X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=c243a2e02fbf34f52a0fa167ec6ee29190189a93;hb=8548008f4fbd321b445c7e69fbdffda26e21f457;hp=f9ab0156721ee9f892cb37be967ef5d761238b9b;hpb=09b64bea954c283bde1d21c0a230f51f1ae89373;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index f9ab015..c243a2e 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -10,14 +10,12 @@ public class SeqCanvas extends JPanel
 {
      FeatureRenderer fr;
     Image             img;
-    Graphics          gg;
+    Graphics2D          gg;
     int               imgWidth;
     int               imgHeight;
 
     AlignViewport     av;
 
-    public boolean paintFlag = false;
-
     boolean showScores = false;
     boolean displaySearch = false;
     int [] searchResults = null;
@@ -25,6 +23,8 @@ public class SeqCanvas extends JPanel
     int chunkHeight;
     int chunkWidth;
 
+    boolean fastPaint = false;
+
 
     public SeqCanvas(AlignViewport av)
     {
@@ -35,23 +35,129 @@ public class SeqCanvas extends JPanel
 
     }
 
-  public void drawScale(Graphics g, int startx, int endx,int ypos) {
-      int scalestartx = startx - startx%10 + 10;
+  void drawNorthScale(Graphics g, int startx, int endx,int ypos) {
+    int scalestartx = startx - startx % 10 + 10;
+
+    g.setColor(Color.black);
 
-      g.setColor(Color.black);
+    // NORTH SCALE
+    for (int i = scalestartx; i < endx; i += 10)
+    {
+      String string = String.valueOf(i);
+      g.drawString(string, (i - startx - 1) * av.charWidth,
+                   ypos - av.charHeight / 2);
+
+      g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,
+                 ypos + 2 - av.charHeight / 2,
+                 (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);
 
-      for (int i=scalestartx;i < endx;i+= 10)
+    }
+  }
+
+  void drawWestScale(Graphics g, int startx, int endx, int ypos)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
+    ypos+= av.charHeight;
+      // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = startx;
+      int value = -1;
+      while (index < endx)
       {
-          String string = String.valueOf(i);
-          g.drawString(string,(i-startx-1)*av.charWidth,ypos - av.charHeight/2);
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index++;
+          continue;
+        }
 
-          g.drawLine( (i-startx-1)*av.charWidth +av.charWidth/2, ypos+2 - av.charHeight/2,
-                    (i-startx-1)*av.charWidth +av.charWidth/2, ypos-2 );
+        value = av.alignment.getSequenceAt(i).findPosition(index);
+        break;
+      }
+      if(value!=-1)
+      {
+        int x = fm.stringWidth("000") - fm.stringWidth(value+"");
+        g.drawString(value + "", x,  ypos +  i*av.charHeight - av.charHeight/5);
+      }
+    }
+  }
 
+  void drawEastScale(Graphics g, int startx, int endx, int ypos)
+{
+    ypos+= av.charHeight;
+    // EAST SCALE
+  for (int i = 0; i < av.alignment.getHeight(); i++)
+  {
+    SequenceI seq = av.alignment.getSequenceAt(i);
+    int index = endx;
+    int value = -1;
+    while (index > startx)
+    {
+      if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+      {
+        index--;
+        continue;
       }
 
+      value = av.alignment.getSequenceAt(i).findPosition(index);
+      break;
+    }
+    if(value!=-1)
+       g.drawString(value + "", 0,  ypos +  i*av.charHeight - av.charHeight/5);
   }
 
+}
+
+
+
+
+
+public void fastPaint(int horizontal, int vertical)
+{
+    if (horizontal == 0 && vertical == 0 || gg==null)
+      return;
+
+    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,
+        transX = 0, transY = 0;
+    if (horizontal > 0) // scrollbar pulled right, image to the left
+    {
+      transX = (er - sr - horizontal) * av.charWidth;
+      sr = er - horizontal;
+    }
+    else if (horizontal < 0)
+      er = sr - horizontal;
+
+    else if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
+      if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time
+        ss = av.startSeq;
+      else
+        transY = imgHeight - vertical * av.charHeight;
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
+      if(es > av.endSeq)
+        es = av.endSeq;
+    }
+
+
+    gg.translate(transX, transY);
+
+    gg.setColor(Color.white);
+    gg.fillRect(0,0, (er-sr)*av.charWidth, (es-ss)*av.charHeight);
+    drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+    gg.translate( -transX, -transY);
+
+    fastPaint = true;
+    repaint();
+
+}
 
