X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2Fappletgui%2FAlignmentPanel.java;h=36c50285690955068bb538db7dde8a6987348412;hb=6319110ce33faa76ee6cf9832e78faa224510fed;hp=92e6267b9205272afd4a43b6d1040d7e96e227cd;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44;p=jalviewjs.git

diff --git a/unused/appletgui/AlignmentPanel.java b/unused/appletgui/AlignmentPanel.java
index 92e6267..36c5028 100644
--- a/unused/appletgui/AlignmentPanel.java
+++ b/unused/appletgui/AlignmentPanel.java
@@ -1,1166 +1,1166 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- * 
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.analysis.AnnotationSorter;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.JalviewLite;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureSelectionManager;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-import java.awt.event.AdjustmentEvent;
-import java.awt.event.AdjustmentListener;
-import java.awt.event.ComponentAdapter;
-import java.awt.event.ComponentEvent;
-import java.util.List;
-
-import javax.swing.JPanel;
-import javax.swing.JFrame;
-import javax.swing.JScrollBar;
-
-public class AlignmentPanel extends JPanel implements AdjustmentListener,
-        AlignmentViewPanel
-{
-
-  public AlignViewport av;
-
-  OverviewPanel overviewPanel;
-
-  SeqPanel seqPanel;
-
-  IdPanel idPanel;
-
-  IdwidthAdjuster idwidthAdjuster;
-
-  public AlignFrame alignFrame;
-
-  ScalePanel scalePanel;
-
-  AnnotationPanel annotationPanel;
-
-  AnnotationLabels alabels;
-
-  // this value is set false when selection area being dragged
-  boolean fastPaint = true;
-
-  public void finalize()
-  {
-    alignFrame = null;
-    av = null;
-    seqPanel = null;
-    seqPanelHolder = null;
-    sequenceHolderPanel = null;
-    scalePanel = null;
-    scalePanelHolder = null;
-    annotationPanel = null;
-    annotationPanelHolder = null;
-    annotationSpaceFillerHolder = null;
-  }
-
-  public AlignmentPanel(AlignFrame af, final AlignViewport av)
-  {
-    try
-    {
-      jbInit();
-    } catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
-    alignFrame = af;
-    this.av = av;
-    seqPanel = new SeqPanel(av, this);
-    idPanel = new IdPanel(av, this);
-    scalePanel = new ScalePanel(av, this);
-    idwidthAdjuster = new IdwidthAdjuster(this);
-    annotationPanel = new AnnotationPanel(this);
-    annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
-
-    sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
-    alabels = new AnnotationLabels(this);
-
-    setAnnotationVisible(av.isShowAnnotation());
-
-    idPanelHolder.add(idPanel, BorderLayout.CENTER);
-    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
-    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
-    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-
-    fontChanged();
-    setScrollValues(0, 0);
-
-    apvscroll.addAdjustmentListener(this);
-    hscroll.addAdjustmentListener(this);
-    vscroll.addAdjustmentListener(this);
-
-    addComponentListener(new ComponentAdapter()
-    {
-      public void componentResized(ComponentEvent evt)
-      {
-        setScrollValues(av.getStartRes(), av.getStartSeq());
-        if (getSize().height > 0
-                && annotationPanelHolder.getSize().height > 0)
-        {
-          validateAnnotationDimensions(false);
-        }
-        repaint();
-      }
-
-    });
-
-    Dimension d = calculateIdWidth();
-    idPanel.idCanvas.setSize(d);
-
-    hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
-
-    idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
-    annotationSpaceFillerHolder.setSize(d.width,
-            annotationPanel.getSize().height);
-    alabels.setSize(d.width, annotationPanel.getSize().height);
-    final AlignmentPanel ap = this;
-    av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
-    {
-      public void propertyChange(java.beans.PropertyChangeEvent evt)
-      {
-        if (evt.getPropertyName().equals("alignment"))
-        {
-          PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
-          alignmentChanged();
-        }
-      }
-    });
-  }
-
-  @Override
-  public AlignViewportI getAlignViewport()
-  {
-    return av;
-  }
-  public SequenceRenderer getSequenceRenderer()
-  {
-    return seqPanel.seqCanvas.sr;
-  }
-  @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer()
-  {
-    return seqPanel.seqCanvas.fr;
-  }
-  @Override
-  public jalview.api.FeatureRenderer cloneFeatureRenderer()
-  {
-    FeatureRenderer nfr = new FeatureRenderer(av);
-    nfr.transferSettings(seqPanel.seqCanvas.fr);
-    return nfr;
-  }
-  public void alignmentChanged()
-  {
-    av.alignmentChanged(this);
-
-    if (overviewPanel != null)
-    {
-      overviewPanel.updateOverviewImage();
-    }
-
-    alignFrame.updateEditMenuBar();
-
-    repaint();
-  }
-
-  public void fontChanged()
-  {
-    // set idCanvas bufferedImage to null
-    // to prevent drawing old image
-    idPanel.idCanvas.image = null;
-    FontMetrics fm = getFontMetrics(av.getFont());
-
-    scalePanel.setSize(new Dimension(10, av.getCharHeight()
-            + fm.getDescent()));
-    idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
-            + fm.getDescent()));
-    av.updateSequenceIdColours();
-    annotationPanel.image = null;
-    int ap = annotationPanel.adjustPanelHeight(false);
-    Dimension d = calculateIdWidth();
-    d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
-    alabels.setSize(d.width + 4, ap);
-
-    idPanel.idCanvas.setSize(d);
-    hscrollFillerPanel.setSize(d);
-
-    validateAnnotationDimensions(false);
-    annotationPanel.repaint();
-    validate();
-    repaint();
-
-    if (overviewPanel != null)
-    {
-      overviewPanel.updateOverviewImage();
-    }
-  }
-
-  public void setIdWidth(int w, int h)
-  {
-    idPanel.idCanvas.setSize(w, h);
-    idPanelHolder.setSize(w, idPanelHolder.getSize().height);
-    annotationSpaceFillerHolder.setSize(w,
-            annotationSpaceFillerHolder.getSize().height);
-    alabels.setSize(w, alabels.getSize().height);
-    validate();
-  }
-
-  Dimension calculateIdWidth()
-  {
-    if (av.nullFrame == null)
-    {
-      av.nullFrame = new JFrame();
-      av.nullFrame.addNotify();
-    }
-
-    Graphics g = av.nullFrame.getGraphics();
-
-    FontMetrics fm = g.getFontMetrics(av.font);
-    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);
-      }
-      i++;
-    }
-
-    // Also check annotation label widths
-    i = 0;
-    if (al.getAlignmentAnnotation() != null)
-    {
-      fm = g.getFontMetrics(av.nullFrame.getFont());
-      while (i < al.getAlignmentAnnotation().length)
-      {
-        String label = al.getAlignmentAnnotation()[i].label;
-        if (fm.stringWidth(label) > idWidth)
-        {
-          idWidth = fm.stringWidth(label);
-        }
-        i++;
-      }
-    }
-
-    return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
-  }
-
-  /**
-   * Highlight the given results on the alignment.
