X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=1ddcaf742368b16241ca88f94f9475318c70d424;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=f6ef5779f0e3433e508c8d38b14370e3301c15e9;hpb=f7d45a21db810c5f8f7ca668d1a28f1403defe32;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index f6ef577..1ddcaf7 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,649 +1,815 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class SeqCanvas
-    extends Panel
-{
-  FeatureRenderer fr;
-  SequenceRenderer sr;
-  Image img;
-  Graphics gg;
-  int imgWidth;
-  int imgHeight;
-
-  AlignViewport av;
-
-  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;
-
-    g.setColor(Color.black);
-
-    // NORTH SCALE
-    for (int i = scalestartx; i < endx; i += 10)
-    {
-      String string = String.valueOf(i);
-      g.drawString(string, (i - startx - 1) * av.charWidth,
-                   ypos - av.charHeight / 2);
-
-      g.drawLine( (i - startx - 1) * av.charWidth + av.charWidth / 2,
-                 ypos + 2 - av.charHeight / 2,
-                 (i - startx - 1) * av.charWidth + av.charWidth / 2, ypos - 2);
-
-    }
-  }
-
-  void drawWestScale(Graphics g, int startx, int endx, int ypos)
-  {
-    FontMetrics fm = getFontMetrics(av.getFont());
-    ypos += av.charHeight;
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = startx;
-      int value = -1;
-      while (index < endx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-        {
-          index++;
-          continue;
-        }
-
-        value = av.alignment.getSequenceAt(i).findPosition(index);
-        break;
-      }
-      if (value != -1)
-      {
-        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))-av.charWidth/2;
-        g.drawString(value + "", x,
-                     ypos + i * av.charHeight - av.charHeight / 5);
-      }
-    }
-  }
-
-  void drawEastScale(Graphics g, int startx, int endx, int ypos)
-  {
-    ypos += av.charHeight;
-    // EAST SCALE
-    for (int i = 0; i < av.alignment.getHeight(); i++)
-    {
-      SequenceI seq = av.alignment.getSequenceAt(i);
-      int index = endx;
-      int value = -1;
-      while (index > startx)
-      {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
-        {
-          index--;
-          continue;
-        }
-
-        value = av.alignment.getSequenceAt(i).findPosition(index);
-        break;
-      }
-      if (value != -1)
-      {
-        g.drawString(value + "", av.charWidth/2,
-                     ypos + i * av.charHeight - av.charHeight / 5);
-      }
-    }
-
-  }
-
-  int lastsr=0;
-  void fastPaint(int horizontal, int vertical)
-  {
-    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 - 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;
-      sr = er - horizontal;
-    }
-    else if (horizontal < 0)
-    {
-      er = sr - horizontal;
-    }
-
-    else if (vertical > 0) // scroll down
-    {
-      ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
-      {
-        ss = av.startSeq;
-      }
-      else
-      {
-        transY = imgHeight - vertical * av.charHeight;
-      }
-    }
-    else if (vertical < 0)
-    {
-      es = ss - vertical;
-      if (es > av.endSeq)
-      {
-        es = av.endSeq;
-      }
-    }
-
-    gg.translate(transX, transY);
-
-    drawPanel(gg, sr, er, ss, es, 0);
-    gg.translate( -transX, -transY);
-
-    repaint();
-
-  }
-
-  /**
-   * Definitions of startx and endx (hopefully):
-   * SMJS This is what I'm working towards!
-   *   startx is the first residue (starting at 0) to display.
-   *   endx   is the last residue to display (starting at 0).
-   *   starty is the first sequence to display (starting at 0).
-   *   endy   is the last sequence to display (starting at 0).
-   * NOTE 1: The av limits are set in setFont in this class and
-   * in the adjustment listener in SeqPanel when the scrollbars move.
