X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8548c426fde26194e0b873c2c0ffc4d16dcf3590;hb=5dd663636925f44c6f964fa32fed2f584223b295;hp=ed00d3379d6c59bec106afe6b8878f4a64c18a68;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ed00d33..8548c42 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -27,10 +27,10 @@ import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
-
 import java.io.*;
-
 import javax.swing.*;
+import java.beans.*;
+
 
 
 /**
@@ -81,67 +81,55 @@ public class AlignmentPanel extends GAlignmentPanel
     annotationPanel = new AnnotationPanel(this);
     alabels = new AnnotationLabels(this);
 
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
     annotationScroller.setViewportView(annotationPanel);
     annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
 
     fontChanged();
 
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+   seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
 
     setScrollValues(0, 0);
 
-    annotationPanel.adjustPanelHeight();
-    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.
-                                                 getPreferredSize());
-    annotationScroller.setPreferredSize(annotationPanel.
-                                        getPreferredSize());
     setAnnotationVisible(av.getShowAnnotation());
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-    af.addKeyListener(new KeyAdapter()
+    final AlignmentPanel ap = this;
+    av.addPropertyChangeListener(new PropertyChangeListener()
     {
-      public void keyPressed(KeyEvent evt)
+      public void propertyChange(PropertyChangeEvent evt)
       {
-        switch (evt.getKeyCode())
+        if (evt.getPropertyName().equals("alignment"))
         {
-          case 27: // escape key
-            av.setSelectionGroup(null);
-            repaint();
-
-            break;
+          PaintRefresher.Refresh(ap,
+                                 av.getSequenceSetId(),
+                                 true,
+                                 true);
+          alignmentChanged();
+        }
+      }
+      });
 
-          case KeyEvent.VK_DOWN:
-            alignFrame.moveSelectedSequences(false);
+    adjustAnnotationHeight();
 
-            break;
+  }
 
-          case KeyEvent.VK_UP:
-            alignFrame.moveSelectedSequences(true);
+  public void alignmentChanged()
+  {
+    av.alignmentChanged(this);
 
-            break;
+    if (overviewPanel != null)
+      overviewPanel.updateOverviewImage();
 
-          case KeyEvent.VK_BACK_SPACE:
-          case KeyEvent.VK_DELETE:
-            alignFrame.cut_actionPerformed(null);
-            break;
+    alignFrame.updateEditMenuBar();
 
-          case KeyEvent.VK_P:
-            seqPanel.seqCanvas.increaseAARatio();
-            break;
-          case KeyEvent.VK_L:
-            seqPanel.seqCanvas.decreaseAARation();
-            break;
-        }
-      }
-    });
+    repaint();
   }
 
+
+
   /**
    * DOCUMENT ME!
    */
@@ -165,19 +153,6 @@ public class AlignmentPanel extends GAlignmentPanel
     idPanel.idCanvas.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
-    if (av.getWrapAlignment())
-    {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
-      vscroll.setMaximum(max);
-      vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
-    }
-    else
-    {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
-    }
-
     if (overviewPanel != null)
       overviewPanel.setBoxPosition();
 
@@ -193,7 +168,9 @@ public class AlignmentPanel extends GAlignmentPanel
   {
     Container c = new Container();
 
-    FontMetrics fm = c.getFontMetrics(av.font);
+    FontMetrics fm = c.getFontMetrics(
+      new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
+
     AlignmentI al = av.getAlignment();
 
     int i = 0;
@@ -242,26 +219,43 @@ public class AlignmentPanel extends GAlignmentPanel
    *
    * @param results DOCUMENT ME!
    */
-  public void highlightSearchResults(int[] results)
+  public void highlightSearchResults(SearchResults results)
   {
     seqPanel.seqCanvas.highlightSearchResults(results);
 
     // do we need to scroll the panel?
     if (results != null)
     {
-      SequenceI seq = av.alignment.getSequenceAt(results[0]);
-      int start = seq.findIndex(results[1]) - 1;
-      int end = seq.findIndex(results[2]) - 1;
+      SequenceI seq = results.getResultSequence(0);
+      int seqIndex = av.alignment.findIndex(seq);
+      int start = seq.findIndex(results.getResultStart(0)) - 1;
+      int end = seq.findIndex(results.getResultEnd(0)) - 1;
 
