2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.api.AlignViewportI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.SearchResults;
27 import jalview.datamodel.SequenceI;
28 import jalview.structure.StructureSelectionManager;
30 import java.awt.BorderLayout;
31 import java.awt.Color;
32 import java.awt.Dimension;
33 import java.awt.FontMetrics;
34 import java.awt.Frame;
35 import java.awt.Graphics;
36 import java.awt.Panel;
37 import java.awt.Scrollbar;
38 import java.awt.event.AdjustmentEvent;
39 import java.awt.event.AdjustmentListener;
40 import java.awt.event.ComponentAdapter;
41 import java.awt.event.ComponentEvent;
43 public class AlignmentPanel extends Panel implements AdjustmentListener,
47 public AlignViewport av;
49 OverviewPanel overviewPanel;
55 IdwidthAdjuster idwidthAdjuster;
57 public AlignFrame alignFrame;
59 ScalePanel scalePanel;
61 AnnotationPanel annotationPanel;
63 AnnotationLabels alabels;
65 // this value is set false when selection area being dragged
66 boolean fastPaint = true;
68 public void finalize()
73 seqPanelHolder = null;
74 sequenceHolderPanel = null;
76 scalePanelHolder = null;
77 annotationPanel = null;
78 annotationPanelHolder = null;
79 annotationSpaceFillerHolder = null;
82 public AlignmentPanel(AlignFrame af, final AlignViewport av)
94 seqPanel = new SeqPanel(av, this);
95 idPanel = new IdPanel(av, this);
96 scalePanel = new ScalePanel(av, this);
97 idwidthAdjuster = new IdwidthAdjuster(this);
98 annotationPanel = new AnnotationPanel(this);
99 annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
101 sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
102 alabels = new AnnotationLabels(this);
104 setAnnotationVisible(av.isShowAnnotation());
106 idPanelHolder.add(idPanel, BorderLayout.CENTER);
107 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
108 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
109 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
110 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
113 setScrollValues(0, 0);
115 apvscroll.addAdjustmentListener(this);
116 hscroll.addAdjustmentListener(this);
117 vscroll.addAdjustmentListener(this);
119 addComponentListener(new ComponentAdapter()
121 public void componentResized(ComponentEvent evt)
123 setScrollValues(av.getStartRes(), av.getStartSeq());
124 if (getSize().height > 0
125 && annotationPanelHolder.getSize().height > 0)
127 validateAnnotationDimensions(false);
134 Dimension d = calculateIdWidth();
135 idPanel.idCanvas.setSize(d);
137 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
139 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
140 annotationSpaceFillerHolder.setSize(d.width,
141 annotationPanel.getSize().height);
142 alabels.setSize(d.width, annotationPanel.getSize().height);
143 final AlignmentPanel ap = this;
144 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
146 public void propertyChange(java.beans.PropertyChangeEvent evt)
148 if (evt.getPropertyName().equals("alignment"))
150 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
158 public AlignViewportI getAlignViewport()
162 public SequenceRenderer getSequenceRenderer()
164 return seqPanel.seqCanvas.sr;
167 public jalview.api.FeatureRenderer getFeatureRenderer()
169 return seqPanel.seqCanvas.fr;
172 public jalview.api.FeatureRenderer cloneFeatureRenderer()
174 FeatureRenderer nfr = new FeatureRenderer(av);
175 nfr.transferSettings(seqPanel.seqCanvas.fr);
178 public void alignmentChanged()
180 av.alignmentChanged(this);
182 if (overviewPanel != null)
184 overviewPanel.updateOverviewImage();
187 alignFrame.updateEditMenuBar();
192 public void fontChanged()
194 // set idCanvas bufferedImage to null
195 // to prevent drawing old image
196 idPanel.idCanvas.image = null;
197 FontMetrics fm = getFontMetrics(av.getFont());
199 scalePanel.setSize(new Dimension(10, av.getCharHeight()
201 idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
203 av.updateSequenceIdColours();
204 annotationPanel.image = null;
205 int ap = annotationPanel.adjustPanelHeight(false);
206 Dimension d = calculateIdWidth();
207 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
208 alabels.setSize(d.width + 4, ap);
210 idPanel.idCanvas.setSize(d);
211 hscrollFillerPanel.setSize(d);
213 validateAnnotationDimensions(false);
214 annotationPanel.repaint();
218 if (overviewPanel != null)
220 overviewPanel.updateOverviewImage();
224 public void setIdWidth(int w, int h)
226 idPanel.idCanvas.setSize(w, h);
227 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
228 annotationSpaceFillerHolder.setSize(w,
229 annotationSpaceFillerHolder.getSize().height);
230 alabels.setSize(w, alabels.getSize().height);
