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.analysis.AnnotationSorter;
24 import jalview.api.AlignViewportI;
25 import jalview.api.AlignmentViewPanel;
26 import jalview.bin.JalviewLite;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.SearchResultsI;
29 import jalview.datamodel.SequenceI;
30 import jalview.structure.StructureSelectionManager;
31 import jalview.viewmodel.ViewportListenerI;
32 import jalview.viewmodel.ViewportRanges;
34 import java.awt.BorderLayout;
35 import java.awt.Color;
36 import java.awt.Dimension;
37 import java.awt.FontMetrics;
38 import java.awt.Frame;
39 import java.awt.Graphics;
40 import java.awt.Panel;
41 import java.awt.Scrollbar;
42 import java.awt.event.AdjustmentEvent;
43 import java.awt.event.AdjustmentListener;
44 import java.awt.event.ComponentAdapter;
45 import java.awt.event.ComponentEvent;
46 import java.beans.PropertyChangeEvent;
47 import java.util.List;
49 public class AlignmentPanel extends Panel implements AdjustmentListener,
50 AlignmentViewPanel, ViewportListenerI
53 public AlignViewport av;
55 OverviewPanel overviewPanel;
61 IdwidthAdjuster idwidthAdjuster;
63 public AlignFrame alignFrame;
65 ScalePanel scalePanel;
67 AnnotationPanel annotationPanel;
69 AnnotationLabels alabels;
71 ViewportRanges vpRanges;
73 // this value is set false when selection area being dragged
74 boolean fastPaint = true;
77 public void finalize() throws Throwable
83 seqPanelHolder = null;
84 sequenceHolderPanel = null;
86 scalePanelHolder = null;
87 annotationPanel = null;
88 annotationPanelHolder = null;
89 annotationSpaceFillerHolder = null;
93 public AlignmentPanel(AlignFrame af, final AlignViewport av)
105 vpRanges = av.getRanges();
106 seqPanel = new SeqPanel(av, this);
107 idPanel = new IdPanel(av, this);
108 scalePanel = new ScalePanel(av, this);
109 idwidthAdjuster = new IdwidthAdjuster(this);
110 annotationPanel = new AnnotationPanel(this);
111 annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
113 sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
114 alabels = new AnnotationLabels(this);
116 setAnnotationVisible(av.isShowAnnotation());
118 idPanelHolder.add(idPanel, BorderLayout.CENTER);
119 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
120 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
121 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
122 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
125 setScrollValues(0, 0);
127 apvscroll.addAdjustmentListener(this);
128 hscroll.addAdjustmentListener(this);
129 vscroll.addAdjustmentListener(this);
131 addComponentListener(new ComponentAdapter()
134 public void componentResized(ComponentEvent evt)
136 // reset the viewport ranges when the alignment panel is resized
137 // in particular, this initialises the end residue value when Jalview
139 if (av.getWrapAlignment())
141 int widthInRes = seqPanel.seqCanvas
142 .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
143 vpRanges.setViewportWidth(widthInRes);
147 int widthInRes = seqPanel.seqCanvas.getWidth()
149 int heightInSeq = seqPanel.seqCanvas.getHeight()
150 / av.getCharHeight();
152 vpRanges.setViewportWidth(widthInRes);
153 vpRanges.setViewportHeight(heightInSeq);
155 // setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
156 if (getSize().height > 0
157 && annotationPanelHolder.getSize().height > 0)
159 validateAnnotationDimensions(false);
166 Dimension d = calculateIdWidth();
167 idPanel.idCanvas.setSize(d);
169 hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
171 idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
172 annotationSpaceFillerHolder.setSize(d.width,
173 annotationPanel.getSize().height);
174 alabels.setSize(d.width, annotationPanel.getSize().height);
175 final AlignmentPanel ap = this;
176 av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
