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 = end + offset - 1;
411 // end = Math.min(end + offset, seq.getEnd() - 1);
418 if (end == seq.getEnd())
424 * allow for offset of target sequence (actually scroll to one above it)
426 seqIndex = Math.max(0, seqIndex - verticalOffset);
427 return scrollTo(start, end, seqIndex, false, redrawOverview);
432 public boolean scrollTo(int ostart, int end, int seqIndex,
433 boolean scrollToNearest, boolean redrawOverview)
435 int startv, endv, starts, ends, width;
438 if (av.hasHiddenColumns())
440 AlignmentI al = av.getAlignment();
441 start = al.getHiddenColumns().findColumnPosition(ostart);
442 end = al.getHiddenColumns().findColumnPosition(end);
445 if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
447 // don't scroll - position isn't visible
457 if (!av.getWrapAlignment())
460 * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
461 * av.getStartRes()) >= start) { spos=start-1; // seqIn //
462 * setScrollValues(start - 1, seqIndex); } else if ((endv =
463 * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
464 * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
465 * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
466 * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
467 * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
470 // below is scrolling logic up to Jalview 2.8.2
471 // if ((av.getStartRes() > end)
472 // || (av.getEndRes() < start)
473 // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
475 // if (start > av.getAlignment().getWidth() - hextent)
477 // start = av.getAlignment().getWidth() - hextent;
484 // if (seqIndex > av.getAlignment().getHeight() - vextent)
486 // seqIndex = av.getAlignment().getHeight() - vextent;
492 // setScrollValues(start, seqIndex);
494 // logic copied from jalview.gui.AlignmentPanel:
495 if ((startv = vpRanges.getStartRes()) >= start)
498 * Scroll left to make start of search results visible
500 setScrollValues(start - 1, seqIndex);
502 else if ((endv = vpRanges.getEndRes()) <= end)
505 * Scroll right to make end of search results visible
507 setScrollValues(startv + 1 + end - endv, seqIndex);
509 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
512 * Scroll up to make start of search results visible
514 setScrollValues(vpRanges.getStartRes(), seqIndex);
516 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
519 * Scroll down to make end of search results visible
521 setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
525 * Else results are already visible - no need to scroll
530 vpRanges.scrollToWrappedVisible(start);
533 paintAlignment(redrawOverview);
537 public OverviewPanel getOverviewPanel()
539 return overviewPanel;
542 public void setOverviewPanel(OverviewPanel op)
547 public void setAnnotationVisible(boolean b)
549 if (!av.getWrapAlignment())
551 annotationSpaceFillerHolder.setVisible(b);
552 annotationPanelHolder.setVisible(b);
556 annotationSpaceFillerHolder.setVisible(false);
557 annotationPanelHolder.setVisible(false);
564 * automatically adjust annotation panel height for new annotation whilst
565 * ensuring the alignment is still visible.
568 public void adjustAnnotationHeight()
570 // TODO: display vertical annotation scrollbar if necessary
571 // this is called after loading new annotation onto alignment
572 if (alignFrame.getSize().height == 0)
575 .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
578 validateAnnotationDimensions(true);
579 apvscroll.addNotify();
582 paintAlignment(true);
586 * Calculate the annotation dimensions and refresh slider values accordingly.
587 * Need to do repaints/notifys afterwards.
