JAL-2665 Code tidies

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 646ecf8..c6a8825 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -55,7 +55,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 {
   final FeatureRenderer fr;
 
-  final SequenceRenderer sr;
+  final SequenceRenderer seqRdr;
 
   BufferedImage img;
 
@@ -73,6 +73,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   int cursorY = 0;
 
+  int charHeight = 0;
+
+  int charWidth = 0;
+
+  boolean fastpainting = false;
+
   /**
    * Creates a new SeqCanvas object.
    * 
@@ -84,7 +90,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     this.av = ap.av;
     updateViewport();
     fr = new FeatureRenderer(ap);
-    sr = new SequenceRenderer(av);
+    seqRdr = new SequenceRenderer(av);
     setLayout(new BorderLayout());
     PaintRefresher.Register(this, av.getSequenceSetId());
     setBackground(Color.white);
@@ -94,7 +100,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   public SequenceRenderer getSequenceRenderer()
   {
-    return sr;
+    return seqRdr;
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -102,8 +108,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     return fr;
   }
 
-  int charHeight = 0, charWidth = 0;
-
   private void updateViewport()
   {
     charHeight = av.getCharHeight();
@@ -263,7 +267,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     }
   }
 
-  boolean fastpainting = false;
 
   /**
    * need to make this thread safe move alignment rendering in response to
@@ -353,13 +356,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     updateViewport();
 
-    // img is a cached version of the last view we drew
-    // selectImage will hold any selection we have
-    // lcimg is a local *copy* of img which we'll draw selectImage on top of
-
     ViewportRanges ranges = av.getRanges();
+
+    int width = getWidth();
+    int height = getHeight();
+
+    width -= (width % charWidth);
+    height -= (height % charHeight);
+
+    // selectImage is the selection group outline image
     BufferedImage selectImage = drawSelectionGroup(
-            av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+            ranges.getStartRes(), ranges.getEndRes(),
             ranges.getStartSeq(), ranges.getEndSeq());
 
     if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
@@ -367,55 +374,47 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     {
       BufferedImage lcimg = buildLocalImage(selectImage);
       g.drawImage(lcimg, 0, 0, this);
-
       fastPaint = false;
-      return;
     }
+    else if ((width > 0) && (height > 0))
+    {
+      // img is a cached version of the last view we drew, if any
+      // if we have no img or the size has changed, make a new one
+      if (img == null || width != img.getWidth()
+              || height != img.getHeight())
+      {
+        img = setupImage();
+        if (img == null)
+        {
+          return;
+        }
+        gg = (Graphics2D) img.getGraphics();
+        gg.setFont(av.getFont());
+      }
 
-    int width = getWidth();
-    int height = getHeight();
+      if (av.antiAlias)
+      {
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                RenderingHints.VALUE_ANTIALIAS_ON);
+      }
 
-    width -= (width % charWidth);
-    height -= (height % charHeight);
+      gg.setColor(Color.white);
+      gg.fillRect(0, 0, img.getWidth(), img.getHeight());
 
-    if ((width < 1) || (height < 1))
-    {
-      return;
-    }
-
-    if (img == null || width != img.getWidth() || height != img.getHeight())
-    {
-      img = setupImage();
-      gg = (Graphics2D) img.getGraphics();
-      gg.setFont(av.getFont());
-    }
-    if (img == null)
-    {
-      return;
-    }
+      if (av.getWrapAlignment())
+      {
+        drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
+      }
+      else
+      {
+        drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+                ranges.getStartSeq(), ranges.getEndSeq(), 0);
+      }
 
-    
-    if (av.antiAlias)
-    {
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-              RenderingHints.VALUE_ANTIALIAS_ON);
-    }
-    
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, img.getWidth(), img.getHeight());
-    
-    if (av.getWrapAlignment())
-    {
-      drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
-    }
-    else
-    {
-      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
-              ranges.getStartSeq(), ranges.getEndSeq(), 0);
+      // lcimg is a local *copy* of img which we'll draw selectImage on top of
+      BufferedImage lcimg = buildLocalImage(selectImage);
+      g.drawImage(lcimg, 0, 0, this);
     }
-
-    BufferedImage lcimg = buildLocalImage(selectImage);
-    g.drawImage(lcimg, 0, 0, this);
   }
 