-   * 
-   */
-  public void highlightSearchResults(SearchResults results)
-  {
-    scrollToPosition(results);
-    seqPanel.seqCanvas.highlightSearchResults(results);
-  }
-
-  /**
-   * scroll the view to show the position of the highlighted region in results
-   * (if any) and redraw the overview
-   * 
-   * @param results
-   * @return false if results were not found
-   */
-  public boolean scrollToPosition(SearchResults results)
-  {
-    return scrollToPosition(results, true);
-  }
-
-  /**
-   * scroll the view to show the position of the highlighted region in results
-   * (if any)
-   * 
-   * @param results
-   * @param redrawOverview
-   *          - when set, the overview will be recalculated (takes longer)
-   * @return false if results were not found
-   */
-  public boolean scrollToPosition(SearchResults results,
-          boolean redrawOverview)
-  {
-    return scrollToPosition(results, redrawOverview, false);
-  }
-
-  /**
-   * scroll the view to show the position of the highlighted region in results
-   * (if any)
-   * 
-   * @param results
-   * @param redrawOverview
-   *          - when set, the overview will be recalculated (takes longer)
-   * @return false if results were not found
-   */
-  public boolean scrollToPosition(SearchResults results,
-          boolean redrawOverview, boolean centre)
-  {
-    // do we need to scroll the panel?
-    if (results != null && results.getSize() > 0)
-    {
-      AlignmentI alignment = av.getAlignment();
-      int seqIndex = alignment.findIndex(results);
-      if (seqIndex == -1)
-      {
-        return false;
-      }
-      SequenceI seq = alignment.getSequenceAt(seqIndex);
-      int[] r = results.getResults(seq, 0, alignment.getWidth());
-      if (r == null)
-      {
-        if (JalviewLite.debug)
-        {// DEBUG
-          System.out
-                  .println("DEBUG: scroll didn't happen - results not within alignment : "
-                          + seq.getStart() + "," + seq.getEnd());
-        }
-        return false;
-      }
-      if (JalviewLite.debug)
-      {
-        // DEBUG
-        /*
-         * System.out.println("DEBUG: scroll: start=" + r[0] +
-         * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
-         * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
-         * " hextent=" + hextent);
-         */
-      }
-      int start = r[0];
-      int end = r[1];
-
-      /*
-       * To centre results, scroll to positions half the visible width
-       * left/right of the start/end positions
-       */
-      if (centre)
-      {
-        int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
-        start = Math.max(start - offset, 0);
-        end = Math.min(end + offset, seq.getEnd() - 1);
-      }
-
-      if (start < 0)
-      {
-        return false;
-      }
-      if (end == seq.getEnd())
-      {
-        return false;
-      }
-      return scrollTo(start, end, seqIndex, false, redrawOverview);
-    }
-    return true;
-  }
-
-  public boolean scrollTo(int ostart, int end, int seqIndex,
-          boolean scrollToNearest, boolean redrawOverview)
-  {
-    int startv, endv, starts, ends, width;
-
-    int start = -1;
-    if (av.hasHiddenColumns())
-    {
-      start = av.getColumnSelection().findColumnPosition(ostart);
-      end = av.getColumnSelection().findColumnPosition(end);
-      if (start == end)
-      {
-        if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
-        {
-          // don't scroll - position isn't visible
-          return false;
-        }
-      }
-    }
-    else
-    {
-      start = ostart;
-    }
-    if (!av.getWrapAlignment())
-    {
-      /*
-       * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
-       * av.getStartRes()) >= start) { spos=start-1; // seqIn //
-       * setScrollValues(start - 1, seqIndex); } else if ((endv =
-       * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
-       * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
-       * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
-       * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
-       * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
-       */
-
-      // below is scrolling logic up to Jalview 2.8.2
-      // if ((av.getStartRes() > end)
-      // || (av.getEndRes() < start)
-      // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
-      // {
-      // if (start > av.getAlignment().getWidth() - hextent)
-      // {
-      // start = av.getAlignment().getWidth() - hextent;
-      // if (start < 0)
-      // {
-      // start = 0;
-      // }
-      //
-      // }
-      // if (seqIndex > av.getAlignment().getHeight() - vextent)
-      // {
-      // seqIndex = av.getAlignment().getHeight() - vextent;
-      // if (seqIndex < 0)
-      // {
-      // seqIndex = 0;
-      // }
-      // }
-      // setScrollValues(start, seqIndex);
-      // }
-      // logic copied from jalview.gui.AlignmentPanel:
-        if ((startv = av.getStartRes()) >= start)
-        {
-          /*
-           * Scroll left to make start of search results visible
-           */
-          setScrollValues(start - 1, seqIndex);
-        }
-        else if ((endv = av.getEndRes()) <= end)
-        {
-          /*
-           * Scroll right to make end of search results visible
-           */
-          setScrollValues(startv + 1 + end - endv, seqIndex);
-        }
-        else if ((starts = av.getStartSeq()) > seqIndex)
-        {
-          /*
-           * Scroll up to make start of search results visible
-           */
-          setScrollValues(av.getStartRes(), seqIndex);
-        }
-        else if ((ends = av.getEndSeq()) <= seqIndex)
-        {
-          /*
-           * Scroll down to make end of search results visible
-           */
-          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
-        }
-        /*
-         * Else results are already visible - no need to scroll
-         */
-    }
-    else
-    {
-      scrollToWrappedVisible(start);
-    }
-    if (redrawOverview && overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
-    }
-    paintAlignment(redrawOverview);
-    return true;
-  }
-
-  void scrollToWrappedVisible(int res)
-  {
-    int cwidth = seqPanel.seqCanvas
-            .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
-    {
-      vscroll.setValue(res / cwidth);
-      av.startRes = vscroll.getValue() * cwidth;
-    }
-  }
-
-  public OverviewPanel getOverviewPanel()
-  {
-    return overviewPanel;
-  }
-
-  public void setOverviewPanel(OverviewPanel op)
-  {
-    overviewPanel = op;
-  }
-
-  public void setAnnotationVisible(boolean b)
-  {
-    if (!av.getWrapAlignment())
-    {
-      annotationSpaceFillerHolder.setVisible(b);
-      annotationPanelHolder.setVisible(b);
-    }
-    else
-    {
-      annotationSpaceFillerHolder.setVisible(false);
-      annotationPanelHolder.setVisible(false);
-    }
-    validate();
-    repaint();
-  }
-
-  /**
-   * automatically adjust annotation panel height for new annotation whilst
-   * ensuring the alignment is still visible.
-   */
-  public void adjustAnnotationHeight()
-  {
-    // TODO: display vertical annotation scrollbar if necessary
-    // this is called after loading new annotation onto alignment
-    if (alignFrame.getSize().height == 0)
-    {
-      System.out
-              .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
-    }
-    fontChanged();
-    validateAnnotationDimensions(true);
-    apvscroll.addNotify();
-    hscroll.addNotify();
-    validate();
-    paintAlignment(true);
-  }
-
-  /**
-   * Calculate the annotation dimensions and refresh slider values accordingly.
-   * Need to do repaints/notifys afterwards.
