X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=b2e9d3ead108b105ba18a00fa8bde011e2ec21e6;hb=c521a798765bb3672e89ea8cda3241a97d6c6e73;hp=c243a2e02fbf34f52a0fa167ec6ee29190189a93;hpb=79f4b175e12f4c16d598b4cb56ffe62532b592a1;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c243a2e..b2e9d3e 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -1,15 +1,17 @@
 package jalview.gui;
 
 import java.awt.*;
+import java.awt.image.*;
 import javax.swing.*;
 import jalview.datamodel.*;
 import jalview.analysis.*;
 
 
-public class SeqCanvas extends JPanel
+public class SeqCanvas extends JComponent
 {
      FeatureRenderer fr;
-    Image             img;
+     SequenceRenderer sr;
+    BufferedImage             img;
     Graphics2D          gg;
     int               imgWidth;
     int               imgHeight;
@@ -30,6 +32,7 @@ public class SeqCanvas extends JPanel
     {
 	this.av         = av;
        fr = new FeatureRenderer(av);
+       sr = new SequenceRenderer(av);
        setLayout(new BorderLayout());
        PaintRefresher.Register(this);
 
@@ -77,7 +80,7 @@ public class SeqCanvas extends JPanel
       }
       if(value!=-1)
       {
-        int x = fm.stringWidth("000") - fm.stringWidth(value+"");
+        int x = LABEL_WEST - fm.stringWidth(value+"");
         g.drawString(value + "", x,  ypos +  i*av.charHeight - av.charHeight/5);
       }
     }
@@ -121,7 +124,7 @@ public void fastPaint(int horizontal, int vertical)
     gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
                 -vertical * av.charHeight);
 
-    int sr = av.startRes, er = av.endRes + 1, ss = av.startSeq, es = av.endSeq,
+    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
         transX = 0, transY = 0;
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -150,7 +153,7 @@ public void fastPaint(int horizontal, int vertical)
     gg.translate(transX, transY);
 
     gg.setColor(Color.white);
-    gg.fillRect(0,0, (er-sr)*av.charWidth, (es-ss)*av.charHeight);
+    gg.fillRect(0,0, (er-sr+1)*av.charWidth, (es-ss)*av.charHeight);
     drawPanel(gg, sr, er, ss, es, sr, ss, 0);
     gg.translate( -transX, -transY);
 
@@ -185,13 +188,14 @@ public void fastPaint(int horizontal, int vertical)
     // this draws the whole of the alignment
       imgWidth  = getWidth();
       imgHeight = getHeight();
-      if(imgWidth==0 || imgHeight==0)
-        return;
 
       imgWidth -= imgWidth%av.charWidth;
       imgHeight-= imgHeight%av.charHeight;
 
-      img = createImage(imgWidth,imgHeight);
+      if(imgWidth<1 || imgHeight<1)
+        return;
+
+      img = new BufferedImage(imgWidth,imgHeight,BufferedImage.TYPE_INT_RGB);
       gg  = (Graphics2D)img.getGraphics();
       gg.setFont(av.getFont());
       gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
@@ -215,16 +219,19 @@ public void fastPaint(int horizontal, int vertical)
 
   }
 
+  int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    int LABEL_EAST = 0;
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
+
     if(av.scaleRightWrapped)
       LABEL_EAST = fm.stringWidth( av.alignment.getWidth()+"000" );
-    int LABEL_WEST = 0;
+
     if(av.scaleLeftWrapped)
-      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"0" );
+      LABEL_WEST = fm.stringWidth( av.alignment.getWidth()+"" );
 
     return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
   }
@@ -240,16 +247,18 @@ public void fastPaint(int horizontal, int vertical)
         LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );
       int LABEL_WEST = 0;
       if(av.scaleLeftWrapped)
-        LABEL_WEST = fm.stringWidth( al.getWidth()+"0" );
+        LABEL_WEST = fm.stringWidth(al.getWidth()+"0");
+
 
       int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
       int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
+      av.endRes = av.startRes + cWidth;
+
       int  endx   = startRes+cWidth-1;
       int  ypos  = 2*av.charHeight;
 
-
-      while (ypos <= canvasHeight && endx <al.getWidth())
+      while (ypos <= canvasHeight && startRes<av.alignment.getWidth() )
       {
         g.setColor(Color.black);
 
