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.
23 import java.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.Container;
26 import java.awt.Dimension;
28 import java.awt.FontMetrics;
29 import java.awt.Graphics;
30 import java.awt.Graphics2D;
31 import java.awt.event.AdjustmentEvent;
32 import java.awt.event.AdjustmentListener;
33 import java.awt.event.ComponentAdapter;
34 import java.awt.event.ComponentEvent;
35 import java.awt.print.PageFormat;
36 import java.awt.print.Printable;
37 import java.awt.print.PrinterException;
38 import java.beans.PropertyChangeEvent;
39 import java.beans.PropertyChangeListener;
41 import java.io.FileWriter;
42 import java.io.PrintWriter;
43 import java.util.List;
45 import javax.swing.SwingUtilities;
47 import jalview.analysis.AnnotationSorter;
48 import jalview.api.AlignViewportI;
49 import jalview.api.AlignmentViewPanel;
50 import jalview.bin.Cache;
51 import jalview.bin.Jalview;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.HiddenColumns;
54 import jalview.datamodel.SearchResultsI;
55 import jalview.datamodel.SequenceFeature;
56 import jalview.datamodel.SequenceGroup;
57 import jalview.datamodel.SequenceI;
58 import jalview.gui.ImageExporter.ImageWriterI;
59 import jalview.io.HTMLOutput;
60 import jalview.jbgui.GAlignmentPanel;
61 import jalview.math.AlignmentDimension;
62 import jalview.schemes.ResidueProperties;
63 import jalview.structure.StructureSelectionManager;
64 import jalview.util.Comparison;
65 import jalview.util.ImageMaker;
66 import jalview.util.MessageManager;
67 import jalview.viewmodel.AlignmentViewport;
68 import jalview.viewmodel.ViewportListenerI;
69 import jalview.viewmodel.ViewportRanges;
75 * @version $Revision: 1.161 $
77 @SuppressWarnings("serial")
78 public class AlignmentPanel extends GAlignmentPanel implements
79 AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
82 * spare space in pixels between sequence id and alignment panel
84 private static final int ID_WIDTH_PADDING = 4;
86 public AlignViewport av;
88 OverviewPanel overviewPanel;
90 private SeqPanel seqPanel;
92 private IdPanel idPanel;
94 IdwidthAdjuster idwidthAdjuster;
96 public AlignFrame alignFrame;
98 private ScalePanel scalePanel;
100 private AnnotationPanel annotationPanel;
102 private AnnotationLabels alabels;
104 private int hextent = 0;
106 private int vextent = 0;
109 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
110 * false, suppresses invoking the same method recursively.
112 private boolean scrollComplementaryPanel = true;
114 private PropertyChangeListener propertyChangeListener;
116 private CalculationChooser calculationDialog;
119 * Creates a new AlignmentPanel object.
124 public AlignmentPanel(AlignFrame af, final AlignViewport av)
126 setName("AligmentPanel");
127 // setBackground(Color.white); // BH 2019
130 setSeqPanel(new SeqPanel(av, this));
131 setIdPanel(new IdPanel(av, this));
133 setScalePanel(new ScalePanel(av, this));
135 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
136 idwidthAdjuster = new IdwidthAdjuster(this);
137 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
139 setAnnotationPanel(new AnnotationPanel(this));
140 setAlabels(new AnnotationLabels(this));
142 annotationScroller.setViewportView(getAnnotationPanel());
143 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
145 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
146 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
148 setScrollValues(0, 0);
150 hscroll.addAdjustmentListener(this);
151 vscroll.addAdjustmentListener(this);
153 addComponentListener(new ComponentAdapter()
156 public void componentResized(ComponentEvent evt)
158 // reset the viewport ranges when the alignment panel is resized
159 // in particular, this initialises the end residue value when Jalview
161 ViewportRanges ranges = av.getRanges();
162 if (av.getWrapAlignment())
164 int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
165 getSeqPanel().seqCanvas.getWidth());
166 ranges.setViewportWidth(widthInRes);
170 int widthInRes = getSeqPanel().seqCanvas.getWidth()
172 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
173 / av.getCharHeight();
175 ranges.setViewportWidth(widthInRes);
176 ranges.setViewportHeight(heightInSeq);
183 final AlignmentPanel ap = this;
184 propertyChangeListener = new PropertyChangeListener()
187 public void propertyChange(PropertyChangeEvent evt)
189 switch (evt.getPropertyName()) {
190 case AlignmentViewport.PROPERTY_SEQUENCE:
191 updateScrollBarsFromRanges();
192 if (annotationPanel != null)
193 annotationPanel.paintImmediately(0, 0, getWidth(), getHeight());
195 case AlignmentViewport.PROPERTY_ALIGNMENT:
196 updateScrollBarsFromRanges();
197 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
203 av.addPropertyChangeListener(propertyChangeListener);
205 av.getRanges().addPropertyChangeListener(this);
207 adjustAnnotationHeight();
212 public AlignViewportI getAlignViewport()
217 public void alignmentChanged()
219 av.alignmentChanged(this);