589 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
591 int rowHeight = av.getCharHeight();
592 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
593 int annotationHeight = av.calcPanelHeight();
595 int mheight = annotationHeight;
596 Dimension d = sequenceHolderPanel.getSize();
598 int availableHeight = d.height - scalePanelHolder.getHeight();
600 if (adjustPanelHeight)
603 * If not enough vertical space, maximize annotation height while keeping
604 * at least two rows of alignment visible
606 if (annotationHeight + alignmentHeight > availableHeight)
608 annotationHeight = Math.min(annotationHeight, availableHeight - 2
614 // maintain same window layout whilst updating sliders
615 annotationHeight = annotationPanelHolder.getSize().height;
618 if (availableHeight - annotationHeight < 5)
620 annotationHeight = availableHeight;
623 annotationPanel.setSize(new Dimension(d.width, annotationHeight));
624 annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
625 // seqPanelHolder.setSize(d.width, seqandannot - height);
627 .setSize(d.width, seqPanel.seqCanvas.getSize().height);
629 Dimension e = idPanel.getSize();
630 alabels.setSize(new Dimension(e.width, annotationHeight));
631 annotationSpaceFillerHolder.setSize(new Dimension(e.width,
634 int s = apvscroll.getValue();
635 if (s > mheight - annotationHeight)
639 apvscroll.setValues(s, annotationHeight, 0, mheight);
640 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
641 alabels.setScrollOffset(apvscroll.getValue(), false);
644 public void setWrapAlignment(boolean wrap)
646 vpRanges.setStartSeq(0);
647 vpRanges.setStartRes(0);
648 scalePanelHolder.setVisible(!wrap);
650 hscroll.setVisible(!wrap);
651 idwidthAdjuster.setVisible(!wrap);
655 annotationPanelHolder.setVisible(false);
656 annotationSpaceFillerHolder.setVisible(false);
658 else if (av.isShowAnnotation())
660 annotationPanelHolder.setVisible(true);
661 annotationSpaceFillerHolder.setVisible(true);
664 idSpaceFillerPanel1.setVisible(!wrap);
666 fontChanged(); // This is so that the scalePanel is resized correctly
669 sequenceHolderPanel.validate();
678 public void setScrollValues(int xpos, int ypos)
683 if (av.getWrapAlignment())
685 setScrollingForWrappedPanel(x);
689 int width = av.getAlignment().getWidth();
690 int height = av.getAlignment().getHeight();
692 if (av.hasHiddenColumns())
694 width = av.getAlignment().getHiddenColumns()
695 .findColumnPosition(width);
702 hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
703 vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
710 if (vextent > height)
715 if ((hextent + x) > width)
717 System.err.println("hextent was " + hextent + " and x was " + x);
722 if ((vextent + y) > height)
724 y = height - vextent;
734 System.err.println("x was " + x);
738 hscroll.setValues(x, hextent, 0, width);
739 vscroll.setValues(y, vextent, 0, height);
741 // AWT scrollbar does not fire adjustmentValueChanged for setValues
742 // so also call adjustment code!
751 * Respond to adjustment event when horizontal or vertical scrollbar is
755 * adjustment event encoding whether apvscroll, hscroll or vscroll
759 public void adjustmentValueChanged(AdjustmentEvent evt)
761 // Note that this event is NOT fired by the AWT scrollbar when setValues is
762 // called. Instead manually call adjustHorizontal and adjustVertical
764 if (evt == null || evt.getSource() == apvscroll)
766 annotationPanel.setScrollOffset(apvscroll.getValue(), false);
767 alabels.setScrollOffset(apvscroll.getValue(), false);
769 if (evt == null || evt.getSource() == hscroll)
771 int x = hscroll.getValue();
775 if (evt == null || evt.getSource() == vscroll)
777 int offy = vscroll.getValue();
778 adjustVertical(offy);
783 private void adjustHorizontal(int x)
785 int oldX = vpRanges.getStartRes();
786 int oldwidth = vpRanges.getViewportWidth();
787 int width = seqPanel.seqCanvas.getWidth() / av.getCharWidth();
789 // if we're scrolling to the position we're already at, stop
790 // this prevents infinite recursion of events when the scroll/viewport
791 // ranges values are the same
792 if ((x == oldX) && (width == oldwidth))
796 vpRanges.setViewportStartAndWidth(x, width);
798 if (av.getWrapAlignment() || !fastPaint)
805 private void adjustVertical(int offy)
807 int oldX = vpRanges.getStartRes();
808 int oldwidth = vpRanges.getViewportWidth();
809 int oldY = vpRanges.getStartSeq();
810 int oldheight = vpRanges.getViewportHeight();
812 if (av.getWrapAlignment())
814 int rowSize = seqPanel.seqCanvas
815 .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
817 // if we're scrolling to the position we're already at, stop
818 // this prevents infinite recursion of events when the scroll/viewport
819 // ranges values are the same
820 if ((offy * rowSize == oldX) && (oldwidth == rowSize))
826 vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
831 int height = seqPanel.seqCanvas.getHeight() / av.getCharHeight();
833 // if we're scrolling to the position we're already at, stop
834 // this prevents infinite recursion of events when the scroll/viewport
835 // ranges values are the same
836 if ((offy == oldY) && (height == oldheight))
840 vpRanges.setViewportStartAndHeight(offy, height);
842 if (av.getWrapAlignment() || !fastPaint)
850 * A helper method to return the AlignmentPanel in the other (complementary)
851 * half of a SplitFrame view. Returns null if not in a SplitFrame.
