X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=c5b4324561f3394bde31feaf82f86cde12b6cbdf;hb=3b5ad2b93c9765e2f381ef66dc755184657d7d71;hp=3202fc44e803b1a56999cbabd7d2b827e0b71edf;hpb=019042a9f87d94260b3060cdf45ab93ca714a46d;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 3202fc4..c5b4324 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -21,7 +21,6 @@ package jalview.appletgui;
 
 import java.awt.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 
 public class SeqCanvas
@@ -36,23 +35,45 @@ public class SeqCanvas
 
   AlignViewport av;
 
-  boolean displaySearch = false;
-  int[] searchResults = null;
-
-  int chunkHeight;
-  int chunkWidth;
+  SearchResults searchResults = null;
 
   boolean fastPaint = false;
 
+
+  int cursorX = 0;
+  int cursorY = 0;
+
+
   public SeqCanvas(AlignViewport av)
   {
     this.av = av;
     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;
@@ -120,7 +141,7 @@ public class SeqCanvas
           continue;
         }
 
-        value = av.alignment.getSequenceAt(i).findPosition(index);
+        value = seq.findPosition(index);
         break;
       }
       if (value != -1)
@@ -132,18 +153,38 @@ public class SeqCanvas
 
   }
 
-  public void fastPaint(int horizontal, int vertical)
+  int lastsr=0;
+  void fastPaint(int horizontal, int vertical)
   {
-    if (horizontal == 0 && vertical == 0 || gg == null)
+    if ( fastPaint || gg == null)
     {
       return;
     }
 
-    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
+
+    // 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 - horizontal * av.charWidth,
+                imgHeight - vertical * av.charHeight,
+                -horizontal * av.charWidth,
                 -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;
@@ -177,12 +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();
 
   }
@@ -204,6 +242,7 @@ public class SeqCanvas
 
   public void paint(Graphics g)
   {
+
     if (fastPaint)
     {
       g.drawImage(img, 0, 0, this);
@@ -234,24 +273,22 @@ public class SeqCanvas
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
-    chunkWidth = getWrappedCanvasWidth(getSize().width);
-    chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
-
-    av.setChunkHeight(chunkHeight);
-    av.setChunkWidth(chunkWidth);
 
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, getSize().width, getSize().height, av.startRes);
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
     }
     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;
@@ -264,7 +301,7 @@ public class SeqCanvas
 
       if (av.scaleRightWrapped)
       {
-          LABEL_EAST = fm.stringWidth(getMask()+"0");
+          LABEL_EAST = fm.stringWidth(getMask());
       }
 
       if (av.scaleLeftWrapped)
@@ -282,7 +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";
@@ -297,9 +334,11 @@ public class SeqCanvas
 
     FontMetrics fm = getFontMetrics(av.getFont());
 
+    int LABEL_EAST = 0;
+
     if (av.scaleRightWrapped)
     {
-        LABEL_EAST = fm.stringWidth(getMask()+"0");
+        LABEL_EAST = fm.stringWidth(getMask());
     }
 
     int LABEL_WEST = 0;
@@ -309,264 +348,299 @@ public class SeqCanvas
         LABEL_WEST = fm.stringWidth(getMask());
     }
 
+    int hgap = av.charHeight;
+    if(av.scaleAboveWrapped)
+      hgap += av.charHeight;
+
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
-    int cHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+    int cHeight = av.getAlignment().getHeight() * av.charHeight;
+
+    av.setWrappedWidth(cWidth);
 
     av.endRes = av.startRes + cWidth;
 
-    int endx = startRes + cWidth - 1;
-    int ypos = 2 * av.charHeight;
 
-    while (ypos <= canvasHeight && startRes < av.alignment.getWidth())
+    int endx;
+    int ypos = hgap;
+
+
+    while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
     {
-      g.setColor(Color.black);
+      endx = startRes + cWidth -1;
 
-      if (av.scaleLeftWrapped)
+      if (endx > al.getWidth())
       {
-        drawWestScale(g, startRes, endx, ypos);
+        endx = al.getWidth();
       }
 
-      if (av.scaleRightWrapped)
-      {
-        g.translate(canvasWidth - LABEL_EAST, 0);
-        drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST), 0);
-      }
+        g.setColor(Color.black);
 
-      g.translate(LABEL_WEST, 0);
-      if (av.scaleAboveWrapped)
-      {
-        drawNorthScale(g, startRes, endx, ypos);
-      }
+        if (av.scaleLeftWrapped)
+        {
+            drawWestScale(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().y,
-                  cWidth * av.charWidth,
-                  (int) clip.getBounds().height
-            );
-      }
+        if (av.scaleRightWrapped)
+        {
+            g.translate(canvasWidth - LABEL_EAST, 0);
+            drawEastScale(g, startRes, endx, ypos);
+            g.translate(-(canvasWidth - LABEL_EAST), 0);
+        }
 
-      drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
-      g.setClip(clip);
-      g.translate( -LABEL_WEST, 0);
+        g.translate(LABEL_WEST, 0);
 