234 Dimension calculateIdWidth()
236 if (av.nullFrame == null)
238 av.nullFrame = new Frame();
239 av.nullFrame.addNotify();
242 Graphics g = av.nullFrame.getGraphics();
244 FontMetrics fm = g.getFontMetrics(av.font);
245 AlignmentI al = av.getAlignment();
250 while (i < al.getHeight() && al.getSequenceAt(i) != null)
252 SequenceI s = al.getSequenceAt(i);
253 id = s.getDisplayId(av.getShowJVSuffix());
255 if (fm.stringWidth(id) > idWidth)
257 idWidth = fm.stringWidth(id);
262 // Also check annotation label widths
264 if (al.getAlignmentAnnotation() != null)
266 fm = g.getFontMetrics(av.nullFrame.getFont());
267 while (i < al.getAlignmentAnnotation().length)
269 String label = al.getAlignmentAnnotation()[i].label;
270 if (fm.stringWidth(label) > idWidth)
272 idWidth = fm.stringWidth(label);
278 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
282 * Highlight the given results on the alignment.
285 public void highlightSearchResults(SearchResults results)
287 scrollToPosition(results);
288 seqPanel.seqCanvas.highlightSearchResults(results);
292 * scroll the view to show the position of the highlighted region in results
293 * (if any) and redraw the overview
296 * @return false if results were not found
298 public boolean scrollToPosition(SearchResults results)
300 return scrollToPosition(results, true);
304 * scroll the view to show the position of the highlighted region in results
308 * @param redrawOverview
309 * - when set, the overview will be recalculated (takes longer)
310 * @return false if results were not found
312 public boolean scrollToPosition(SearchResults results,
313 boolean redrawOverview)
316 // do we need to scroll the panel?
317 if (results != null && results.getSize() > 0)
319 AlignmentI alignment = av.getAlignment();
320 int seqIndex = alignment.findIndex(results);
325 SequenceI seq = alignment.getSequenceAt(seqIndex);
326 int[] r = results.getResults(seq, 0, alignment.getWidth());
332 .println("DEBUG: scroll didn't happen - results not within alignment : "
333 + seq.getStart() + "," + seq.getEnd());
341 * System.out.println("DEBUG: scroll: start=" + r[0] +
342 * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
343 * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
344 * " hextent=" + hextent);
353 if (end == seq.getEnd())
357 return scrollTo(start, end, seqIndex, false, redrawOverview);
362 public boolean scrollTo(int ostart, int end, int seqIndex,
363 boolean scrollToNearest, boolean redrawOverview)
365 int startv, endv, starts, ends, width;
368 if (av.hasHiddenColumns())
370 start = av.getColumnSelection().findColumnPosition(ostart);
371 end = av.getColumnSelection().findColumnPosition(end);
374 if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
376 // don't scroll - position isn't visible
385 if (!av.getWrapAlignment())
388 * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
389 * av.getStartRes()) >= start) { spos=start-1; // seqIn //
390 * setScrollValues(start - 1, seqIndex); } else if ((endv =
391 * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
392 * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
393 * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
394 * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
395 * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
399 if ((av.getStartRes() > end)
400 || (av.getEndRes() < start)
401 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
403 if (start > av.getAlignment().getWidth() - hextent)
405 start = av.getAlignment().getWidth() - hextent;
412 if (seqIndex > av.getAlignment().getHeight() - vextent)
414 seqIndex = av.getAlignment().getHeight() - vextent;
420 // System.out.println("trying to scroll to: "+start+" "+seqIndex);
421 setScrollValues(start, seqIndex);
426 scrollToWrappedVisible(start);
428 if (redrawOverview && overviewPanel != null)
430 overviewPanel.setBoxPosition();
432 paintAlignment(redrawOverview);
436 void scrollToWrappedVisible(int res)
438 int cwidth = seqPanel.seqCanvas
439 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
440 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
442 vscroll.setValue(res / cwidth);
443 av.startRes = vscroll.getValue() * cwidth;
447 public OverviewPanel getOverviewPanel()
449 return overviewPanel;
452 public void setOverviewPanel(OverviewPanel op)
457 public void setAnnotationVisible(boolean b)
459 if (!av.getWrapAlignment())
461 annotationSpaceFillerHolder.setVisible(b);
462 annotationPanelHolder.setVisible(b);
466 annotationSpaceFillerHolder.setVisible(false);
467 annotationPanelHolder.setVisible(false);
474 * automatically adjust annotation panel height for new annotation whilst
475 * ensuring the alignment is still visible.