-   */
-  protected void validateAnnotationDimensions(boolean adjustPanelHeight)
-  {
-    int rowHeight = av.getCharHeight();
-    int alignmentHeight = rowHeight * av.getAlignment().getHeight();
-    int annotationHeight = av.calcPanelHeight();
-
-    int mheight = annotationHeight;
-    Dimension d = sequenceHolderPanel.getSize();
-
-    int availableHeight = d.height - scalePanelHolder.getHeight();
-
-    if (adjustPanelHeight)
-    {
-      /*
-       * 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 = annotationPanelHolder.getSize().height;
-    }
-
-    if (availableHeight - annotationHeight < 5)
-    {
-      annotationHeight = availableHeight;
-    }
-
-    annotationPanel.setSize(new Dimension(d.width, annotationHeight));
-    annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
-    // seqPanelHolder.setSize(d.width, seqandannot - height);
-    seqPanel.seqCanvas
-            .setSize(d.width, seqPanel.seqCanvas.getSize().height);
-
-    Dimension e = idPanel.getSize();
-    alabels.setSize(new Dimension(e.width, annotationHeight));
-    annotationSpaceFillerHolder.setSize(new Dimension(e.width,
-            annotationHeight));
-
-    int s = apvscroll.getValue();
-    if (s > mheight - annotationHeight)
-    {
-      s = 0;
-    }
-    apvscroll.setValues(s, annotationHeight, 0, mheight);
-    annotationPanel.setScrollOffset(apvscroll.getValue(), false);
-    alabels.setScrollOffset(apvscroll.getValue(), false);
-  }
-
-  public void setWrapAlignment(boolean wrap)
-  {
-    av.startSeq = 0;
-    av.startRes = 0;
-    scalePanelHolder.setVisible(!wrap);
-
-    hscroll.setVisible(!wrap);
-    idwidthAdjuster.setVisible(!wrap);
-
-    if (wrap)
-    {
-      annotationPanelHolder.setVisible(false);
-      annotationSpaceFillerHolder.setVisible(false);
-    }
-    else if (av.isShowAnnotation())
-    {
-      annotationPanelHolder.setVisible(true);
-      annotationSpaceFillerHolder.setVisible(true);
-    }
-
-    idSpaceFillerPanel1.setVisible(!wrap);
-
-    fontChanged(); // This is so that the scalePanel is resized correctly
-
-    validate();
-    sequenceHolderPanel.validate();
-    repaint();
-
-  }
-
-  int hextent = 0;
-
-  int vextent = 0;
-
-  // return value is true if the scroll is valid
-  public boolean scrollUp(boolean up)
-  {
-    if (up)
-    {
-      if (vscroll.getValue() < 1)
-      {
-        return false;
-      }
-      setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
-    }
-    else
-    {
-      if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
-      {
-        return false;
-      }
-      setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
-    }
-
-    repaint();
-    return true;
-  }
-
-  public boolean scrollRight(boolean right)
-  {
-    if (!right)
-    {
-      if (hscroll.getValue() < 1)
-      {
-        return false;
-      }
-      setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
-    }
-    else
-    {
-      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
-      {
-        return false;
-      }
-      setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
-    }
-
-    repaint();
-    return true;
-  }
-
-  public void setScrollValues(int x, int y)
-  {
-    int width = av.getAlignment().getWidth();
-    int height = av.getAlignment().getHeight();
-
-    if (av.hasHiddenColumns())
-    {
-      width = av.getColumnSelection().findColumnPosition(width);
-    }
-    if (x < 0)
-    {
-      x = 0;
-    }
-    ;
-
-    hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
-    vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
-
-    if (hextent > width)
-    {
-      hextent = width;
-    }
-
-    if (vextent > height)
-    {
-      vextent = height;
-    }
-
-    if ((hextent + x) > width)
-    {
-      System.err.println("hextent was " + hextent + " and x was " + x);
-
-      x = width - hextent;
-    }
-
-    if ((vextent + y) > height)
-    {
-      y = height - vextent;
-    }
-
-    if (y < 0)
-    {
-      y = 0;
-    }
-
-    if (x < 0)
-    {
-      System.err.println("x was " + x);
-      x = 0;
-    }
-
-    av.setStartSeq(y);
-
-    int endSeq = y + vextent;
-    if (endSeq > av.getAlignment().getHeight())
-    {
-      endSeq = av.getAlignment().getHeight();
-    }
-
-    av.setEndSeq(endSeq);
-    av.setStartRes(x);
-    av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
-            .getCharWidth())) - 1);
-
-    hscroll.setValues(x, hextent, 0, width);
-    vscroll.setValues(y, vextent, 0, height);
-
-    if (overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
-    }
-    sendViewPosition();
-
-  }
-
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
-
-    if (evt == null || evt.getSource() == apvscroll)
-    {
-      annotationPanel.setScrollOffset(apvscroll.getValue(), false);
-      alabels.setScrollOffset(apvscroll.getValue(), false);
-      // annotationPanel.image=null;
-      // alabels.image=null;
-      // alabels.repaint();
-      // annotationPanel.repaint();
-    }
-    if (evt == null || evt.getSource() == hscroll)
-    {
-      int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getSize().width
-              / av.getCharWidth() - 1);
-    }
-
-    if (evt == null || evt.getSource() == vscroll)
-    {
-      int offy = vscroll.getValue();
-      if (av.getWrapAlignment())
-      {
-        int rowSize = seqPanel.seqCanvas
-                .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes((vscroll.getValue() + 1) * rowSize);
-      }
-      else
-      {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
-                / av.getCharHeight());
-      }
-    }
-
-    if (overviewPanel != null)
-    {
-      overviewPanel.setBoxPosition();
-    }
-
-    int scrollX = av.startRes - oldX;
-    int scrollY = av.startSeq - oldY;
-
-    if (av.getWrapAlignment() || !fastPaint || av.MAC)
-    {
-      repaint();
-    }
-    else
-    {
-      // 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;
-      }
-
-      idPanel.idCanvas.fastPaint(scrollY);
-      seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
-
-      scalePanel.repaint();
-      if (av.isShowAnnotation())
-      {
-        annotationPanel.fastPaint(av.getStartRes() - oldX);
-      }
-    }
-    sendViewPosition();
-
-    /*
-     * If there is one, scroll the (Protein/cDNA) complementary alignment to
-     * match, unless we are ourselves doing that.
-     */
-    if (isFollowingComplementScroll())
-    {
-      setFollowingComplementScroll(false);
-    }
-    else
-    {
-      AlignmentPanel ap = getComplementPanel();
-      av.scrollComplementaryAlignment(ap);
-    }
-
-  }
-
-  /**
-   * A helper method to return the AlignmentPanel in the other (complementary)
-   * half of a SplitFrame view. Returns null if not in a SplitFrame.
-   * 
-   * @return
-   */
-  private AlignmentPanel getComplementPanel()
-  {
-    AlignmentPanel ap = null;
-    if (alignFrame != null)
-    {
-      SplitFrame sf = alignFrame.getSplitFrame();
-      if (sf != null)
-      {
-        AlignFrame other = sf.getComplement(alignFrame);
-        if (other != null)
-        {
-          ap = other.alignPanel;
-        }
-      }
-    }
-    return ap;
-  }
-
-  /**
-   * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
-   * The aim is to keep the two alignments 'lined up' on their centre columns.