855 private AlignmentPanel getComplementPanel()
857 AlignmentPanel ap = null;
858 if (alignFrame != null)
860 SplitFrame sf = alignFrame.getSplitFrame();
863 AlignFrame other = sf.getComplement(alignFrame);
866 ap = other.alignPanel;
874 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
875 * The aim is to keep the two alignments 'lined up' on their centre columns.
878 * holds mapped region(s) of this alignment that we are scrolling
879 * 'to'; may be modified for sequence offset by this method
881 * the number of visible sequences to show above the mapped region
883 protected void scrollToCentre(SearchResultsI sr, int seqOffset)
886 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
887 * mapped), we can make the scroll-to location a sequence above the one
890 SequenceI mappedTo = sr.getResults().get(0).getSequence();
891 List<SequenceI> seqs = av.getAlignment().getSequences();
894 * This is like AlignmentI.findIndex(seq) but here we are matching the
895 * dataset sequence not the aligned sequence
897 boolean matched = false;
898 for (SequenceI seq : seqs)
900 if (mappedTo == seq.getDatasetSequence())
908 return; // failsafe, shouldn't happen
912 * Scroll to position but centring the target residue. Also set a state flag
913 * to prevent adjustmentValueChanged performing this recursively.
915 scrollToPosition(sr, seqOffset, true, true);
918 private void sendViewPosition()
920 StructureSelectionManager.getStructureSelectionManager(av.applet)
921 .sendViewPosition(this, vpRanges.getStartRes(),
922 vpRanges.getEndRes(), vpRanges.getStartSeq(),
923 vpRanges.getEndSeq());
927 * Repaint the alignment and annotations, and, optionally, any overview window
930 public void paintAlignment(boolean updateOverview)
932 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
933 av.isShowAutocalculatedAbove());
934 sorter.sort(getAlignment().getAlignmentAnnotation(),
935 av.getSortAnnotationsBy());
940 // TODO: determine if this paintAlignment changed structure colours
941 jalview.structure.StructureSelectionManager
942 .getStructureSelectionManager(av.applet)
943 .sequenceColoursChanged(this);
945 if (overviewPanel != null)
947 overviewPanel.updateOverviewImage();
953 public void update(Graphics g)
959 public void paint(Graphics g)
962 Dimension d = idPanel.idCanvas.getSize();
963 final int canvasHeight = seqPanel.seqCanvas.getSize().height;
964 if (canvasHeight != d.height)
966 idPanel.idCanvas.setSize(d.width, canvasHeight);
969 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
971 seqPanel.seqCanvas.repaint();
972 idPanel.idCanvas.repaint();
973 if (!av.getWrapAlignment())
975 if (av.isShowAnnotation())
978 annotationPanel.repaint();
980 scalePanel.repaint();
986 * Set vertical scroll bar parameters for wrapped panel
988 * the residue to scroll to
990 private void setScrollingForWrappedPanel(int res)
992 // get the width of the alignment in residues
993 int maxwidth = av.getAlignment().getWidth();
994 if (av.hasHiddenColumns())
996 maxwidth = av.getAlignment().getHiddenColumns()
997 .findColumnPosition(maxwidth) - 1;
1000 // get the width of the canvas in residues
1001 int canvasWidth = seqPanel.seqCanvas
1002 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
1003 if (canvasWidth > 0)
1005 // position we want to scroll to is number of canvasWidth's to get there
1006 int current = res / canvasWidth;
1008 // max scroll position: add one because extent is 1 and scrollbar value
1009 // can only be set to at most max - extent
1010 int max = maxwidth / canvasWidth + 1;
1011 vscroll.setUnitIncrement(1);
1012 vscroll.setValues(current, 1, 0, max);
1016 protected Panel sequenceHolderPanel = new Panel();
1018 protected Scrollbar vscroll = new Scrollbar();
1020 protected Scrollbar hscroll = new Scrollbar();
1022 protected Panel seqPanelHolder = new Panel();
1024 protected Panel scalePanelHolder = new Panel();
1026 protected Panel idPanelHolder = new Panel();
1028 protected Panel idSpaceFillerPanel1 = new Panel();
1030 public Panel annotationSpaceFillerHolder = new Panel();
1032 protected Panel hscrollFillerPanel = new Panel();
1034 Panel annotationPanelHolder = new Panel();
1036 protected Scrollbar apvscroll = new Scrollbar();
1039 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
1040 * false, suppresses invoking the same method recursively.
