X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=ac5ff899b871c443fe80a41691f4cbb77fe86b50;hb=42ae188a9819c341cd345baeab442cd0606ff157;hp=46ddf37833140146f3422f444b53e5a43f3245ba;hpb=ee53965807b83bf93a21cbc341cee9a9e005b2cb;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 46ddf37..ac5ff89 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -35,15 +35,13 @@ public class SeqCanvas
 
   AlignViewport av;
 
-  boolean displaySearch = false;
-  int[] searchResults = null;
+  SearchResults searchResults = null;
 
   int chunkHeight;
   int chunkWidth;
 
   boolean fastPaint = false;
 
-  boolean isOverview = false;
 
   public SeqCanvas(AlignViewport av)
   {
@@ -51,9 +49,30 @@ public class SeqCanvas
     fr = new FeatureRenderer(av);
     sr = new SequenceRenderer(av);
     PaintRefresher.Register(this, av.alignment);
+  }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
 
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return fr;
+  }
+
+  MCview.AppletPDBCanvas pdbCanvas;
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
+  }
+
+  public void setPDBCanvas(MCview.AppletPDBCanvas pc)
+  {
+    pdbCanvas = pc;
   }
 
+
   void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
     int scalestartx = startx - startx % 10 + 10;
@@ -135,11 +154,13 @@ public class SeqCanvas
 
   public void fastPaint(int horizontal, int vertical)
   {
-    if (gg == null)
+    if (fastPaint || gg == null)
     {
+      repaint();
       return;
     }
 
+    fastPaint = true;
     gg.copyArea(horizontal * av.charWidth,
                 vertical * av.charHeight,
                 imgWidth,
@@ -149,6 +170,7 @@ public class SeqCanvas
 
     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
     {
       transX = (er - sr - horizontal) * av.charWidth;
@@ -182,12 +204,9 @@ public class SeqCanvas
 
     gg.translate(transX, transY);
 
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, (es - ss) * av.charHeight);
-    drawPanel(gg, sr, er, ss, es, sr, ss, 0);
+    drawPanel(gg, sr, er, ss, es, 0);
     gg.translate( -transX, -transY);
 
-    fastPaint = true;
     repaint();
 
   }
@@ -209,7 +228,6 @@ public class SeqCanvas
 
   public void paint(Graphics g)
   {
-    sr.renderGaps(av.renderGaps);
 
     if (fastPaint)
     {
@@ -248,12 +266,15 @@ public class SeqCanvas
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, av.startRes,
-                av.startSeq, 0);
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
     }
 
     g.drawImage(img, 0, 0, this);
 
+    if (pdbCanvas != null)
+    {
+      pdbCanvas.updateSeqColours();
+    }
   }
 
   int LABEL_WEST, LABEL_EAST;
@@ -266,7 +287,7 @@ public class SeqCanvas
 
       if (av.scaleRightWrapped)
       {
-          LABEL_EAST = fm.stringWidth(getMask()+"0");
+          LABEL_EAST = fm.stringWidth(getMask());
       }
 
       if (av.scaleLeftWrapped)
@@ -284,7 +305,7 @@ public class SeqCanvas
    */
   String getMask()
   {
-    String mask = "0";
+    String mask = "00";
     for (int i = av.alignment.getWidth(); i > 0; i /= 10)
     {
       mask += "0";
@@ -303,7 +324,7 @@ public class SeqCanvas
 
     if (av.scaleRightWrapped)
     {
-        LABEL_EAST = fm.stringWidth(getMask()+"0");
+        LABEL_EAST = fm.stringWidth(getMask());
     }
 
     int LABEL_WEST = 0;
@@ -359,16 +380,21 @@ public class SeqCanvas
         }
 
 
-        drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
+        if(g.getClip()==null)
+          g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+
+        drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+         g.setClip(null);
+
 
         if(av.showAnnotation)
         {
-          g.translate(0, cHeight + ypos);
+          g.translate(0, cHeight + ypos+4);
           if(annotations==null)
             annotations = new AnnotationPanel(av);
 
           annotations.drawComponent( g, startRes, endx + 1);
-          g.translate(0, -cHeight - ypos);
+          g.translate(0, -cHeight - ypos-4);
         }
         g.translate(-LABEL_WEST, 0);
 
@@ -398,8 +424,7 @@ public class SeqCanvas
     return annotations.adjustPanelHeight();
     }
 
-  synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2,
-                                     int startx, int starty, int offset)
+  synchronized public void drawPanel(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset)
   {
 
     g.setFont(av.getFont());
@@ -408,24 +433,37 @@ public class SeqCanvas
     SequenceI nextSeq;
     /// First draw the sequences
   /////////////////////////////
-  for (int i = y1; i < y2; i++)
+  for (int i = startSeq; i < endSeq; i++)
   {
     nextSeq = av.alignment.getSequenceAt(i);
 
