X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=5366913f16385a2681de458607ee87d94385b6b8;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=58aa645eb156091058a019476feadd7fb32a8e85;hpb=f9f0b83445a2da848d21614d94a909888484e25e;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 58aa645..5366913 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
@@ -40,7 +41,6 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.Comparison;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
-import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
@@ -51,6 +51,7 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
+import java.awt.Graphics2D;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
@@ -73,9 +74,15 @@ import javax.swing.SwingUtilities;
  * @author $author$
  * @version $Revision: 1.161 $
  */
+@SuppressWarnings("serial")
 public class AlignmentPanel extends GAlignmentPanel implements
         AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
 {
+  /*
+   * spare space in pixels between sequence id and alignment panel
+   */
+  private static final int ID_WIDTH_PADDING = 4;
+
   public AlignViewport av;
 
   OverviewPanel overviewPanel;
@@ -116,6 +123,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
+//	setBackground(Color.white);  // BH 2019
     alignFrame = af;
     this.av = av;
     setSeqPanel(new SeqPanel(av, this));
@@ -228,13 +236,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
             new Dimension(10, av.getCharHeight() + fm.getDescent()));
     idwidthAdjuster.invalidate();
     scalePanelHolder.invalidate();
-    getIdPanel().getIdCanvas().gg = null;
+    // BH 2018 getIdPanel().getIdCanvas().gg = null;
     getSeqPanel().seqCanvas.img = null;
     getAnnotationPanel().adjustPanelHeight();
 
     Dimension d = calculateIdWidth();
-
-    d.setSize(d.width + 4, d.height);
     getIdPanel().getIdCanvas().setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(d);
 
@@ -242,20 +248,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * Calculate the width of the alignment labels based on the displayed names
-   * and any bounds on label width set in preferences.
+   * Calculates the width of the alignment labels based on the displayed names
+   * and any bounds on label width set in preferences. The calculated width is
+   * also set as a property of the viewport.
    * 
    * @return Dimension giving the maximum width of the alignment label panel
    *         that should be used.
    */
   public Dimension calculateIdWidth()
   {
+    int oldWidth = av.getIdWidth();
+
     // calculate sensible default width when no preference is available
     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));
+      int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
+      int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
       r = calculateIdWidth(maxwidth);
       av.setIdWidth(r.width);
     }
@@ -265,6 +275,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
       r.width = av.getIdWidth();
       r.height = 0;
     }
+
+    /*
+     * fudge: if desired width has changed, update layout
+     * (see also paintComponent - updates layout on a repaint)
+     */
+    if (r.width != oldWidth)
+    {
+      idPanelHolder.setPreferredSize(r);
+      validate();
+    }
     return r;
   }
 
@@ -277,7 +297,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return Dimension giving the maximum width of the alignment label panel
    *         that should be used.
    */
-  public Dimension calculateIdWidth(int maxwidth)
+  protected Dimension calculateIdWidth(int maxwidth)
   {
     Container c = new Container();
 
@@ -287,19 +307,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     AlignmentI al = av.getAlignment();
     int i = 0;
     int idWidth = 0;
-    String id;
 
     while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
     {
       SequenceI s = al.getSequenceAt(i);
-
-      id = s.getDisplayId(av.getShowJVSuffix());
-
-      if (fm.stringWidth(id) > idWidth)
-      {
-        idWidth = fm.stringWidth(id);
-      }
-
+      String id = s.getDisplayId(av.getShowJVSuffix());
+      int stringWidth = fm.stringWidth(id);
+      idWidth = Math.max(idWidth, stringWidth);
       i++;
     }
 
@@ -313,27 +327,25 @@ public class AlignmentPanel extends GAlignmentPanel implements
       while (i < al.getAlignmentAnnotation().length)
       {
         String label = al.getAlignmentAnnotation()[i].label;
-
-        if (fm.stringWidth(label) > idWidth)
-        {
-          idWidth = fm.stringWidth(label);
-        }
-
+        int stringWidth = fm.stringWidth(label);
+        idWidth = Math.max(idWidth, stringWidth);
         i++;
       }
     }
 
