X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f493fcf946176cafec07070c8e04f4706ab80f54;hb=7b0ab0889b9ecaf301c2259fe63e843fa9a895b3;hp=d2670f452a4a14dd9c9a5c56ea44e0899ca9556a;hpb=a3b4ec9805c4cee4c2dbe2a4c98913ee9c189c6b;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d2670f4..f493fcf 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -28,6 +30,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -65,20 +68,21 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   OverviewPanel overviewPanel;
 
-  SeqPanel seqPanel;
+  private SeqPanel seqPanel;
 
-  IdPanel idPanel;
+  private IdPanel idPanel;
 
+  private boolean headless;
   IdwidthAdjuster idwidthAdjuster;
 
   /** DOCUMENT ME!! */
   public AlignFrame alignFrame;
 
-  ScalePanel scalePanel;
+  private ScalePanel scalePanel;
 
-  AnnotationPanel annotationPanel;
+  private AnnotationPanel annotationPanel;
 
-  AnnotationLabels alabels;
+  private AnnotationLabels alabels;
 
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
@@ -99,28 +103,26 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     alignFrame = af;
     this.av = av;
-    seqPanel = new SeqPanel(av, this);
-    idPanel = new IdPanel(av, this);
+    setSeqPanel(new SeqPanel(av, this));
+    setIdPanel(new IdPanel(av, this));
 
-    scalePanel = new ScalePanel(av, this);
+    setScalePanel(new ScalePanel(av, this));
 
-    idPanelHolder.add(idPanel, BorderLayout.CENTER);
+    idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
     idwidthAdjuster = new IdwidthAdjuster(this);
     idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
 
-    annotationPanel = new AnnotationPanel(this);
-    alabels = new AnnotationLabels(this);
+    setAnnotationPanel(new AnnotationPanel(this));
+    setAlabels(new AnnotationLabels(this));
 
-    annotationScroller.setViewportView(annotationPanel);
-    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+    annotationScroller.setViewportView(getAnnotationPanel());
+    annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
 
-    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+    scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
+    seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
 
     setScrollValues(0, 0);
 
-    setAnnotationVisible(av.getShowAnnotation());
-
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
@@ -138,9 +140,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
     });
     fontChanged();
     adjustAnnotationHeight();
-
+    updateLayout();
   }
 
+  @Override
+  public AlignViewportI getAlignViewport()
+  {
+    return av;
+  }
   public void alignmentChanged()
   {
     av.alignmentChanged(this);
@@ -160,18 +167,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // to prevent drawing old image
     FontMetrics fm = getFontMetrics(av.getFont());
 
-    scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
+    scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
             + fm.getDescent()));
-    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+    idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
+            .getCharHeight()
             + fm.getDescent()));
 
-    idPanel.idCanvas.gg = null;
-    seqPanel.seqCanvas.img = null;
-    annotationPanel.adjustPanelHeight();
+    getIdPanel().getIdCanvas().gg = null;
+    getSeqPanel().seqCanvas.img = null;
+    getAnnotationPanel().adjustPanelHeight();
 
     Dimension d = calculateIdWidth();
+
     d.setSize(d.width + 4, d.height);
-    idPanel.idCanvas.setPreferredSize(d);
+    getIdPanel().getIdCanvas().setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
     if (overviewPanel != null)
@@ -192,11 +201,21 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public Dimension calculateIdWidth()
   {
     // calculate sensible default width when no preference is available
-
-    int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
-    int maxwidth = Math.max(20,
-            Math.min(afwidth - 200, 2 * afwidth / 3));
-    return calculateIdWidth(maxwidth);
+    Dimension r = null;
+    if (av.getIdWidth() < 0)
+    {
+      int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+      int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
+      r = calculateIdWidth(maxwidth);
+      av.setIdWidth(r.width);
+    }
+    else
+    {
+      r = new Dimension();
+      r.width = av.getIdWidth();
+      r.height = 0;
+    }
+    return r;
   }
 