477 public void adjustAnnotationHeight()
479 // TODO: display vertical annotation scrollbar if necessary
480 // this is called after loading new annotation onto alignment
481 if (alignFrame.getSize().height == 0)
484 .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
487 validateAnnotationDimensions(true);
488 apvscroll.addNotify();
491 paintAlignment(true);
495 * calculate the annotation dimensions and refresh slider values accordingly.
496 * need to do repaints/notifys afterwards.
498 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
500 boolean modified = false;
501 int height = av.calcPanelHeight();
503 if (hscroll.isVisible())
505 height += (minsize = hscroll.getPreferredSize().height);
507 if (apvscroll.isVisible())
509 minsize += apvscroll.getPreferredSize().height;
511 int mheight = height;
512 Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
513 int seqandannot = d.height - scalePanelHolder.getSize().height;
515 if (adjustPanelHeight)
517 // NOTE: this logic is different in the application. Need a better
518 // algorithm to define behaviour
519 // sets initial preferred height
520 // try and set height according to alignment
521 float sscaling = (float) ((av.getCharHeight() * av.getAlignment()
522 .getHeight()) / (1.0 * mheight));
525 // if the alignment is too big then
526 // default is 0.5 split
527 height = seqandannot / 2;
531 // otherwise just set the panel so that one row of sequence is visible
532 height = -av.getCharHeight() * 1
533 + (int) (seqandannot * (1 - sscaling));
538 // maintain same window layout whilst updating sliders
539 height = annotationPanelHolder.getSize().height;
542 if (seqandannot - height < 5)
544 height = seqandannot;
546 annotationPanel.setSize(new Dimension(d.width, height));
547 alabels.setSize(new Dimension(e.width, height));
548 annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
549 annotationPanelHolder.setSize(new Dimension(d.width, height));
550 // seqPanelHolder.setSize(d.width, seqandannot - height);
552 .setSize(d.width, seqPanel.seqCanvas.getSize().height);
553 int s = apvscroll.getValue();
554 if (s > mheight - height)
558 apvscroll.setValues(s, height, 0, mheight);
559 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
560 alabels.setScrollOffset(apvscroll.getValue(), false);
563 public void setWrapAlignment(boolean wrap)
567 scalePanelHolder.setVisible(!wrap);
569 hscroll.setVisible(!wrap);
570 idwidthAdjuster.setVisible(!wrap);
574 annotationPanelHolder.setVisible(false);
575 annotationSpaceFillerHolder.setVisible(false);
577 else if (av.isShowAnnotation())
579 annotationPanelHolder.setVisible(true);
580 annotationSpaceFillerHolder.setVisible(true);
583 idSpaceFillerPanel1.setVisible(!wrap);
585 fontChanged(); // This is so that the scalePanel is resized correctly
588 sequenceHolderPanel.validate();
597 // return value is true if the scroll is valid
598 public boolean scrollUp(boolean up)
602 if (vscroll.getValue() < 1)
606 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
610 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
614 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
621 public boolean scrollRight(boolean right)
625 if (hscroll.getValue() < 1)
629 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
633 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
637 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
644 public void setScrollValues(int x, int y)
646 int width = av.getAlignment().getWidth();
647 int height = av.getAlignment().getHeight();
649 if (av.hasHiddenColumns())
651 width = av.getColumnSelection().findColumnPosition(width);
659 hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
660 vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
667 if (vextent > height)
672 if ((hextent + x) > width)
674 System.err.println("hextent was " + hextent + " and x was " + x);
