X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=fe8122aece254fe8f63c8b908d4de66b8aefc5d3;hb=92c8f4e119ed0b5b362ee9538ef65781dbf50136;hp=438d7ad7d69019f61de55860eac831b77c1198cf;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 438d7ad..fe8122a 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
@@ -36,7 +35,6 @@ public class SeqCanvas
 
   AlignViewport av;
 
-  boolean showScores = false;
   boolean displaySearch = false;
   int[] searchResults = null;
 
@@ -45,15 +43,37 @@ public class SeqCanvas
 
   boolean fastPaint = false;
 
+
   public SeqCanvas(AlignViewport av)
   {
     this.av = av;
     fr = new FeatureRenderer(av);
     sr = new SequenceRenderer(av);
-    PaintRefresher.Register(this);
+    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;
@@ -97,7 +117,7 @@ public class SeqCanvas
       }
       if (value != -1)
       {
-        int x = LABEL_WEST - fm.stringWidth(value + "");
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
         g.drawString(value + "", x,
                      ypos + i * av.charHeight - av.charHeight / 5);
       }
@@ -126,7 +146,7 @@ public class SeqCanvas
       }
       if (value != -1)
       {
-        g.drawString(value + "", 0,
+        g.drawString(value + "", av.charWidth/2,
                      ypos + i * av.charHeight - av.charHeight / 5);
       }
     }
@@ -135,13 +155,17 @@ public class SeqCanvas
 
   public void fastPaint(int horizontal, int vertical)
   {
-    if (horizontal == 0 && vertical == 0 || gg == null)
+    if (gg == null)
     {
       return;
     }
 
-    gg.copyArea(0, 0, imgWidth, imgHeight, -horizontal * av.charWidth,
-                -vertical * av.charHeight);
+    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;
@@ -205,6 +229,8 @@ public class SeqCanvas
 
   public void paint(Graphics g)
   {
+    sr.renderGaps(av.renderGaps);
+
     if (fastPaint)
     {
       g.drawImage(img, 0, 0, this);
@@ -235,15 +261,10 @@ 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
     {
@@ -253,29 +274,48 @@ public class SeqCanvas
 
     g.drawImage(img, 0, 0, this);
 
+    if (pdbCanvas != null)
+    {
+      pdbCanvas.updateSeqColours();
+    }
   }
 
   int LABEL_WEST, LABEL_EAST;
   public int getWrappedCanvasWidth(int cwidth)
   {
-    FontMetrics fm = getFontMetrics(av.getFont());
+      FontMetrics fm = getFontMetrics(av.getFont());
 
-    LABEL_EAST = 0;
-    LABEL_WEST = 0;
+      LABEL_EAST = 0;
+      LABEL_WEST = 0;
 
-    if (av.scaleRightWrapped)
-    {
-      LABEL_EAST = fm.stringWidth(av.alignment.getWidth() + "000");
-    }
+      if (av.scaleRightWrapped)
+      {
+          LABEL_EAST = fm.stringWidth(getMask());
+      }
 
-    if (av.scaleLeftWrapped)
-    {
-      LABEL_WEST = fm.stringWidth(av.alignment.getWidth() + "");
-    }
+      if (av.scaleLeftWrapped)
+      {
+          LABEL_WEST = fm.stringWidth(getMask());
+      }
 
-    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+      return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
   }
 
+
+  /**
+   * Generates a string of zeroes.
+   * @return String
+   */
+  String getMask()
+  {
+    String mask = "00";
+    for (int i = av.alignment.getWidth(); i > 0; i /= 10)
+    {
+      mask += "0";
+    }
+    return mask;
+    }
+
   public void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight,
                                int startRes)
   {
@@ -284,78 +324,109 @@ public class SeqCanvas
     FontMetrics fm = getFontMetrics(av.getFont());
 
     int LABEL_EAST = 0;
+
     if (av.scaleRightWrapped)
     {
-      LABEL_EAST = fm.stringWidth(al.getWidth() + "000");
+        LABEL_EAST = fm.stringWidth(getMask());
     }
+
     int LABEL_WEST = 0;
+
     if (av.scaleLeftWrapped)
     {
-      LABEL_WEST = fm.stringWidth(al.getWidth() + "0");
+        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 + av.charWidth, 0);
-        drawEastScale(g, startRes, endx, ypos);
-        g.translate( - (canvasWidth - LABEL_EAST + av.charWidth), 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);
 
-      // 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.scaleAboveWrapped)
+        {
+            drawNorthScale(g, startRes, endx, ypos);
+        }
 