   /**
@@ -239,7 +258,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (al.getAlignmentAnnotation() != null)
     {
-      fm = c.getFontMetrics(alabels.getFont());
+      fm = c.getFontMetrics(getAlabels().getFont());
 
       while (i < al.getAlignmentAnnotation().length)
       {
@@ -265,7 +284,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void highlightSearchResults(SearchResults results)
   {
     scrollToPosition(results);
-    seqPanel.seqCanvas.highlightSearchResults(results);
+    getSeqPanel().seqCanvas.highlightSearchResults(results);
   }
 
   /**
@@ -336,7 +355,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           }
         }
       }
-      if (!av.wrapAlignment)
+      if (!av.getWrapAlignment())
       {
         if ((startv = av.getStartRes()) >= start)
         {
@@ -370,8 +389,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   void scrollToWrappedVisible(int res)
   {
-    int cwidth = seqPanel.seqCanvas
-            .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+    int cwidth = getSeqPanel().seqCanvas
+            .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
     if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue((res / cwidth));
@@ -409,7 +428,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void setAnnotationVisible(boolean b)
   {
-    if (!av.wrapAlignment)
+    if (!av.getWrapAlignment())
     {
       annotationSpaceFillerHolder.setVisible(b);
       annotationScroller.setVisible(b);
@@ -440,7 +459,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void validateAnnotationDimensions(boolean adjustPanelHeight)
   {
-    int height = annotationPanel.adjustPanelHeight();
+    int height = getAnnotationPanel().adjustPanelHeight();
 
     int theight = av.getCharHeight()
             * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0
@@ -485,13 +504,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * update alignment layout for viewport settings
    * 
    * @param wrap
    *          DOCUMENT ME!
    */
-  public void setWrapAlignment(boolean wrap)
+  public void updateLayout()
   {
+    fontChanged();
+    setAnnotationVisible(av.isShowAnnotation());
+    boolean wrap = av.getWrapAlignment();
     av.startSeq = 0;
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
@@ -502,7 +524,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       annotationScroller.setVisible(false);
       annotationSpaceFillerHolder.setVisible(false);
     }
-    else if (av.showAnnotation)
+    else if (av.isShowAnnotation())
     {
       annotationScroller.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
@@ -602,10 +624,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
       width = av.getColumnSelection().findColumnPosition(width);
     }
 
-    av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+    av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+            .getCharWidth())) - 1);
 
-    hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
-    vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+    hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+    vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
     if (hextent > width)
     {
@@ -657,7 +680,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
     }
 
     if (evt.getSource() == vscroll)
@@ -668,8 +691,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         if (offy > -1)
         {
-          int rowSize = seqPanel.seqCanvas
-                  .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+          int rowSize = getSeqPanel().seqCanvas
+                  .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
           av.setStartRes(offy * rowSize);
           av.setEndRes((offy + 1) * rowSize);
         }
@@ -691,7 +714,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         av.setStartSeq(offy);
         av.setEndSeq(offy
-                + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
       }
     }
 
@@ -722,20 +745,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
       if (scrollX != 0 || scrollY != 0)
       {
-        idPanel.idCanvas.fastPaint(scrollY);
-        seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
-        scalePanel.repaint();
+        getIdPanel().getIdCanvas().fastPaint(scrollY);
+        getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
+        getScalePanel().repaint();
 
-        if (av.getShowAnnotation() && scrollX != 0)
+        if (av.isShowAnnotation() && scrollX != 0)
         {
-          annotationPanel.fastPaint(scrollX);
+          getAnnotationPanel().fastPaint(scrollX);
         }
       }
     }
   }
 
+  /**
+   * Repaint the alignment including the annotations and overview panels (if
+   * shown).
+   */
   public void paintAlignment(boolean updateOverview)
   {
+    final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+            av.isShowAutocalculatedAbove());
+    sorter.sort(getAlignment()
+            .getAlignmentAnnotation(),
+            av.getSortAnnotationsBy());
     repaint();
 
     if (updateOverview)
@@ -759,7 +791,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     invalidate();
 
