X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=1e1105f86d1a8413d931835502e8cd1a7e19ebb0;hb=f5cadfa2a55d78a08268a0df9a7c3f64d1c43e8a;hp=394a0b642d03cdb7be0ade6f7350931e71c4e861;hpb=f02e65ac3b489b25e5514d9972838af04298c148;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 394a0b6..1e1105f 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -296,47 +296,48 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       int transX = 0;
       int transY = 0;
 
-    gg.copyArea(horizontal * charWidth, vertical * charHeight,
-            img.getWidth(), img.getHeight(), -horizontal * charWidth,
-            -vertical * charHeight);
+      gg.copyArea(horizontal * charWidth, vertical * charHeight,
+              img.getWidth(), img.getHeight(), -horizontal * charWidth,
+              -vertical * charHeight);
 
-    if (horizontal > 0) // scrollbar pulled right, image to the left
-    {
-      transX = (endRes - startRes - horizontal) * charWidth;
-      startRes = endRes - horizontal;
-    }
-    else if (horizontal < 0)
-    {
-      endRes = startRes - horizontal;
-    }
-    else if (vertical > 0) // scroll down
-    {
-      startSeq = endSeq - vertical;
-
-      if (startSeq < ranges.getStartSeq())
-      { // ie scrolling too fast, more than a page at a time
-        startSeq = ranges.getStartSeq();
+      if (horizontal > 0) // scrollbar pulled right, image to the left
+      {
+        transX = (endRes - startRes - horizontal) * charWidth;
+        startRes = endRes - horizontal;
       }
-      else
+      else if (horizontal < 0)
       {
-        transY = img.getHeight() - ((vertical + 1) * charHeight);
+        endRes = startRes - horizontal;
       }
-    }
-    else if (vertical < 0)
-    {
-      endSeq = startSeq - vertical;
 
-      if (endSeq > ranges.getEndSeq())
+      if (vertical > 0) // scroll down
       {
-        endSeq = ranges.getEndSeq();
+        startSeq = endSeq - vertical;
+
+        if (startSeq < ranges.getStartSeq())
+        { // ie scrolling too fast, more than a page at a time
+          startSeq = ranges.getStartSeq();
+        }
+        else
+        {
+          transY = img.getHeight() - ((vertical + 1) * charHeight);
+        }
       }
-    }
+      else if (vertical < 0)
+      {
+        endSeq = startSeq - vertical;
 
-    gg.translate(transX, transY);
-    drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
-    gg.translate(-transX, -transY);
+        if (endSeq > ranges.getEndSeq())
+        {
+          endSeq = ranges.getEndSeq();
+        }
+      }
 
-    repaint();
+      gg.translate(transX, transY);
+      drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
+      gg.translate(-transX, -transY);
+
+      repaint();
     } finally
     {
       fastpainting = false;
@@ -364,14 +365,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
             ranges.getStartRes(), ranges.getEndRes(),
             ranges.getStartSeq(), ranges.getEndSeq());
 
-    BufferedImage cursorImage = drawCursor(ranges.getStartRes(),
-            ranges.getEndRes(), ranges.getStartSeq(), ranges.getEndSeq());
-
     if ((img != null) && (fastPaint
             || (getVisibleRect().width != g.getClipBounds().width)
             || (getVisibleRect().height != g.getClipBounds().height)))
     {
-      BufferedImage lcimg = buildLocalImage(selectImage, cursorImage);
+      BufferedImage lcimg = buildLocalImage(selectImage);
       g.drawImage(lcimg, 0, 0, this);
       fastPaint = false;
     }
@@ -411,8 +409,15 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
 
       // lcimg is a local *copy* of img which we'll draw selectImage on top of
-      BufferedImage lcimg = buildLocalImage(selectImage, cursorImage);
+      BufferedImage lcimg = buildLocalImage(selectImage);
       g.drawImage(lcimg, 0, 0, this);
+
+    }
+
+    if (av.cursorMode)
+    {
+      drawCursor(g, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq());
     }
   }
   
@@ -496,8 +501,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    * Make a local image by combining the cached image img
    * with any selection
    */
-  private BufferedImage buildLocalImage(BufferedImage selectImage,
-          BufferedImage cursorImage)
+  private BufferedImage buildLocalImage(BufferedImage selectImage)
   {
     // clone the cached image
     BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
@@ -512,12 +516,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
       g2d.drawImage(selectImage, 0, 0, this);
     }
-    // overlay cursor on lcimg
-    if (cursorImage != null)
-    {
-      g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
-      g2d.drawImage(cursorImage, 0, 0, this);
-    }
+
     g2d.dispose();
 
     return lcimg;
@@ -781,8 +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,
@@ -922,9 +921,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           int canvasWidth,
           int canvasHeight, int startRes)
   {
-	int charHeight = av.getCharHeight();
-	int charWidth = av.getCharWidth();
-	  
+    int charHeight = av.getCharHeight();
+    int charWidth = av.getCharWidth();
+      
     // height gap above each panel
     int hgap = charHeight;
     if (av.getScaleAboveWrapped())
@@ -1151,13 +1150,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           }
         }
       }
-
-      /*      if (av.cursorMode && cursorY == i && cursorX >= startRes
-              && cursorX <= endRes)
-      {
-        seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
-                offset + ((i - startSeq) * charHeight));
-      }*/
     }
 
     if (av.getSelectionGroup() != null
@@ -1269,74 +1261,77 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    * @return a transparent image of the same size as the sequence canvas, with
    *         the cursor drawn on it, if any
    */
-  private BufferedImage drawCursor(int startRes, int endRes, int startSeq,
+  private void drawCursor(Graphics g, int startRes, int endRes,
+          int startSeq,
           int endSeq)
   {
-    // define our cursor image
-    BufferedImage cursorImage = null;
+    // convert the cursorY into a position on the visible alignment
+    int cursor_ypos = cursorY;
 