@@ -263,12 +272,25 @@ public void fastPaint(int horizontal, int vertical)
           g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);
         }
 
-
         g.translate(LABEL_WEST,0);
         if(av.scaleAboveWrapped)
           drawNorthScale(g, startRes, endx, ypos);
 
+
+        // When printing we have an extra clipped region,
+        // the Printable page which we need to account for here
+        Shape clip = g.getClip();
+        if(clip==null)
+          g.setClip(0, 0, cWidth*av.charWidth, canvasHeight);
+        else
+          g.setClip(0,
+                    (int)clip.getBounds().getY(),
+                    cWidth*av.charWidth,
+                    (int)clip.getBounds().getHeight()
+                    );
+
         drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+        g.setClip(clip);
         g.translate(-LABEL_WEST,0);
 
         ypos += cHeight;
@@ -282,37 +304,12 @@ public void fastPaint(int horizontal, int vertical)
   }
 
 
-  public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
+  synchronized public void drawPanel(Graphics g1,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
 
     Graphics2D g = (Graphics2D)g1;
     g.setFont(av.getFont());
-    RendererI sr = av.getRenderer();
-
-    /*Vector    pid    = av.getConsensus(false);
-    Vector tmpseq = new Vector();
-    for (int i = 0; i < av.getAlignment().getHeight(); i++)
-	if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
-	    tmpseq.addElement(av.getAlignment().getSequenceAt(i));
-
-    if (sr instanceof SequenceRenderer)
-	pid    = AAFrequency.calculate(tmpseq,x1,x2);
-
-    else if (sr instanceof GraphRenderer)
-	pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
-				       av.getAlignment().getSequences(),
-				       av.getPIDWindow(),x1,x2);
+    sr.renderGaps(av.renderGaps);
 
-*/
-
-   /* if (y2 > starty && y1 < av.getEndSeq())
-    {
-       fillBackground(g,
-                   Color.red,
-                   (x1-startx)*charWidth,
-                   offset + AlignmentUtil.getPixelHeight(starty,y1,av.getCharHeight()),
-                   (x2-x1+1)*charWidth,
-                   offset + AlignmentUtil.getPixelHeight(y1,y2,av.getCharHeight()));
-    }*/
 
     SequenceI nextSeq;
 
@@ -325,7 +322,7 @@ public void fastPaint(int horizontal, int vertical)
      sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,
                  (x1 - startx) * av.charWidth,
                  offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                 av.charWidth,av.charHeight,null, i);
+                 av.charWidth,av.charHeight);
 
      if(av.showSequenceFeatures)
      {
@@ -333,7 +330,7 @@ public void fastPaint(int horizontal, int vertical)
                        (x1 - startx) * av.charWidth,
                        offset +
                        AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                       av.charWidth, av.charHeight, null, i);
+                       av.charWidth, av.charHeight);
      }
     }
     //
@@ -363,23 +360,7 @@ public void fastPaint(int horizontal, int vertical)
         {
           sx = (group.getStartRes() - startx) * av.charWidth;
           sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth;
-
-          if (av.getWrapAlignment())
-          {
-            if (sx < 0)
-              sx = 0;
-
-            if (ex > getWidth())
-            {
-              if (av.getWrapAlignment())
-                ex = getWrappedCanvasWidth(getWidth()) * av.charWidth;
-
-            }
-          }
-          else if(ex>getWidth())
-            ex -= av.charWidth;
-
+          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth -1;
 
           if (sx < getWidth()
               && ex > 0
@@ -470,17 +451,21 @@ public void fastPaint(int horizontal, int vertical)
       for(int r=0; r<searchResults.length; r+=3)
       {
         int searchSeq = searchResults[r];
-        int searchStart = searchResults[r+1];
-        int searchEnd = searchResults[r+2];
 
         if (searchSeq >= y1 && searchSeq < y2)
         {
+          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
+
+          int searchStart = seq.findIndex( searchResults[r+1] )-1;
+          int searchEnd =  seq.findIndex(  searchResults[r+2] )-1;
+
           SequenceRenderer ssr = (SequenceRenderer) sr;
           if(searchStart<x1)
             searchStart = x1;
           if(searchEnd > x2)
             searchEnd = x2;
-          ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
+
+          ssr.drawHighlightedText(seq,
                                   searchStart,
                                   searchEnd,
                                   (searchStart - startx) * av.charWidth,