2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.AlignmentViewPanel;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.SearchResults;
26 import jalview.datamodel.SequenceI;
27 import jalview.structure.StructureSelectionManager;
29 import java.awt.BorderLayout;
30 import java.awt.Color;
31 import java.awt.Dimension;
32 import java.awt.FontMetrics;
33 import java.awt.Frame;
34 import java.awt.Graphics;
35 import java.awt.Panel;
36 import java.awt.Scrollbar;
37 import java.awt.event.AdjustmentEvent;
38 import java.awt.event.AdjustmentListener;
39 import java.awt.event.ComponentAdapter;
40 import java.awt.event.ComponentEvent;
42 public class AlignmentPanel extends Panel implements AdjustmentListener,
46 public AlignViewport av;
48 OverviewPanel overviewPanel;
54 IdwidthAdjuster idwidthAdjuster;
56 public AlignFrame alignFrame;
58 ScalePanel scalePanel;
60 AnnotationPanel annotationPanel;
62 AnnotationLabels alabels;
64 // this value is set false when selection area being dragged
65 boolean fastPaint = true;
67 public void finalize()
72 seqPanelHolder = null;
73 sequenceHolderPanel = null;
75 scalePanelHolder = null;
76 annotationPanel = null;
77 annotationPanelHolder = null;
78 annotationSpaceFillerHolder = null;
81 public AlignmentPanel(AlignFrame af, final AlignViewport av)
93 seqPanel = new SeqPanel(av, this);
94 idPanel = new IdPanel(av, this);
95 scalePanel = new ScalePanel(av, this);
96 idwidthAdjuster = new IdwidthAdjuster(this);
97 annotationPanel = new AnnotationPanel(this);
98 annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
100 sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
101 alabels = new AnnotationLabels(this);
103 setAnnotationVisible(av.showAnnotation);
105 idPanelHolder.add(idPanel, BorderLayout.CENTER);
106 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
107 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
108 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
109 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
112 setScrollValues(0, 0);
114 apvscroll.addAdjustmentListener(this);
115 hscroll.addAdjustmentListener(this);
116 vscroll.addAdjustmentListener(this);
118 addComponentListener(new ComponentAdapter()
120 public void componentResized(ComponentEvent evt)
122 setScrollValues(av.getStartRes(), av.getStartSeq());
123 if (getSize().height > 0
124 && annotationPanelHolder.getSize().height > 0)
126 validateAnnotationDimensions(false);
133 Dimension d = calculateIdWidth();
134 idPanel.idCanvas.setSize(d);
136 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
138 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
139 annotationSpaceFillerHolder.setSize(d.width,
140 annotationPanel.getSize().height);
141 alabels.setSize(d.width, annotationPanel.getSize().height);
142 final AlignmentPanel ap = this;
143 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
145 public void propertyChange(java.beans.PropertyChangeEvent evt)
147 if (evt.getPropertyName().equals("alignment"))
149 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
156 public SequenceRenderer getSequenceRenderer()
158 return seqPanel.seqCanvas.sr;
161 public jalview.api.FeatureRenderer getFeatureRenderer()
163 return seqPanel.seqCanvas.fr;
166 public jalview.api.FeatureRenderer cloneFeatureRenderer()
168 FeatureRenderer nfr = new FeatureRenderer(av);
169 nfr.transferSettings(seqPanel.seqCanvas.fr);
172 public void alignmentChanged()
174 av.alignmentChanged(this);
176 if (overviewPanel != null)
178 overviewPanel.updateOverviewImage();
181 alignFrame.updateEditMenuBar();
186 public void fontChanged()
188 // set idCanvas bufferedImage to null
189 // to prevent drawing old image
190 idPanel.idCanvas.image = null;
191 FontMetrics fm = getFontMetrics(av.getFont());
193 scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
194 idwidthAdjuster.setSize(new Dimension(10, av.charHeight
196 av.updateSequenceIdColours();
197 annotationPanel.image = null;
198 int ap = annotationPanel.adjustPanelHeight(false);
199 Dimension d = calculateIdWidth();
200 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
201 alabels.setSize(d.width + 4, ap);
203 idPanel.idCanvas.setSize(d);
204 hscrollFillerPanel.setSize(d);
206 validateAnnotationDimensions(false);
207 annotationPanel.repaint();
211 if (overviewPanel != null)
213 overviewPanel.updateOverviewImage();
217 public void setIdWidth(int w, int h)
219 idPanel.idCanvas.setSize(w, h);
220 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
221 annotationSpaceFillerHolder.setSize(w,
222 annotationSpaceFillerHolder.getSize().height);
223 alabels.setSize(w, alabels.getSize().height);
227 Dimension calculateIdWidth()