-      if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||
-          ( (av.getStartSeq() > results[0]) ||
-           (av.getEndSeq() < results[0])))
+      if(!av.wrapAlignment)
+      {
+        if ( (av.getStartRes() > end)  || (av.getEndRes() < start) ||
+           ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+        {
+          setScrollValues(start, seqIndex);
+        }
+      }
+      else
       {
-        setScrollValues(start, results[0]);
+        scrollToWrappedVisible(start);
       }
     }
   }
 
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    if( res<=av.getStartRes() || res>=(av.getStartRes()+cwidth) )
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -297,6 +291,31 @@ public class AlignmentPanel extends GAlignmentPanel
     repaint();
   }
 
+  public void adjustAnnotationHeight()
+  {
+    if (alignFrame.getHeight() == 0)
+    {
+      System.out.println("NEEDS FIXING");
+    }
+
+    int height = annotationPanel.adjustPanelHeight();
+
+    if (height > alignFrame.getHeight() / 2)
+    {
+      height = alignFrame.getHeight() / 2;
+    }
+
+    annotationScroller.setPreferredSize(
+        new Dimension(annotationScroller.getWidth(),
+                      height));
+
+    annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+        annotationSpaceFillerHolder.getWidth(),
+        height));
+
+    repaint();
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -363,7 +382,7 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public boolean scrollRight(boolean right)
   {
-    if (right)
+    if (!right)
     {
       if (hscroll.getValue() < 1)
       {
@@ -397,30 +416,36 @@ public class AlignmentPanel extends GAlignmentPanel
    */
   public void setScrollValues(int x, int y)
   {
-    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -
-                 1);
+
+    int width = av.alignment.getWidth();
+    int height = av.alignment.getHeight();
+
+    if(av.hasHiddenColumns)
+     width = av.getColumnSelection().findColumnPosition(width);
+
+    av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) -1);
 
     hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
     vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
 
-    if (hextent > av.alignment.getWidth())
+    if (hextent > width)
     {
-      hextent = av.alignment.getWidth();
+      hextent = width;
     }
 
-    if (vextent > av.alignment.getHeight())
+    if (vextent > height)
     {
-      vextent = av.alignment.getHeight();
+      vextent = height;
     }
 
-    if ( (hextent + x) > av.getAlignment().getWidth())
+    if ( (hextent + x) > width)
     {
-      x = av.getAlignment().getWidth() - hextent;
+      x = width - hextent;
     }
 
-    if ( (vextent + y) > av.getAlignment().getHeight())
+    if ( (vextent + y) > height)
     {
-      y = av.getAlignment().getHeight() - vextent;
+      y = height - vextent;
     }
 
     if (y < 0)
@@ -433,8 +458,8 @@ public class AlignmentPanel extends GAlignmentPanel
       x = 0;
     }
 
-    hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());
-    vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());
+    hscroll.setValues(x, hextent, 0, width);
+    vscroll.setValues(y, vextent, 0, height);
   }
 
   /**
@@ -462,10 +487,26 @@ public class AlignmentPanel extends GAlignmentPanel
 
       if (av.getWrapAlignment())
       {
-        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
-            seqCanvas.getWidth());
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes( (vscroll.getValue() + 1) * rowSize);
+        if(offy>-1)
+        {
+          int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
+              seqCanvas.getWidth());
+          av.setStartRes(offy * rowSize);
+          av.setEndRes( (offy + 1) * rowSize);
+        }
+        else
+        {
+          //This is only called if file loaded is a jar file that
+          //was wrapped when saved and user has wrap alignment true
+          //as preference setting
+          SwingUtilities.invokeLater(new Runnable()
+              {
+                public void run()
+                {
+                  setScrollValues(av.getStartRes(), av.getStartSeq());
+                }
+              });
+        }
       }
       else
       {
@@ -480,28 +521,33 @@ public class AlignmentPanel extends GAlignmentPanel
       overviewPanel.setBoxPosition();
     }
 
-    int xShift = av.getStartRes() - oldX;
-    int yShift = av.getStartSeq() - oldY;
+    int scrollX = av.startRes - oldX;
+    int scrollY = av.startSeq - oldY;
 
