X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=3d8b8aafeb3e5874138e20417f53fa0daecf6893;hb=b7b29fb6c0b015ac4798ec4718ab0cfbdd79b20a;hp=c6a8825bd86b43f5e2d48aa535bd88a5ce60f3e7;hpb=e3df4942a8d6e95b622a4abe916f9d2b27ec523b;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c6a8825..3d8b8aa 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -79,6 +79,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
   boolean fastpainting = false;
 
+  AnnotationPanel annotations;
+
   /**
    * Creates a new SeqCanvas object.
    * 
@@ -145,9 +147,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         {
           g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
         }
-        g.drawLine((mpos * charWidth) + (charWidth / 2), (ypos + 2)
-                - (charHeight / 2), (mpos * charWidth) + (charWidth / 2),
-                ypos - 2);
+        g.drawLine((mpos * charWidth) + (charWidth / 2),
+                (ypos + 2) - (charHeight / 2),
+                (mpos * charWidth) + (charWidth / 2), ypos - 2);
       }
     }
   }
@@ -209,8 +211,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       {
         int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
                 - charWidth / 2;
-        g.drawString(value + "", x, (ypos + (i * charHeight))
-                - (charHeight / 5));
+        g.drawString(value + "", x,
+                (ypos + (i * charHeight)) - (charHeight / 5));
       }
     }
   }
@@ -261,8 +263,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       if (value != -1)
       {
-        g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
-                - (charHeight / 5));
+        g.drawString(String.valueOf(value), 0,
+                (ypos + (i * charHeight)) - (charHeight / 5));
       }
     }
   }
@@ -369,8 +371,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
             ranges.getStartRes(), ranges.getEndRes(),
             ranges.getStartSeq(), ranges.getEndSeq());
 
-    if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
-            || (getVisibleRect().height != g.getClipBounds().height))
+    if ((img != null) && (fastPaint
+            || (getVisibleRect().width != g.getClipBounds().width)
+            || (getVisibleRect().height != g.getClipBounds().height)))
     {
       BufferedImage lcimg = buildLocalImage(selectImage);
       g.drawImage(lcimg, 0, 0, this);
@@ -417,6 +420,78 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     }
   }
 
+  /**
+   * Draw an alignment panel for printing
+   * 
+   * @param g1
+   *          Graphics object to draw with
+   * @param startRes
+   *          start residue of print area
+   * @param endRes
+   *          end residue of print area
+   * @param startSeq
+   *          start sequence of print area
+   * @param endSeq
+   *          end sequence of print area
+   */
+  public void drawPanelForPrinting(Graphics g1, int startRes, int endRes,
+          int startSeq, int endSeq)
+  {
+    BufferedImage selectImage = drawSelectionGroup(startRes, endRes,
+            startSeq, endSeq);
+    drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
+    ((Graphics2D) g1).setComposite(
+            AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+    g1.drawImage(selectImage, 0, 0, this);
+  }
+
+  /**
+   * Draw a wrapped alignment panel for printing
+   * 
+   * @param g
+   *          Graphics object to draw with
+   * @param canvasWidth
+   *          width of drawing area
+   * @param canvasHeight
+   *          height of drawing area
+   * @param startRes
+   *          start residue of print area
+   */
+  public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth,
+          int canvasHeight, int startRes)
+  {
+    SequenceGroup group = av.getSelectionGroup();
+
+    drawWrappedPanel(g, canvasWidth, canvasHeight, startRes);
+
+    if (group != null)
+    {
+      BufferedImage selectImage = null;
+      try
+      {
+        selectImage = new BufferedImage(canvasWidth, canvasHeight,
+                BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+      } catch (OutOfMemoryError er)
+      {
+        System.gc();
+        System.err.println("Print image OutOfMemory Error.\n" + er);
+        new OOMWarning("Creating wrapped alignment image for printing", er);
+      }
+      if (selectImage != null)
+      {
+        Graphics2D g2 = selectImage.createGraphics();
+        setupSelectionGroup(g2, selectImage);
+        drawWrappedSelection(g2, group, canvasWidth, canvasHeight,
+                startRes);
+
+        g2.setComposite(
+                AlphaComposite.getInstance(AlphaComposite.SRC_OVER));
+        g.drawImage(selectImage, 0, 0, this);
+        g2.dispose();
+      }
+    }
+  }
+
   /*
    * Make a local image by combining the cached image img
    * with any selection
@@ -441,12 +516,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     return lcimg;
   }
 