229 if (av.nullFrame == null)
231 av.nullFrame = new Frame();
232 av.nullFrame.addNotify();
235 Graphics g = av.nullFrame.getGraphics();
237 FontMetrics fm = g.getFontMetrics(av.font);
238 AlignmentI al = av.getAlignment();
243 while (i < al.getHeight() && al.getSequenceAt(i) != null)
245 SequenceI s = al.getSequenceAt(i);
246 id = s.getDisplayId(av.getShowJVSuffix());
248 if (fm.stringWidth(id) > idWidth)
250 idWidth = fm.stringWidth(id);
255 // Also check annotation label widths
257 if (al.getAlignmentAnnotation() != null)
259 fm = g.getFontMetrics(av.nullFrame.getFont());
260 while (i < al.getAlignmentAnnotation().length)
262 String label = al.getAlignmentAnnotation()[i].label;
263 if (fm.stringWidth(label) > idWidth)
265 idWidth = fm.stringWidth(label);
271 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
275 * Highlight the given results on the alignment.
278 public void highlightSearchResults(SearchResults results)
280 scrollToPosition(results);
281 seqPanel.seqCanvas.highlightSearchResults(results);
285 * scroll the view to show the position of the highlighted region in results
286 * (if any) and redraw the overview
289 * @return false if results were not found
291 public boolean scrollToPosition(SearchResults results)
293 return scrollToPosition(results, true);
297 * scroll the view to show the position of the highlighted region in results
301 * @param redrawOverview
302 * - when set, the overview will be recalculated (takes longer)
303 * @return false if results were not found
305 public boolean scrollToPosition(SearchResults results,
306 boolean redrawOverview)
309 // do we need to scroll the panel?
310 if (results != null && results.getSize() > 0)
312 AlignmentI alignment = av.getAlignment();
313 int seqIndex = alignment.findIndex(results);
318 SequenceI seq = alignment.getSequenceAt(seqIndex);
319 int[] r = results.getResults(seq, 0, alignment.getWidth());
325 .println("DEBUG: scroll didn't happen - results not within alignment : "
326 + seq.getStart() + "," + seq.getEnd());
334 * System.out.println("DEBUG: scroll: start=" + r[0] +
335 * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
336 * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
337 * " hextent=" + hextent);
346 if (end == seq.getEnd())
350 return scrollTo(start, end, seqIndex, false, redrawOverview);
355 public boolean scrollTo(int ostart, int end, int seqIndex,
356 boolean scrollToNearest, boolean redrawOverview)
358 int startv, endv, starts, ends, width;
361 if (av.hasHiddenColumns())
363 start = av.getColumnSelection().findColumnPosition(ostart);
364 end = av.getColumnSelection().findColumnPosition(end);
367 if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
369 // don't scroll - position isn't visible
378 if (!av.wrapAlignment)
381 * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
382 * av.getStartRes()) >= start) { spos=start-1; // seqIn //
383 * setScrollValues(start - 1, seqIndex); } else if ((endv =
384 * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
385 * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
386 * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
387 * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
388 * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
392 if ((av.getStartRes() > end)
393 || (av.getEndRes() < start)
394 || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
396 if (start > av.getAlignment().getWidth() - hextent)
398 start = av.getAlignment().getWidth() - hextent;
405 if (seqIndex > av.getAlignment().getHeight() - vextent)
407 seqIndex = av.getAlignment().getHeight() - vextent;
413 // System.out.println("trying to scroll to: "+start+" "+seqIndex);
414 setScrollValues(start, seqIndex);
419 scrollToWrappedVisible(start);
421 if (redrawOverview && overviewPanel != null)
423 overviewPanel.setBoxPosition();
425 paintAlignment(redrawOverview);
429 void scrollToWrappedVisible(int res)
431 int cwidth = seqPanel.seqCanvas
432 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
433 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
435 vscroll.setValue(res / cwidth);
436 av.startRes = vscroll.getValue() * cwidth;
440 public OverviewPanel getOverviewPanel()
442 return overviewPanel;
445 public void setOverviewPanel(OverviewPanel op)
450 public void setAnnotationVisible(boolean b)
452 if (!av.wrapAlignment)
454 annotationSpaceFillerHolder.setVisible(b);
455 annotationPanelHolder.setVisible(b);
459 annotationSpaceFillerHolder.setVisible(false);
460 annotationPanelHolder.setVisible(false);
467 * automatically adjust annotation panel height for new annotation whilst
468 * ensuring the alignment is still visible.