221 if (getCalculationDialog() != null)
223 getCalculationDialog().validateCalcTypes();
226 alignFrame.updateEditMenuBar();
228 // no idea if we need to update structure
229 paintAlignment(true, true);
236 public void fontChanged()
238 // set idCanvas bufferedImage to null
239 // to prevent drawing old image
240 FontMetrics fm = getFontMetrics(av.getFont());
242 scalePanelHolder.setPreferredSize(
243 new Dimension(10, av.getCharHeight() + fm.getDescent()));
244 idSpaceFillerPanel1.setPreferredSize(
245 new Dimension(10, av.getCharHeight() + fm.getDescent()));
246 idwidthAdjuster.invalidate();
247 scalePanelHolder.invalidate();
248 // BH 2018 getIdPanel().getIdCanvas().gg = null;
249 getSeqPanel().seqCanvas.img = null;
250 getAnnotationPanel().adjustPanelHeight();
252 Dimension d = calculateIdWidth();
253 getIdPanel().getIdCanvas().setPreferredSize(d);
254 hscrollFillerPanel.setPreferredSize(d);
260 * Calculates the width of the alignment labels based on the displayed names
261 * and any bounds on label width set in preferences. The calculated width is
262 * also set as a property of the viewport.
264 * @return Dimension giving the maximum width of the alignment label panel
265 * that should be used.
267 public Dimension calculateIdWidth()
269 int oldWidth = av.getIdWidth();
271 // calculate sensible default width when no preference is available
273 if (av.getIdWidth() < 0)
275 int maxWidth = getMaxWidth();
276 d = calculateIdWidth(maxWidth);
277 av.setIdWidth(d.width);
282 d.width = av.getIdWidth();
287 * fudge: if desired width has changed, update layout
288 * (see also paintComponent - updates layout on a repaint)
290 if (d.width != oldWidth)
292 idPanelHolder.setPreferredSize(d);
298 public int getMaxWidth()
300 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
301 int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
302 return Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
306 * Calculate the width of the alignment labels based on the displayed names
307 * and any bounds on label width set in preferences.
310 * -1 or maximum width allowed for IdWidth
311 * @return Dimension giving the maximum width of the alignment label panel
312 * that should be used.
314 public Dimension calculateIdWidth(int maxwidth)
316 Container c = this;// new Container();
317 FontMetrics fm = c.getFontMetrics(
318 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
320 AlignmentI al = av.getAlignment();
324 boolean withSuffix = av.getShowJVSuffix();
326 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
328 SequenceI s = al.getSequenceAt(i);
329 String id = s.getDisplayId(withSuffix);
330 int stringWidth = fm.stringWidth(id);
331 idWidth = Math.max(idWidth, stringWidth);
335 // Also check annotation label widths
338 if (al.getAlignmentAnnotation() != null)
340 fm = c.getFontMetrics(getAlabels().getFont());
342 while (i < al.getAlignmentAnnotation().length)
344 String label = al.getAlignmentAnnotation()[i].label;
345 int stringWidth = fm.stringWidth(label);
346 idWidth = Math.max(idWidth, stringWidth);
351 int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth);
352 w += ID_WIDTH_PADDING;
354 return new Dimension(w, 12);
358 * Highlight the given results on the alignment
361 public void highlightSearchResults(SearchResultsI results)
363 boolean scrolled = scrollToPosition(results, 0, false);
365 boolean fastPaint = !(scrolled && av.getWrapAlignment());
367 getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint);
371 * Scroll the view to show the position of the highlighted region in results
374 * @param searchResults
377 public boolean scrollToPosition(SearchResultsI searchResults)
379 return scrollToPosition(searchResults, 0, false);
383 * Scrolls the view (if necessary) to show the position of the first
384 * highlighted region in results (if any). Answers true if the view was
385 * scrolled, or false if no matched region was found, or it is already
389 * @param verticalOffset
390 * if greater than zero, allows scrolling to a position below the
391 * first displayed sequence
393 * if true, try to centre the search results horizontally in the view
396 protected boolean scrollToPosition(SearchResultsI results,
397 int verticalOffset, boolean centre)
399 int startv, endv, starts, ends;
400 ViewportRanges ranges = av.getRanges();
402 if (results == null || results.isEmpty() || av == null
403 || av.getAlignment() == null)
407 int seqIndex = av.getAlignment().findIndex(results);
412 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
414 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
423 * To centre results, scroll to positions half the visible width
424 * left/right of the start/end positions
428 int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
429 start = Math.max(start - offset, 0);
430 end = end + offset - 1;
436 if (end == seq.getEnd())
441 if (av.hasHiddenColumns())
443 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
444 start = hidden.absoluteToVisibleColumn(start);