-   */
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-
-    if (fastPaint)
-    {
-      g.drawImage(img, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
-
-    // this draws the whole of the alignment
-    imgWidth = this.getSize().width;
-    imgHeight = this.getSize().height;
-
-    imgWidth -= imgWidth % av.charWidth;
-    imgHeight -= imgHeight % av.charHeight;
-
-    if (imgWidth < 1 || imgHeight < 1)
-    {
-      return;
-    }
-
-    if (img == null || imgWidth != img.getWidth(this) ||
-        imgHeight != img.getHeight(this))
-    {
-      img = createImage(imgWidth, imgHeight);
-      gg = img.getGraphics();
-      gg.setFont(av.getFont());
-    }
-
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, imgWidth, imgHeight);
-
-
-    if (av.getWrapAlignment())
-    {
-      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
-    }
-    else
-    {
-      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;
-  public int getWrappedCanvasWidth(int cwidth)
-  {
-      FontMetrics fm = getFontMetrics(av.getFont());
-
-      LABEL_EAST = 0;
-      LABEL_WEST = 0;
-
-      if (av.scaleRightWrapped)
-      {
-          LABEL_EAST = fm.stringWidth(getMask());
-      }
-
-      if (av.scaleLeftWrapped)
-      {
-          LABEL_WEST = fm.stringWidth(getMask());
-      }
-
-      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)
-  {
-    AlignmentI al = av.getAlignment();
-
-    FontMetrics fm = getFontMetrics(av.getFont());
-
-    int LABEL_EAST = 0;
-
-    if (av.scaleRightWrapped)
-    {
-        LABEL_EAST = fm.stringWidth(getMask());
-    }
-
-    int LABEL_WEST = 0;
-
-    if (av.scaleLeftWrapped)
-    {
-        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() * av.charHeight;
-
-    av.setWrappedWidth(cWidth);
-
-    av.endRes = av.startRes + cWidth;
-
-
-    int endx;
-    int ypos = hgap;
-
-
-    while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))
-    {
-      endx = startRes + cWidth;
-
-      if (endx > al.getWidth())
-      {
-        endx = al.getWidth();
-      }
-
-        g.setColor(Color.black);
-
-        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);
-        }
-
-        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);
-
-        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 );
-          g.translate(0, -cHeight - ypos-4);
-        }
-        g.translate(-LABEL_WEST, 0);
-
-        ypos += cHeight+getAnnotationHeight()+hgap;
-
-
-        startRes += cWidth;
-        }
-
-  }
-
-  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 = startSeq; i < endSeq; i++)
-  {
-    nextSeq = av.alignment.getSequenceAt(i);
-
-    sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), startRes, endRes,
-                    offset + ( (i - startSeq) * 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();
-
-  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)
-  {
-      do
-      {
-          int oldY = -1;
-          int i = 0;
-          boolean inGroup = false;
-          int top = -1;
-          int bottom = -1;
-
-          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 <= (endRes-startRes)*av.charWidth) &&
-                      group.sequences.contains(av.alignment.getSequenceAt(
-                              i)))
-              {
-                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)
-                {
-                  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 (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);
-
-            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 - 1, sx + ex, bottom - 1);
-              bottom = -1;
-            }
-
-              inGroup = false;
-          }
-
-          groupIndex++;
-
-          if (groupIndex >= av.alignment.getGroups().size())
-          {
-              break;
-          }
-
-          group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);
-      }
-      while (groupIndex < av.alignment.getGroups().size());
-    }
-  }
-
-  public void highlightSearchResults(SearchResults results)
-  {
-    searchResults = results;
-
-    repaint();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class SeqCanvas extends Panel