-    if ( (xShift != 0 && yShift != 0) ||
-        (Math.abs(xShift) > av.getEndRes() - av.getStartRes()
-         || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())
-        || av.getWrapAlignment()
-        || !fastPaint)
+    if (av.getWrapAlignment() || !fastPaint)
     {
-      // Either no shift at all, or shift greater than visible amount
       repaint();
     }
     else
     {
-      idPanel.idCanvas.fastPaint(yShift);
-      seqPanel.seqCanvas.fastPaint(xShift, yShift);
-
-      scalePanel.repaint();
-
-      if (av.getShowAnnotation())
+      // Make sure we're not trying to draw a panel
+      // larger than the visible window
+      if(scrollX>av.endRes-av.startRes)
+        scrollX = av.endRes-av.startRes;
+      else if(scrollX<av.startRes-av.endRes)
+        scrollX = av.startRes - av.endRes;
+
+      if(scrollX!=0 || scrollY!=0)
       {
-        annotationPanel.fastPaint(xShift);
+        idPanel.idCanvas.fastPaint(scrollY);
+        seqPanel.seqCanvas.fastPaint(scrollX,
+                                     scrollY);
+        scalePanel.repaint();
+
+        if (av.getShowAnnotation())
+        {
+          annotationPanel.fastPaint(scrollX);
+        }
       }
     }
   }
@@ -522,23 +568,31 @@ public class AlignmentPanel extends GAlignmentPanel
 
     if (av.getWrapAlignment())
     {
-      int max = av.alignment.getWidth() /
-          seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;
-      vscroll.setMaximum(max);
-      vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
+      int maxwidth = av.alignment.getWidth();
+
+      if (av.hasHiddenColumns)
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+      int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+            if(canvasWidth>0)
+      {
+        int max = maxwidth /
+            seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
+            getWidth()) +
+            1;
+        vscroll.setMaximum(max);
+        vscroll.setUnitIncrement(1);
+        vscroll.setVisibleAmount(1);
+      }
     }
     else
     {
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
-
-    if( this.getVisibleRect().getBounds() == g.getClipBounds() )
-    {
-      if (overviewPanel != null)
+    if( this.getVisibleRect().getBounds() == g.getClipBounds()
+        && overviewPanel != null)
         overviewPanel.updateOverviewImage();
-    }
   }
 
   /**
@@ -585,7 +639,7 @@ public class AlignmentPanel extends GAlignmentPanel
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
       throws PrinterException
   {
-    int idWidth = calculateIdWidth().width + 4;
+    int idWidth = getVisibleIdWidth();
     FontMetrics fm = getFontMetrics(av.getFont());
     int scaleHeight = av.charHeight + fm.getDescent();
 
@@ -657,18 +711,21 @@ public class AlignmentPanel extends GAlignmentPanel
     Color currentColor = null;
     Color currentTextColor = null;
 
+    pg.setFont(idPanel.idCanvas.idfont);
+
+    SequenceI seq;
     for (int i = startSeq; i < endSeq; i++)
     {
+      seq = av.getAlignment().getSequenceAt(i);
       if ( (av.getSelectionGroup() != null) &&
-          av.getSelectionGroup().sequences.contains(
-              av.getAlignment().getSequenceAt(i)))
+          av.getSelectionGroup().getSequences(null).contains(seq))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
       }
       else
       {
-        currentColor = av.getAlignment().getSequenceAt(i).getColor();
+        currentColor = av.getSequenceColour(seq);
         currentTextColor = Color.black;
       }
 
@@ -678,24 +735,32 @@ public class AlignmentPanel extends GAlignmentPanel
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId
-          ( av.getShowJVSuffix());
+      int xPos = 0;
+      if (av.rightAlignIds)
+      {
+        fm = pg.getFontMetrics();
+        xPos = idWidth - fm.stringWidth(
+            seq.getDisplayId(av.getShowJVSuffix())
+            ) - 4;
+      }
 
-      pg.drawString(string, 0,
+      pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),
+                    xPos,
                     ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
                     (av.getCharHeight() / 5));
     }
 
+    pg.setFont(av.getFont());
+
     // draw main sequence panel
     pg.translate(idWidth, 0);
-    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,
-                                 startRes, startSeq, 0);
+    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
 
     if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
     {
-      pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3);
+      pg.translate( -idWidth-3, (endSeq - startSeq) * av.charHeight + 3);
       alabels.drawComponent( (Graphics2D) pg, idWidth);
-      pg.translate(idWidth, 0);
+      pg.translate(idWidth+3, 0);
       annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
                                     1);
     }
@@ -736,12 +801,17 @@ public class AlignmentPanel extends GAlignmentPanel
         + hgap
         + annotationHeight;
 
-    int idWidth = calculateIdWidth().width + 4;
+    int idWidth = getVisibleIdWidth();
+
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
 
     int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
         idWidth);
 