 /**
  * Definitions of startx and endx (hopefully):
@@ -66,65 +172,119 @@ public class SeqCanvas extends JPanel
 
   public void paintComponent(Graphics g)
   {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
 
-    if (img==null ||  imgWidth!=getWidth() || imgHeight!=getHeight() || paintFlag)
+    if (fastPaint)
     {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    // 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);
-      gg  = img.getGraphics();
+      gg  = (Graphics2D)img.getGraphics();
       gg.setFont(av.getFont());
-      paintFlag = false;
-    }
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
 
+      gg.setColor(Color.white);
+      gg.fillRect(0,0,imgWidth,imgHeight);
 
-    chunkWidth  =   getWidth()/av.charWidth;
+    chunkWidth  =   getWrappedCanvasWidth( getWidth() );
     chunkHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
     av.setChunkHeight(chunkHeight);
     av.setChunkWidth(chunkWidth);
 
-    fillBackground(gg,Color.WHITE,0,0,imgWidth,imgHeight);
 
     if (av.getWrapAlignment())
       drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
     else
       drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes, av.startSeq, 0);
 
+    g.drawImage(img, 0, 0, this);
 
-    g.drawImage(img,0,0,this);
+  }
+
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
 
+    int LABEL_EAST = 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" );
+
+    return  (cwidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
   }
 
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes)
   {
-      AlignmentI da = av.getAlignment();
+      AlignmentI al = av.getAlignment();
+
+      FontMetrics fm = getFontMetrics(av.getFont());
 
-      int cWidth  =   canvasWidth/av.charWidth;
+      int LABEL_EAST = 0;
+      if(av.scaleRightWrapped)
+        LABEL_EAST = fm.stringWidth( al.getWidth()+"000" );
+      int LABEL_WEST = 0;
+      if(av.scaleLeftWrapped)
+        LABEL_WEST = fm.stringWidth( al.getWidth()+"0" );
+
+      int cWidth  =   (canvasWidth - LABEL_EAST -LABEL_WEST)/av.charWidth;
       int cHeight =  (av.getAlignment().getHeight() + 2)*av.charHeight;
 
       int  endx   = startRes+cWidth-1;
-      int ypos  = 2*av.charHeight;
+      int  ypos  = 2*av.charHeight;
+
 
-      while (ypos <= canvasHeight)
+      while (ypos <= canvasHeight && endx <al.getWidth())
       {
-        drawScale(g, startRes, endx, ypos);
-        drawPanel(g, startRes, endx, 0, da.getHeight(), startRes, 0, ypos);
+        g.setColor(Color.black);
+
+        if(av.scaleLeftWrapped)
+          drawWestScale(g, startRes, endx, ypos);
+
+        if(av.scaleRightWrapped)
+        {
+          g.translate(canvasWidth - LABEL_EAST +av.charWidth, 0);
+          drawEastScale(g, startRes, endx, ypos);
+          g.translate( - (canvasWidth - LABEL_EAST+av.charWidth), 0);
+        }
+
+
+        g.translate(LABEL_WEST,0);
+        if(av.scaleAboveWrapped)
+          drawNorthScale(g, startRes, endx, ypos);
+
+        drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+        g.translate(-LABEL_WEST,0);
 
         ypos += cHeight;
         startRes += cWidth;
         endx = startRes + cWidth - 1;
 
-        if (endx > da.getWidth())
-          endx = da.getWidth();
+        if (endx > al.getWidth())
+          endx = al.getWidth();
       }
 