-  private void paintSeqGroup()
-  {
-    fastPaint = true;
-    repaint();
-  }
-
+  /*
+   * Set up a buffered image of the correct height and size for the sequence canvas
+   */
   private BufferedImage setupImage()
   {
     BufferedImage lcimg = null;
@@ -470,7 +542,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     {
       System.gc();
       System.err.println(
-              "Selection Group image OutOfMemory Redraw Error.\n" + er);
+              "Group image OutOfMemory Redraw Error.\n" + er);
       new OOMWarning("Creating alignment image for display", er);
 
       return null;
@@ -545,7 +617,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
    * @param startRes
    *          DOCUMENT ME!
    */
-  public void drawWrappedPanel(Graphics g, int canvasWidth,
+  private void drawWrappedPanel(Graphics g, int canvasWidth,
           int canvasHeight, int startRes)
   {
     updateViewport();
@@ -636,10 +708,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           }
 
           gg.fillPolygon(
-                  new int[] { res * charWidth - charHeight / 4,
+                  new int[]
+                  { res * charWidth - charHeight / 4,
                       res * charWidth + charHeight / 4, res * charWidth },
-                  new int[] { ypos - (charHeight / 2),
-                      ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+                  new int[]
+                  { ypos - (charHeight / 2), ypos - (charHeight / 2),
+                      ypos - (charHeight / 2) + 8 },
                   3);
 
         }
@@ -669,8 +743,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
           annotations = new AnnotationPanel(av);
         }
 
-        annotations.renderer.drawComponent(annotations, av, g, -1,
-                startRes, endx + 1);
+        annotations.renderer.drawComponent(annotations, av, g, -1, startRes,
+                endx + 1);
         g.translate(0, -cHeight - ypos - 3);
       }
       g.setClip(clip);
@@ -738,8 +812,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     }
   }
 
-  AnnotationPanel annotations;
-
   int getAnnotationHeight()
   {
     if (!av.isShowAnnotation())
@@ -755,23 +827,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     return annotations.adjustPanelHeight();
   }
 
-  /**
-   * DOCUMENT ME!
+  /*
+   * Draw an alignment panel for printing
    * 
    * @param g1
-   *          DOCUMENT ME!
+   *          Graphics object to draw with
    * @param startRes
-   *          DOCUMENT ME!
+   *          start residue of print area
    * @param endRes
-   *          DOCUMENT ME!
+   *          end residue of print area
    * @param startSeq
-   *          DOCUMENT ME!
+   *          start sequence of print area
    * @param endSeq
-   *          DOCUMENT ME!
+   *          end sequence of print area
    * @param offset
-   *          DOCUMENT ME!
+   *          vertical offset
    */
-  public void drawPanel(Graphics g1, int startRes, int endRes,
+  private void drawPanel(Graphics g1, int startRes, int endRes,
           int startSeq, int endSeq, int offset)
   {
     updateViewport();
@@ -860,8 +932,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       if (av.isShowSequenceFeatures())
       {
-        fr.drawSequence(g, nextSeq, startRes, endRes, offset
-                + ((i - startSeq) * charHeight), false);
+        fr.drawSequence(g, nextSeq, startRes, endRes,
+                offset + ((i - startSeq) * charHeight), false);
       }
 
       // / Highlight search Results once all sequences have been drawn
@@ -908,12 +980,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // ///////////////////////////////////
 
     SequenceGroup group = null;
-
-    int sx = -1;
-    int sy = -1;
-    int ex = -1;
     int groupIndex = -1;
-    int visWidth = (endRes - startRes + 1) * charWidth;
 