     // don't do work unless we have to
-    if (av.cursorMode && cursorY >= startSeq && cursorY <= endSeq)
+    if (cursor_ypos >= startSeq && cursor_ypos <= endSeq)
     {
       int yoffset = 0;
       int xoffset = 0;
       int startx = startRes;
       int endx = endRes;
-      if (av.getWrapAlignment())
-      {
-        // 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;
+      // convert the cursorX into a position on the visible alignment
+      int cursor_xpos = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(cursorX);
 
-        endx = startx + cWidth - 1;
-        int ypos = hgap; // vertical offset
+      if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
+      {
 
-        // iterate down the wrapped panels
-        while ((ypos <= canvasHeight) && (endx < cursorX))
+        if (av.getWrapAlignment())
         {
-          // update vertical offset
-          ypos += cHeight + getAnnotationHeight() + hgap;
+          // 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;
 
-          // update horizontal offset
-          startx += cWidth;
           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;
+
+            // 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 (cursorX >= startx && cursorX <= endx)
-      {
-        // get a new image of the correct size
-        cursorImage = setupImage();
-        Graphics2D g = (Graphics2D) cursorImage.getGraphics();
-
-        // get the character the cursor is drawn at
-        SequenceI seq = av.getAlignment().getSequenceAt(cursorY);
-        char s = seq.getCharAt(cursorX);
-
-        seqRdr.drawCursor(g, s,
-                xoffset + (cursorX - startx) * av.getCharWidth(),
-                yoffset + (cursorY - startSeq) * av.getCharHeight());
-        g.dispose();
+        // 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());
+        }
       }
     }
-
-    return cursorImage;
   }
 
 
@@ -1371,8 +1366,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
           int startRes, int endRes, int startSeq, int endSeq, int offset)
   {
-	int charWidth = av.getCharWidth();
-	  
+    int charWidth = av.getCharWidth();
+          
     if (!av.hasHiddenColumns())
     {
       drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
@@ -1434,9 +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;
@@ -1444,140 +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;
-        }
-
-        if (!inGroup)
-        {
-          if (((top == -1) && (i == 0)) || !group.getSequences(null)
-                  .contains(av.getAlignment().getSequenceAt(i - 1)))
-          {
-            top = sy;
-          }
+        sy = verticalOffset + (i - startSeq) * charHeight;
 
-          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)
-          {
-            g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
-          }
-
-          if (sx < 0)
+          if ((bottom == -1)
+                  && !seqs.contains(av.getAlignment().getSequenceAt(i + 1)))
           {
-            xwidth += sx;
-            sx = 0;
+            bottom = sy + charHeight;
           }
 
-          // 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);
     }
   }
   
@@ -1664,7 +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;
     }
@@ -1755,15 +1750,31 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       repaint();
       return;
     }
+    else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
+    {
+      fastPaint = false;
+      repaint();
+      return;
+    }
 
     int scrollX = 0;
-    if (eventName.equals(ViewportRanges.STARTRES))
+    if (eventName.equals(ViewportRanges.STARTRES)
+            || eventName.equals(ViewportRanges.STARTRESANDSEQ))
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
+      if (eventName.equals(ViewportRanges.STARTRES))
+      {
+        scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+      }
+      else
+      {
+        scrollX = ((int[]) evt.getNewValue())[0]
+                - ((int[]) evt.getOldValue())[0];
+      }
       ViewportRanges vpRanges = av.getRanges();
-      scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
-      int range = vpRanges.getViewportWidth();
+
+      int range = vpRanges.getEndRes() - vpRanges.getStartRes();
       if (scrollX > range)
       {
         scrollX = range;
@@ -1773,17 +1784,30 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         scrollX = -range;
       }
     }
-
     // Both scrolling and resizing change viewport ranges: scrolling changes
     // both start and end points, but resize only changes end values.
     // Here we only want to fastpaint on a scroll, with resize using a normal
     // paint, so scroll events are identified as changes to the horizontal or
     // vertical start value.
-
-    // scroll - startres and endres both change
     if (eventName.equals(ViewportRanges.STARTRES))
     {
       if (av.getWrapAlignment())
+        {
+          fastPaintWrapped(scrollX);
+        }
+        else
+        {
+          fastPaint(scrollX, 0);
+        }
+    }
+    else if (eventName.equals(ViewportRanges.STARTSEQ))
+    {
+      // scroll
+      fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+    }
+    else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+    {
+      if (av.getWrapAlignment())
       {
         fastPaintWrapped(scrollX);
       }
@@ -1791,11 +1815,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       {
         fastPaint(scrollX, 0);
       }
-    }
-    else if (eventName.equals(ViewportRanges.STARTSEQ))
-    {
-      // scroll
-      fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+      // bizarrely, we only need to scroll on the x value here as fastpaint
+      // copies the full height of the image anyway. Passing in the y value
+      // causes nasty repaint artefacts, which only disappear on a full
+      // repaint.
     }
   }
 
@@ -1812,7 +1835,9 @@ 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 
@@ -2062,7 +2087,7 @@ 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;
     }