1042 private boolean scrollComplementaryPanel = true;
1044 private void jbInit() throws Exception
1046 // idPanelHolder.setPreferredSize(new Dimension(70, 10));
1047 this.setLayout(new BorderLayout());
1049 // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
1050 sequenceHolderPanel.setLayout(new BorderLayout());
1051 seqPanelHolder.setLayout(new BorderLayout());
1052 scalePanelHolder.setBackground(Color.white);
1054 // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
1055 scalePanelHolder.setLayout(new BorderLayout());
1056 idPanelHolder.setLayout(new BorderLayout());
1057 idSpaceFillerPanel1.setBackground(Color.white);
1059 // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
1060 idSpaceFillerPanel1.setLayout(new BorderLayout());
1061 annotationSpaceFillerHolder.setBackground(Color.white);
1063 // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
1064 annotationSpaceFillerHolder.setLayout(new BorderLayout());
1065 hscroll.setOrientation(Scrollbar.HORIZONTAL);
1067 Panel hscrollHolder = new Panel();
1068 hscrollHolder.setLayout(new BorderLayout());
1069 hscrollFillerPanel.setBackground(Color.white);
1070 apvscroll.setOrientation(Scrollbar.VERTICAL);
1071 apvscroll.setVisible(true);
1072 apvscroll.addAdjustmentListener(this);
1074 annotationPanelHolder.setBackground(Color.white);
1075 annotationPanelHolder.setLayout(new BorderLayout());
1076 annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
1077 // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
1078 hscrollHolder.setBackground(Color.white);
1080 // annotationScroller.setPreferredSize(new Dimension(10, 80));
1081 // this.setPreferredSize(new Dimension(220, 166));
1082 seqPanelHolder.setBackground(Color.white);
1083 idPanelHolder.setBackground(Color.white);
1084 sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
1085 sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
1086 seqPanelHolder.add(vscroll, BorderLayout.EAST);
1088 // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
1089 this.add(idPanelHolder, BorderLayout.WEST);
1090 idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
1091 idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
1092 this.add(hscrollHolder, BorderLayout.SOUTH);
1093 hscrollHolder.add(hscroll, BorderLayout.CENTER);
1094 hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
1095 this.add(sequenceHolderPanel, BorderLayout.CENTER);
1099 * hides or shows dynamic annotation rows based on groups and av state flags
1101 public void updateAnnotation()
1103 updateAnnotation(false);
1106 public void updateAnnotation(boolean applyGlobalSettings)
1108 updateAnnotation(applyGlobalSettings, false);
1111 public void updateAnnotation(boolean applyGlobalSettings,
1112 boolean preserveNewGroupSettings)
1114 av.updateGroupAnnotationSettings(applyGlobalSettings,
1115 preserveNewGroupSettings);
1116 adjustAnnotationHeight();
1120 public AlignmentI getAlignment()
1122 return av.getAlignment();
1126 public String getViewName()
1132 public StructureSelectionManager getStructureSelectionManager()
1134 return StructureSelectionManager
1135 .getStructureSelectionManager(av.applet);
1139 public void raiseOOMWarning(String string, OutOfMemoryError error)
1142 System.err.println("Out of memory whilst '" + string + "'");
1143 error.printStackTrace();
1147 * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
1151 protected void setToScrollComplementPanel(boolean b)
1153 this.scrollComplementaryPanel = b;
1157 * Get whether to scroll complement panel
1159 * @return true if cDNA/protein complement panels should be scrolled
1161 protected boolean isSetToScrollComplementPanel()
1163 return this.scrollComplementaryPanel;
1168 * Property change event fired when a change is made to the viewport ranges
1169 * object associated with this alignment panel's viewport
1171 public void propertyChange(PropertyChangeEvent evt)
1173 // update this panel's scroll values based on the new viewport ranges values
1174 int x = vpRanges.getStartRes();
1175 int y = vpRanges.getStartSeq();
1176 setScrollValues(x, y);
1178 // now update any complementary alignment (its viewport ranges object
1179 // is different so does not get automatically updated)
1180 if (isSetToScrollComplementPanel())
1182 setToScrollComplementPanel(false);
1183 av.scrollComplementaryAlignment(getComplementPanel());
1184 setToScrollComplementPanel(true);