-      ypos += cHeight;
-      startRes += cWidth;
-      endx = startRes + cWidth - 1;
+        if (av.scaleAboveWrapped)
+        {
+            drawNorthScale(g, startRes, endx, 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 (endx > al.getWidth())
-      {
-        endx = al.getWidth();
-      }
-    }
+
+        if(av.showAnnotation)
+        {
+          g.translate(0, cHeight + ypos+4);
+          if(annotations==null)
+            annotations = new AnnotationPanel(av);
+
+          annotations.drawComponent( g, startRes, endx+1 );
+          g.translate(0, -cHeight - ypos-4);
+        }
+        g.translate(-LABEL_WEST, 0);
+
+        ypos += cHeight+getAnnotationHeight()+hgap;
+
+
+        startRes += cWidth;
+        }
 
   }
 
-  synchronized public void drawPanel(Graphics g, int x1, int x2, int y1, int y2,
-                                     int startx, int starty, int offset)
+  AnnotationPanel annotations;
+  int getAnnotationHeight()
+  {
+    if(!av.showAnnotation)
+      return 0;
+
+    if(annotations==null)
+      annotations = new AnnotationPanel(av);
+
+    return annotations.adjustPanelHeight();
+    }
+
+  void drawPanel(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset)
   {
 
     g.setFont(av.getFont());
     sr.renderGaps(av.renderGaps);
 
     SequenceI nextSeq;
-
     /// First draw the sequences
-    /////////////////////////////
-    for (int i = y1; i < y2; i++)
-    {
-      nextSeq = av.alignment.getSequenceAt(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,
-                        av.charWidth, av.charHeight);
-      }
+    if (av.showSequenceFeatures)
+    {
+      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();
-    java.util.Vector groups = av.alignment.getGroups();
+  }
 
-    int sx = -1, sy = -1, ex = -1;
-    int groupIndex = -1;
-    if (group == null && groups.size() > 0)
-    {
-      group = (SequenceGroup) groups.elementAt(0);
+  //
+  /////////////////////////////////////
+  // Now outline any areas if necessary
+  /////////////////////////////////////
+  SequenceGroup group = av.getSelectionGroup();
+
+  int sx = -1;
+  int sy = -1;
+  int ex = -1;
+  int groupIndex = -1;
+
+  if ((group == null) && (av.alignment.getGroups().size() > 0))
+  {
+      group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
       groupIndex = 0;
-    }
+  }
 
-    if (group != null)
-    {
+  if ( group != null)
+  {
       do
       {
-        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 + (i-starty)*av.charHeight;
-          ex = (group.getEndRes() + 1 - group.getStartRes()) * av.charWidth - 1;
+          int oldY = -1;
+          int i = 0;
+          boolean inGroup = false;
+          int top = -1;
+          int bottom = -1;
 
-          if (sx < getSize().width
-              && ex > 0
-              && group.sequences.contains(av.alignment.getSequenceAt(i)))
+          for (i = startSeq; i < endSeq; i++)
           {
-            if (bottom == -1 && (i == av.alignment.getHeight() - 1 ||
-                                 !group.sequences.contains(av.alignment.
-                getSequenceAt(i + 1))))
-            {
-              bottom = sy + av.charHeight;
-            }
+              sx = (group.getStartRes() - startRes) * av.charWidth;
+              sy = offset + ((i - startSeq) * av.charHeight);
+              ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) -
+                  1;
 
-            if (!inGroup)
-            {
-              if (top == -1 && i == 0 ||
-                  !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
+              if(sx+ex<0 || sx>imgWidth)
               {
-                top = sy;
+                continue;
               }
 
-              oldY = sy;
-              inGroup = true;
-              if (group == av.getSelectionGroup())
+              if ( (sx <= (endRes-startRes)*av.charWidth) &&
+                      group.sequences.contains(av.alignment.getSequenceAt(
+                              i)))
               {
-                g.setColor(new Color(255, 0, 0));
+                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;
+                }
+
+                  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
               {
-                g.setColor(group.getOutlineColour());
+                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)
+                  {
+                    ex += sx;
+                    sx = 0;
+                  }
+
+                  if (sx + ex > imgWidth)
+                    ex = imgWidth;
+
+                  else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                    ex = (endRes - startRes + 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;
+                  }
               }
-            }
           }
-          else
+
+          if (inGroup)
           {
-            if (inGroup)
-            {
+            sy = offset + ( (i - startSeq) * av.charHeight);
+            if (sx >= 0 && sx < imgWidth)
               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;
-              }
+            if (sx + ex < imgWidth)
+              g.drawLine(sx + ex, oldY, sx + ex, sy);
 
-              inGroup = false;
+            if (sx < 0)
+            {
+              ex += sx;
+              sx = 0;
             }
-          }
-        }
-
-        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 + (i-starty)*av.charHeight;
-          g.drawLine(sx, oldY, sx, sy);
-          g.drawLine(sx + ex, oldY, sx + ex, sy);
-          inGroup = false;
-        }
-        groupIndex++;
-        if (groupIndex >= groups.size())
-        {
-          break;
-        }
-
-        group = (SequenceGroup) groups.elementAt(groupIndex);
+            if (sx + ex > imgWidth)
+              ex = imgWidth;
+            else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+              ex = (endRes - startRes + 1) * av.charWidth;
 
-      }
-      while (groupIndex < groups.size());
-    }
+            if (top != -1)
+            {
+              g.drawLine(sx, top, sx + ex, top);
+              top = -1;
+            }
 
-    /// 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();