X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=c5b4324561f3394bde31feaf82f86cde12b6cbdf;hb=3b5ad2b93c9765e2f381ef66dc755184657d7d71;hp=46ddf37833140146f3422f444b53e5a43f3245ba;hpb=ee53965807b83bf93a21cbc341cee9a9e005b2cb;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 46ddf37..c5b4324 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -35,15 +35,14 @@ public class SeqCanvas
 
   AlignViewport av;
 
-  boolean displaySearch = false;
-  int[] searchResults = null;
-
-  int chunkHeight;
-  int chunkWidth;
+  SearchResults searchResults = null;
 
   boolean fastPaint = false;
 
-  boolean isOverview = false;
+
+  int cursorX = 0;
+  int cursorY = 0;
+
 
   public SeqCanvas(AlignViewport av)
   {
@@ -51,9 +50,30 @@ 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;
@@ -121,7 +141,7 @@ public class SeqCanvas
           continue;
         }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+        value = seq.findPosition(index);
         break;
       }
       if (value != -1)
@@ -133,22 +153,38 @@ public class SeqCanvas
 
   }
 
-  public void fastPaint(int horizontal, int vertical)
+  int lastsr=0;
+  void fastPaint(int horizontal, int vertical)
   {
-    if (gg == null)
+    if ( fastPaint || gg == null)
     {
       return;
     }
 
+
+    // Its possible on certain browsers that the call to fastpaint
+    // is faster than it can paint, so this check here catches
+    // this possibility
+    if(lastsr + horizontal != av.startRes)
+    {
+      horizontal = av.startRes - lastsr;
+    }
+
+    lastsr = av.startRes;
+
+    fastPaint = true;
     gg.copyArea(horizontal * av.charWidth,
                 vertical * av.charHeight,
-                imgWidth,
-                imgHeight,
+                imgWidth - horizontal * av.charWidth,
+                imgHeight - vertical * av.charHeight,
                 -horizontal * av.charWidth,
-                    -vertical * av.charHeight);
+                -vertical * av.charHeight);
+
+
 
     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 +218,9 @@ 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 +242,6 @@ public class SeqCanvas
 
   public void paint(Graphics g)
   {
-    sr.renderGaps(av.renderGaps);
 
     if (fastPaint)
     {
@@ -248,12 +280,15 @@ 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 +301,7 @@ public class SeqCanvas
 
       if (av.scaleRightWrapped)
       {
-          LABEL_EAST = fm.stringWidth(getMask()+"0");
+          LABEL_EAST = fm.stringWidth(getMask());
       }
 
       if (av.scaleLeftWrapped)
@@ -284,7 +319,7 @@ 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 +338,7 @@ public class SeqCanvas
 
     if (av.scaleRightWrapped)
     {
-        LABEL_EAST = fm.stringWidth(getMask()+"0");
+        LABEL_EAST = fm.stringWidth(getMask());
     }
 
     int LABEL_WEST = 0;
@@ -325,12 +360,19 @@ public class SeqCanvas
     av.endRes = av.startRes + cWidth;
 
 
-    int endx = (startRes + cWidth) - 1;
+    int endx;
     int ypos = hgap;
 
 
     while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
     {
+      endx = startRes + cWidth -1;
+
+      if (endx > al.getWidth())
+      {
+        endx = al.getWidth();
+      }
+
         g.setColor(Color.black);
 
         if (av.scaleLeftWrapped)
@@ -352,23 +394,21 @@ public class SeqCanvas
             drawNorthScale(g, startRes, endx, ypos);
         }
 
+        if(g.getClip()==null)
+          g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
 
-        if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
-        {
-          endx = av.vconsensus.size() - 2;
-        }
-
+        drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+         g.setClip(null);
 
-        drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
 
         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);
+          annotations.drawComponent( g, startRes, endx+1 );
+          g.translate(0, -cHeight - ypos-4);
         }
         g.translate(-LABEL_WEST, 0);
 
@@ -376,12 +416,6 @@ public class SeqCanvas
 
 
         startRes += cWidth;
-        endx = (startRes + cWidth) - 1;
-
-        if (endx > al.getWidth())
-        {
-            endx = al.getWidth();
-        }
         }
 
   }
@@ -398,8 +432,7 @@ 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)
+  void drawPanel(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset)
   {
 
     g.setFont(av.getFont());
@@ -408,233 +441,206 @@ 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,
-                    offset +
-                    (i - starty) * av.charHeight,
-                    av.charWidth, av.charHeight);
+    sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), startRes, endRes,
+                    offset + ( (i - startSeq) * 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);
+       }
+   }
+
+   if (av.cursorMode && cursorY == i
+       && cursorX >= startRes && cursorX <= endRes)
+   {
+     sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * av.charWidth,
+                   offset + ( (i - startSeq) * av.charHeight));
+   }
+
   }
 
-    /////////////////////////////////////
+  //
+  /////////////////////////////////////
+  // Now outline any areas if necessary
+  /////////////////////////////////////
+  SequenceGroup group = av.getSelectionGroup();
 
-    // Now outline any areas if necessary
-    /////////////////////////////////////
-    SequenceGroup group = av.getSelectionGroup();
-    java.util.Vector groups = av.alignment.getGroups();
+  int sx = -1;
+  int sy = -1;
+  int ex = -1;
+  int groupIndex = -1;
 
-    int sx = -1, sy = -1, ex = -1;
-    int groupIndex = -1;
-    if (group == null && groups.size() > 0)
-    {
-      group = (SequenceGroup) groups.elementAt(0);
+  if ((group == null) && (av.alignment.getGroups().size() > 0))
+  {
+      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
       groupIndex = 0;
-    }
-    if (group != null && !isOverview)
-    {
-        do
-        {
-            int oldY = -1;
-            int i = 0;
-            boolean inGroup = false;
-            int top = -1;
-            int bottom = -1;
+  }
 