679 if ((vextent + y) > height)
681 y = height - vextent;
691 System.err.println("x was " + x);
697 int endSeq = y + vextent;
698 if (endSeq > av.getAlignment().getHeight())
700 endSeq = av.getAlignment().getHeight();
703 av.setEndSeq(endSeq);
705 av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
706 .getCharWidth())) - 1);
708 hscroll.setValues(x, hextent, 0, width);
709 vscroll.setValues(y, vextent, 0, height);
711 if (overviewPanel != null)
713 overviewPanel.setBoxPosition();
719 public void adjustmentValueChanged(AdjustmentEvent evt)
721 int oldX = av.getStartRes();
722 int oldY = av.getStartSeq();
724 if (evt == null || evt.getSource() == apvscroll)
726 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
727 alabels.setScrollOffset(apvscroll.getValue(), false);
728 // annotationPanel.image=null;
729 // alabels.image=null;
730 // alabels.repaint();
731 // annotationPanel.repaint();
733 if (evt == null || evt.getSource() == hscroll)
735 int x = hscroll.getValue();
737 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
738 / av.getCharWidth() - 1);
741 if (evt == null || evt.getSource() == vscroll)
743 int offy = vscroll.getValue();
744 if (av.getWrapAlignment())
746 int rowSize = seqPanel.seqCanvas
747 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
748 av.setStartRes(vscroll.getValue() * rowSize);
749 av.setEndRes((vscroll.getValue() + 1) * rowSize);
753 av.setStartSeq(offy);
754 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
755 / av.getCharHeight());
759 if (overviewPanel != null)
761 overviewPanel.setBoxPosition();
764 int scrollX = av.startRes - oldX;
765 int scrollY = av.startSeq - oldY;
767 if (av.getWrapAlignment() || !fastPaint || av.MAC)
773 // Make sure we're not trying to draw a panel
774 // larger than the visible window
775 if (scrollX > av.endRes - av.startRes)
777 scrollX = av.endRes - av.startRes;
779 else if (scrollX < av.startRes - av.endRes)
781 scrollX = av.startRes - av.endRes;
784 idPanel.idCanvas.fastPaint(scrollY);
785 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
787 scalePanel.repaint();
788 if (av.isShowAnnotation())
790 annotationPanel.fastPaint(av.getStartRes() - oldX);
797 private void sendViewPosition()
799 StructureSelectionManager.getStructureSelectionManager(av.applet)
800 .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
804 public void paintAlignment(boolean updateOverview)
810 jalview.structure.StructureSelectionManager
811 .getStructureSelectionManager(av.applet)
812 .sequenceColoursChanged(this);
814 if (overviewPanel != null)
816 overviewPanel.updateOverviewImage();
821 public void update(Graphics g)
826 public void paint(Graphics g)
829 Dimension d = idPanel.idCanvas.getSize();
830 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
832 if (av.getWrapAlignment())
834 int maxwidth = av.getAlignment().getWidth();
836 if (av.hasHiddenColumns())
838 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
841 int canvasWidth = seqPanel.seqCanvas
842 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
846 int max = maxwidth / canvasWidth;
847 vscroll.setMaximum(1 + max);
848 vscroll.setUnitIncrement(1);
849 vscroll.setVisibleAmount(1);
854 setScrollValues(av.getStartRes(), av.getStartSeq());
857 seqPanel.seqCanvas.repaint();
858 idPanel.idCanvas.repaint();
859 if (!av.getWrapAlignment())
861 if (av.isShowAnnotation())
864 annotationPanel.repaint();
866 scalePanel.repaint();
871 protected Panel sequenceHolderPanel = new Panel();
873 protected Scrollbar vscroll = new Scrollbar();
875 protected Scrollbar hscroll = new Scrollbar();
877 protected Panel seqPanelHolder = new Panel();
879 BorderLayout borderLayout1 = new BorderLayout();
881 BorderLayout borderLayout3 = new BorderLayout();
883 protected Panel scalePanelHolder = new Panel();
885 protected Panel idPanelHolder = new Panel();