-    return new Dimension(
-            maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
+    int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth);
+    w += ID_WIDTH_PADDING;
+
+    return new Dimension(w, 12);
   }
 
   /**
-   * Highlight the given results on the alignment.
+   * Highlight the given results on the alignment
    * 
    */
   public void highlightSearchResults(SearchResultsI results)
   {
-    boolean scrolled = scrollToPosition(results, 0, true, false);
+    boolean scrolled = scrollToPosition(results, 0, false);
 
     boolean fastPaint = !(scrolled && av.getWrapAlignment());
 
@@ -345,13 +357,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * (if any)
    * 
    * @param searchResults
-   * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResultsI searchResults,
-          boolean redrawOverview)
+  public boolean scrollToPosition(SearchResultsI searchResults)
   {
-    return scrollToPosition(searchResults, 0, redrawOverview, false);
+    return scrollToPosition(searchResults, 0, false);
   }
 
   /**
@@ -364,14 +374,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param verticalOffset
    *          if greater than zero, allows scrolling to a position below the
    *          first displayed sequence
-   * @param redrawOverview
-   *          - when set, the overview will be recalculated (takes longer)
    * @param centre
    *          if true, try to centre the search results horizontally in the view
    * @return
    */
   protected boolean scrollToPosition(SearchResultsI results,
-          int verticalOffset, boolean redrawOverview, boolean centre)
+          int verticalOffset, boolean centre)
   {
     int startv, endv, starts, ends;
     ViewportRanges ranges = av.getRanges();
@@ -477,7 +485,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       scrollNeeded = ranges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview, false);
+    paintAlignment(false, false);
 
     return scrollNeeded;
   }
@@ -536,7 +544,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     addNotify();
     // TODO: many places call this method and also paintAlignment with various
     // different settings. this means multiple redraws are triggered...
-    paintAlignment(true, false);
+    paintAlignment(true, av.needToUpdateStructureViews());
   }
 
   /**
@@ -545,44 +553,27 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void validateAnnotationDimensions(boolean adjustPanelHeight)
   {
-    int annotationHeight = getAnnotationPanel().adjustPanelHeight();
-
-    if (adjustPanelHeight)
-    {
-      int rowHeight = av.getCharHeight();
-      int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+    // BH 2018.04.18 comment: addNotify() is not appropriate here. We
+    // are not changing ancestors, and keyboard action listeners do
+    // not need to be reset. addNotify() is a very expensive operation,
+    // requiring a full re-layout of all parents and children.
+    // Note in JComponent:
+    // This method is called by the toolkit internally and should
+    // not be called directly by programs.
+    // I note that addNotify() is called in several areas of Jalview.
 
-      /*
-       * Estimate available height in the AlignFrame for alignment +
-       * annotations. Deduct an estimate for title bar, menu bar, scale panel,
-       * hscroll, status bar, insets. 
-       */
-      int stuff = Platform.isAMac() ? 120 : 140;
-      int availableHeight = alignFrame.getHeight() - stuff;
+    int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+    annotationHeight = getAnnotationPanel()
+            .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
 
-      /*
-       * If not enough vertical space, maximize annotation height while keeping
-       * at least two rows of alignment visible
-       */
-      if (annotationHeight + alignmentHeight > availableHeight)
-      {
-        annotationHeight = Math.min(annotationHeight,
-                availableHeight - 2 * rowHeight);
-      }
-    }
-    else
-    {
-      // maintain same window layout whilst updating sliders
-      annotationHeight = annotationScroller.getSize().height;
-    }
     hscroll.addNotify();
-
     annotationScroller.setPreferredSize(
             new Dimension(annotationScroller.getWidth(), annotationHeight));
 
     Dimension e = idPanel.getSize();
     alabels.setSize(new Dimension(e.width, annotationHeight));
 