-    Dimension d = idPanel.idCanvas.getPreferredSize();
+    Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
     idPanelHolder.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
     validate();
@@ -773,13 +805,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
         maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
       }
 
-      int canvasWidth = seqPanel.seqCanvas
-              .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      int canvasWidth = getSeqPanel().seqCanvas
+              .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
       if (canvasWidth > 0)
       {
         int max = maxwidth
-                / seqPanel.seqCanvas
-                        .getWrappedCanvasWidth(seqPanel.seqCanvas
+                / getSeqPanel().seqCanvas
+                        .getWrappedCanvasWidth(getSeqPanel().seqCanvas
                                 .getWidth()) + 1;
         vscroll.setMaximum(max);
         vscroll.setUnitIncrement(1);
@@ -847,7 +879,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
-    int scaleHeight = av.charHeight + fm.getDescent();
+    int scaleHeight = av.getCharHeight() + fm.getDescent();
 
     pg.setColor(Color.white);
     pg.fillRect(0, 0, pwidth, pheight);
@@ -895,9 +927,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
             * pheight;
 
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+      pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
     }
 
     pagesHigh /= pheight;
@@ -909,7 +941,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // draw Scale
     pg.translate(idWidth, 0);
-    scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
+    getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth,
             scaleHeight);
     pg.translate(-idWidth, scaleHeight);
 
@@ -918,7 +950,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Color currentColor = null;
     Color currentTextColor = null;
 
-    pg.setFont(idPanel.idCanvas.idfont);
+    pg.setFont(getIdPanel().getIdCanvas().getIdfont());
 
     SequenceI seq;
     for (int i = startSeq; i < endSeq; i++)
@@ -937,13 +969,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
 
       pg.setColor(currentColor);
-      pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+      pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
               av.getCharHeight());
 
       pg.setColor(currentTextColor);
 
       int xPos = 0;
-      if (av.rightAlignIds)
+      if (av.isRightAlignIds())
       {
         fm = pg.getFontMetrics();
         xPos = idWidth
@@ -954,7 +986,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       pg.drawString(
               seq.getDisplayId(av.getShowJVSuffix()),
               xPos,
-              (((i - startSeq) * av.charHeight) + av.getCharHeight())
+              (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
 
@@ -962,17 +994,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // draw main sequence panel
     pg.translate(idWidth, 0);
-    seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+    getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
 
-    if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
+    if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
     {
       // draw annotation - need to offset for current scroll position
-      int offset = -alabels.scrollOffset;
+      int offset = -getAlabels().getScrollOffset();
       pg.translate(0, offset);
-      pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
-      alabels.drawComponent(pg, idWidth);
+      pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight()
+              + 3);
+      getAlabels().drawComponent(pg, idWidth);
       pg.translate(idWidth + 3, 0);
-      annotationPanel.renderer.drawComponent(annotationPanel, av,
+      getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
               pg, -1, startRes, endRes + 1);
       pg.translate(0, -offset);
     }
@@ -1000,22 +1033,21 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
           int pi) throws PrinterException
   {
-
     int annotationHeight = 0;
     AnnotationLabels labels = null;
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      annotationHeight = annotationPanel.adjustPanelHeight();
+      annotationHeight = getAnnotationPanel().adjustPanelHeight();
       labels = new AnnotationLabels(av);
     }
 
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
+    int hgap = av.getCharHeight();
+    if (av.getScaleAboveWrapped())
     {
-      hgap += av.charHeight;
+      hgap += av.getCharHeight();
     }
 
-    int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+    int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
             + annotationHeight;
 
     int idWidth = getVisibleIdWidth(false);
@@ -1026,7 +1058,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
 