-    sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
-                    (x1 - startx) * av.charWidth,
+    sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), startRes, endRes,
+                    (startRes - startRes) * av.charWidth,
                     offset +
-                    (i - starty) * av.charHeight,
+                    (i - startSeq) * av.charHeight,
                     av.charWidth, av.charHeight);
 
     if (av.showSequenceFeatures)
     {
-      fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
-                      (x1 - startx) * av.charWidth,
-                      offset +
-                      (i - starty) * av.charHeight,
+      fr.drawSequence(g, nextSeq, startRes, endRes,
+                      offset +(i - startSeq) * av.charHeight,
                       av.charWidth, av.charHeight);
     }
+    /// Highlight search Results once all sequences have been drawn
+   //////////////////////////////////////////////////////////
+   if (searchResults != null)
+   {
+     int[] visibleResults = searchResults.getResults(nextSeq, startRes, endRes);
+     if (visibleResults != null)
+       for (int r = 0; r < visibleResults.length; r += 2)
+       {
+         sr.drawHighlightedText(nextSeq, visibleResults[r],
+                                visibleResults[r + 1],
+                                (visibleResults[r] - startRes) * av.charWidth,
+                                offset + ( (i - startSeq) * av.charHeight),
+                                av.charWidth, av.charHeight);
+       }
+   }
   }
 
     /////////////////////////////////////
@@ -442,7 +480,7 @@ public class SeqCanvas
       group = (SequenceGroup) groups.elementAt(0);
       groupIndex = 0;
     }
-    if (group != null && !isOverview)
+    if (group != null)
     {
         do
         {
@@ -452,10 +490,10 @@ public class SeqCanvas
             int top = -1;
             int bottom = -1;
 
-            for (i = y1; i < y2; i++)
+            for (i = startSeq; i < endSeq; i++)
             {
-                sx = (group.getStartRes() - startx) * av.charWidth;
-                sy = offset + ((i - starty) * av.charHeight);
+                sx = (group.getStartRes() - startRes) * av.charWidth;
+                sy = offset + ((i - startSeq) * av.charHeight);
                 ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
                     1;
 
@@ -464,14 +502,16 @@ public class SeqCanvas
                   continue;
                 }
 
-                if ( (sx <= (x2-x1)*av.charWidth) &&
+                if ( (sx <= (endRes-startRes)*av.charWidth) &&
                         group.sequences.contains(av.alignment.getSequenceAt(
                                 i)))
                 {
-                    if ((bottom == -1) &&
-                            !group.sequences.contains(
-                                av.alignment.getSequenceAt(i + 1)))
-                    {
+
+                    if (bottom == -1)
+                   {
+                     if(i == endSeq-1 || // Dont check for i+1 if on the bottom row
+                      !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))
+
                         bottom = sy + av.charHeight;
                     }
 
@@ -517,8 +557,8 @@ public class SeqCanvas
                     if (sx + ex > imgWidth)
                       ex = imgWidth;
 
-                    else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                      ex = (x2 - x1 + 1) * av.charWidth;
+                    else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                      ex = (endRes - startRes + 1) * av.charWidth;
 
                     if (top != -1)
                     {
@@ -539,7 +579,7 @@ public class SeqCanvas
 
             if (inGroup)
             {
-              sy = offset + ( (i - starty) * av.charHeight);
+              sy = offset + ( (i - startSeq) * av.charHeight);
               if (sx >= 0 && sx < imgWidth)
                 g.drawLine(sx, oldY, sx, sy);
 
@@ -554,8 +594,8 @@ public class SeqCanvas
 
               if (sx + ex > imgWidth)
                 ex = imgWidth;
-              else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                ex = (x2 - x1 + 1) * av.charWidth;
+              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                ex = (endRes - startRes + 1) * av.charWidth;
 
               if (top != -1)
               {
@@ -583,58 +623,10 @@ public class SeqCanvas
         }
         while (groupIndex < groups.size());
     }
-
-    /// Highlight search Results once all sequences have been drawn
-    //////////////////////////////////////////////////////////
-    if (displaySearch)
-    {
-      for (int r = 0; r < searchResults.length; r += 3)
-      {
-        int searchSeq = searchResults[r];
-
-        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(seq,
-                                  searchStart,
-                                  searchEnd,
-                                  (searchStart - startx) * av.charWidth,
-                                  offset +
-                                  (searchSeq-starty)*av.charHeight,
-                                  av.charWidth,
-                                  av.charHeight);
-        }
-      }
-    }
-
   }
 
-  public void highlightSearchResults(int[] results)
+  public void highlightSearchResults(SearchResults results)
   {
-    // results are in the order sequence, startRes, endRes
-    if (results == null)
-    {
-      displaySearch = false;
-    }
-    else
-    {
-      displaySearch = true;
-    }
-
     searchResults = results;
 
     repaint();