+
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -615,6 +606,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       annotationScroller.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
+      validateAnnotationDimensions(false);
     }
 
     int canvasWidth = getSeqPanel().seqCanvas.getWidth();
@@ -667,16 +659,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      int width = av.getAlignment().getWidth();
+      int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns())
-      {
-        // reset the width to exclude hidden columns
-        width = av.getAlignment().getHiddenColumns()
-                .absoluteToVisibleColumn(width);
-      }
-
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
       vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
@@ -822,7 +807,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // could not be validated and it is not clear if it is now being
           // called. Log warning here in case it is called and unforeseen
           // problems occur
-          Cache.log.warn(
+          Console.warn(
                   "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
 
           // scroll to start of panel
@@ -861,12 +846,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param g
-   *          DOCUMENT ME!
-   */
   @Override
   public void paintComponent(Graphics g)
   {
@@ -884,6 +863,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      */
     ViewportRanges ranges = av.getRanges();
     setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+    super.paintComponent(g);
   }
 
   /**
@@ -942,30 +922,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param pg
-   *          DOCUMENT ME!
-   * @param pwidth
-   *          DOCUMENT ME!
-   * @param pheight
-   *          DOCUMENT ME!
-   * @param pi
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   * 
-   * @throws PrinterException
-   *           DOCUMENT ME!
-   */
-  /**
    * Draws the alignment image, including sequence ids, sequences, and
    * annotation labels and annotations if shown, on either one or two Graphics
-   * context.
+   * contexts.
    * 
    * @param pageWidth
+   *          in pixels
    * @param pageHeight
-   * @param pi
+   *          in pixels
+   * @param pageIndex
+   *          (0, 1, ...)
    * @param idGraphics
    *          the graphics context for sequence ids and annotation labels
    * @param alignmentGraphics
@@ -974,7 +940,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return
    * @throws PrinterException
    */
-  public int printUnwrapped(int pageWidth, int pageHeight, int pi,
+  public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
           Graphics idGraphics, Graphics alignmentGraphics)
           throws PrinterException
   {
@@ -988,8 +954,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             : idWidth;
 
     FontMetrics fm = getFontMetrics(av.getFont());
-    int charHeight = av.getCharHeight();
-    int scaleHeight = charHeight + fm.getDescent();
+    final int charHeight = av.getCharHeight();
+    final int scaleHeight = charHeight + fm.getDescent();
 
     idGraphics.setColor(Color.white);
     idGraphics.fillRect(0, 0, pageWidth, pageHeight);
@@ -998,29 +964,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
     /*
      * How many sequences and residues can we fit on a printable page?
      */
-    int totalRes = (pageWidth - idWidth) / av.getCharWidth();
+    final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
 
-    int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
+    final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
 
-    int alignmentWidth = av.getAlignment().getWidth();
+    final int alignmentWidth = av.getAlignment().getVisibleWidth();
     int pagesWide = (alignmentWidth / totalRes) + 1;
 
-    final int startRes = (pi % pagesWide) * totalRes;
-    int endRes = (startRes + totalRes) - 1;
-
-    if (endRes > (alignmentWidth - 1))
-    {
-      endRes = alignmentWidth - 1;
-    }
-
-    final int startSeq = (pi / pagesWide) * totalSeq;
-    int endSeq = startSeq + totalSeq;
+    final int startRes = (pageIndex % pagesWide) * totalRes;
+    final int endRes = Math.min(startRes + totalRes - 1,
+            alignmentWidth - 1);
 
-    int alignmentHeight = av.getAlignment().getHeight();
-    if (endSeq > alignmentHeight)
-    {
-      endSeq = alignmentHeight;
-    }
+    final int startSeq = (pageIndex / pagesWide) * totalSeq;
+    final int alignmentHeight = av.getAlignment().getHeight();
+    final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
 
     int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
 
@@ -1031,7 +988,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     pagesHigh /= pageHeight;
 
-    if (pi >= (pagesWide * pagesHigh))
+    if (pageIndex >= (pagesWide * pagesHigh))
     {
       return Printable.NO_SUCH_PAGE;
     }
@@ -1050,47 +1007,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * then reset to top left (0, 0)
      */
     idGraphics.translate(0, scaleHeight);
-    idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
-    Color currentColor = null;
-    Color currentTextColor = null;
+    IdCanvas idCanvas = getIdPanel().getIdCanvas();
+    List<SequenceI> selection = av.getSelectionGroup() == null ? null
+            : av.getSelectionGroup().getSequences(null);
+    idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
+            selection);
 