445 end = hidden.absoluteToVisibleColumn(end);
448 if (!hidden.isVisible(r[0]))
450 // don't scroll - position isn't visible
457 * allow for offset of target sequence (actually scroll to one above it)
459 seqIndex = Math.max(0, seqIndex - verticalOffset);
460 boolean scrollNeeded = true;
462 if (!av.getWrapAlignment())
464 if ((startv = ranges.getStartRes()) >= start)
467 * Scroll left to make start of search results visible
469 setScrollValues(start, seqIndex);
471 else if ((endv = ranges.getEndRes()) <= end)
474 * Scroll right to make end of search results visible
476 setScrollValues(startv + end - endv, seqIndex);
478 else if ((starts = ranges.getStartSeq()) > seqIndex)
481 * Scroll up to make start of search results visible
483 setScrollValues(ranges.getStartRes(), seqIndex);
485 else if ((ends = ranges.getEndSeq()) <= seqIndex)
488 * Scroll down to make end of search results visible
490 setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
493 * Else results are already visible - no need to scroll
495 scrollNeeded = false;
499 scrollNeeded = ranges.scrollToWrappedVisible(start);
502 paintAlignment(false, false);
510 * @return DOCUMENT ME!
512 public OverviewPanel getOverviewPanel()
514 return overviewPanel;
523 public void setOverviewPanel(OverviewPanel op)
531 * Hide or show annotation panel
534 public void setAnnotationVisible(boolean b)
536 if (!av.getWrapAlignment())
538 annotationSpaceFillerHolder.setVisible(b);
539 annotationScroller.setVisible(b);
545 * automatically adjust annotation panel height for new annotation whilst
546 * ensuring the alignment is still visible.
549 public void adjustAnnotationHeight()
551 // TODO: display vertical annotation scrollbar if necessary
552 // this is called after loading new annotation onto alignment
553 if (alignFrame.getHeight() == 0)
555 System.out.println("NEEDS FIXING");
557 validateAnnotationDimensions(true);
559 // TODO: many places call this method and also paintAlignment with various
560 // different settings. this means multiple redraws are triggered...
561 paintAlignment(true, av.needToUpdateStructureViews());
565 * calculate the annotation dimensions and refresh slider values accordingly.
566 * need to do repaints/notifys afterwards.
568 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
570 // BH 2018.04.18 comment: addNotify() is not appropriate here. We
571 // are not changing ancestors, and keyboard action listeners do
572 // not need to be reset, and most importantly, we can't be sure we are actually
573 // connected to resources.
575 // addNotify() is a very expensive operation,
576 // requiring a full re-layout of all parents and children.
578 // Note in JComponent:
580 // This method is called by the toolkit internally and should
581 // not be called directly by programs.
583 // I note that addNotify() is called in several areas of Jalview.
585 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
586 annotationHeight = getAnnotationPanel()
587 .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
591 annotationScroller.setPreferredSize(
592 new Dimension(annotationScroller.getWidth(), annotationHeight));
594 Dimension e = idPanel.getSize();
595 alabels.setSize(new Dimension(e.width, annotationHeight));
597 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
598 annotationSpaceFillerHolder.getWidth(), annotationHeight));
599 annotationScroller.validate();
600 annotationScroller.addNotify();
604 * update alignment layout for viewport settings
606 public void updateLayout()
608 ViewportRanges ranges = av.getRanges();
610 setAnnotationVisible(av.isShowAnnotation());
611 boolean wrap = av.getWrapAlignment();
612 ranges.setStartSeq(0);
613 scalePanelHolder.setVisible(!wrap);
614 hscroll.setVisible(!wrap);
615 idwidthAdjuster.setVisible(!wrap);
619 annotationScroller.setVisible(false);
620 annotationSpaceFillerHolder.setVisible(false);
622 else if (av.isShowAnnotation())
624 annotationScroller.setVisible(true);
625 annotationSpaceFillerHolder.setVisible(true);
628 idSpaceFillerPanel1.setVisible(!wrap);
631 * defer dimension calculations if panel not yet added to a Window
634 if (getTopLevelAncestor() == null)
640 if (!wrap && av.isShowAnnotation())
642 validateAnnotationDimensions(false);
644 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
646 { // may not yet be laid out
649 int widthInRes = getSeqPanel().seqCanvas
650 .getWrappedCanvasWidth(canvasWidth);
651 ranges.setViewportWidth(widthInRes);
655 int widthInRes = (canvasWidth / av.getCharWidth());
656 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
657 / av.getCharHeight());
659 ranges.setViewportWidth(widthInRes);
660 ranges.setViewportHeight(heightInSeq);
664 // System.out.println("ap dim = " + getSize());
665 // these values will go negative if getSize() returns (0,0):
666 // System.out.println("seqpan dim = " + getSeqPanel().getSize());
667 // System.out.println("seqcan dim = " + getSeqPanel().seqCanvas.getSize());
673 * Adjust row/column scrollers to show a visible position in the alignment.