-      drawPanel(g, startRes, endx, 0, al.getHeight(), startRes, 0, ypos);
-      g.setClip(clip);
-      g.translate( -LABEL_WEST, 0);
 
-      ypos += cHeight;
-      startRes += cWidth;
-      endx = startRes + cWidth - 1;
+        if (av.vconsensus!=null && av.alignment.getWidth() >= av.vconsensus.size())
+        {
+          endx = av.vconsensus.size() - 2;
+        }
 
-      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(), startRes, 0, 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();
+        }
+        }
 
   }
 
+  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 x1, int x2, int y1, int y2,
                                      int startx, int starty, int offset)
   {
@@ -364,29 +435,28 @@ public class SeqCanvas
     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 = y1; i < y2; 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), x1, x2,
+    if (av.showSequenceFeatures)
+    {
+      fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
                       (x1 - startx) * av.charWidth,
                       offset +
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
+                      (i - starty) * av.charHeight,
                       av.charWidth, av.charHeight);
-
-      if (av.showSequenceFeatures)
-      {
-        fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
-                        (x1 - startx) * av.charWidth,
-                        offset +
-                        AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                        av.charWidth, av.charHeight);
-      }
     }
-    //
+  }
+
     /////////////////////////////////////
 
     // Now outline any areas if necessary
@@ -401,104 +471,148 @@ public class SeqCanvas
       group = (SequenceGroup) groups.elementAt(0);
       groupIndex = 0;
     }
-
     if (group != null)
     {
-      do
-      {
-        int oldY = -1;
-        int i = 0;
-        boolean inGroup = false;
-        int top = -1, bottom = -1;
-        for (i = y1; i < y2; i++)
+        do
         {
-          sx = (group.getStartRes() - startx) * av.charWidth;
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, 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)))
-          {
-            if (bottom == -1 && (i == av.alignment.getHeight() - 1 ||
-                                 !group.sequences.contains(av.alignment.
-                getSequenceAt(i + 1))))
+            for (i = y1; i < y2; i++)
             {
-              bottom = sy + av.charHeight;
+                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;
+                }
+
+                if ( (sx <= (x2-x1)*av.charWidth) &&
+                        group.sequences.contains(av.alignment.getSequenceAt(
+                                i)))
+                {
+
+                    if (bottom == -1)
+                   {
+                     if(i == y2-1 || // 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)
+                  {
+                    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;
+                    }
+                }
             }
 
-            if (!inGroup)
+            if (inGroup)
             {
-              if (top == -1 && i == 0 ||
-                  !group.sequences.contains(av.alignment.getSequenceAt(i - 1)))
-              {
-                top = sy;
-              }
+              sy = offset + ( (i - starty) * av.charHeight);
+              if (sx >= 0 && sx < imgWidth)
+                g.drawLine(sx, oldY, sx, sy);
 
-              oldY = sy;
-              inGroup = true;
-              if (group == av.getSelectionGroup())
-              {
-                g.setColor(new Color(255, 0, 0));
-              }
-              else
+              if (sx + ex < imgWidth)
+                g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+              if (sx < 0)
               {
-                g.setColor(group.getOutlineColour());
+                ex += sx;
+                sx = 0;
               }
-            }
-          }
-          else
-          {
-            if (inGroup)
-            {
-              g.drawLine(sx, oldY, sx, sy);
-              g.drawLine(sx + ex, oldY, sx + ex, sy);
+
+              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);
+                g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
                 bottom = -1;
               }
 
-              inGroup = false;
+                inGroup = false;
             }
-          }
-        }
 
-        if (inGroup)
-        {
+            groupIndex++;
 
-          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;
+            if (groupIndex >= groups.size())
+            {
+                break;
+            }
 
-          }
-          sy = offset + AlignmentUtil.getPixelHeight(starty, i, 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);
         }
-
-        group = (SequenceGroup) groups.elementAt(groupIndex);
-
-      }
-      while (groupIndex < groups.size());
+        while (groupIndex < groups.size());
     }
 
     /// Highlight search Results once all sequences have been drawn
@@ -531,9 +645,7 @@ public class SeqCanvas
                                   searchEnd,
                                   (searchStart - startx) * av.charWidth,
                                   offset +
-                                  AlignmentUtil.getPixelHeight(starty,
-              searchSeq,
-              av.charHeight),
+                                  (searchSeq-starty)*av.charHeight,
                                   av.charWidth,
                                   av.charHeight);
         }