-    int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);
+    int totalHeight = cHeight * (maxwidth / resWidth + 1);
 
     pg.setColor(Color.white);
     pg.fillRect(0, 0, pwidth, pheight);
@@ -756,31 +826,35 @@ public class AlignmentPanel extends GAlignmentPanel
     pg.setClip(0, pi * pheight, pwidth, pheight);
 
     int ypos = hgap;
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
-    pg.setFont(italic);
+
+
 
     do
     {
       for (int i = 0; i < av.alignment.getHeight(); i++)
       {
+        pg.setFont(idPanel.idCanvas.idfont);
         SequenceI s = av.alignment.getSequenceAt(i);
         String string = s.getDisplayId( av.getShowJVSuffix());
-
-        pg.drawString(string, 0,
+        int xPos = 0;
+        if (av.rightAlignIds)
+        {
+          FontMetrics fm = pg.getFontMetrics();
+          xPos = idWidth - fm.stringWidth( string ) - 4;
+        }
+        pg.drawString(string, xPos,
                       ( (i * av.charHeight) + ypos + av.charHeight) -
                       (av.charHeight / 5));
       }
       if (labels != null)
       {
-        pg.translate(0,
+        pg.translate(-3,
                      ypos +
                      (av.getAlignment().getHeight() * av.charHeight));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
-        pg.setFont(italic);
-        pg.translate(0,
+        pg.translate(+3,
                      -ypos -
                      (av.getAlignment().getHeight() * av.charHeight));
       }
@@ -804,21 +878,42 @@ public class AlignmentPanel extends GAlignmentPanel
     }
   }
 
+  int getVisibleIdWidth()
+  {
+    return
+        idPanel.getWidth() > 0 ? idPanel.getWidth() :
+        calculateIdWidth().width + 4;
+  }
+
   void makeAlignmentImage(int type, File file)
   {
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+
     int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
-    int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);
+    int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
 
     if (av.getWrapAlignment())
     {
       height = getWrappedHeight();
-      width = seqPanel.getWidth() + idPanel.getWidth();
+      if (System.getProperty("java.awt.headless") != null
+          && System.getProperty("java.awt.headless").equals("true"))
+      {
+        width = alignFrame.getWidth() - 22;
+      }
+      else
+        width = seqPanel.getWidth() + getVisibleIdWidth();
+
     }
     else if (av.getShowAnnotation())
     {
       height += annotationPanel.adjustPanelHeight() + 3;
     }
 
+    try
+    {
+
     jalview.util.ImageMaker im;
     if(type==jalview.util.ImageMaker.PNG)
       im  = new jalview.util.ImageMaker(this,
@@ -831,20 +926,22 @@ public class AlignmentPanel extends GAlignmentPanel
                                        "Create EPS file from alignment",
                                         width, height, file, alignFrame.getTitle() );
 
-    try
-    {
       if (av.getWrapAlignment())
       {
         if(im.getGraphics()!=null)
+        {
           printWrappedAlignment(im.getGraphics(), width, height, 0);
+          im.writeImage();
+        }
       }
       else
       {
         if(im.getGraphics()!=null)
+        {
           printUnwrapped(im.getGraphics(), width, height, 0);
+          im.writeImage();
+        }
       }
-
-      im.writeImage();
     }
     catch (OutOfMemoryError err)
     {
@@ -887,7 +984,7 @@ public class AlignmentPanel extends GAlignmentPanel
   {
     ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
     //////////////////////////////////////////////
-    int idWidth = calculateIdWidth().width + 4;
+    int idWidth = getVisibleIdWidth();
     FontMetrics fm = getFontMetrics(av.getFont());
     int scaleHeight = av.charHeight + fm.getDescent();
 
@@ -897,45 +994,106 @@ public class AlignmentPanel extends GAlignmentPanel
     {
       try
       {
+        int s, sSize = av.alignment.getHeight(),
+            res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
+        StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
         out.println(jalview.io.HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName +
                     "\" border=\"0\" usemap=\"#Map\" >"
                     + "<map name=\"Map\">");
 