-    int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
+    int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
             - idWidth);
 
     int totalHeight = cHeight * (maxwidth / resWidth + 1);
@@ -1049,28 +1081,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       for (int i = 0; i < av.getAlignment().getHeight(); i++)
       {
-        pg.setFont(idPanel.idCanvas.idfont);
+        pg.setFont(getIdPanel().getIdCanvas().getIdfont());
         SequenceI s = av.getAlignment().getSequenceAt(i);
         String string = s.getDisplayId(av.getShowJVSuffix());
         int xPos = 0;
-        if (av.rightAlignIds)
+        if (av.isRightAlignIds())
         {
           FontMetrics fm = pg.getFontMetrics();
           xPos = idWidth - fm.stringWidth(string) - 4;
         }
         pg.drawString(string, xPos,
-                ((i * av.charHeight) + ypos + av.charHeight)
-                        - (av.charHeight / 5));
+                ((i * av.getCharHeight()) + ypos + av.getCharHeight())
+                        - (av.getCharHeight() / 5));
       }
       if (labels != null)
       {
         pg.translate(-3, ypos
-                + (av.getAlignment().getHeight() * av.charHeight));
+ + (av.getAlignment().getHeight() * av.getCharHeight()));
 
         pg.setFont(av.getFont());
         labels.drawComponent(pg, idWidth);
         pg.translate(+3, -ypos
-                - (av.getAlignment().getHeight() * av.charHeight));
+                        - (av.getAlignment().getHeight() * av
+                                .getCharHeight()));
       }
 
       ypos += cHeight;
@@ -1078,7 +1111,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pg.translate(idWidth, 0);
 
-    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
+    getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
             0);
 
     if ((pi * pheight) < totalHeight)
@@ -1098,7 +1131,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @return
    */
-  int getVisibleIdWidth()
+  public int getVisibleIdWidth()
   {
     return getVisibleIdWidth(true);
   }
@@ -1112,7 +1145,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          be returned
    * @return
    */
-  int getVisibleIdWidth(boolean onscreen)
+  public int getVisibleIdWidth(boolean onscreen)
   {
     // see if rendering offscreen - check preferences and calc width accordingly
     if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
@@ -1123,7 +1156,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (onscreen
             || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
     {
-      return (idPanel.getWidth() > 0 ? idPanel.getWidth()
+      return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
               : calculateIdWidth().width + 4);
     }
     return idwidth.intValue() + 4;
@@ -1132,7 +1165,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
   {
     long progress = System.currentTimeMillis();
-    boolean headless = (System.getProperty("java.awt.headless") != null && System
+    headless = (System.getProperty("java.awt.headless") != null && System
             .getProperty("java.awt.headless").equals("true"));
     if (alignFrame != null && !headless)
     {
@@ -1143,44 +1176,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     try
     {
-      int maxwidth = av.getAlignment().getWidth();
-      if (av.hasHiddenColumns())
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
-      }
-
-      int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
-              + scalePanel.getHeight();
-      int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
-
-      if (av.getWrapAlignment())
-      {
-        height = getWrappedHeight();
-        if (headless)
-        {
-          // need to obtain default alignment width and then add in any
-          // additional allowance for id margin
-          // this duplicates the calculation in getWrappedHeight but adjusts for
-          // offscreen idWith
-          width = alignFrame.getWidth() - vscroll.getPreferredSize().width
-                  - alignFrame.getInsets().left
-                  - alignFrame.getInsets().right - getVisibleIdWidth()
-                  + getVisibleIdWidth(false);
-        }
-        else
-        {
-          width = seqPanel.getWidth() + getVisibleIdWidth(false);
-        }
-
-      }
-      else if (av.getShowAnnotation())
-      {
-        height += annotationPanel.adjustPanelHeight() + 3;
-      }
-
+      AlignmentDimension aDimension = getAlignmentDimension();
       try
       {
-
         jalview.util.ImageMaker im;
         final String imageAction, imageTitle;
         if (type == jalview.util.ImageMaker.TYPE.PNG)
@@ -1199,13 +1197,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
           imageTitle = alignFrame.getTitle();
         }
 