676 * visible column to scroll to
678 * visible row to scroll to
681 public void setScrollValues(int x, int y)
684 if (av == null || av.getAlignment() == null)
689 if (av.getWrapAlignment())
691 setScrollingForWrappedPanel(x);
695 int width = av.getAlignment().getVisibleWidth();
696 int height = av.getAlignment().getHeight();
698 hextent = Math.min(getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(), width);
699 vextent = Math.min(getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(), height);
701 x = Math.max(0, Math.min(x, width - hextent));
702 y = Math.max(0, Math.min(y, height - vextent));
705 updateScrollBars(x, y, width, height);
709 private void updateScrollBars(int x, int y, int width, int height)
711 hscroll.setValues(x, hextent, 0, width);
712 vscroll.setValues(y, vextent, 0, height);
716 * Respond to adjustment event when horizontal or vertical scrollbar is
720 * adjustment event encoding whether hscroll or vscroll changed
723 public void adjustmentValueChanged(AdjustmentEvent evt)
725 if (av.getWrapAlignment())
727 adjustScrollingWrapped(evt);
731 if (evt.getSource() == hscroll)
733 if (!updateRanges(hscroll.getValue(), Integer.MIN_VALUE))
736 else if (evt.getSource() == vscroll)
738 if (!updateRanges(Integer.MIN_VALUE, vscroll.getValue()))
744 private boolean updateRanges(int x, int y)
746 ViewportRanges ranges = av.getRanges();
747 boolean isChanged = false;
748 if (x != Integer.MIN_VALUE)
750 int oldX = ranges.getStartRes();
751 int oldwidth = ranges.getViewportWidth();
752 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
754 // if we're scrolling to the position we're already at, stop
755 // this prevents infinite recursion of events when the scroll/viewport
756 // ranges values are the same
757 if (width > 0 && (x != oldX || width != oldwidth))
759 ranges.setViewportStartAndWidth(x, width);
763 if (y != Integer.MIN_VALUE)
765 int oldY = ranges.getStartSeq();
766 int oldheight = ranges.getViewportHeight();
767 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
769 // if we're scrolling to the position we're already at, stop
770 // this prevents infinite recursion of events when the scroll/viewport
771 // ranges values are the same
772 if (height > 0 && (y != oldY || height != oldheight))
774 ranges.setViewportStartAndHeight(y, height);
782 * Responds to a scroll change by setting the start position of the viewport.
787 protected void adjustScrollingWrapped(AdjustmentEvent evt)
789 if (evt.getSource() == hscroll)
791 return; // no horizontal scroll when wrapped
793 final ViewportRanges ranges = av.getRanges();
795 if (evt.getSource() == vscroll)
797 int newY = vscroll.getValue();
800 * if we're scrolling to the position we're already at, stop
801 * this prevents infinite recursion of events when the scroll/viewport
802 * ranges values are the same
804 int oldX = ranges.getStartRes();
805 int oldY = ranges.getWrappedScrollPosition(oldX);
813 * limit page up/down to one width's worth of positions
815 int rowSize = ranges.getViewportWidth();
816 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
817 ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
822 // This is only called if file loaded is a jar file that
823 // was wrapped when saved and user has wrap alignment true
824 // as preference setting
825 SwingUtilities.invokeLater(new Runnable()
830 // When updating scrolling to use ViewportChange events, this code
831 // could not be validated and it is not clear if it is now being
832 // called. Log warning here in case it is called and unforeseen
835 "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
837 // scroll to start of panel
838 ranges.setStartRes(0);
839 ranges.setStartSeq(0);
847 * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
850 public void paintAlignment(boolean updateOverview,
851 boolean updateStructures)
853 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
854 av.isShowAutocalculatedAbove());
855 sorter.sort(getAlignment().getAlignmentAnnotation(),
856 av.getSortAnnotationsBy());
858 if (updateStructures)
860 av.getStructureSelectionManager().sequenceColoursChanged(this);
864 alignFrame.repaint();
865 if (overviewPanel != null)
867 overviewPanel.updateOverviewImage();
870 invalidate(); // needed so that the id width adjuster works correctly
876 public void paintComponent(Graphics g)
879 invalidate(); // needed so that the id width adjuster works correctly
881 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
882 idPanelHolder.setPreferredSize(d);
883 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
885 validate(); // needed so that the id width adjuster works correctly
888 * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
889 * though I still think this call should be elsewhere.
