx = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(startx);
+      endx = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(endx);
     }
 
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     // WEST SCALE
@@ -223,7 +232,8 @@ public class SeqCanvas extends JComponent
 
     if (av.hasHiddenColumns())
     {
-      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+      endx = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(endx);
     }
 
     SequenceI seq;
@@ -279,43 +289,43 @@ public class SeqCanvas extends JComponent
     gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
             imgHeight, -horizontal * charWidth, -vertical * charHeight);
 
-    int sr = av.startRes;
-    int er = av.endRes;
-    int ss = av.startSeq;
-    int es = av.endSeq;
+    ViewportRanges ranges = av.getRanges();
+    int sr = ranges.getStartRes();
+    int er = ranges.getEndRes();
+    int ss = ranges.getStartSeq();
+    int es = ranges.getEndSeq();
     int transX = 0;
     int transY = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
-      er++;
       transX = (er - sr - horizontal) * charWidth;
       sr = er - horizontal;
     }
     else if (horizontal < 0)
     {
-      er = sr - horizontal - 1;
+      er = sr - horizontal;
     }
     else if (vertical > 0) // scroll down
     {
       ss = es - vertical;
 
-      if (ss < av.startSeq)
+      if (ss < ranges.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
+        ss = ranges.getStartSeq();
       }
       else
       {
-        transY = imgHeight - (vertical * charHeight);
+        transY = imgHeight - ((vertical + 1) * charHeight);
       }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
 
-      if (es > av.endSeq)
+      if (es > ranges.getEndSeq())
       {
-        es = av.endSeq;
+        es = ranges.getEndSeq();
       }
     }
 
@@ -395,13 +405,15 @@ public class SeqCanvas extends JComponent
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
+    ViewportRanges ranges = av.getRanges();
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+      drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq(), 0);
     }
 
     g.drawImage(lcimg, 0, 0, this);
@@ -503,7 +515,7 @@ public class SeqCanvas extends JComponent
 
     av.setWrappedWidth(cWidth);
 
-    av.endRes = av.startRes + cWidth;
+    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth - 1);
 
     int endx;
     int ypos = hgap;
@@ -511,7 +523,8 @@ public class SeqCanvas extends JComponent
 
     if (av.hasHiddenColumns())
     {
-      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
     }
 
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
@@ -549,11 +562,10 @@ public class SeqCanvas extends JComponent
       {
         g.setColor(Color.blue);
         int res;
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
-                .size(); i++)
+        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+        for (int i = 0; i < hidden.getHiddenRegions().size(); i++)
         {
-          res = av.getColumnSelection().findHiddenRegionPosition(i)
-                  - startRes;
+          res = hidden.findHiddenRegionPosition(i) - startRes;
 
           if (res < 0 || res > endx - startRes)
           {
@@ -584,7 +596,7 @@ public class SeqCanvas extends JComponent
                 (int) clip.getBounds().getHeight());
       }
 
-      drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+      drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
 
       if (av.isShowAnnotation())
       {
@@ -650,7 +662,8 @@ public class SeqCanvas extends JComponent
     }
     else
     {
-      List<int[]> regions = av.getColumnSelection().getHiddenColumns();
+      List<int[]> regions = av.getAlignment().getHiddenColumns()
+              .getHiddenRegions();
 
       int screenY = 0;
       int blockStart = startRes;
@@ -679,7 +692,7 @@ public class SeqCanvas extends JComponent
 
           g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
                   0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
-                  (endSeq - startSeq) * charHeight + offset);
+                  (endSeq - startSeq + 1) * charHeight + offset);
         }
 
         g1.translate(-screenY * charWidth, 0);
@@ -718,7 +731,7 @@ public class SeqCanvas extends JComponent
 
     // / First draw the sequences
     // ///////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
+    for (int i = startSeq; i <= endSeq; i++)
     {
       nextSeq = av.getAlignment().getSequenceAt(i);
       if (nextSeq == null)
@@ -733,7 +746,7 @@ public class SeqCanvas extends JComponent
       if (av.isShowSequenceFeatures())
       {
         fr.drawSequence(g, nextSeq, startRes, endRes, offset
-                + ((i - startSeq) * charHeight));
+                + ((i - startSeq) * charHeight), false);
       }
 
       // / Highlight search Results once all sequences have been drawn
@@ -802,7 +815,7 @@ public class SeqCanvas extends JComponent
         int top = -1;
         int bottom = -1;
 
-        for (i = startSeq; i < endSeq; i++)
+        for (i = startSeq; i <= endSeq; i++)
         {
           sx = (group.getStartRes() - startRes) * charWidth;
           sy = offset + ((i - startSeq) * charHeight);
@@ -971,4 +984,34 @@ public class SeqCanvas extends JComponent
 
     repaint();
   }
+
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    if (!av.getWrapAlignment())
+    {
+      if (evt.getPropertyName().equals("startres")
+              || evt.getPropertyName().equals("endres"))
+      {
+        // Make sure we're not trying to draw a panel
+        // larger than the visible window
+        ViewportRanges vpRanges = av.getRanges();
+        int scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+        if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
+        {
+          scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
+        }
+        else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
+        {
+          scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
+        }
+        fastPaint(scrollX, 0);
+      }
+      else if (evt.getPropertyName().equals("startseq")
+              || evt.getPropertyName().equals("endseq"))
+      {
+        fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+      }
+    }
+  }
 }