   /*
@@ -683,10 +682,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     }
   }
 
-  public void drawWrappedSelection(Graphics2D g, SequenceGroup group,
+  /*
+   * Draw a selection group over a wrapped alignment
+   */
+  private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
           int canvasWidth,
           int canvasHeight, int startRes)
   {
+    // height gap above each panel
     int hgap = charHeight;
     if (av.getScaleAboveWrapped())
     {
@@ -696,8 +699,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
     int cHeight = av.getAlignment().getHeight() * charHeight;
 
+    int startx = startRes;
     int endx;
-    int ypos = hgap;
+    int ypos = hgap; // vertical offset
     int maxwidth = av.getAlignment().getWidth();
 
     if (av.hasHiddenColumns())
@@ -706,9 +710,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               .findColumnPosition(maxwidth);
     }
 
-    while ((ypos <= canvasHeight) && (startRes < maxwidth))
+    // chop the wrapped alignment extent up into panel-sized blocks and treat
+    // each block as if it were a block from an unwrapped alignment
+    while ((ypos <= canvasHeight) && (startx < maxwidth))
     {
-      endx = startRes + cWidth - 1;
+      // set end value to be start + width, or maxwidth, whichever is smaller
+      endx = startx + cWidth - 1;
 
       if (endx > maxwidth)
       {
@@ -717,15 +724,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       g.translate(LABEL_WEST, 0);
 
-      drawUnwrappedSelection(g, group, startRes, endx, 0,
+      drawUnwrappedSelection(g, group, startx, endx, 0,
               av.getAlignment().getHeight() - 1,
               ypos);
 
       g.translate(-LABEL_WEST, 0);
 
+      // update vertical offset
       ypos += cHeight + getAnnotationHeight() + hgap;
 
-      startRes += cWidth;
+      // update horizontal offset
+      startx += cWidth;
     }
   }
 
@@ -831,7 +840,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           int endSeq, int offset)
   {
     g.setFont(av.getFont());
-    sr.prepare(g, av.isRenderGaps());
+    seqRdr.prepare(g, av.isRenderGaps());
 
     SequenceI nextSeq;
 
@@ -846,7 +855,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         // empty
         continue;
       }
-      sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+      seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
               startRes, endRes, offset + ((i - startSeq) * charHeight));
 
       if (av.isShowSequenceFeatures())
@@ -865,7 +874,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         {
           for (int r = 0; r < visibleResults.length; r += 2)
           {
-            sr.drawHighlightedText(nextSeq, visibleResults[r],
+            seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
                     visibleResults[r + 1], (visibleResults[r] - startRes)
                             * charWidth, offset
                             + ((i - startSeq) * charHeight));
@@ -876,7 +885,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       if (av.cursorMode && cursorY == i && cursorX >= startRes
               && cursorX <= endRes)
       {
-        sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+        seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
                 offset + ((i - startSeq) * charHeight));
       }
     }
@@ -1099,11 +1108,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     // set up drawing colour
     Graphics2D g = (Graphics2D) selectionImage.getGraphics();
-    // g.translate(LABEL_WEST, 0);
+
     // set background to transparent
     g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f));
     g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight());
 
+    // set up foreground to draw red dashed line
     g.setComposite(AlphaComposite.Src);
     g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
             BasicStroke.JOIN_ROUND, 3f, new float[]
@@ -1125,6 +1135,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     return selectionImage;
   }
 
+  /*
+   * Draw a selection group over an unwrapped alignment
+   * @param g graphics object to draw with
+   * @param group selection group
+   * @param startRes start residue of area to draw
+   * @param endRes end residue of area to draw
+   * @param startSeq start sequence of area to draw
+   * @param endSeq end sequence of area to draw
+   * @param offset vertical offset (used when called from wrapped alignment code)
+   */
   private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
           int startRes, int endRes, int startSeq, int endSeq, int offset)
   {