-        for (int s = 0; s < av.alignment.getHeight(); s++)
+        for (s = 0; s < sSize; s++)
         {
+          sy = s * av.charHeight + scaleHeight;
+
           SequenceI seq = av.alignment.getSequenceAt(s);
+          SequenceFeature [] features = seq.getDatasetSequence().getSequenceFeatures();
           SequenceGroup[] groups = av.alignment.findAllGroups(seq);
-          for (int i = 0; i < groups.length; i++)
+          for(res =0; res<alwidth; res++)
           {
-            int sy = s * av.charHeight + scaleHeight;
-            for (int res = groups[i].getStartRes();
-                 res < groups[i].getEndRes() + 1; res++)
-            {
-              int alIndex = seq.findPosition(res);
-              Object obj = ResidueProperties.aa2Triplet.get(
-                  seq.getCharAt(res) + "");
+            text = new StringBuffer();
+            Object obj = null;
+            if(av.alignment.isNucleotide())
+              obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)+"" );
+            else
+              obj = ResidueProperties.aa2Triplet.get(
+                    seq.getCharAt(res) + "");
+
               if (obj == null)
-                continue;
+                  continue;
+
+            String triplet = obj.toString();
+            int alIndex = seq.findPosition(res);
+            gSize = groups.length;
+            for (g = 0; g < gSize; g++)
+            {
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
+                  + (idWidth + res * av.charWidth) + ","
+                  + sy + ","
+                  + (idWidth + (res + 1) * av.charWidth) + ","
+                  + (av.charHeight + sy) + "\""
+                  + " onMouseOver=\"toolTip('"
+                  + alIndex + " " + triplet );
+              }
 
-              String triplet = obj.toString();
+              if(groups[g].getStartRes()<res && groups[g].getEndRes()>res)
+                text.append("<br><em>" + groups[g].getName() + "</em>");
+            }
 
-              out.println(
-                  "<area shape=\"rect\" coords=\""
+            if (features != null)
+            {
+              if(text.length()<1)
+              {
+                text.append("<area shape=\"rect\" coords=\""
                   + (idWidth + res * av.charWidth) + ","
                   + sy + ","
                   + (idWidth + (res + 1) * av.charWidth) + ","
                   + (av.charHeight + sy) + "\""
                   + " onMouseOver=\"toolTip('"
-                  + alIndex + " " + triplet +
-                  "<br><em>" + groups[i].getName() +
-                  "</em>')\"; onMouseOut=\"toolTip()\"; "
-                  + " href=\"#\">");
+                  + alIndex + " " + triplet );
+              }
+                fSize = features.length;
+                for (f = 0; f < fSize; f++)
+                {
+
+                  if ( (features[f].getBegin() <= seq.findPosition(res)) &&
+                      (features[f].getEnd() >= seq.findPosition(res)))
+                  {
+                    if (features[f].getType().equals("disulfide bond"))
+                    {
+                      if (features[f].getBegin() == seq.findPosition(res)
+                          || features[f].getEnd() == seq.findPosition(res))
+                      {
+                        text.append("<br>disulfide bond " + features[f].getBegin() + ":" +
+                                       features[f].getEnd());
+                      }
+                    }
+                    else
+                    {
+                      text.append("<br>");
+                      text.append(features[f].getType());
+                      if (features[f].getDescription() != null && !features[f].getType().equals(features[f].getDescription()))
+                        text.append(" " + features[f].getDescription());
+
+                      if (features[f].getValue("status") != null )
+                      {
+                        text.append(" (" + features[f].getValue("status") + ")");
+                      }
+                    }
+                  }
+
+                }
+              }
+              if(text.length()>1)
+              {
+                text.append("')\"; onMouseOut=\"toolTip()\";  href=\"#\">");
+                out.println(text.toString());
+              }
             }
           }
-        }
-
         out.println("</map></body></html>");
         out.close();
 
@@ -950,9 +1108,18 @@ public class AlignmentPanel extends GAlignmentPanel
 
   int getWrappedHeight()
   {
+    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+
+    //If headless, seqPanel will have 0 width
+    if (System.getProperty("java.awt.headless") != null
+              && System.getProperty("java.awt.headless").equals("true"))
+    {
+      seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth();
+    }
 
     int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
-        seqPanel.seqCanvas.getWidth());
+        seqPanelWidth
+          );
 
     int hgap = av.charHeight;
     if (av.scaleAboveWrapped)
@@ -968,7 +1135,12 @@ public class AlignmentPanel extends GAlignmentPanel
         + hgap
         + annotationHeight;
 
-    int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;
+    int maxwidth = av.alignment.getWidth();
+    if (av.hasHiddenColumns)
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+
+    int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
 
     return height;
   }