-    SequenceI seq;
-    for (int i = startSeq; i < endSeq; i++)
-    {
-      seq = av.getAlignment().getSequenceAt(i);
-      if ((av.getSelectionGroup() != null)
-              && av.getSelectionGroup().getSequences(null).contains(seq))
-      {
-        /*
-         * gray out ids of sequences in selection group (if any)
-         */
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
-      {
-        currentColor = av.getSequenceColour(seq);
-        currentTextColor = Color.black;
-      }
-
-      idGraphics.setColor(currentColor);
-      idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
-              charHeight);
-
-      idGraphics.setColor(currentTextColor);
-
-      int xPos = 0;
-      String displayId = seq.getDisplayId(av.getShowJVSuffix());
-      if (av.isRightAlignIds())
-      {
-        fm = idGraphics.getFontMetrics();
-        xPos = idWidth - fm.stringWidth(displayId) - 4;
-      }
-
-      idGraphics.drawString(displayId, xPos,
-              (((i - startSeq) * charHeight) + charHeight)
-                      - (charHeight / 5));
-    }
     idGraphics.setFont(av.getFont());
     idGraphics.translate(0, -scaleHeight);
 
@@ -1100,7 +1022,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
     getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
-            endRes, startSeq, endSeq);
+            endRes, startSeq, endSeq - 1);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
@@ -1130,31 +1052,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * DOCUMENT ME!
+   * Prints one page of an alignment in wrapped mode. Returns
+   * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
+   * no page could be drawn (page number out of range).
    * 
-   * @param pg
-   *          DOCUMENT ME!
-   * @param pwidth
-   *          DOCUMENT ME!
-   * @param pheight
-   *          DOCUMENT ME!
-   * @param pi
-   *          DOCUMENT ME!
+   * @param pageWidth
+   * @param pageHeight
+   * @param pageNumber
+   *          (0, 1, ...)
+   * @param g
    * 
-   * @return DOCUMENT ME!
+   * @return
    * 
    * @throws PrinterException
-   *           DOCUMENT ME!
    */
-  public int printWrappedAlignment(int pwidth, int pheight, int pi,
-          Graphics pg) throws PrinterException
+  public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
+          Graphics g) throws PrinterException
   {
+    getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
+            getHeight());
     int annotationHeight = 0;
-    AnnotationLabels labels = null;
     if (av.isShowAnnotation())
     {
       annotationHeight = getAnnotationPanel().adjustPanelHeight();
-      labels = new AnnotationLabels(av);
     }
 
     int hgap = av.getCharHeight();
@@ -1168,72 +1088,43 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int idWidth = getVisibleIdWidth(false);
 
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     int resWidth = getSeqPanel().seqCanvas
-            .getWrappedCanvasWidth(pwidth - idWidth);
+            .getWrappedCanvasWidth(pageWidth - idWidth);
+    av.getRanges().setViewportStartAndWidth(0, resWidth);
 
     int totalHeight = cHeight * (maxwidth / resWidth + 1);
 
-    pg.setColor(Color.white);
-    pg.fillRect(0, 0, pwidth, pheight);
-    pg.setFont(av.getFont());
-
-    // //////////////
-    // Draw the ids
-    pg.setColor(Color.black);
-
-    pg.translate(0, -pi * pheight);
-
-    pg.setClip(0, pi * pheight, pwidth, pheight);
+    g.setColor(Color.white);
+    g.fillRect(0, 0, pageWidth, pageHeight);
+    g.setFont(av.getFont());
+    g.setColor(Color.black);
 