+{
+  FeatureRenderer fr;
+
+  SequenceRenderer sr;
+
+  Image img;
+
+  Graphics gg;
+
+  int imgWidth;
+
+  int imgHeight;
+
+  AlignViewport av;
+
+  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.getSequenceSetId());
+  }
+
+  public AlignViewport getViewport()
+  {
+    return av;
+  }
+
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return fr;
+  }
+
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
+  }
+
+  void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+  {
+    int scalestartx = startx - startx % 10 + 10;
+
+    g.setColor(Color.black);
+
+    // NORTH SCALE
+    for (int i = scalestartx; i < endx; i += 10)
+    {
+      int value = i;
+      if (av.hasHiddenColumns)
+      {
+        value = av.getColumnSelection().adjustForHiddenColumns(value);
+      }
+
+      g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
+              ypos - (av.charHeight / 2));
+
+      g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+              (ypos + 2) - (av.charHeight / 2),
+              ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+              ypos - 2);
+    }
+  }
+
+  void drawWestScale(Graphics g, int startx, int endx, int ypos)
+  {
+    FontMetrics fm = getFontMetrics(av.getFont());
+    ypos += av.charHeight;
+    if (av.hasHiddenColumns)
+    {
+      startx = av.getColumnSelection().adjustForHiddenColumns(startx);
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+    }
+
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    // WEST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      SequenceI seq = av.alignment.getSequenceAt(i);
+      int index = startx;
+      int value = -1;
+
+      while (index < endx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index++;
+
+          continue;
+        }
+
+        value = av.alignment.getSequenceAt(i).findPosition(index);
+
+        break;
+      }
+
+      if (value != -1)
+      {
+        int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
+                - av.charWidth / 2;
+        g.drawString(value + "", x, (ypos + (i * av.charHeight))
+                - (av.charHeight / 5));
+      }
+    }
+  }
+
+  void drawEastScale(Graphics g, int startx, int endx, int ypos)
+  {
+    ypos += av.charHeight;
+
+    if (av.hasHiddenColumns)
+    {
+      endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+    }
+
+    SequenceI seq;
+    // EAST SCALE
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      seq = av.alignment.getSequenceAt(i);
+      int index = endx;
+      int value = -1;
+
+      while (index > startx)
+      {
+        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        {
+          index--;
+
+          continue;
+        }
+
+        value = seq.findPosition(index);
+
+        break;
+      }
+
+      if (value != -1)
+      {
+        g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
+                - (av.charHeight / 5));
+      }
+    }
+  }
+
+  int lastsr = 0;
+
+  void fastPaint(int horizontal, int vertical)
+  {
+    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 - 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;
+      sr = er - horizontal;
+    }
+    else if (horizontal < 0)
+    {
+      er = sr - horizontal;
+    }
+
+    else if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
+      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      {
+        ss = av.startSeq;
+      }
+      else
+      {
+        transY = imgHeight - vertical * av.charHeight;
+      }
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
+
+    gg.translate(transX, transY);
+
+    drawPanel(gg, sr, er, ss, es, 0);
+    gg.translate(-transX, -transY);
+
+    repaint();
+
+  }
+
+  /**
+   * Definitions of startx and endx (hopefully): SMJS This is what I'm working
+   * towards! startx is the first residue (starting at 0) to display. endx is
+   * the last residue to display (starting at 0). starty is the first sequence
+   * to display (starting at 0). endy is the last sequence to display (starting
+   * at 0). NOTE 1: The av limits are set in setFont in this class and in the
+   * adjustment listener in SeqPanel when the scrollbars move.
