X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=433d2ec9e5b29cca26e9780c77817f95045689f6;hb=refs%2Ftags%2FRelease_2_10_3;hp=8d9e537b7d5b74069bc704e8f3b9d6a31686845a;hpb=accb26f3cc680534a35c012accbfb7e7383cc606;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 8d9e537..433d2ec 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -780,8 +780,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
      * white fill the region to be drawn (so incremental fast paint doesn't
      * scribble over an existing image)
      */
-    gg.setColor(Color.white);
-    gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
+    g.setColor(Color.white);
+    g.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
             wrappedRepeatHeightPx);
 
     drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
@@ -1266,8 +1266,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           int endSeq)
   {
     // convert the cursorY into a position on the visible alignment
-    int cursor_ypos = av.getAlignment().getHiddenSequences()
-            .findIndexWithoutHiddenSeqs(cursorY);
+    int cursor_ypos = cursorY;
 
     // don't do work unless we have to
     if (cursor_ypos >= startSeq && cursor_ypos <= endSeq)
@@ -1281,52 +1280,56 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       int cursor_xpos = av.getAlignment().getHiddenColumns()
               .findColumnPosition(cursorX);
 
-      if (av.getWrapAlignment())
+      if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
       {
-        // work out the correct offsets for the cursor
-        int charHeight = av.getCharHeight();
-        int charWidth = av.getCharWidth();
-        int canvasWidth = getWidth();
-        int canvasHeight = getHeight();
-
-        // height gap above each panel
-        int hgap = charHeight;
-        if (av.getScaleAboveWrapped())
+
+        if (av.getWrapAlignment())
         {
-          hgap += charHeight;
-        }
+          // work out the correct offsets for the cursor
+          int charHeight = av.getCharHeight();
+          int charWidth = av.getCharWidth();
+          int canvasWidth = getWidth();
+          int canvasHeight = getHeight();
+
+          // height gap above each panel
+          int hgap = charHeight;
+          if (av.getScaleAboveWrapped())
+          {
+            hgap += charHeight;
+          }
 
-        int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
-                / charWidth;
-        int cHeight = av.getAlignment().getHeight() * charHeight;
+          int cWidth = (canvasWidth - labelWidthEast - labelWidthWest)
+                  / charWidth;
+          int cHeight = av.getAlignment().getHeight() * charHeight;
 
-        endx = startx + cWidth - 1;
-        int ypos = hgap; // vertical offset
+          endx = startx + cWidth - 1;
+          int ypos = hgap; // vertical offset
 
-        // iterate down the wrapped panels
-        while ((ypos <= canvasHeight) && (endx < cursor_xpos))
-        {
-          // update vertical offset
-          ypos += cHeight + getAnnotationHeight() + hgap;
+          // iterate down the wrapped panels
+          while ((ypos <= canvasHeight) && (endx < cursor_xpos))
+          {
+            // update vertical offset
+            ypos += cHeight + getAnnotationHeight() + hgap;
 
-          // update horizontal offset
-          startx += cWidth;
-          endx = startx + cWidth - 1;
+            // update horizontal offset
+            startx += cWidth;
+            endx = startx + cWidth - 1;
+          }
+          yoffset = ypos;
+          xoffset = labelWidthWest;
         }
-        yoffset = ypos;
-        xoffset = labelWidthWest;
-      }
 
-      // now check if cursor is within range for x values
-      if (cursor_xpos >= startx && cursor_xpos <= endx)
-      {
-        // get the character the cursor is drawn at
-        SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
-        char s = seq.getCharAt(cursorX);
+        // now check if cursor is within range for x values
+        if (cursor_xpos >= startx && cursor_xpos <= endx)
+        {
+          // get the character the cursor is drawn at
+          SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
+          char s = seq.getCharAt(cursorX);
 
-        seqRdr.drawCursor(g, s,
-                xoffset + (cursor_xpos - startx) * av.getCharWidth(),
-                yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
+          seqRdr.drawCursor(g, s,
+                  xoffset + (cursor_xpos - startx) * av.getCharWidth(),
+                  yoffset + (cursor_ypos - startSeq) * av.getCharHeight());
+        }
       }
     }
   }
@@ -1426,9 +1429,8 @@ 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;
@@ -1436,140 +1438,141 @@ 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;
 
-      // width of group in pixels
-      xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
-              - 1;
+    List<SequenceI> seqs = group.getSequences(null);
 
-      sy = verticalOffset + (i - startSeq) * charHeight;
+    // position of start residue of group relative to startRes, in pixels
+    int sx = (group.getStartRes() - startRes) * charWidth;
 
-      if (sx + xwidth < 0 || sx > visWidth)
-      {
-        continue;
-      }
+    // width of group in pixels
+    int xwidth = (((group.getEndRes() + 1) - group.getStartRes())
+            * charWidth) - 1;
 
-      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 ((sx <= (endRes - startRes) * charWidth)
+                && seqs.contains(av.getAlignment().getSequenceAt(i)))
         {
-          if (((top == -1) && (i == 0)) || !group.getSequences(null)
-                  .contains(av.getAlignment().getSequenceAt(i - 1)))
+          if ((bottom == -1)
+                  && !seqs.contains(av.getAlignment().getSequenceAt(i + 1)))
           {
-            top = sy;
+            bottom = sy + charHeight;
           }
 
-          oldY = sy;
-          inGroup = true;
-        }
-      }
-      else
-      {
-        if (inGroup)
-        {
-          // 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)
-          {
-            g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
-          }
-
-          if (sx < 0)
-          {
-            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)
+          if (!inGroup)
           {
-            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);
     }
   }
   
@@ -1656,7 +1659,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   protected boolean drawMappedPositions(SearchResultsI results)
   {
-    if (results == null)
+    if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
     {
       return false;
     }
@@ -1833,7 +1836,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   {
     ViewportRanges ranges = av.getRanges();
 
-    if (Math.abs(scrollX) > ranges.getViewportWidth())
+    // if (Math.abs(scrollX) > ranges.getViewportWidth())
+    // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3
+    if (true)
     {
       /*
        * shift of more than one view width is 
@@ -2083,7 +2088,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    */
   protected boolean drawMappedPositionsWrapped(SearchResultsI results)
   {
-    if (results == null)
+    if ((results == null) || (gg == null)) // JAL-2784 check gg is not null
     {
       return false;
     }