X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=ac5ff899b871c443fe80a41691f4cbb77fe86b50;hb=42ae188a9819c341cd345baeab442cd0606ff157;hp=fd8330977705d18b7b81a13e6639bdb5c23941c2;hpb=8878681ec11f85c050248236a96ffbcaf2f0497b;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index fd83309..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;
@@ -135,16 +154,23 @@ public class SeqCanvas
 
   public void fastPaint(int horizontal, int vertical)
   {
-    if (gg == null)
+    if (fastPaint || gg == null)
     {
+      repaint();
       return;
     }
 
-    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
-                -vertical * av.charHeight);
+    fastPaint = true;
+    gg.copyArea(horizontal * av.charWidth,
+                vertical * av.charHeight,
+                imgWidth,
+                imgHeight,
+                -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;
@@ -178,12 +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();
 
   }
@@ -205,7 +228,6 @@ public class SeqCanvas
 
   public void paint(Graphics g)
   {
-    sr.renderGaps(av.renderGaps);
 
     if (fastPaint)
     {
@@ -237,11 +259,6 @@ 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())
     {
@@ -249,12 +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;
@@ -267,7 +287,7 @@ public class SeqCanvas
 
       if (av.scaleRightWrapped)
       {
-          LABEL_EAST = fm.stringWidth(getMask()+"0");
+          LABEL_EAST = fm.stringWidth(getMask());
       }
 
       if (av.scaleLeftWrapped)
@@ -285,7 +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";
@@ -300,9 +320,11 @@ 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;
@@ -312,91 +334,138 @@ 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 = (startRes + cWidth) - 1;
+    int ypos = hgap;
+
+
+    while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
     {
-      g.setColor(Color.black);
+        g.setColor(Color.black);
 
-      if (av.scaleLeftWrapped)
-      {
-        drawWestScale(g, startRes, endx, ypos);
-      }
+        if (av.scaleLeftWrapped)
+        {
+            drawWestScale(g, startRes, endx, ypos);
+        }
 
-      if (av.scaleRightWrapped)
-      {
-        g.translate(canvasWidth - LABEL_EAST, 0);
-        drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST), 0);
-      }
+        if (av.scaleRightWrapped)
+        {
+            g.translate(canvasWidth - LABEL_EAST, 0);
+            drawEastScale(g, startRes, endx, ypos);
+            g.translate(-(canvasWidth - LABEL_EAST), 0);
+        }
 
-      g.translate(LABEL_WEST, 0);
-      if (av.scaleAboveWrapped)
-      {
-        drawNorthScale(g, startRes, endx, ypos);
-      }
+        g.translate(LABEL_WEST, 0);
 
+        if (av.scaleAboveWrapped)
+        {
+            drawNorthScale(g, startRes, endx, ypos);
+        }
 
-     if(g.getClip()==null)
-       g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
 
-     if (av.alignment.getWidth() >= av.vconsensus.size())
-     {
-       endx = av.vconsensus.size() - 2;
-     }
-     drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
-      g.setClip(null);
-      g.translate( -LABEL_WEST, 0);
+        if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
+        {
+          endx = av.vconsensus.size() - 2;
+        }
 
-      ypos += cHeight;
-      startRes += cWidth;
-      endx = startRes + cWidth - 1;
 
-      if (endx > al.getWidth())
-      {
-        endx = al.getWidth();
-      }
-    }
+        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+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;
+        endx = (startRes + cWidth) - 1;
+
+        if (endx > al.getWidth())
+        {
+            endx = al.getWidth();
+        }
+        }
 
   }
 
-  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();
+    }
+
+  synchronized public 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,
+                    (startRes - startRes) * av.charWidth,
+                    offset +
+                    (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,
-                        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);
+       }
+   }
+  }
+
     /////////////////////////////////////
 
     // Now outline any areas if necessary
@@ -411,199 +480,153 @@ public class SeqCanvas
       group = (SequenceGroup) groups.elementAt(0);
       groupIndex = 0;
     }
-
-    if (group != null && !isOverview)
+    if (group != null)
     {
-      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(sx+ex<0 || sx>imgWidth)
-              {
-                continue;
-              }
+        do
+        {
+            int oldY = -1;
+            int i = 0;
+            boolean inGroup = false;
+            int top = -1;
+            int bottom = -1;
 
-              if ( (sx <= (x2-x1)*av.charWidth) &&
-                      group.sequences.contains(av.alignment.getSequenceAt(
-                              i)))
-              {
-                  if ((bottom == -1) &&
-                          !group.sequences.contains(
-                              av.alignment.getSequenceAt(i + 1)))
-                  {
-                      bottom = sy + av.charHeight;
-                  }
+            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 (!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(sx+ex<0 || sx>imgWidth)
                 {
-                  if (sx >= 0 && sx < imgWidth)
-                    g.drawLine(sx, oldY, sx, sy);
+                  continue;
+                }
 
-                  if (sx + ex < imgWidth)
-                    g.drawLine(sx + ex, oldY, sx + ex, sy);
+                if ( (sx <= (endRes-startRes)*av.charWidth) &&
+                        group.sequences.contains(av.alignment.getSequenceAt(
+                                i)))
+                {
 
-                  if (sx < 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
+                {
+                  if (inGroup)
                   {
-                    ex += sx;
-                    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 >= (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;
+                    }
+                }
+            }
 
-                  if (sx + ex > imgWidth)
-                    ex = imgWidth;
+            if (inGroup)
+            {
+              sy = offset + ( (i - startSeq) * av.charHeight);
+              if (sx >= 0 && sx < imgWidth)
+                g.drawLine(sx, oldY, sx, sy);
 
-                  else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-                    ex = (x2 - x1 + 1) * av.charWidth;
+              if (sx + ex < imgWidth)
+                g.drawLine(sx + ex, oldY, sx + ex, sy);
 
-                  if (top != -1)
-                  {
-                    g.drawLine(sx, top, sx + ex, top);
-                    top = -1;
-                  }
+              if (sx < 0)
+              {
+                ex += sx;
+                sx = 0;
+              }
 
-                  if (bottom != -1)
-                  {
-                    g.drawLine(sx, bottom, sx + ex, bottom);
-                    bottom = -1;
-                  }
+              if (sx + ex > imgWidth)
+                ex = imgWidth;
+              else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+                ex = (endRes - startRes + 1) * av.charWidth;
 
-                  inGroup = false;
-                  }
+              if (top != -1)
+              {
+                g.drawLine(sx, top, sx + ex, top);
+                top = -1;
               }
-          }
-
-          if (inGroup)
-          {
-            sy = offset + ( (i - starty) * 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);
+              if (bottom != -1)
+              {
+                g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
+                bottom = -1;
+              }
 
-            if (sx < 0)
-            {
-              ex += sx;
-              sx = 0;
+                inGroup = false;
             }
 
-            if (sx + ex > imgWidth)
-              ex = imgWidth;
-            else if (sx + ex >= (x2 - x1 + 1) * av.charWidth)
-              ex = (x2 - x1 + 1) * av.charWidth;
+            groupIndex++;
 
-            if (top != -1)
+            if (groupIndex >= groups.size())
             {
-              g.drawLine(sx, top, sx + ex, top);
-              top = -1;
+                break;
             }
 
-            if (bottom != -1)
-            {
-              g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
-              bottom = -1;
-            }
-
-              inGroup = false;
-          }
-
-          groupIndex++;
-
-          if (groupIndex >= groups.size())
-          {
-              break;
-          }
-
-          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 (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);
+            group = (SequenceGroup) groups.elementAt(groupIndex);
         }
-      }
+        while (groupIndex < groups.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();