-            for (i = y1; i < y2; i++)
-            {
-                sx = (group.getStartRes() - startx) * av.charWidth;
-                sy = offset + ((i - starty) * av.charHeight);
-                ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
-                    1;
+  if ( group != null)
+  {
+      do
+      {
+          int oldY = -1;
+          int i = 0;
+          boolean inGroup = false;
+          int top = -1;
+          int bottom = -1;
 
-                if(sx+ex<0 || sx>imgWidth)
-                {
-                  continue;
-                }
+          for (i = startSeq; i < endSeq; i++)
+          {
+              sx = (group.getStartRes() - startRes) * av.charWidth;
+              sy = offset + ((i - startSeq) * av.charHeight);
+              ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
+                  1;
+
+              if(sx+ex<0 || sx>imgWidth)
+              {
+                continue;
+              }
 
-                if ( (sx <= (x2-x1)*av.charWidth) &&
-                        group.sequences.contains(av.alignment.getSequenceAt(
-                                i)))
+              if ( (sx <= (endRes-startRes)*av.charWidth) &&
+                      group.sequences.contains(av.alignment.getSequenceAt(
+                              i)))
+              {
+                if (bottom == -1)
                 {
-                    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);
-                        }
-                        else
-                        {
-                            g.setColor(group.getOutlineColour());
-                        }
-                    }
+                 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;
                 }
-                else
+
+                  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);
+                      }
+                      else
+                      {
+                          g.setColor(group.getOutlineColour());
+                      }
+                  }
+              }
+              else
+              {
+                if (inGroup)
                 {
-                  if (inGroup)
+                  if (sx >= 0 && sx < imgWidth)
+                    g.drawLine(sx, oldY, sx, sy);
+
+                  if (sx + ex < imgWidth)
+                    g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+                  if (sx < 0)
                   {
-                    if (sx >= 0 && sx < imgWidth)
-                      g.drawLine(sx, oldY, sx, sy);
-
-                    if (sx + ex < imgWidth)
-                      g.drawLine(sx + ex, oldY, sx + ex, sy);
-
-                    if (sx < 0)
-                    {
-                      ex += sx;
-                      sx = 0;
-                    }
-
-                    if (sx + ex > imgWidth)
-                      ex = imgWidth;
-
-                    else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                      ex = (x2 - x1 + 1) * av.charWidth;
-
-                    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;
-                    }
-                }
-            }
+                    ex += sx;
+                    sx = 0;
+                  }
 
-            if (inGroup)
-            {
-              sy = offset + ( (i - starty) * av.charHeight);
-              if (sx >= 0 && sx < imgWidth)
-                g.drawLine(sx, oldY, sx, sy);
+                  if (sx + ex > imgWidth)
+                    ex = imgWidth;
 
-              if (sx + ex < imgWidth)
-                g.drawLine(sx + ex, oldY, sx + ex, sy);
+                  else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                    ex = (endRes - startRes + 1) * av.charWidth;
 
-              if (sx < 0)
-              {
-                ex += sx;
-                sx = 0;
-              }
+                  if (top != -1)
+                  {
+                    g.drawLine(sx, top, sx + ex, top);
+                    top = -1;
+                  }
 
-              if (sx + ex > imgWidth)
-                ex = imgWidth;
-              else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                ex = (x2 - x1 + 1) * av.charWidth;
+                  if (bottom != -1)
+                  {
+                    g.drawLine(sx, bottom, sx + ex, bottom);
+                    bottom = -1;
+                  }
 
-              if (top != -1)
-              {
-                g.drawLine(sx, top, sx + ex, top);
-                top = -1;
+                  inGroup = false;
+                  }
               }
+          }
 
-              if (bottom != -1)
-              {
-                g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
-                bottom = -1;
-              }
+          if (inGroup)
+          {
+            sy = offset + ( (i - startSeq) * av.charHeight);
+            if (sx >= 0 && sx < imgWidth)
+              g.drawLine(sx, oldY, sx, sy);
+
+            if (sx + ex < imgWidth)
+              g.drawLine(sx + ex, oldY, sx + ex, sy);
 
-                inGroup = false;
+            if (sx < 0)
+            {
+              ex += sx;
+              sx = 0;
             }
 
-            groupIndex++;
+            if (sx + ex > imgWidth)
+              ex = imgWidth;
+            else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+              ex = (endRes - startRes + 1) * av.charWidth;
 
-            if (groupIndex >= groups.size())
+            if (top != -1)
             {
-                break;
+              g.drawLine(sx, top, sx + ex, top);
+              top = -1;
             }
 
-            group = (SequenceGroup) groups.elementAt(groupIndex);
-        }
-        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 (bottom != -1)
+            {
+              g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+              bottom = -1;
+            }
 
-        if (searchSeq >= y1 && searchSeq < y2)
-        {
-          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
+              inGroup = false;
+          }
 
-          int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
-          int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
+          groupIndex++;
 
-          SequenceRenderer ssr = (SequenceRenderer) sr;
-          if (searchStart < x1)
-          {
-            searchStart = x1;
-          }
-          if (searchEnd > x2)
+          if (groupIndex >= av.alignment.getGroups().size())
           {
-            searchEnd = x2;
+              break;
           }
 
-          ssr.drawHighlightedText(seq,
-                                  searchStart,
-                                  searchEnd,
-                                  (searchStart - startx) * av.charWidth,
-                                  offset +
-                                  (searchSeq-starty)*av.charHeight,
-                                  av.charWidth,
-                                  av.charHeight);
-        }
+          group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
       }
+      while (groupIndex < av.alignment.getGroups().size());
     }
-
   }
 
-  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();