179 public void propertyChange(java.beans.PropertyChangeEvent evt)
181 if (evt.getPropertyName().equals("alignment"))
183 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
188 av.getRanges().addPropertyChangeListener(this);
192 public AlignViewportI getAlignViewport()
197 public SequenceRenderer getSequenceRenderer()
199 return seqPanel.seqCanvas.sr;
203 public jalview.api.FeatureRenderer getFeatureRenderer()
205 return seqPanel.seqCanvas.fr;
209 public jalview.api.FeatureRenderer cloneFeatureRenderer()
211 FeatureRenderer nfr = new FeatureRenderer(av);
212 nfr.transferSettings(seqPanel.seqCanvas.fr);
216 public void alignmentChanged()
218 av.alignmentChanged(this);
220 if (overviewPanel != null)
222 overviewPanel.updateOverviewImage();
225 alignFrame.updateEditMenuBar();
230 public void fontChanged()
232 // set idCanvas bufferedImage to null
233 // to prevent drawing old image
234 idPanel.idCanvas.image = null;
235 FontMetrics fm = getFontMetrics(av.getFont());
237 scalePanel.setSize(new Dimension(10, av.getCharHeight()
239 idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
241 av.updateSequenceIdColours();
242 annotationPanel.image = null;
243 int ap = annotationPanel.adjustPanelHeight(false);
244 Dimension d = calculateIdWidth();
245 d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
246 alabels.setSize(d.width + 4, ap);
248 idPanel.idCanvas.setSize(d);
249 hscrollFillerPanel.setSize(d);
251 validateAnnotationDimensions(false);
252 annotationPanel.repaint();
257 public void setIdWidth(int w, int h)
259 idPanel.idCanvas.setSize(w, h);
260 idPanelHolder.setSize(w, idPanelHolder.getSize().height);
261 annotationSpaceFillerHolder.setSize(w,
262 annotationSpaceFillerHolder.getSize().height);
263 alabels.setSize(w, alabels.getSize().height);
267 Dimension calculateIdWidth()
269 if (av.nullFrame == null)
271 av.nullFrame = new Frame();
272 av.nullFrame.addNotify();
275 Graphics g = av.nullFrame.getGraphics();
277 FontMetrics fm = g.getFontMetrics(av.font);
278 AlignmentI al = av.getAlignment();
283 while (i < al.getHeight() && al.getSequenceAt(i) != null)
285 SequenceI s = al.getSequenceAt(i);
286 id = s.getDisplayId(av.getShowJVSuffix());
288 if (fm.stringWidth(id) > idWidth)
290 idWidth = fm.stringWidth(id);
295 // Also check annotation label widths
297 if (al.getAlignmentAnnotation() != null)
299 fm = g.getFontMetrics(av.nullFrame.getFont());
300 while (i < al.getAlignmentAnnotation().length)
302 String label = al.getAlignmentAnnotation()[i].label;
303 if (fm.stringWidth(label) > idWidth)
305 idWidth = fm.stringWidth(label);
311 return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
315 * Highlight the given results on the alignment.
318 public void highlightSearchResults(SearchResultsI results)
320 scrollToPosition(results);
321 seqPanel.seqCanvas.highlightSearchResults(results);
325 * scroll the view to show the position of the highlighted region in results
326 * (if any) and redraw the overview
329 * @return false if results were not found
331 public boolean scrollToPosition(SearchResultsI results)
333 return scrollToPosition(results, true);
337 * scroll the view to show the position of the highlighted region in results
341 * @param redrawOverview
342 * - when set, the overview will be recalculated (takes longer)
343 * @return false if results were not found
345 public boolean scrollToPosition(SearchResultsI results,
346 boolean redrawOverview)
348 return scrollToPosition(results, 0, redrawOverview, false);
352 * scroll the view to show the position of the highlighted region in results
356 * @param redrawOverview
357 * - when set, the overview will be recalculated (takes longer)
358 * @return false if results were not found
360 public boolean scrollToPosition(SearchResultsI results,
362 boolean redrawOverview, boolean centre)
364 // do we need to scroll the panel?