470 public void adjustAnnotationHeight()
472 // TODO: display vertical annotation scrollbar if necessary
473 // this is called after loading new annotation onto alignment
474 if (alignFrame.getSize().height == 0)
476 System.out.println("NEEDS FIXING");
479 validateAnnotationDimensions(true);
480 apvscroll.addNotify();
483 paintAlignment(true);
487 * calculate the annotation dimensions and refresh slider values accordingly.
488 * need to do repaints/notifys afterwards.
490 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
492 boolean modified = false;
493 int height = av.calcPanelHeight();
495 if (hscroll.isVisible())
497 height += (minsize = hscroll.getPreferredSize().height);
499 if (apvscroll.isVisible())
501 minsize += apvscroll.getPreferredSize().height;
503 int mheight = height;
504 Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
505 int seqandannot = d.height - scalePanelHolder.getSize().height;
507 if (adjustPanelHeight)
509 // NOTE: this logic is different in the application. Need a better
510 // algorithm to define behaviour
511 // sets initial preferred height
512 // try and set height according to alignment
513 float sscaling = (float) ((av.getCharHeight() * av.getAlignment()
514 .getHeight()) / (1.0 * mheight));
517 // if the alignment is too big then
518 // default is 0.5 split
519 height = seqandannot / 2;
523 // otherwise just set the panel so that one row of sequence is visible
524 height = -av.getCharHeight() * 1
525 + (int) (seqandannot * (1 - sscaling));
530 // maintain same window layout whilst updating sliders
531 height = annotationPanelHolder.getSize().height;
534 if (seqandannot - height < 5)
536 height = seqandannot;
538 annotationPanel.setSize(new Dimension(d.width, height));
539 alabels.setSize(new Dimension(e.width, height));
540 annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
541 annotationPanelHolder.setSize(new Dimension(d.width, height));
542 // seqPanelHolder.setSize(d.width, seqandannot - height);
544 .setSize(d.width, seqPanel.seqCanvas.getSize().height);
545 int s = apvscroll.getValue();
546 if (s > mheight - height)
550 apvscroll.setValues(s, height, 0, mheight);
551 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
552 alabels.setScrollOffset(apvscroll.getValue(), false);
555 public void setWrapAlignment(boolean wrap)
559 scalePanelHolder.setVisible(!wrap);
561 hscroll.setVisible(!wrap);
562 idwidthAdjuster.setVisible(!wrap);
566 annotationPanelHolder.setVisible(false);
567 annotationSpaceFillerHolder.setVisible(false);
569 else if (av.showAnnotation)
571 annotationPanelHolder.setVisible(true);
572 annotationSpaceFillerHolder.setVisible(true);
575 idSpaceFillerPanel1.setVisible(!wrap);
577 fontChanged(); // This is so that the scalePanel is resized correctly
580 sequenceHolderPanel.validate();
589 // return value is true if the scroll is valid
590 public boolean scrollUp(boolean up)
594 if (vscroll.getValue() < 1)
598 setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
602 if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
606 setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
613 public boolean scrollRight(boolean right)
617 if (hscroll.getValue() < 1)
621 setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
625 if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
629 setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
636 public void setScrollValues(int x, int y)
638 int width = av.getAlignment().getWidth();
639 int height = av.getAlignment().getHeight();
641 if (av.hasHiddenColumns())
643 width = av.getColumnSelection().findColumnPosition(width);
651 hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
652 vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
659 if (vextent > height)
664 if ((hextent + x) > width)
666 System.err.println("hextent was " + hextent + " and x was " + x);
