JAL-2821 refactored drawPartialGroupOutline

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 2a9c704..881afe5 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1339,9 +1339,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           int startRes, int endRes, int startSeq, int endSeq,
           int verticalOffset)
   {
-       int charHeight = av.getCharHeight();
-       int charWidth = av.getCharWidth();
-         
+    int charHeight = av.getCharHeight();
+    int charWidth = av.getCharWidth();
     int visWidth = (endRes - startRes + 1) * charWidth;
 
     int oldY = -1;
@@ -1349,140 +1348,141 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     boolean inGroup = false;
     int top = -1;
     int bottom = -1;
-
-    int sx = -1;
     int sy = -1;
-    int xwidth = -1;
 
-    for (i = startSeq; i <= endSeq; i++)
-    {
-      // position of start residue of group relative to startRes, in pixels
-      sx = (group.getStartRes() - startRes) * charWidth;
+    List<SequenceI> seqs = group.getSequences(null);
 
-      // width of group in pixels
-      xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
-              - 1;
+    // position of start residue of group relative to startRes, in pixels
+    int sx = (group.getStartRes() - startRes) * charWidth;
 
-      sy = verticalOffset + (i - startSeq) * charHeight;
+    // width of group in pixels
+    int xwidth = (((group.getEndRes() + 1) - group.getStartRes())
+            * charWidth) - 1;
 
-      if (sx + xwidth < 0 || sx > visWidth)
-      {
-        continue;
-      }
-
-      if ((sx <= (endRes - startRes) * charWidth)
-              && group.getSequences(null)
-                      .contains(av.getAlignment().getSequenceAt(i)))
+    if (!(sx + xwidth < 0 || sx > visWidth))
+    {
+      for (i = startSeq; i <= endSeq; i++)
       {
-        if ((bottom == -1) && !group.getSequences(null)
-                .contains(av.getAlignment().getSequenceAt(i + 1)))
-        {
-          bottom = sy + charHeight;
-        }
+        sy = verticalOffset + (i - startSeq) * charHeight;
 
-        if (!inGroup)
-        {
-          if (((top == -1) && (i == 0)) || !group.getSequences(null)
-                  .contains(av.getAlignment().getSequenceAt(i - 1)))
-          {
-            top = sy;
-          }
-
-          oldY = sy;
-          inGroup = true;
-        }
-      }
-      else
-      {
-        if (inGroup)
+        if ((sx <= (endRes - startRes) * charWidth)
+                && seqs.contains(av.getAlignment().getSequenceAt(i)))
         {
-          // if start position is visible, draw vertical line to left of
-          // group
-          if (sx >= 0 && sx < visWidth)
-          {
-            g.drawLine(sx, oldY, sx, sy);
-          }
-
-          // if end position is visible, draw vertical line to right of
-          // group
-          if (sx + xwidth < visWidth)
+          if ((bottom == -1)
+                  && !seqs.contains(av.getAlignment().getSequenceAt(i + 1)))
           {
-            g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
+            bottom = sy + charHeight;
           }
 
-          if (sx < 0)
+          if (!inGroup)
           {
-            xwidth += sx;
-            sx = 0;
-          }
-
-          // don't let width extend beyond current block, or group extent
-          // fixes JAL-2672
-          if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
-          {
-            xwidth = (endRes - startRes + 1) * charWidth - sx;
-          }
-          
-          // draw horizontal line at top of group
-          if (top != -1)
-          {
-            g.drawLine(sx, top, sx + xwidth, top);
-            top = -1;
-          }
+            if (((top == -1) && (i == 0)) || !seqs
+                    .contains(av.getAlignment().getSequenceAt(i - 1)))
+            {
+              top = sy;
+            }
 
-          // draw horizontal line at bottom of group
-          if (bottom != -1)
-          {
-            g.drawLine(sx, bottom, sx + xwidth, bottom);
-            bottom = -1;
+            oldY = sy;
+            inGroup = true;
           }
+        }
+        else if (inGroup)
+        {
+          drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+          drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
 
+          // reset top and bottom
+          top = -1;
+          bottom = -1;
           inGroup = false;
         }
       }
-    }
-
-    if (inGroup)
-    {
-      sy = verticalOffset + ((i - startSeq) * charHeight);
-      if (sx >= 0 && sx < visWidth)
+      if (inGroup)
       {
-        g.drawLine(sx, oldY, sx, sy);
+        sy = verticalOffset + ((i - startSeq) * charHeight);
+        drawVerticals(g, sx, xwidth, visWidth, oldY, sy);
+        drawHorizontals(g, sx, xwidth, visWidth, top, bottom);
       }
+    }
+  }
 
-      if (sx + xwidth < visWidth)
-      {
-        g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
-      }
+  /**
+   * Draw horizontal selection group boundaries at top and bottom positions
+   * 
+   * @param g
+   *          graphics object to draw on
+   * @param sx
+   *          start x position
+   * @param xwidth
+   *          width of gap
+   * @param visWidth
+   *          visWidth maximum available width
+   * @param top
+   *          position to draw top of group at
+   * @param bottom
+   *          position to draw bottom of group at
+   */
+  private void drawHorizontals(Graphics2D g, int sx, int xwidth,
+          int visWidth, int top, int bottom)
+  {
+    int width = xwidth;
+    int startx = sx;
+    if (startx < 0)
+    {
+      width += startx;
+      startx = 0;
+    }
 
-      if (sx < 0)
-      {
-        xwidth += sx;
-        sx = 0;
-      }
+    // don't let width extend beyond current block, or group extent
+    // fixes JAL-2672
+    if (startx + width >= visWidth)
+    {
+      width = visWidth - startx;
+    }
 
-      if (sx + xwidth > visWidth)
-      {
-        xwidth = visWidth;
-      }
-      else if (sx + xwidth >= (endRes - startRes + 1) * charWidth)
-      {
-        xwidth = (endRes - startRes + 1) * charWidth;
-      }
+    if (top != -1)
+    {
+      g.drawLine(startx, top, startx + width, top);
+    }
 
-      if (top != -1)
-      {
-        g.drawLine(sx, top, sx + xwidth, top);
-        top = -1;
-      }
+    if (bottom != -1)
+    {
+      g.drawLine(startx, bottom - 1, startx + width, bottom - 1);
+    }
+  }
 
-      if (bottom != -1)
-      {
-        g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1);
-        bottom = -1;
-      }
+  /**
+   * Draw vertical lines at sx and sx+xwidth providing they lie within
+   * [0,visWidth)
+   * 
+   * @param g
+   *          graphics object to draw on
+   * @param sx
+   *          start x position
+   * @param xwidth
+   *          width of gap
+   * @param visWidth
+   *          visWidth maximum available width
+   * @param oldY
+   *          top y value
+   * @param sy
+   *          bottom y value
+   */
+  private void drawVerticals(Graphics2D g, int sx, int xwidth, int visWidth,
+          int oldY, int sy)
+  {
+    // if start position is visible, draw vertical line to left of
+    // group
+    if (sx >= 0 && sx < visWidth)
+    {
+      g.drawLine(sx, oldY, sx, sy);
+    }
 
-      inGroup = false;
+    // if end position is visible, draw vertical line to right of
+    // group
+    if (sx + xwidth < visWidth)
+    {
+      g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
     }
   }