365 if (results != null && results.getSize() > 0)
367 AlignmentI alignment = av.getAlignment();
368 int seqIndex = alignment.findIndex(results);
374 * allow for offset of target sequence (actually scroll to one above it)
377 SequenceI seq = alignment.getSequenceAt(seqIndex);
378 int[] r = results.getResults(seq, 0, alignment.getWidth());
381 if (JalviewLite.debug)
384 .println("DEBUG: scroll didn't happen - results not within alignment : "
385 + seq.getStart() + "," + seq.getEnd());
389 if (JalviewLite.debug)
393 * System.out.println("DEBUG: scroll: start=" + r[0] +
394 * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
395 * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
396 * " hextent=" + hextent);
403 * To centre results, scroll to positions half the visible width
404 * left/right of the start/end positions
408 int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
409 start = Math.max(start - offset, 0);
410 end = Math.min(end + offset, seq.getEnd() - 1);
417 if (end == seq.getEnd())
423 * allow for offset of target sequence (actually scroll to one above it)
425 seqIndex = Math.max(0, seqIndex - verticalOffset);
426 return scrollTo(start, end, seqIndex, false, redrawOverview);
431 public boolean scrollTo(int ostart, int end, int seqIndex,
432 boolean scrollToNearest, boolean redrawOverview)
434 int startv, endv, starts, ends, width;
437 if (av.hasHiddenColumns())
439 AlignmentI al = av.getAlignment();
440 start = al.getHiddenColumns().findColumnPosition(ostart);
441 end = al.getHiddenColumns().findColumnPosition(end);
444 if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
446 // don't scroll - position isn't visible
456 if (!av.getWrapAlignment())
459 * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
460 * av.getStartRes()) >= start) { spos=start-1; // seqIn //
461 * setScrollValues(start - 1, seqIndex); } else if ((endv =
462 * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
463 * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
464 * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
465 * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
466 * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
469 // below is scrolling logic up to Jalview 2.8.2
470 // if ((av.getStartRes() > end)
471 // || (av.getEndRes() < start)
472 // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
474 // if (start > av.getAlignment().getWidth() - hextent)
476 // start = av.getAlignment().getWidth() - hextent;
483 // if (seqIndex > av.getAlignment().getHeight() - vextent)
485 // seqIndex = av.getAlignment().getHeight() - vextent;
491 // setScrollValues(start, seqIndex);
493 // logic copied from jalview.gui.AlignmentPanel:
494 if ((startv = vpRanges.getStartRes()) >= start)
497 * Scroll left to make start of search results visible
499 setScrollValues(start - 1, seqIndex);
501 else if ((endv = vpRanges.getEndRes()) <= end)
504 * Scroll right to make end of search results visible
506 setScrollValues(startv + 1 + end - endv, seqIndex);
508 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
511 * Scroll up to make start of search results visible
513 setScrollValues(vpRanges.getStartRes(), seqIndex);
515 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
518 * Scroll down to make end of search results visible
520 setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
524 * Else results are already visible - no need to scroll
529 vpRanges.scrollToWrappedVisible(start);
532 paintAlignment(redrawOverview);
536 public OverviewPanel getOverviewPanel()
538 return overviewPanel;
541 public void setOverviewPanel(OverviewPanel op)
546 public void setAnnotationVisible(boolean b)
548 if (!av.getWrapAlignment())
550 annotationSpaceFillerHolder.setVisible(b);
551 annotationPanelHolder.setVisible(b);
555 annotationSpaceFillerHolder.setVisible(false);
556 annotationPanelHolder.setVisible(false);
563 * automatically adjust annotation panel height for new annotation whilst
564 * ensuring the alignment is still visible.
567 public void adjustAnnotationHeight()
569 // TODO: display vertical annotation scrollbar if necessary
570 // this is called after loading new annotation onto alignment
571 if (alignFrame.getSize().height == 0)
574 .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
577 validateAnnotationDimensions(true);
578 apvscroll.addNotify();
581 paintAlignment(true);
585 * Calculate the annotation dimensions and refresh slider values accordingly.
586 * Need to do repaints/notifys afterwards.