671 if ((vextent + y) > height)
673 y = height - vextent;
683 System.err.println("x was " + x);
689 int endSeq = y + vextent;
690 if (endSeq > av.getAlignment().getHeight())
692 endSeq = av.getAlignment().getHeight();
695 av.setEndSeq(endSeq);
697 av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
699 hscroll.setValues(x, hextent, 0, width);
700 vscroll.setValues(y, vextent, 0, height);
702 if (overviewPanel != null)
704 overviewPanel.setBoxPosition();
710 public void adjustmentValueChanged(AdjustmentEvent evt)
712 int oldX = av.getStartRes();
713 int oldY = av.getStartSeq();
715 if (evt == null || evt.getSource() == apvscroll)
717 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
718 alabels.setScrollOffset(apvscroll.getValue(), false);
719 // annotationPanel.image=null;
720 // alabels.image=null;
721 // alabels.repaint();
722 // annotationPanel.repaint();
724 if (evt == null || evt.getSource() == hscroll)
726 int x = hscroll.getValue();
728 av.setEndRes(x + seqPanel.seqCanvas.getSize().width
729 / av.getCharWidth() - 1);
732 if (evt == null || evt.getSource() == vscroll)
734 int offy = vscroll.getValue();
735 if (av.getWrapAlignment())
737 int rowSize = seqPanel.seqCanvas
738 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
739 av.setStartRes(vscroll.getValue() * rowSize);
740 av.setEndRes((vscroll.getValue() + 1) * rowSize);
744 av.setStartSeq(offy);
745 av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
746 / av.getCharHeight());
750 if (overviewPanel != null)
752 overviewPanel.setBoxPosition();
755 int scrollX = av.startRes - oldX;
756 int scrollY = av.startSeq - oldY;
758 if (av.getWrapAlignment() || !fastPaint || av.MAC)
764 // Make sure we're not trying to draw a panel
765 // larger than the visible window
766 if (scrollX > av.endRes - av.startRes)
768 scrollX = av.endRes - av.startRes;
770 else if (scrollX < av.startRes - av.endRes)
772 scrollX = av.startRes - av.endRes;
775 idPanel.idCanvas.fastPaint(scrollY);
776 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
778 scalePanel.repaint();
779 if (av.getShowAnnotation())
781 annotationPanel.fastPaint(av.getStartRes() - oldX);
788 private void sendViewPosition()
790 StructureSelectionManager.getStructureSelectionManager(av.applet)
791 .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
795 public void paintAlignment(boolean updateOverview)
801 jalview.structure.StructureSelectionManager
802 .getStructureSelectionManager(av.applet)
803 .sequenceColoursChanged(this);
805 if (overviewPanel != null)
807 overviewPanel.updateOverviewImage();
812 public void update(Graphics g)
817 public void paint(Graphics g)
820 Dimension d = idPanel.idCanvas.getSize();
821 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
823 if (av.getWrapAlignment())
825 int maxwidth = av.getAlignment().getWidth();
827 if (av.hasHiddenColumns())
829 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
832 int canvasWidth = seqPanel.seqCanvas
833 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
837 int max = maxwidth / canvasWidth;
838 vscroll.setMaximum(1 + max);
839 vscroll.setUnitIncrement(1);
840 vscroll.setVisibleAmount(1);
845 setScrollValues(av.getStartRes(), av.getStartSeq());
848 seqPanel.seqCanvas.repaint();
849 idPanel.idCanvas.repaint();
850 if (!av.wrapAlignment)
852 if (av.showAnnotation)
855 annotationPanel.repaint();
857 scalePanel.repaint();
862 protected Panel sequenceHolderPanel = new Panel();
864 protected Scrollbar vscroll = new Scrollbar();
866 protected Scrollbar hscroll = new Scrollbar();
868 protected Panel seqPanelHolder = new Panel();
870 BorderLayout borderLayout1 = new BorderLayout();
872 BorderLayout borderLayout3 = new BorderLayout();
874 protected Panel scalePanelHolder = new Panel();
876 protected Panel idPanelHolder = new Panel();