-   * 
-   * @param sr
-   *          holds mapped region(s) of this alignment that we are scrolling
-   *          'to'; may be modified for sequence offset by this method
-   * @param seqOffset
-   *          the number of visible sequences to show above the mapped region
-   */
-  protected void scrollToCentre(SearchResults sr, int seqOffset)
-  {
-    /*
-     * To avoid jumpy vertical scrolling (if some sequences are gapped or not
-     * mapped), we can make the scroll-to location a sequence above the one
-     * actually mapped.
-     */
-    SequenceI mappedTo = sr.getResultSequence(0);
-    List<SequenceI> seqs = av.getAlignment().getSequences();
-
-    /*
-     * This is like AlignmentI.findIndex(seq) but here we are matching the
-     * dataset sequence not the aligned sequence
-     */
-    int sequenceIndex = 0;
-    boolean matched = false;
-    for (SequenceI seq : seqs)
-    {
-      if (mappedTo == seq.getDatasetSequence())
-      {
-        matched = true;
-        break;
-      }
-      sequenceIndex++;
-    }
-    if (!matched)
-    {
-      return; // failsafe, shouldn't happen
-    }
-    sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
-    sr.getResults().get(0)
-            .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
-
-    /*
-     * Scroll to position but centring the target residue. Also set a state flag
-     * to prevent adjustmentValueChanged performing this recursively.
-     */
-    setFollowingComplementScroll(true);
-    scrollToPosition(sr, true, true);
-  }
-
-  private void sendViewPosition()
-  {
-    StructureSelectionManager.getStructureSelectionManager(av.applet)
-            .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
-                    av.endSeq);
-  }
-
-  /**
-   * Repaint the alignment and annotations, and, optionally, any overview window
-   */
-  public void paintAlignment(boolean updateOverview)
-  {
-    final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
-            av.isShowAutocalculatedAbove());
-    sorter.sort(getAlignment().getAlignmentAnnotation(),
-            av.getSortAnnotationsBy());
-    repaint();
-
-    if (updateOverview)
-    {
-      StructureSelectionManager.getStructureSelectionManager(av.applet)
-              .sequenceColoursChanged(this);
-
-      if (overviewPanel != null)
-      {
-        overviewPanel.updateOverviewImage();
-      }
-    }
-  }
-
-  public void update(Graphics g)
-  {
-    paint(g);
-  }
-
-  public void paint(Graphics g)
-  {
-    invalidate();
-    Dimension d = idPanel.idCanvas.getSize();
-    final int canvasHeight = seqPanel.seqCanvas.getSize().height;
-    if (canvasHeight != d.height)
-    {
-      idPanel.idCanvas.setSize(d.width, canvasHeight);
-    }
-
-    if (av.getWrapAlignment())
-    {
-      int maxwidth = av.getAlignment().getWidth();
-
-      if (av.hasHiddenColumns())
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-      }
-
-      int canvasWidth = seqPanel.seqCanvas
-              .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-
-      if (canvasWidth > 0)
-      {
-        int max = maxwidth / canvasWidth;
-        vscroll.setMaximum(1 + max);
-        vscroll.setUnitIncrement(1);
-        vscroll.setVisibleAmount(1);
-      }
-    }
-    else
-    {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
-    }
-
-    seqPanel.seqCanvas.repaint();
-    idPanel.idCanvas.repaint();
-    if (!av.getWrapAlignment())
-    {
-      if (av.isShowAnnotation())
-      {
-        alabels.repaint();
-        annotationPanel.repaint();
-      }
-      scalePanel.repaint();
-    }
-
-  }
-
-  protected JPanel sequenceHolderPanel = new JPanel();
-
-  protected JScrollBar vscroll = new JScrollBar();
-
-  protected JScrollBar hscroll = new JScrollBar();
-
-  protected JPanel seqPanelHolder = new JPanel();
-
-  protected JPanel scalePanelHolder = new JPanel();
-
-  protected JPanel idPanelHolder = new JPanel();
-
-  protected JPanel idSpaceFillerPanel1 = new JPanel();
-
-  public JPanel annotationSpaceFillerHolder = new JPanel();
-
-  protected JPanel hscrollFillerPanel = new JPanel();
-
-  JPanel annotationPanelHolder = new JPanel();
-
-  protected JScrollBar apvscroll = new JScrollBar();
-
-  /*
-   * Flag set while scrolling to follow complementary cDNA/protein scroll. When
-   * true, suppresses invoking the same method recursively.
-   */
-  private boolean followingComplementScroll;
-
-  private void jbInit() throws Exception
-  {
-    // idPanelHolder.setPreferredSize(new Dimension(70, 10));
-    this.setLayout(new BorderLayout());
-
-    // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
-    sequenceHolderPanel.setLayout(new BorderLayout());
-    seqPanelHolder.setLayout(new BorderLayout());
-    scalePanelHolder.setBackground(Color.white);
-
-    // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
-    scalePanelHolder.setLayout(new BorderLayout());
-    idPanelHolder.setLayout(new BorderLayout());
-    idSpaceFillerPanel1.setBackground(Color.white);
-
-    // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
-    idSpaceFillerPanel1.setLayout(new BorderLayout());
-    annotationSpaceFillerHolder.setBackground(Color.white);
-
-    // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
-    annotationSpaceFillerHolder.setLayout(new BorderLayout());
-    hscroll.setOrientation(JScrollBar.HORIZONTAL);
-
-    JPanel hscrollHolder = new JPanel();
-    hscrollHolder.setLayout(new BorderLayout());
-    hscrollFillerPanel.setBackground(Color.white);
-    apvscroll.setOrientation(JScrollBar.VERTICAL);
-    apvscroll.setVisible(true);
-    apvscroll.addAdjustmentListener(this);
-
-    annotationPanelHolder.setBackground(Color.white);
-    annotationPanelHolder.setLayout(new BorderLayout());
-    annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
-    // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
-    hscrollHolder.setBackground(Color.white);
-
-    // annotationScroller.setPreferredSize(new Dimension(10, 80));
-    // this.setPreferredSize(new Dimension(220, 166));
-    seqPanelHolder.setBackground(Color.white);
-    idPanelHolder.setBackground(Color.white);
-    sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
-    sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
-    seqPanelHolder.add(vscroll, BorderLayout.EAST);
-
-    // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
-    this.add(idPanelHolder, BorderLayout.WEST);
-    idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
-    idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
-    this.add(hscrollHolder, BorderLayout.SOUTH);
-    hscrollHolder.add(hscroll, BorderLayout.CENTER);
-    hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
-    this.add(sequenceHolderPanel, BorderLayout.CENTER);
-  }
-
-  /**
-   * hides or shows dynamic annotation rows based on groups and av state flags
-   */
-  public void updateAnnotation()
-  {
-    updateAnnotation(false);
-  }
-
-  public void updateAnnotation(boolean applyGlobalSettings)