588 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
590 int rowHeight = av.getCharHeight();
591 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
592 int annotationHeight = av.calcPanelHeight();
594 int mheight = annotationHeight;
595 Dimension d = sequenceHolderPanel.getSize();
597 int availableHeight = d.height - scalePanelHolder.getHeight();
599 if (adjustPanelHeight)
602 * If not enough vertical space, maximize annotation height while keeping
603 * at least two rows of alignment visible
605 if (annotationHeight + alignmentHeight > availableHeight)
607 annotationHeight = Math.min(annotationHeight, availableHeight - 2
613 // maintain same window layout whilst updating sliders
614 annotationHeight = annotationPanelHolder.getSize().height;
617 if (availableHeight - annotationHeight < 5)
619 annotationHeight = availableHeight;
622 annotationPanel.setSize(new Dimension(d.width, annotationHeight));
623 annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
624 // seqPanelHolder.setSize(d.width, seqandannot - height);
626 .setSize(d.width, seqPanel.seqCanvas.getSize().height);
628 Dimension e = idPanel.getSize();
629 alabels.setSize(new Dimension(e.width, annotationHeight));
630 annotationSpaceFillerHolder.setSize(new Dimension(e.width,
633 int s = apvscroll.getValue();
634 if (s > mheight - annotationHeight)
638 apvscroll.setValues(s, annotationHeight, 0, mheight);
639 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
640 alabels.setScrollOffset(apvscroll.getValue(), false);
643 public void setWrapAlignment(boolean wrap)
645 vpRanges.setStartSeq(0);
646 vpRanges.setStartRes(0);
647 scalePanelHolder.setVisible(!wrap);
649 hscroll.setVisible(!wrap);
650 idwidthAdjuster.setVisible(!wrap);
654 annotationPanelHolder.setVisible(false);
655 annotationSpaceFillerHolder.setVisible(false);
657 else if (av.isShowAnnotation())
659 annotationPanelHolder.setVisible(true);
660 annotationSpaceFillerHolder.setVisible(true);
663 idSpaceFillerPanel1.setVisible(!wrap);
665 fontChanged(); // This is so that the scalePanel is resized correctly
668 sequenceHolderPanel.validate();
677 public void setScrollValues(int xpos, int ypos)
682 if (av.getWrapAlignment())
684 setScrollingForWrappedPanel(x);
688 int width = av.getAlignment().getWidth();
689 int height = av.getAlignment().getHeight();
691 if (av.hasHiddenColumns())
693 width = av.getAlignment().getHiddenColumns()
694 .findColumnPosition(width);
701 hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
702 vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
709 if (vextent > height)
714 if ((hextent + x) > width)
716 System.err.println("hextent was " + hextent + " and x was " + x);
721 if ((vextent + y) > height)
723 y = height - vextent;
733 System.err.println("x was " + x);
737 hscroll.setValues(x, hextent, 0, width);
738 vscroll.setValues(y, vextent, 0, height);
740 // AWT scrollbar does not fire adjustmentValueChanged for setValues
741 // so also call adjustment code!
750 * Respond to adjustment event when horizontal or vertical scrollbar is
754 * adjustment event encoding whether apvscroll, hscroll or vscroll
758 public void adjustmentValueChanged(AdjustmentEvent evt)
760 // Note that this event is NOT fired by the AWT scrollbar when setValues is
761 // called. Instead manually call adjustHorizontal and adjustVertical
763 if (evt == null || evt.getSource() == apvscroll)
765 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
766 alabels.setScrollOffset(apvscroll.getValue(), false);
768 if (evt == null || evt.getSource() == hscroll)
770 int x = hscroll.getValue();
774 if (evt == null || evt.getSource() == vscroll)
776 int offy = vscroll.getValue();
777 adjustVertical(offy);
782 private void adjustHorizontal(int x)
784 int oldX = vpRanges.getStartRes();
785 int oldwidth = vpRanges.getViewportWidth();
786 int width = seqPanel.seqCanvas.getWidth() / av.getCharWidth();
788 // if we're scrolling to the position we're already at, stop
789 // this prevents infinite recursion of events when the scroll/viewport
790 // ranges values are the same
791 if ((x == oldX) && (width == oldwidth))
795 vpRanges.setViewportStartAndWidth(x, width);
797 if (av.getWrapAlignment() || !fastPaint)
804 private void adjustVertical(int offy)
806 int oldX = vpRanges.getStartRes();
807 int oldwidth = vpRanges.getViewportWidth();
808 int oldY = vpRanges.getStartSeq();
809 int oldheight = vpRanges.getViewportHeight();
811 if (av.getWrapAlignment())
813 int rowSize = seqPanel.seqCanvas
814 .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
816 // if we're scrolling to the position we're already at, stop
817 // this prevents infinite recursion of events when the scroll/viewport
818 // ranges values are the same
819 if ((offy * rowSize == oldX) && (oldwidth == rowSize))
825 vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
830 int height = seqPanel.seqCanvas.getHeight() / av.getCharHeight();
832 // if we're scrolling to the position we're already at, stop
833 // this prevents infinite recursion of events when the scroll/viewport
834 // ranges values are the same
835 if ((offy == oldY) && (height == oldheight))
839 vpRanges.setViewportStartAndHeight(offy, height);
841 if (av.getWrapAlignment() || !fastPaint)
849 * A helper method to return the AlignmentPanel in the other (complementary)
850 * half of a SplitFrame view. Returns null if not in a SplitFrame.