878 BorderLayout borderLayout5 = new BorderLayout();
880 protected Panel idSpaceFillerPanel1 = new Panel();
882 public Panel annotationSpaceFillerHolder = new Panel();
884 BorderLayout borderLayout6 = new BorderLayout();
886 BorderLayout borderLayout7 = new BorderLayout();
888 Panel hscrollHolder = new Panel();
890 BorderLayout borderLayout10 = new BorderLayout();
892 protected Panel hscrollFillerPanel = new Panel();
894 BorderLayout borderLayout11 = new BorderLayout();
896 BorderLayout borderLayout4 = new BorderLayout();
898 BorderLayout borderLayout2 = new BorderLayout();
900 Panel annotationPanelHolder = new Panel();
902 protected Scrollbar apvscroll = new Scrollbar();
904 BorderLayout borderLayout12 = new BorderLayout();
906 private void jbInit() throws Exception
908 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
909 this.setLayout(borderLayout7);
911 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
912 sequenceHolderPanel.setLayout(borderLayout3);
913 seqPanelHolder.setLayout(borderLayout1);
914 scalePanelHolder.setBackground(Color.white);
916 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
917 scalePanelHolder.setLayout(borderLayout6);
918 idPanelHolder.setLayout(borderLayout5);
919 idSpaceFillerPanel1.setBackground(Color.white);
921 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
922 idSpaceFillerPanel1.setLayout(borderLayout11);
923 annotationSpaceFillerHolder.setBackground(Color.white);
925 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
926 annotationSpaceFillerHolder.setLayout(borderLayout4);
927 hscroll.setOrientation(Scrollbar.HORIZONTAL);
928 hscrollHolder.setLayout(borderLayout10);
929 hscrollFillerPanel.setBackground(Color.white);
930 apvscroll.setOrientation(Scrollbar.VERTICAL);
931 apvscroll.setVisible(true);
932 apvscroll.addAdjustmentListener(this);
934 annotationPanelHolder.setBackground(Color.white);
935 annotationPanelHolder.setLayout(borderLayout12);
936 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
937 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
938 hscrollHolder.setBackground(Color.white);
940 // annotationScroller.setPreferredSize(new Dimension(10, 80));
941 // this.setPreferredSize(new Dimension(220, 166));
942 seqPanelHolder.setBackground(Color.white);
943 idPanelHolder.setBackground(Color.white);
944 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
945 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
946 seqPanelHolder.add(vscroll, BorderLayout.EAST);
948 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
949 this.add(idPanelHolder, BorderLayout.WEST);
950 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
951 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
952 this.add(hscrollHolder, BorderLayout.SOUTH);
953 hscrollHolder.add(hscroll, BorderLayout.CENTER);
954 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
955 this.add(sequenceHolderPanel, BorderLayout.CENTER);
959 * hides or shows dynamic annotation rows based on groups and av state flags
961 public void updateAnnotation()
963 updateAnnotation(false);
966 public void updateAnnotation(boolean applyGlobalSettings)
968 updateAnnotation(applyGlobalSettings, false);
971 public void updateAnnotation(boolean applyGlobalSettings,
972 boolean preserveNewGroupSettings)
974 av.updateGroupAnnotationSettings(applyGlobalSettings,
975 preserveNewGroupSettings);
976 adjustAnnotationHeight();
980 public AlignmentI getAlignment()
982 return av.getAlignment();
986 public String getViewName()
992 public StructureSelectionManager getStructureSelectionManager()
994 return StructureSelectionManager
995 .getStructureSelectionManager(av.applet);
999 public void raiseOOMWarning(String string, OutOfMemoryError error)
1002 System.err.println("Out of memory whilst '" + string + "'");
1003 error.printStackTrace();