+   */
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+
+    if (img != null
+            && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
+                    .getClipBounds().height)))
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    if (fastPaint)
+    {
+      g.drawImage(img, 0, 0, this);
+      fastPaint = false;
+      return;
+    }
+
+    // this draws the whole of the alignment
+    imgWidth = this.getSize().width;
+    imgHeight = this.getSize().height;
+
+    imgWidth -= imgWidth % av.charWidth;
+    imgHeight -= imgHeight % av.charHeight;
+
+    if (imgWidth < 1 || imgHeight < 1)
+    {
+      return;
+    }
+
+    if (img == null || imgWidth != img.getWidth(this)
+            || imgHeight != img.getHeight(this))
+    {
+      img = createImage(imgWidth, imgHeight);
+      gg = img.getGraphics();
+      gg.setFont(av.getFont());
+    }
+
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, imgWidth, imgHeight);
+
+    if (av.getWrapAlignment())
+    {
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+    }
+    else
+    {
+      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+    }
+
+    g.drawImage(img, 0, 0, this);
+
+  }
+
+  int LABEL_WEST, LABEL_EAST;
+
+  public int getWrappedCanvasWidth(int cwidth)
+  {
+    cwidth -= cwidth % av.charWidth;
+
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    LABEL_EAST = 0;
+    LABEL_WEST = 0;
+
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(getMask());
+    }
+
+    if (av.scaleLeftWrapped)
+    {
+      LABEL_WEST = fm.stringWidth(getMask());
+    }
+
+    return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+  }
+
+  /**
+   * Generates a string of zeroes.
+   * 
+   * @return String
+   */
+  String getMask()
+  {
+    String mask = "0";
+    int maxWidth = 0;
+    int tmp;
+    for (int i = 0; i < av.alignment.getHeight(); i++)
+    {
+      tmp = av.alignment.getSequenceAt(i).getEnd();
+      if (tmp > maxWidth)
+      {
+        maxWidth = tmp;
+      }
+    }
+
+    for (int i = maxWidth; i > 0; i /= 10)
+    {
+      mask += "0";
+    }
+    return mask;
+  }
+
+  public void drawWrappedPanel(Graphics g, int canvasWidth,
+          int canvasHeight, int startRes)
+  {
+    AlignmentI al = av.getAlignment();
+
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    if (av.scaleRightWrapped)
+    {
+      LABEL_EAST = fm.stringWidth(getMask());
+    }
+
+    if (av.scaleLeftWrapped)
+    {
+      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() * av.charHeight;
+
+    av.setWrappedWidth(cWidth);
+
+    av.endRes = av.startRes + cWidth;
+
+    int endx;
+    int ypos = hgap;
+
+    int maxwidth = av.alignment.getWidth() - 1;
+
+    if (av.hasHiddenColumns)
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+    }
+
+    while ((ypos <= canvasHeight) && (startRes < maxwidth))
+    {
+      endx = startRes + cWidth - 1;
+
+      if (endx > maxwidth)
+      {
+        endx = maxwidth;
+      }
+
+      g.setColor(Color.black);
+
+      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);
+      }
+
+      g.translate(LABEL_WEST, 0);
+
+      if (av.scaleAboveWrapped)
+      {
+        drawNorthScale(g, startRes, endx, ypos);
+      }
+      if (av.hasHiddenColumns && av.showHiddenMarkers)
+      {
+        g.setColor(Color.blue);
+        int res;
+        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
+                .size(); i++)
+        {
+          res = av.getColumnSelection().findHiddenRegionPosition(i)
+                  - startRes;
+
+          if (res < 0 || res > endx - startRes)
+          {
+            continue;
+          }
+
+          gg.fillPolygon(new int[]
+          { res * av.charWidth - av.charHeight / 4,
+              res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+                  new int[]
+                  { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
+                      ypos - (av.charHeight / 2) + 8 }, 3);
+
+        }
+      }
+
+      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;
+    }
+
+  }
+
+  AnnotationPanel annotations;
+
+  int getAnnotationHeight()
+  {
+    if (!av.showAnnotation)
+    {
+      return 0;
+    }
+
+    if (annotations == null)
+    {
+      annotations = new AnnotationPanel(av);
+    }
+
+    return annotations.adjustPanelHeight();
+  }
+
+  void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
+          int endSeq, int offset)
+  {
+    if (!av.hasHiddenColumns)
+    {
+      draw(g1, startRes, endRes, startSeq, endSeq, offset);
+    }
+    else
+    {