     if (av.getAlignment().getGroups().size() > 0)
     {
@@ -923,149 +990,13 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     if (group != null)
     {
+      g.setStroke(new BasicStroke());
+      g.setColor(group.getOutlineColour());
+      
       do
       {
-        int oldY = -1;
-        int i = 0;
-        boolean inGroup = false;
-        int top = -1;
-        int bottom = -1;
-
-        for (i = startSeq; i <= endSeq; i++)
-        {
-          // position of start residue of group relative to startRes, in pixels
-          sx = (group.getStartRes() - startRes) * charWidth;
-          sy = offset + ((i - startSeq) * charHeight);
-          // width of group in pixels
-          ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth)
-                  - 1;
-
-          if (sx + ex < 0 || sx > visWidth)
-          {
-            continue;
-          }
-
-          if ((sx <= (endRes - startRes) * charWidth)
-                  && group.getSequences(null).contains(
-                          av.getAlignment().getSequenceAt(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;
-              }
-
-              oldY = sy;
-              inGroup = true;
-
-              g.setStroke(new BasicStroke());
-              g.setColor(group.getOutlineColour());
-            }
-          }
-          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 + ex < visWidth)
-              {
-                g.drawLine(sx + ex, oldY, sx + ex, sy);
-              }
-
-              if (sx < 0)
-              {
-                ex += sx;
-                sx = 0;
-              }
-
-              if (sx + ex > visWidth)
-              {
-                ex = visWidth;
-              }
-              else if (sx + ex >= (endRes - startRes + 1) * charWidth)
-              {
-                ex = (endRes - startRes + 1) * charWidth;
-              }
-
-              // draw horizontal line at top of group
-              if (top != -1)
-              {
-                g.drawLine(sx, top, sx + ex, top);
-                top = -1;
-              }
-
-              // draw horizontal line at bottom of group
-              if (bottom != -1)
-              {
-                g.drawLine(sx, bottom, sx + ex, bottom);
-                bottom = -1;
-              }
-
-              inGroup = false;
-            }
-          }
-        }
-
-        if (inGroup)
-        {
-          sy = offset + ((i - startSeq) * charHeight);
-          if (sx >= 0 && sx < visWidth)
-          {
-            g.drawLine(sx, oldY, sx, sy);
-          }
-
-          if (sx + ex < visWidth)
-          {
-            g.drawLine(sx + ex, oldY, sx + ex, sy);
-          }
-
-          if (sx < 0)
-          {
-            ex += sx;
-            sx = 0;
-          }
-
-          if (sx + ex > visWidth)
-          {
-            ex = visWidth;
-          }
-          else if (sx + ex >= (endRes - startRes + 1) * charWidth)
-          {
-            ex = (endRes - startRes + 1) * charWidth;
-          }
-
-          if (top != -1)
-          {
-            g.drawLine(sx, top, sx + ex, top);
-            top = -1;
-          }
-
-          if (bottom != -1)
-          {
-            g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
-            bottom = -1;
-          }
-
-          inGroup = false;
-        }
+        drawPartialGroupOutline(g, group, startRes, endRes, startSeq,
+                endSeq, offset);
 
         groupIndex++;
 
@@ -1109,16 +1040,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     // set up drawing colour
     Graphics2D g = (Graphics2D) selectionImage.getGraphics();
 
-    // 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[]
-    { 5f, 3f }, 0f));
-    g.setColor(Color.RED);
+    setupSelectionGroup(g, selectionImage);
 
     if (!av.getWrapAlignment())
     {
@@ -1136,6 +1058,24 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   }
 
   /*
+   * Set up graphics for selection group
+   */
+  private void setupSelectionGroup(Graphics2D g,
+          BufferedImage selectionImage)
+  {
+    // 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[]
+    { 5f, 3f }, 0f));
+    g.setColor(Color.RED);
+  }
+
+  /*
    * Draw a selection group over an unwrapped alignment
    * @param g graphics object to draw with
    * @param group selection group
@@ -1150,7 +1090,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   {
     if (!av.hasHiddenColumns())
     {
-      drawSelectionGroupPart(g, group, startRes, endRes, startSeq, endSeq,
+      drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
               offset);
     }
     else
@@ -1175,7 +1115,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         blockEnd = hideStart - 1;
 
         g.translate(screenY * charWidth, 0);
-        drawSelectionGroupPart(g, group,
+        drawPartialGroupOutline(g, group,
                 blockStart, blockEnd, startSeq, endSeq, offset);
 
         g.translate(-screenY * charWidth, 0);
@@ -1194,7 +1134,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         // remaining visible region to render
         blockEnd = blockStart + (endRes - startRes) - screenY;
         g.translate(screenY * charWidth, 0);
-        drawSelectionGroupPart(g, group,
+        drawPartialGroupOutline(g, group,
                 blockStart, blockEnd, startSeq, endSeq, offset);
         
         g.translate(-screenY * charWidth, 0);
@@ -1205,7 +1145,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   /*
    * Draw the selection group as a separate image and overlay
    */
-  private void drawSelectionGroupPart(Graphics2D g, SequenceGroup group,
+  private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group,
           int startRes, int endRes, int startSeq, int endSeq,
           int verticalOffset)
   {
@@ -1283,6 +1223,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
             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;
@@ -1350,7 +1292,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       inGroup = false;
     }
   }
-
+  
   /**
    * DOCUMENT ME!
    * 
@@ -1373,7 +1315,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
     {
-      paintSeqGroup();
+      fastPaint = true;
+      repaint();
     }
     else if (av.getWrapAlignment())
     {