-  {
-    updateAnnotation(applyGlobalSettings, false);
-  }
-
-  public void updateAnnotation(boolean applyGlobalSettings,
-          boolean preserveNewGroupSettings)
-  {
-    av.updateGroupAnnotationSettings(applyGlobalSettings,
-            preserveNewGroupSettings);
-    adjustAnnotationHeight();
-  }
-
-  @Override
-  public AlignmentI getAlignment()
-  {
-    return av.getAlignment();
-  }
-
-  @Override
-  public String getViewName()
-  {
-    return getName();
-  }
-
-  @Override
-  public StructureSelectionManager getStructureSelectionManager()
-  {
-    return StructureSelectionManager
-            .getStructureSelectionManager(av.applet);
-  }
-
-  @Override
-  public void raiseOOMWarning(String string, OutOfMemoryError error)
-  {
-    // TODO: JAL-960
-    System.err.println("Out of memory whilst '" + string + "'");
-    error.printStackTrace();
-  }
-
-  /**
-   * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
-   * 
-   * @param b
-   */
-  protected void setFollowingComplementScroll(boolean b)
-  {
-    this.followingComplementScroll = b;
-  }
-
-  protected boolean isFollowingComplementScroll()
-  {
-    return this.followingComplementScroll;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.JFrame;
+import javax.swing.JScrollBar;
+
+public class AlignmentPanel extends JPanel implements AdjustmentListener,
+        AlignmentViewPanel
+{
+
+  public AlignViewport av;
+
+  OverviewPanel overviewPanel;
+
+  SeqPanel seqPanel;
+
+  IdPanel idPanel;
+
+  IdwidthAdjuster idwidthAdjuster;
+
+  public AlignFrame alignFrame;
+
+  ScalePanel scalePanel;
+
+  AnnotationPanel annotationPanel;
+
+  AnnotationLabels alabels;
+
+  // this value is set false when selection area being dragged
+  boolean fastPaint = true;
+
+  public void finalize()
+  {
+    alignFrame = null;
+    av = null;
+    seqPanel = null;
+    seqPanelHolder = null;
+    sequenceHolderPanel = null;
+    scalePanel = null;
+    scalePanelHolder = null;
+    annotationPanel = null;
+    annotationPanelHolder = null;
+    annotationSpaceFillerHolder = null;
+  }
+
+  public AlignmentPanel(AlignFrame af, final AlignViewport av)
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    alignFrame = af;
+    this.av = av;
+    seqPanel = new SeqPanel(av, this);
+    idPanel = new IdPanel(av, this);
+    scalePanel = new ScalePanel(av, this);
+    idwidthAdjuster = new IdwidthAdjuster(this);
+    annotationPanel = new AnnotationPanel(this);
+    annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
+
+    sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
+    alabels = new AnnotationLabels(this);
+
+    setAnnotationVisible(av.isShowAnnotation());
+
+    idPanelHolder.add(idPanel, BorderLayout.CENTER);
+    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+
+    fontChanged();
+    setScrollValues(0, 0);
+
+    apvscroll.addAdjustmentListener(this);
+    hscroll.addAdjustmentListener(this);
+    vscroll.addAdjustmentListener(this);
+
+    addComponentListener(new ComponentAdapter()
+    {
+      public void componentResized(ComponentEvent evt)
+      {
+        setScrollValues(av.getStartRes(), av.getStartSeq());
+        if (getSize().height > 0
+                && annotationPanelHolder.getSize().height > 0)
+        {
+          validateAnnotationDimensions(false);
+        }
+        repaint();
+      }
+
+    });
+
+    Dimension d = calculateIdWidth();
+    idPanel.idCanvas.setSize(d);
+
+    hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
+
+    idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+    annotationSpaceFillerHolder.setSize(d.width,
+            annotationPanel.getSize().height);
+    alabels.setSize(d.width, annotationPanel.getSize().height);
+    final AlignmentPanel ap = this;
+    av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+    {
+      public void propertyChange(java.beans.PropertyChangeEvent evt)
+      {
+        if (evt.getPropertyName().equals("alignment"))
+        {
+          PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
+          alignmentChanged();
+        }
+      }
+    });
+  }
+
+  @Override
+  public AlignViewportI getAlignViewport()
+  {
+    return av;
+  }
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return seqPanel.seqCanvas.sr;
+  }
+  @Override
+  public jalview.api.FeatureRenderer getFeatureRenderer()
+  {
+    return seqPanel.seqCanvas.fr;
+  }
+  @Override
+  public jalview.api.FeatureRenderer cloneFeatureRenderer()
+  {
+    FeatureRenderer nfr = new FeatureRenderer(av);
+    nfr.transferSettings(seqPanel.seqCanvas.fr);
+    return nfr;
+  }
+  public void alignmentChanged()
+  {
+    av.alignmentChanged(this);
+
+    if (overviewPanel != null)
+    {
+      overviewPanel.updateOverviewImage();
+    }
+
+    alignFrame.updateEditMenuBar();
+
+    repaint();
+  }
+
+  public void fontChanged()
+  {
+    // set idCanvas bufferedImage to null
+    // to prevent drawing old image
+    idPanel.idCanvas.image = null;
+    FontMetrics fm = getFontMetrics(av.getFont());
+
+    scalePanel.setSize(new Dimension(10, av.getCharHeight()
+            + fm.getDescent()));
+    idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
+            + fm.getDescent()));
+    av.updateSequenceIdColours();
+    annotationPanel.image = null;
+    int ap = annotationPanel.adjustPanelHeight(false);
+    Dimension d = calculateIdWidth();
+    d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
+    alabels.setSize(d.width + 4, ap);
+
+    idPanel.idCanvas.setSize(d);
+    hscrollFillerPanel.setSize(d);
+
+    validateAnnotationDimensions(false);
+    annotationPanel.repaint();
+    validate();
+    repaint();
+
+    if (overviewPanel != null)
+    {
+      overviewPanel.updateOverviewImage();
+    }
+  }
+
+  public void setIdWidth(int w, int h)
+  {
+    idPanel.idCanvas.setSize(w, h);
+    idPanelHolder.setSize(w, idPanelHolder.getSize().height);
+    annotationSpaceFillerHolder.setSize(w,
+            annotationSpaceFillerHolder.getSize().height);
+    alabels.setSize(w, alabels.getSize().height);
+    validate();
+  }
+
+  Dimension calculateIdWidth()
+  {
+    if (av.nullFrame == null)
+    {
+      av.nullFrame = new JFrame();
+      av.nullFrame.addNotify();
+    }
+
+    Graphics g = av.nullFrame.getGraphics();
+
+    FontMetrics fm = g.getFontMetrics(av.font);
+    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);
+      }
+      i++;
+    }
+
+    // Also check annotation label widths
+    i = 0;
+    if (al.getAlignmentAnnotation() != null)
+    {
+      fm = g.getFontMetrics(av.nullFrame.getFont());
+      while (i < al.getAlignmentAnnotation().length)
+      {
+        String label = al.getAlignmentAnnotation()[i].label;
+        if (fm.stringWidth(label) > idWidth)
+        {
+          idWidth = fm.stringWidth(label);
+        }
+        i++;
+      }
+    }
+
+    return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
+  }
+
+  /**
+   * Highlight the given results on the alignment.