-    int ypos = hgap;
-
-    do
-    {
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)
-      {
-        pg.setFont(getIdPanel().getIdCanvas().getIdfont());
-        SequenceI s = av.getAlignment().getSequenceAt(i);
-        String string = s.getDisplayId(av.getShowJVSuffix());
-        int xPos = 0;
-        if (av.isRightAlignIds())
-        {
-          FontMetrics fm = pg.getFontMetrics();
-          xPos = idWidth - fm.stringWidth(string) - 4;
-        }
-        pg.drawString(string, xPos,
-                ((i * av.getCharHeight()) + ypos + av.getCharHeight())
-                        - (av.getCharHeight() / 5));
-      }
-      if (labels != null)
-      {
-        pg.translate(-3, ypos
-                + (av.getAlignment().getHeight() * av.getCharHeight()));
+    /*
+     * method: print the whole wrapped alignment, but with a clip region that
+     * is restricted to the requested page; this supports selective print of 
+     * single pages or ranges, (at the cost of repeated processing in the 
+     * 'normal' case, when all pages are printed)
+     */
+    g.translate(0, -pageNumber * pageHeight);
 
-        pg.setFont(av.getFont());
-        labels.drawComponent(pg, idWidth);
-        pg.translate(+3, -ypos
-                - (av.getAlignment().getHeight() * av.getCharHeight()));
-      }
+    g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
 
-      ypos += cHeight;
-    } while (ypos < totalHeight);
+    /*
+     * draw sequence ids and annotation labels (if shown)
+     */
+    IdCanvas idCanvas = getIdPanel().getIdCanvas();
+    idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
 
-    pg.translate(idWidth, 0);
+    g.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth,
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
             totalHeight, 0);
 
-    if ((pi * pheight) < totalHeight)
+    if ((pageNumber * pageHeight) < totalHeight)
     {
       return Printable.PAGE_EXISTS;
-
     }
     else
     {
@@ -1261,21 +1152,22 @@ public class AlignmentPanel extends GAlignmentPanel implements
    *          be returned
    * @return
    */
-  public int getVisibleIdWidth(boolean onscreen)
+  protected int getVisibleIdWidth(boolean onscreen)
   {
     // see if rendering offscreen - check preferences and calc width accordingly
     if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
     {
-      return calculateIdWidth(-1).width + 4;
+      return calculateIdWidth(-1).width;
     }
-    Integer idwidth = null;
-    if (onscreen || (idwidth = Cache
-            .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
+    Integer idwidth = onscreen ? null
+            : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
+    if (idwidth != null)
     {
-      int w = getIdPanel().getWidth();
-      return (w > 0 ? w : calculateIdWidth().width + 4);
+      return idwidth.intValue() + ID_WIDTH_PADDING;
     }
-    return idwidth.intValue() + 4;
+
+    int w = getIdPanel().getWidth();
+    return (w > 0 ? w : calculateIdWidth().width);
   }
 
   /**
@@ -1326,12 +1218,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentDimension getAlignmentDimension()
   {
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
             + getScalePanel().getHeight();
@@ -1493,6 +1380,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   }
 
+  /**
+   * Answers the height of the entire alignment in pixels, assuming it is in
+   * wrapped mode
+   * 
+   * @return
+   */
   int getWrappedHeight()
   {
     int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
@@ -1517,6 +1410,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int annotationHeight = 0;
     if (av.isShowAnnotation())
     {
+      hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
       annotationHeight = getAnnotationPanel().adjustPanelHeight();
     }
 
@@ -1571,9 +1465,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      if (Cache.log.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.log.warn("Closing alignment panel which is already closed.");
+        Console.warn("Closing alignment panel which is already closed.");
       }
     }
   }
@@ -1625,7 +1519,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public String getViewName()
   {
-    return av.viewName;
+    return av.getViewName();
   }
 
   /**
@@ -1648,13 +1542,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
     } catch (Exception ex)
     {
     }
-
     if (b)
     {
-      alignFrame.setDisplayedView(this);
+      setAlignFrameView();
     }
   }
-
+  public void setAlignFrameView()
+  {
+    alignFrame.setDisplayedView(this);
+  }
+  
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
@@ -1756,7 +1653,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
-    scrollToPosition(sr, verticalOffset, true, true);
+    scrollToPosition(sr, verticalOffset, true);
   }
 
   /**
@@ -1843,4 +1740,5 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     return calculationDialog;
   }
+
 }