854 private AlignmentPanel getComplementPanel()
856 AlignmentPanel ap = null;
857 if (alignFrame != null)
859 SplitFrame sf = alignFrame.getSplitFrame();
862 AlignFrame other = sf.getComplement(alignFrame);
865 ap = other.alignPanel;
873 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
874 * The aim is to keep the two alignments 'lined up' on their centre columns.
877 * holds mapped region(s) of this alignment that we are scrolling
878 * 'to'; may be modified for sequence offset by this method
880 * the number of visible sequences to show above the mapped region
882 protected void scrollToCentre(SearchResultsI sr, int seqOffset)
885 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
886 * mapped), we can make the scroll-to location a sequence above the one
889 SequenceI mappedTo = sr.getResults().get(0).getSequence();
890 List<SequenceI> seqs = av.getAlignment().getSequences();
893 * This is like AlignmentI.findIndex(seq) but here we are matching the
894 * dataset sequence not the aligned sequence
896 boolean matched = false;
897 for (SequenceI seq : seqs)
899 if (mappedTo == seq.getDatasetSequence())
907 return; // failsafe, shouldn't happen
911 * Scroll to position but centring the target residue. Also set a state flag
912 * to prevent adjustmentValueChanged performing this recursively.
914 scrollToPosition(sr, seqOffset, true, true);
917 private void sendViewPosition()
919 StructureSelectionManager.getStructureSelectionManager(av.applet)
920 .sendViewPosition(this, vpRanges.getStartRes(),
921 vpRanges.getEndRes(), vpRanges.getStartSeq(),
922 vpRanges.getEndSeq());
926 * Repaint the alignment and annotations, and, optionally, any overview window
929 public void paintAlignment(boolean updateOverview)
931 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
932 av.isShowAutocalculatedAbove());
933 sorter.sort(getAlignment().getAlignmentAnnotation(),
934 av.getSortAnnotationsBy());
939 // TODO: determine if this paintAlignment changed structure colours
940 jalview.structure.StructureSelectionManager
941 .getStructureSelectionManager(av.applet)
942 .sequenceColoursChanged(this);
944 if (overviewPanel != null)
946 overviewPanel.updateOverviewImage();
952 public void update(Graphics g)
958 public void paint(Graphics g)
961 Dimension d = idPanel.idCanvas.getSize();
962 final int canvasHeight = seqPanel.seqCanvas.getSize().height;
963 if (canvasHeight != d.height)
965 idPanel.idCanvas.setSize(d.width, canvasHeight);
968 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
970 seqPanel.seqCanvas.repaint();
971 idPanel.idCanvas.repaint();
972 if (!av.getWrapAlignment())
974 if (av.isShowAnnotation())
977 annotationPanel.repaint();
979 scalePanel.repaint();
985 * Set vertical scroll bar parameters for wrapped panel
987 * the residue to scroll to
989 private void setScrollingForWrappedPanel(int res)
991 // get the width of the alignment in residues
992 int maxwidth = av.getAlignment().getWidth();
993 if (av.hasHiddenColumns())
995 maxwidth = av.getAlignment().getHiddenColumns()
996 .findColumnPosition(maxwidth) - 1;
999 // get the width of the canvas in residues
1000 int canvasWidth = seqPanel.seqCanvas
1001 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
1002 if (canvasWidth > 0)
1004 // position we want to scroll to is number of canvasWidth's to get there
1005 int current = res / canvasWidth;
1007 // max scroll position: add one because extent is 1 and scrollbar value
1008 // can only be set to at most max - extent
1009 int max = maxwidth / canvasWidth + 1;
1010 vscroll.setUnitIncrement(1);
1011 vscroll.setValues(current, 1, 0, max);
1015 protected Panel sequenceHolderPanel = new Panel();
1017 protected Scrollbar vscroll = new Scrollbar();
1019 protected Scrollbar hscroll = new Scrollbar();
1021 protected Panel seqPanelHolder = new Panel();
1023 protected Panel scalePanelHolder = new Panel();
1025 protected Panel idPanelHolder = new Panel();
1027 protected Panel idSpaceFillerPanel1 = new Panel();
1029 public Panel annotationSpaceFillerHolder = new Panel();
1031 protected Panel hscrollFillerPanel = new Panel();
1033 Panel annotationPanelHolder = new Panel();
1035 protected Scrollbar apvscroll = new Scrollbar();
1038 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
1039 * false, suppresses invoking the same method recursively.