+   * 
+   */
+  public void highlightSearchResults(SearchResults results)
+  {
+    scrollToPosition(results);
+    seqPanel.seqCanvas.highlightSearchResults(results);
+  }
+
+  /**
+   * scroll the view to show the position of the highlighted region in results
+   * (if any) and redraw the overview
+   * 
+   * @param results
+   * @return false if results were not found
+   */
+  public boolean scrollToPosition(SearchResults results)
+  {
+    return scrollToPosition(results, true);
+  }
+
+  /**
+   * scroll the view to show the position of the highlighted region in results
+   * (if any)
+   * 
+   * @param results
+   * @param redrawOverview
+   *          - when set, the overview will be recalculated (takes longer)
+   * @return false if results were not found
+   */
+  public boolean scrollToPosition(SearchResults results,
+          boolean redrawOverview)
+  {
+    return scrollToPosition(results, redrawOverview, false);
+  }
+
+  /**
+   * scroll the view to show the position of the highlighted region in results
+   * (if any)
+   * 
+   * @param results
+   * @param redrawOverview
+   *          - when set, the overview will be recalculated (takes longer)
+   * @return false if results were not found
+   */
+  public boolean scrollToPosition(SearchResults results,
+          boolean redrawOverview, boolean centre)
+  {
+    // do we need to scroll the panel?
+    if (results != null && results.getSize() > 0)
+    {
+      AlignmentI alignment = av.getAlignment();
+      int seqIndex = alignment.findIndex(results);
+      if (seqIndex == -1)
+      {
+        return false;
+      }
+      SequenceI seq = alignment.getSequenceAt(seqIndex);
+      int[] r = results.getResults(seq, 0, alignment.getWidth());
+      if (r == null)
+      {
+        if (JalviewLite.debug)
+        {// DEBUG
+          System.out
+                  .println("DEBUG: scroll didn't happen - results not within alignment : "
+                          + seq.getStart() + "," + seq.getEnd());
+        }
+        return false;
+      }
+      if (JalviewLite.debug)
+      {
+        // DEBUG
+        /*
+         * System.out.println("DEBUG: scroll: start=" + r[0] +
+         * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
+         * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
+         * " hextent=" + hextent);
+         */
+      }
+      int start = r[0];
+      int end = r[1];
+
+      /*
+       * To centre results, scroll to positions half the visible width
+       * left/right of the start/end positions
+       */
+      if (centre)
+      {
+        int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+        start = Math.max(start - offset, 0);
+        end = Math.min(end + offset, seq.getEnd() - 1);
+      }
+
+      if (start < 0)
+      {
+        return false;
+      }
+      if (end == seq.getEnd())
+      {
+        return false;
+      }
+      return scrollTo(start, end, seqIndex, false, redrawOverview);
+    }
+    return true;
+  }
+
+  public boolean scrollTo(int ostart, int end, int seqIndex,
+          boolean scrollToNearest, boolean redrawOverview)
+  {
+    int startv, endv, starts, ends, width;
+
+    int start = -1;
+    if (av.hasHiddenColumns())
+    {
+      start = av.getColumnSelection().findColumnPosition(ostart);
+      end = av.getColumnSelection().findColumnPosition(end);
+      if (start == end)
+      {
+        if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
+        {
+          // don't scroll - position isn't visible
+          return false;
+        }
+      }
+    }
+    else
+    {
+      start = ostart;
+    }
+    if (!av.getWrapAlignment())
+    {
+      /*
+       * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
+       * av.getStartRes()) >= start) { spos=start-1; // seqIn //
+       * setScrollValues(start - 1, seqIndex); } else if ((endv =
+       * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
+       * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
+       * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
+       * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
+       * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
+       */
+
+      // below is scrolling logic up to Jalview 2.8.2
+      // if ((av.getStartRes() > end)
+      // || (av.getEndRes() < start)
+      // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+      // {
+      // if (start > av.getAlignment().getWidth() - hextent)
+      // {
+      // start = av.getAlignment().getWidth() - hextent;
+      // if (start < 0)
+      // {
+      // start = 0;
+      // }
+      //
+      // }
+      // if (seqIndex > av.getAlignment().getHeight() - vextent)
+      // {
+      // seqIndex = av.getAlignment().getHeight() - vextent;
+      // if (seqIndex < 0)
+      // {
+      // seqIndex = 0;
+      // }
+      // }
+      // setScrollValues(start, seqIndex);
+      // }
+      // logic copied from jalview.gui.AlignmentPanel:
+        if ((startv = av.getStartRes()) >= start)
+        {
+          /*
+           * Scroll left to make start of search results visible
+           */
+          setScrollValues(start - 1, seqIndex);
+        }
+        else if ((endv = av.getEndRes()) <= end)
+        {
+          /*
+           * Scroll right to make end of search results visible
+           */
+          setScrollValues(startv + 1 + end - endv, seqIndex);
+        }
+        else if ((starts = av.getStartSeq()) > seqIndex)
+        {
+          /*
+           * Scroll up to make start of search results visible
+           */
+          setScrollValues(av.getStartRes(), seqIndex);
+        }
+        else if ((ends = av.getEndSeq()) <= seqIndex)
+        {
+          /*
+           * Scroll down to make end of search results visible
+           */
+          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+        }
+        /*
+         * Else results are already visible - no need to scroll
+         */
+    }
+    else
+    {
+      scrollToWrappedVisible(start);
+    }
+    if (redrawOverview && overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
+    paintAlignment(redrawOverview);
+    return true;
+  }
+
+  void scrollToWrappedVisible(int res)
+  {
+    int cwidth = seqPanel.seqCanvas
+            .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    {
+      vscroll.setValue(res / cwidth);
+      av.startRes = vscroll.getValue() * cwidth;
+    }
+  }
+
+  public OverviewPanel getOverviewPanel()
+  {
+    return overviewPanel;
+  }
+
+  public void setOverviewPanel(OverviewPanel op)
+  {
+    overviewPanel = op;
+  }
+
+  public void setAnnotationVisible(boolean b)
+  {
+    if (!av.getWrapAlignment())
+    {
+      annotationSpaceFillerHolder.setVisible(b);
+      annotationPanelHolder.setVisible(b);
+    }
+    else
+    {
+      annotationSpaceFillerHolder.setVisible(false);
+      annotationPanelHolder.setVisible(false);
+    }
+    validate();
+    repaint();
+  }
+
+  /**
+   * automatically adjust annotation panel height for new annotation whilst
+   * ensuring the alignment is still visible.
+   */
+  public void adjustAnnotationHeight()
+  {
+    // TODO: display vertical annotation scrollbar if necessary
+    // this is called after loading new annotation onto alignment
+    if (alignFrame.getSize().height == 0)
+    {
+      System.out
+              .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
+    }
+    fontChanged();
+    validateAnnotationDimensions(true);
+    apvscroll.addNotify();
+    hscroll.addNotify();
+    validate();
+    paintAlignment(true);
+  }
+
+  /**
+   * Calculate the annotation dimensions and refresh slider values accordingly.
+   * Need to do repaints/notifys afterwards.