+      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+
+      int screenY = 0;
+      int blockStart = startRes;
+      int blockEnd = endRes;
+
+      for (int i = 0; i < regions.size(); i++)
+      {
+        int[] region = (int[]) regions.elementAt(i);
+        int hideStart = region[0];
+        int hideEnd = region[1];
+
+        if (hideStart <= blockStart)
+        {
+          blockStart += (hideEnd - hideStart) + 1;
+          continue;
+        }
+
+        blockEnd = hideStart - 1;
+
+        g1.translate(screenY * av.charWidth, 0);
+
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+        if (av.getShowHiddenMarkers())
+        {
+          g1.setColor(Color.blue);
+          g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
+                  0 + offset, (blockEnd - blockStart + 1) * av.charWidth
+                          - 1, (endSeq - startSeq) * av.charHeight + offset);
+        }
+
+        g1.translate(-screenY * av.charWidth, 0);
+        screenY += blockEnd - blockStart + 1;
+        blockStart = hideEnd + 1;
+      }
+
+      if (screenY <= (endRes - startRes))
+      {
+        blockEnd = blockStart + (endRes - startRes) - screenY;
+        g1.translate(screenY * av.charWidth, 0);
+        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+
+        g1.translate(-screenY * av.charWidth, 0);
+      }
+    }
+
+  }
+
+  // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
+  // int x1, int x2, int y1, int y2, int startx, int starty,
+  void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
+          int offset)
+  {
+    g.setFont(av.getFont());
+    sr.prepare(g, av.renderGaps);
+
+    SequenceI nextSeq;
+
+    // / First draw the sequences
+    // ///////////////////////////
+    for (int i = startSeq; i < endSeq; i++)
+    {
+      nextSeq = av.alignment.getSequenceAt(i);
+
+      if (nextSeq == null)
+      {
+        continue;
+      }
+
+      sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
+              startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+
+      if (av.showSequenceFeatures)
+      {
+        fr.drawSequence(g, nextSeq, startRes, endRes, offset
+                + ((i - startSeq) * 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));
+          }
+        }
+      }
+
+      if (av.cursorMode && cursorY == i && cursorX >= startRes
+              && cursorX <= endRes)
+      {
+        sr.drawCursor(nextSeq, cursorX,
+                (cursorX - startRes) * av.charWidth, offset
+                        + ((i - startSeq) * av.charHeight));
+      }
+    }
+
+    if (av.getSelectionGroup() != null
+            || av.alignment.getGroups().size() > 0)
+    {
+      drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
+    }
+
+  }
+
+  void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
+          int startSeq, int endSeq, int offset)
+  {
+    //
+    // ///////////////////////////////////
+    // 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)
+    {
+      do
+      {
+        int oldY = -1;
+        int i = 0;
+        boolean inGroup = false;
+        int top = -1;
+        int bottom = -1;
+        int alHeight = av.alignment.getHeight() - 1;
+
+        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 <= (endRes - startRes) * av.charWidth)
+                  && group.getSequences(null).contains(
+                          av.alignment.getSequenceAt(i)))
+          {
+            if ((bottom == -1)
+                    && (i >= alHeight || !group.getSequences(null)
+                            .contains(av.alignment.getSequenceAt(i + 1))))
+            {
+              bottom = sy + av.charHeight;
+            }
+
+            if (!inGroup)
+            {
+              if (((top == -1) && (i == 0))
+                      || !group.getSequences(null).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 >= (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 (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);
+          }
+
+          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 - 1, sx + ex, bottom - 1);
+            bottom = -1;
+          }
+
+          inGroup = false;
+        }
+
+        groupIndex++;
+
+        if (groupIndex >= av.alignment.getGroups().size())
+        {
+          break;
+        }
+
+        group = (SequenceGroup) av.alignment.getGroups().elementAt(
+                groupIndex);
+      } while (groupIndex < av.alignment.getGroups().size());
+
+    }
+  }
+
+  public void highlightSearchResults(SearchResults results)
+  {
+    searchResults = results;
+
+    repaint();
+  }
+
+}