1041 private boolean scrollComplementaryPanel = true;
1043 private void jbInit() throws Exception
1045 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
1046 this.setLayout(new BorderLayout());
1048 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
1049 sequenceHolderPanel.setLayout(new BorderLayout());
1050 seqPanelHolder.setLayout(new BorderLayout());
1051 scalePanelHolder.setBackground(Color.white);
1053 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
1054 scalePanelHolder.setLayout(new BorderLayout());
1055 idPanelHolder.setLayout(new BorderLayout());
1056 idSpaceFillerPanel1.setBackground(Color.white);
1058 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
1059 idSpaceFillerPanel1.setLayout(new BorderLayout());
1060 annotationSpaceFillerHolder.setBackground(Color.white);
1062 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
1063 annotationSpaceFillerHolder.setLayout(new BorderLayout());
1064 hscroll.setOrientation(Scrollbar.HORIZONTAL);
1066 Panel hscrollHolder = new Panel();
1067 hscrollHolder.setLayout(new BorderLayout());
1068 hscrollFillerPanel.setBackground(Color.white);
1069 apvscroll.setOrientation(Scrollbar.VERTICAL);
1070 apvscroll.setVisible(true);
1071 apvscroll.addAdjustmentListener(this);
1073 annotationPanelHolder.setBackground(Color.white);
1074 annotationPanelHolder.setLayout(new BorderLayout());
1075 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
1076 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
1077 hscrollHolder.setBackground(Color.white);
1079 // annotationScroller.setPreferredSize(new Dimension(10, 80));
1080 // this.setPreferredSize(new Dimension(220, 166));
1081 seqPanelHolder.setBackground(Color.white);
1082 idPanelHolder.setBackground(Color.white);
1083 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
1084 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
1085 seqPanelHolder.add(vscroll, BorderLayout.EAST);
1087 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
1088 this.add(idPanelHolder, BorderLayout.WEST);
1089 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
1090 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
1091 this.add(hscrollHolder, BorderLayout.SOUTH);
1092 hscrollHolder.add(hscroll, BorderLayout.CENTER);
1093 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
1094 this.add(sequenceHolderPanel, BorderLayout.CENTER);
1098 * hides or shows dynamic annotation rows based on groups and av state flags
1100 public void updateAnnotation()
1102 updateAnnotation(false);
1105 public void updateAnnotation(boolean applyGlobalSettings)
1107 updateAnnotation(applyGlobalSettings, false);
1110 public void updateAnnotation(boolean applyGlobalSettings,
1111 boolean preserveNewGroupSettings)
1113 av.updateGroupAnnotationSettings(applyGlobalSettings,
1114 preserveNewGroupSettings);
1115 adjustAnnotationHeight();
1119 public AlignmentI getAlignment()
1121 return av.getAlignment();
1125 public String getViewName()
1131 public StructureSelectionManager getStructureSelectionManager()
1133 return StructureSelectionManager
1134 .getStructureSelectionManager(av.applet);
1138 public void raiseOOMWarning(String string, OutOfMemoryError error)
1141 System.err.println("Out of memory whilst '" + string + "'");
1142 error.printStackTrace();
1146 * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
1150 protected void setToScrollComplementPanel(boolean b)
1152 this.scrollComplementaryPanel = b;
1156 * Get whether to scroll complement panel
1158 * @return true if cDNA/protein complement panels should be scrolled
1160 protected boolean isSetToScrollComplementPanel()
1162 return this.scrollComplementaryPanel;
1167 * Property change event fired when a change is made to the viewport ranges
1168 * object associated with this alignment panel's viewport
1170 public void propertyChange(PropertyChangeEvent evt)
1172 // update this panel's scroll values based on the new viewport ranges values
1173 int x = vpRanges.getStartRes();
1174 int y = vpRanges.getStartSeq();
1175 setScrollValues(x, y);
1177 // now update any complementary alignment (its viewport ranges object
1178 // is different so does not get automatically updated)
1179 if (isSetToScrollComplementPanel())
1181 setToScrollComplementPanel(false);
1182 av.scrollComplementaryAlignment(getComplementPanel());
1183 setToScrollComplementPanel(true);