-        im = new jalview.util.ImageMaker(this, type, imageAction, width,
-                height, file, imageTitle);
+        im = new jalview.util.ImageMaker(this, type, imageAction,
+                aDimension.getWidth(), aDimension.getHeight(), file,
+                imageTitle);
         if (av.getWrapAlignment())
         {
           if (im.getGraphics() != null)
           {
-            printWrappedAlignment(im.getGraphics(), width, height, 0);
+            printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
+                    aDimension.getHeight(), 0);
             im.writeImage();
           }
         }
@@ -1213,7 +1213,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           if (im.getGraphics() != null)
           {
-            printUnwrapped(im.getGraphics(), width, height, 0);
+            printUnwrapped(im.getGraphics(), aDimension.getWidth(),
+                    aDimension.getHeight(), 0);
             im.writeImage();
           }
         }
@@ -1237,6 +1238,46 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
   }
 
+  public AlignmentDimension getAlignmentDimension()
+  {
+    int maxwidth = av.getAlignment().getWidth();
+    if (av.hasHiddenColumns())
+    {
+      maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+    }
+
+    int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+            + getScalePanel().getHeight();
+    int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
+
+    if (av.getWrapAlignment())
+    {
+      height = getWrappedHeight();
+      if (headless)
+      {
+        // need to obtain default alignment width and then add in any
+        // additional allowance for id margin
+        // this duplicates the calculation in getWrappedHeight but adjusts for
+        // offscreen idWith
+        width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+                - alignFrame.getInsets().left
+                - alignFrame.getInsets().right - getVisibleIdWidth()
+                + getVisibleIdWidth(false);
+      }
+      else
+      {
+        width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
+      }
+
+    }
+    else if (av.isShowAnnotation())
+    {
+      height += getAnnotationPanel().adjustPanelHeight() + 3;
+    }
+    return new AlignmentDimension(width, height);
+
+  }
+
   /**
    * DOCUMENT ME!
    */
@@ -1263,7 +1304,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // ////////////////////////////////////////////
     int idWidth = getVisibleIdWidth(false);
     FontMetrics fm = getFontMetrics(av.getFont());
-    int scaleHeight = av.charHeight + fm.getDescent();
+    int scaleHeight = av.getCharHeight() + fm.getDescent();
 
     // Gen image map
     // ////////////////////////////////
@@ -1282,7 +1323,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
         for (s = 0; s < sSize; s++)
         {
-          sy = s * av.charHeight + scaleHeight;
+          sy = s * av.getCharHeight() + scaleHeight;
 
           SequenceI seq = av.getAlignment().getSequenceAt(s);
           SequenceFeature[] features = seq.getDatasetSequence()
@@ -1316,9 +1357,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
               if (text.length() < 1)
               {
                 text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.charWidth) + "," + sy + ","
-                        + (idWidth + (res + 1) * av.charWidth) + ","
-                        + (av.charHeight + sy) + "\""
+                        + (idWidth + res * av.getCharWidth()) + "," + sy
+                        + "," + (idWidth + (res + 1) * av.getCharWidth())
+                        + ","
+                        + (av.getCharHeight() + sy) + "\""
                         + " onMouseOver=\"toolTip('" + alIndex + " "
                         + triplet);
               }
@@ -1335,9 +1377,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
               if (text.length() < 1)
               {
                 text.append("<area shape=\"rect\" coords=\""
-                        + (idWidth + res * av.charWidth) + "," + sy + ","
-                        + (idWidth + (res + 1) * av.charWidth) + ","
-                        + (av.charHeight + sy) + "\""
+                        + (idWidth + res * av.getCharWidth()) + "," + sy
+                        + "," + (idWidth + (res + 1) * av.getCharWidth())
+                        + ","
+                        + (av.getCharHeight() + sy) + "\""
                         + " onMouseOver=\"toolTip('" + alIndex + " "
                         + triplet);
               }
@@ -1400,7 +1443,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   int getWrappedHeight()
   {
-    int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+    int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
 
     if (System.getProperty("java.awt.headless") != null
             && System.getProperty("java.awt.headless").equals("true"))
@@ -1410,22 +1453,22 @@ public class AlignmentPanel extends GAlignmentPanel implements
               - alignFrame.getInsets().left - alignFrame.getInsets().right;
     }
 