   }
 
 
-  public void drawPanel(Graphics g,int x1,int x2, int y1, int y2,int startx, int starty,int offset) {
-
+  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();
 
@@ -160,7 +320,7 @@ public class SeqCanvas extends JPanel
     /////////////////////////////
     for (int i = y1 ; i < y2 ;i++)
     {
-     nextSeq = av.getAlignment().getSequenceAt(i);
+     nextSeq = av.alignment.getSequenceAt(i);
 
      sr.drawSequence(g, nextSeq, av.alignment.findAllGroups( nextSeq ),x1,x2,
                  (x1 - startx) * av.charWidth,
@@ -198,42 +358,101 @@ public class SeqCanvas extends JPanel
         int oldY = -1;
         int i = 0;
         boolean inGroup = false;
+        int top=-1, bottom =-1;
         for (i = y1; i < y2; i++)
         {
           sx = (group.getStartRes() - startx) * av.charWidth;
           sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
           ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth;
 
-          if (group.sequences.contains(av.alignment.getSequenceAt(i))
-              && sx < getWidth()
-              && ex > 0)
+          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;
+
+
+          if (sx < getWidth()
+              && ex > 0
+              && group.sequences.contains(av.alignment.getSequenceAt(i)))
+          {
+            if (bottom == -1 &&
+                !group.sequences.contains(av.alignment.getSequenceAt(i + 1)))
+              bottom = sy + av.charHeight ;
+
             if (!inGroup)
             {
+              if (top == -1 && i==0 ||
+                  !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
+                top = sy;
+
+
               oldY = sy;
               inGroup = true;
               if (group == av.getSelectionGroup())
-                g.setColor(Color.RED.brighter());
+              {
+                g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]{5f,3f}, 0f ));
+                g.setColor(Color.RED);
+              }
               else
+              {
+                g.setStroke(new BasicStroke());
                 g.setColor(group.getOutlineColour());
+              }
             }
           }
           else
           {
             if (inGroup)
             {
-              g.drawRect(sx, oldY, ex, (sy - oldY));
+              g.drawLine(sx, oldY, sx, sy );
+              g.drawLine(sx+ex, oldY, sx+ex, sy );
+
+              if (top != -1)
+              {
+                g.drawLine(sx, top, sx + ex, top);
+                top =-1;
+              }
+              if (bottom != -1)
+              {
+                g.drawLine(sx, bottom, sx + ex, bottom);
+                bottom = -1;
+              }
+
+
               inGroup = false;
             }
           }
         }
+
         if (inGroup)
         {
+
+          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;
+
+           }
           sy = offset + AlignmentUtil.getPixelHeight(starty, i, av.charHeight);
-          g.drawRect(sx, oldY, ex, (sy - oldY));
+          g.drawLine(sx, oldY, sx, sy );
+          g.drawLine(sx+ex, oldY, sx+ex, sy );
           inGroup = false;
         }
-
         groupIndex++;
         if (groupIndex >= groups.size())
           break;
@@ -257,6 +476,10 @@ public class SeqCanvas extends JPanel
         if (searchSeq >= y1 && searchSeq < y2)
         {
           SequenceRenderer ssr = (SequenceRenderer) sr;
+          if(searchStart<x1)
+            searchStart = x1;
+          if(searchEnd > x2)
+            searchEnd = x2;
           ssr.drawHighlightedText(av.getAlignment().getSequenceAt(searchSeq),
                                   searchStart,
                                   searchEnd,
@@ -272,14 +495,7 @@ public class SeqCanvas extends JPanel
 
   }
 
-  public void fillBackground(Graphics g,Color c, int x1,int y1,int width,int height) {
-    g.setColor(c);
-    g.fillRect(x1,y1,width,height);
-  }
 
-  public int getChunkWidth() {
-    return chunkWidth;
-  }
 
   public void highlightSearchResults(int [] results)
   {
@@ -291,7 +507,6 @@ public class SeqCanvas extends JPanel
 
     searchResults = results;
 
-    paintFlag = true;
     repaint();
   }