887 BorderLayout borderLayout5 = new BorderLayout();
889 protected Panel idSpaceFillerPanel1 = new Panel();
891 public Panel annotationSpaceFillerHolder = new Panel();
893 BorderLayout borderLayout6 = new BorderLayout();
895 BorderLayout borderLayout7 = new BorderLayout();
897 Panel hscrollHolder = new Panel();
899 BorderLayout borderLayout10 = new BorderLayout();
901 protected Panel hscrollFillerPanel = new Panel();
903 BorderLayout borderLayout11 = new BorderLayout();
905 BorderLayout borderLayout4 = new BorderLayout();
907 BorderLayout borderLayout2 = new BorderLayout();
909 Panel annotationPanelHolder = new Panel();
911 protected Scrollbar apvscroll = new Scrollbar();
913 BorderLayout borderLayout12 = new BorderLayout();
915 private void jbInit() throws Exception
917 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
918 this.setLayout(borderLayout7);
920 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
921 sequenceHolderPanel.setLayout(borderLayout3);
922 seqPanelHolder.setLayout(borderLayout1);
923 scalePanelHolder.setBackground(Color.white);
925 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
926 scalePanelHolder.setLayout(borderLayout6);
927 idPanelHolder.setLayout(borderLayout5);
928 idSpaceFillerPanel1.setBackground(Color.white);
930 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
931 idSpaceFillerPanel1.setLayout(borderLayout11);
932 annotationSpaceFillerHolder.setBackground(Color.white);
934 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
935 annotationSpaceFillerHolder.setLayout(borderLayout4);
936 hscroll.setOrientation(Scrollbar.HORIZONTAL);
937 hscrollHolder.setLayout(borderLayout10);
938 hscrollFillerPanel.setBackground(Color.white);
939 apvscroll.setOrientation(Scrollbar.VERTICAL);
940 apvscroll.setVisible(true);
941 apvscroll.addAdjustmentListener(this);
943 annotationPanelHolder.setBackground(Color.white);
944 annotationPanelHolder.setLayout(borderLayout12);
945 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
946 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
947 hscrollHolder.setBackground(Color.white);
949 // annotationScroller.setPreferredSize(new Dimension(10, 80));
950 // this.setPreferredSize(new Dimension(220, 166));
951 seqPanelHolder.setBackground(Color.white);
952 idPanelHolder.setBackground(Color.white);
953 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
954 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
955 seqPanelHolder.add(vscroll, BorderLayout.EAST);
957 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
958 this.add(idPanelHolder, BorderLayout.WEST);
959 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
960 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
961 this.add(hscrollHolder, BorderLayout.SOUTH);
962 hscrollHolder.add(hscroll, BorderLayout.CENTER);
963 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
964 this.add(sequenceHolderPanel, BorderLayout.CENTER);
968 * hides or shows dynamic annotation rows based on groups and av state flags
970 public void updateAnnotation()
972 updateAnnotation(false);
975 public void updateAnnotation(boolean applyGlobalSettings)
977 updateAnnotation(applyGlobalSettings, false);
980 public void updateAnnotation(boolean applyGlobalSettings,
981 boolean preserveNewGroupSettings)
983 av.updateGroupAnnotationSettings(applyGlobalSettings,
984 preserveNewGroupSettings);
985 adjustAnnotationHeight();
989 public AlignmentI getAlignment()
991 return av.getAlignment();
995 public String getViewName()
1001 public StructureSelectionManager getStructureSelectionManager()
1003 return StructureSelectionManager
1004 .getStructureSelectionManager(av.applet);
1008 public void raiseOOMWarning(String string, OutOfMemoryError error)
1011 System.err.println("Out of memory whilst '" + string + "'");
1012 error.printStackTrace();