-    int chunkWidth = seqPanel.seqCanvas
+    int chunkWidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(seqPanelWidth);
 
-    int hgap = av.charHeight;
-    if (av.scaleAboveWrapped)
+    int hgap = av.getCharHeight();
+    if (av.getScaleAboveWrapped())
     {
-      hgap += av.charHeight;
+      hgap += av.getCharHeight();
     }
 
     int annotationHeight = 0;
-    if (av.showAnnotation)
+    if (av.isShowAnnotation())
     {
-      annotationHeight = annotationPanel.adjustPanelHeight();
+      annotationHeight = getAnnotationPanel().adjustPanelHeight();
     }
 
-    int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+    int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
             + annotationHeight;
 
     int maxwidth = av.getAlignment().getWidth();
@@ -1445,15 +1488,15 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void closePanel()
   {
-    PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
-    PaintRefresher.RemoveComponent(idPanel.idCanvas);
+    PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
+    PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
     if (av != null)
     {
       jalview.structure.StructureSelectionManager ssm = av
               .getStructureSelectionManager();
-      ssm.removeStructureViewerListener(seqPanel, null);
-      ssm.removeSelectionListener(seqPanel);
+      ssm.removeStructureViewerListener(getSeqPanel(), null);
+      ssm.removeSelectionListener(getSeqPanel());
       av.setAlignment(null);
       av = null;
     }
@@ -1493,11 +1536,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return av.getAlignment();
   }
 
-  /**
-   * get the name for this view
-   * 
-   * @return
-   */
+
+  @Override
   public String getViewName()
   {
     return av.viewName;
@@ -1536,22 +1576,77 @@ public class AlignmentPanel extends GAlignmentPanel implements
     new OOMWarning(string, error, this);
   }
 
-  public FeatureRenderer cloneFeatureRenderer()
+  @Override
+  public jalview.api.FeatureRenderer cloneFeatureRenderer()
   {
 
     return new FeatureRenderer(this);
   }
-
-  public void updateFeatureRenderer(FeatureRenderer fr)
+  @Override 
+  public jalview.api.FeatureRenderer getFeatureRenderer()
+  {
+    return seqPanel.seqCanvas.getFeatureRenderer();
+  }
+  public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
   {
-    fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer());
+    fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
   }
 
-  public void updateFeatureRendererFrom(FeatureRenderer fr)
+  public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
   {
-    if (seqPanel.seqCanvas.getFeatureRenderer() != null)
+    if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
     {
-      seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr);
+      getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
     }
   }
+
+  public ScalePanel getScalePanel()
+  {
+    return scalePanel;
+  }
+
+  public void setScalePanel(ScalePanel scalePanel)
+  {
+    this.scalePanel = scalePanel;
+  }
+
+  public SeqPanel getSeqPanel()
+  {
+    return seqPanel;
+  }
+
+  public void setSeqPanel(SeqPanel seqPanel)
+  {
+    this.seqPanel = seqPanel;
+  }
+
+  public AnnotationPanel getAnnotationPanel()
+  {
+    return annotationPanel;
+  }
+
+  public void setAnnotationPanel(AnnotationPanel annotationPanel)
+  {
+    this.annotationPanel = annotationPanel;
+  }
+
+  public AnnotationLabels getAlabels()
+  {
+    return alabels;
+  }
+
+  public void setAlabels(AnnotationLabels alabels)
+  {
+    this.alabels = alabels;
+  }
+
+  public IdPanel getIdPanel()
+  {
+    return idPanel;
+  }
+
+  public void setIdPanel(IdPanel idPanel)
+  {
+    this.idPanel = idPanel;
+  }
 }