+   */
+  protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+  {
+    int rowHeight = av.getCharHeight();
+    int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+    int annotationHeight = av.calcPanelHeight();
+
+    int mheight = annotationHeight;
+    Dimension d = sequenceHolderPanel.getSize();
+
+    int availableHeight = d.height - scalePanelHolder.getHeight();
+
+    if (adjustPanelHeight)
+    {
+      /*
+       * 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 = annotationPanelHolder.getSize().height;
+    }
+
+    if (availableHeight - annotationHeight < 5)
+    {
+      annotationHeight = availableHeight;
+    }
+
+    annotationPanel.setSize(new Dimension(d.width, annotationHeight));
+    annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
+    // seqPanelHolder.setSize(d.width, seqandannot - height);
+    seqPanel.seqCanvas
+            .setSize(d.width, seqPanel.seqCanvas.getSize().height);
+
+    Dimension e = idPanel.getSize();
+    alabels.setSize(new Dimension(e.width, annotationHeight));
+    annotationSpaceFillerHolder.setSize(new Dimension(e.width,
+            annotationHeight));
+
+    int s = apvscroll.getValue();
+    if (s > mheight - annotationHeight)
+    {
+      s = 0;
+    }
+    apvscroll.setValues(s, annotationHeight, 0, mheight);
+    annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+    alabels.setScrollOffset(apvscroll.getValue(), false);
+  }
+
+  public void setWrapAlignment(boolean wrap)
+  {
+    av.startSeq = 0;
+    av.startRes = 0;
+    scalePanelHolder.setVisible(!wrap);
+
+    hscroll.setVisible(!wrap);
+    idwidthAdjuster.setVisible(!wrap);
+
+    if (wrap)
+    {
+      annotationPanelHolder.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
+    else if (av.isShowAnnotation())
+    {
+      annotationPanelHolder.setVisible(true);
+      annotationSpaceFillerHolder.setVisible(true);
+    }
+
+    idSpaceFillerPanel1.setVisible(!wrap);
+
+    fontChanged(); // This is so that the scalePanel is resized correctly
+
+    validate();
+    sequenceHolderPanel.validate();
+    repaint();
+
+  }
+
+  int hextent = 0;
+
+  int vextent = 0;
+
+  // return value is true if the scroll is valid
+  public boolean scrollUp(boolean up)
+  {
+    if (up)
+    {
+      if (vscroll.getValue() < 1)
+      {
+        return false;
+      }
+      setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
+    }
+    else
+    {
+      if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
+      {
+        return false;
+      }
+      setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
+    }
+
+    repaint();
+    return true;
+  }
+
+  public boolean scrollRight(boolean right)
+  {
+    if (!right)
+    {
+      if (hscroll.getValue() < 1)
+      {
+        return false;
+      }
+      setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
+    }
+    else
+    {
+      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+      {
+        return false;
+      }
+      setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
+    }
+
+    repaint();
+    return true;
+  }
+
+  public void setScrollValues(int x, int y)
+  {
+    int width = av.getAlignment().getWidth();
+    int height = av.getAlignment().getHeight();
+
+    if (av.hasHiddenColumns())
+    {
+      width = av.getColumnSelection().findColumnPosition(width);
+    }
+    if (x < 0)
+    {
+      x = 0;
+    }
+    ;
+
+    hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
+    vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
+
+    if (hextent > width)
+    {
+      hextent = width;
+    }
+
+    if (vextent > height)
+    {
+      vextent = height;
+    }
+
+    if ((hextent + x) > width)
+    {
+      System.err.println("hextent was " + hextent + " and x was " + x);
+
+      x = width - hextent;
+    }
+
+    if ((vextent + y) > height)
+    {
+      y = height - vextent;
+    }
+
+    if (y < 0)
+    {
+      y = 0;
+    }
+
+    if (x < 0)
+    {
+      System.err.println("x was " + x);
+      x = 0;
+    }
+
+    av.setStartSeq(y);
+
+    int endSeq = y + vextent;
+    if (endSeq > av.getAlignment().getHeight())
+    {
+      endSeq = av.getAlignment().getHeight();
+    }
+
+    av.setEndSeq(endSeq);
+    av.setStartRes(x);
+    av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+            .getCharWidth())) - 1);
+
+    hscroll.setValues(x, hextent, 0, width);
+    vscroll.setValues(y, vextent, 0, height);
+
+    if (overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
+    sendViewPosition();
+
+  }
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    int oldX = av.getStartRes();
+    int oldY = av.getStartSeq();
+
+    if (evt == null || evt.getSource() == apvscroll)
+    {
+      annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+      alabels.setScrollOffset(apvscroll.getValue(), false);
+      // annotationPanel.image=null;
+      // alabels.image=null;
+      // alabels.repaint();
+      // annotationPanel.repaint();
+    }
+    if (evt == null || evt.getSource() == hscroll)
+    {
+      int x = hscroll.getValue();
+      av.setStartRes(x);
+      av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+              / av.getCharWidth() - 1);
+    }
+
+    if (evt == null || evt.getSource() == vscroll)
+    {
+      int offy = vscroll.getValue();
+      if (av.getWrapAlignment())
+      {
+        int rowSize = seqPanel.seqCanvas
+                .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+        av.setStartRes(vscroll.getValue() * rowSize);
+        av.setEndRes((vscroll.getValue() + 1) * rowSize);
+      }
+      else
+      {
+        av.setStartSeq(offy);
+        av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+                / av.getCharHeight());
+      }
+    }
+
+    if (overviewPanel != null)
+    {
+      overviewPanel.setBoxPosition();
+    }
+
+    int scrollX = av.startRes - oldX;
+    int scrollY = av.startSeq - oldY;
+
+    if (av.getWrapAlignment() || !fastPaint || av.MAC)
+    {
+      repaint();
+    }
+    else
+    {
+      // 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;
+      }
+
+      idPanel.idCanvas.fastPaint(scrollY);
+      seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
+
+      scalePanel.repaint();
+      if (av.isShowAnnotation())
+      {
+        annotationPanel.fastPaint(av.getStartRes() - oldX);
+      }
+    }
+    sendViewPosition();
+
+    /*
+     * If there is one, scroll the (Protein/cDNA) complementary alignment to
+     * match, unless we are ourselves doing that.
+     */
+    if (isFollowingComplementScroll())
+    {
+      setFollowingComplementScroll(false);
+    }
+    else
+    {
+      AlignmentPanel ap = getComplementPanel();
+      av.scrollComplementaryAlignment(ap);
+    }
+
+  }
+
+  /**
+   * A helper method to return the AlignmentPanel in the other (complementary)
+   * half of a SplitFrame view. Returns null if not in a SplitFrame.
+   * 
+   * @return
+   */
+  private AlignmentPanel getComplementPanel()
+  {
+    AlignmentPanel ap = null;
+    if (alignFrame != null)
+    {
+      SplitFrame sf = alignFrame.getSplitFrame();
+      if (sf != null)
+      {
+        AlignFrame other = sf.getComplement(alignFrame);
+        if (other != null)
+        {
+          ap = other.alignPanel;
+        }
+      }
+    }
+    return ap;
+  }
+
+  /**
+   * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
+   * The aim is to keep the two alignments 'lined up' on their centre columns.
+   * 
+   * @param sr
+   *          holds mapped region(s) of this alignment that we are scrolling
+   *          'to'; may be modified for sequence offset by this method
+   * @param seqOffset
+   *          the number of visible sequences to show above the mapped region
+   */
+  protected void scrollToCentre(SearchResults sr, int seqOffset)
+  {
+    /*
+     * To avoid jumpy vertical scrolling (if some sequences are gapped or not
+     * mapped), we can make the scroll-to location a sequence above the one
+     * actually mapped.
+     */
+    SequenceI mappedTo = sr.getResultSequence(0);
+    List<SequenceI> seqs = av.getAlignment().getSequences();
+
+    /*
+     * This is like AlignmentI.findIndex(seq) but here we are matching the
+     * dataset sequence not the aligned sequence
+     */
+    int sequenceIndex = 0;
+    boolean matched = false;
+    for (SequenceI seq : seqs)
+    {
+      if (mappedTo == seq.getDatasetSequence())
+      {
+        matched = true;
+        break;
+      }
+      sequenceIndex++;
+    }
+    if (!matched)
+    {
+      return; // failsafe, shouldn't happen
+    }
+    sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
+    sr.getResults().get(0)
+            .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
+
+    /*
+     * Scroll to position but centring the target residue. Also set a state flag
+     * to prevent adjustmentValueChanged performing this recursively.
+     */
+    setFollowingComplementScroll(true);
+    scrollToPosition(sr, true, true);
+  }
+
+  private void sendViewPosition()
+  {
+    StructureSelectionManager.getStructureSelectionManager(av.applet)
+            .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
+                    av.endSeq);
+  }
+
+  /**
+   * Repaint the alignment and annotations, and, optionally, any overview window
+   */
+  public void paintAlignment(boolean updateOverview)
+  {
+    final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+            av.isShowAutocalculatedAbove());
+    sorter.sort(getAlignment().getAlignmentAnnotation(),
+            av.getSortAnnotationsBy());
+    repaint();
+
+    if (updateOverview)
+    {
+      StructureSelectionManager.getStructureSelectionManager(av.applet)
+              .sequenceColoursChanged(this);
+
+      if (overviewPanel != null)
+      {
+        overviewPanel.updateOverviewImage();
+      }
+    }
+  }
+
+  public void update(Graphics g)
+  {
+    paint(g);
+  }
+
+  public void paint(Graphics g)
+  {
+    invalidate();
+    Dimension d = idPanel.idCanvas.getSize();
+    final int canvasHeight = seqPanel.seqCanvas.getSize().height;
+    if (canvasHeight != d.height)
+    {
+      idPanel.idCanvas.setSize(d.width, canvasHeight);
+    }
+
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.getAlignment().getWidth();
+
+      if (av.hasHiddenColumns())
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
+
+      int canvasWidth = seqPanel.seqCanvas
+              .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+
+      if (canvasWidth > 0)
+      {
+        int max = maxwidth / canvasWidth;
+        vscroll.setMaximum(1 + max);
+        vscroll.setUnitIncrement(1);
+        vscroll.setVisibleAmount(1);
+      }
+    }
+    else
+    {
+      setScrollValues(av.getStartRes(), av.getStartSeq());
+    }
+
+    seqPanel.seqCanvas.repaint();
+    idPanel.idCanvas.repaint();
+    if (!av.getWrapAlignment())
+    {
+      if (av.isShowAnnotation())
+      {
+        alabels.repaint();
+        annotationPanel.repaint();
+      }
+      scalePanel.repaint();
+    }
+
+  }
+
+  protected JPanel sequenceHolderPanel = new JPanel();
+
+  protected JScrollBar vscroll = new JScrollBar();
+
+  protected JScrollBar hscroll = new JScrollBar();
+
+  protected JPanel seqPanelHolder = new JPanel();
+
+  protected JPanel scalePanelHolder = new JPanel();
+
+  protected JPanel idPanelHolder = new JPanel();
+
+  protected JPanel idSpaceFillerPanel1 = new JPanel();
+
+  public JPanel annotationSpaceFillerHolder = new JPanel();
+
+  protected JPanel hscrollFillerPanel = new JPanel();
+
+  JPanel annotationPanelHolder = new JPanel();
+
+  protected JScrollBar apvscroll = new JScrollBar();
+
+  /*
+   * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+   * true, suppresses invoking the same method recursively.
+   */
+  private boolean followingComplementScroll;
+
+  private void jbInit() throws Exception
+  {
+    // idPanelHolder.setPreferredSize(new Dimension(70, 10));
+    this.setLayout(new BorderLayout());
+
+    // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+    sequenceHolderPanel.setLayout(new BorderLayout());
+    seqPanelHolder.setLayout(new BorderLayout());
+    scalePanelHolder.setBackground(Color.white);
+
+    // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
+    scalePanelHolder.setLayout(new BorderLayout());
+    idPanelHolder.setLayout(new BorderLayout());
+    idSpaceFillerPanel1.setBackground(Color.white);
+
+    // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+    idSpaceFillerPanel1.setLayout(new BorderLayout());
+    annotationSpaceFillerHolder.setBackground(Color.white);
+
+    // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+    annotationSpaceFillerHolder.setLayout(new BorderLayout());
+    hscroll.setOrientation(JScrollBar.HORIZONTAL);
+
+    JPanel hscrollHolder = new JPanel();
+    hscrollHolder.setLayout(new BorderLayout());
+    hscrollFillerPanel.setBackground(Color.white);
+    apvscroll.setOrientation(JScrollBar.VERTICAL);
+    apvscroll.setVisible(true);
+    apvscroll.addAdjustmentListener(this);
+
+    annotationPanelHolder.setBackground(Color.white);
+    annotationPanelHolder.setLayout(new BorderLayout());
+    annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
+    // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+    hscrollHolder.setBackground(Color.white);
+
+    // annotationScroller.setPreferredSize(new Dimension(10, 80));
+    // this.setPreferredSize(new Dimension(220, 166));
+    seqPanelHolder.setBackground(Color.white);
+    idPanelHolder.setBackground(Color.white);
+    sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+    sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
+    seqPanelHolder.add(vscroll, BorderLayout.EAST);
+
+    // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
+    this.add(idPanelHolder, BorderLayout.WEST);
+    idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
+    idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
+    this.add(hscrollHolder, BorderLayout.SOUTH);
+    hscrollHolder.add(hscroll, BorderLayout.CENTER);
+    hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
+    this.add(sequenceHolderPanel, BorderLayout.CENTER);
+  }
+
+  /**
+   * hides or shows dynamic annotation rows based on groups and av state flags
+   */
+  public void updateAnnotation()
+  {
+    updateAnnotation(false);
+  }
+
+  public void updateAnnotation(boolean applyGlobalSettings)
+  {
+    updateAnnotation(applyGlobalSettings, false);
+  }
+
+  public void updateAnnotation(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings)
+  {
+    av.updateGroupAnnotationSettings(applyGlobalSettings,
+            preserveNewGroupSettings);
+    adjustAnnotationHeight();
+  }
+
+  @Override
+  public AlignmentI getAlignment()
+  {
+    return av.getAlignment();
+  }
+
+  @Override
+  public String getViewName()
+  {
+    return getName();
+  }
+
+  @Override
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return StructureSelectionManager
+            .getStructureSelectionManager(av.applet);
+  }
+
+  @Override
+  public void raiseOOMWarning(String string, OutOfMemoryError error)
+  {
+    // TODO: JAL-960
+    System.err.println("Out of memory whilst '" + string + "'");
+    error.printStackTrace();
+  }
+
+  /**
+   * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+   * 
+   * @param b
+   */
+  protected void setFollowingComplementScroll(boolean b)
+  {
+    this.followingComplementScroll = b;
+  }
+
+  protected boolean isFollowingComplementScroll()
+  {
+    return this.followingComplementScroll;
+  }
+
+}