891 ViewportRanges ranges = av.getRanges();
892 // setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
893 super.paintComponent(g);
897 * Set vertical scroll bar position, and number of increments, for wrapped
900 * @param topLeftColumn
901 * the column position at top left (0..)
903 private void setScrollingForWrappedPanel(int topLeftColumn)
905 ViewportRanges ranges = av.getRanges();
906 int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
907 int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
910 * a scrollbar's value can be set to at most (maximum-extent)
911 * so we add extent (1) to the maxScroll value
913 vscroll.setUnitIncrement(1);
914 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
927 * @return DOCUMENT ME!
929 * @throws PrinterException
933 public int print(Graphics pg, PageFormat pf, int pi)
934 throws PrinterException
936 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
938 int pwidth = (int) pf.getImageableWidth();
939 int pheight = (int) pf.getImageableHeight();
941 if (av.getWrapAlignment())
943 return printWrappedAlignment(pwidth, pheight, pi, pg);
947 return printUnwrapped(pwidth, pheight, pi, pg, pg);
952 * Draws the alignment image, including sequence ids, sequences, and
953 * annotation labels and annotations if shown, on either one or two Graphics
963 * the graphics context for sequence ids and annotation labels
964 * @param alignmentGraphics
965 * the graphics context for sequences and annotations (may or may not
966 * be the same context as idGraphics)
968 * @throws PrinterException
970 public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
971 Graphics idGraphics, Graphics alignmentGraphics)
972 throws PrinterException
974 final int idWidth = getVisibleIdWidth(false);
977 * Get the horizontal offset to where we draw the sequences.
978 * This is idWidth if using a single Graphics context, else zero.
980 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
983 FontMetrics fm = getFontMetrics(av.getFont());
984 final int charHeight = av.getCharHeight();
985 final int scaleHeight = charHeight + fm.getDescent();
987 idGraphics.setColor(Color.white);
988 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
989 idGraphics.setFont(av.getFont());
992 * How many sequences and residues can we fit on a printable page?
994 final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
996 final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
998 final int alignmentWidth = av.getAlignment().getVisibleWidth();
999 int pagesWide = (alignmentWidth / totalRes) + 1;
1001 final int startRes = (pageIndex % pagesWide) * totalRes;
1002 final int endRes = Math.min(startRes + totalRes - 1,
1003 alignmentWidth - 1);
1005 final int startSeq = (pageIndex / pagesWide) * totalSeq;
1006 final int alignmentHeight = av.getAlignment().getHeight();
1007 final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
1009 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
1011 if (av.isShowAnnotation())
1013 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1016 pagesHigh /= pageHeight;
1018 if (pageIndex >= (pagesWide * pagesHigh))
1020 return Printable.NO_SUCH_PAGE;
1022 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
1025 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1027 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1028 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1029 pageWidth - idWidth, scaleHeight);
1030 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1033 * Draw the sequence ids, offset for scale height,
1034 * then reset to top left (0, 0)
1036 idGraphics.translate(0, scaleHeight);
1037 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1038 List<SequenceI> selection = av.getSelectionGroup() == null ? null
1039 : av.getSelectionGroup().getSequences(null);
1040 idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
1043 idGraphics.setFont(av.getFont());
1044 idGraphics.translate(0, -scaleHeight);
1047 * draw the sequences, offset for scale height, and id width (if using a
1048 * single graphics context), then reset to (0, scale height)
1050 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1051 getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
1052 startRes, endRes, startSeq, endSeq - 1);
1053 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1055 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1058 * draw annotation labels; drawComponent() translates by
1059 * getScrollOffset(), so compensate for that first;
1060 * then reset to (0, scale height)
1062 int offset = getAlabels().getScrollOffset();
1063 idGraphics.translate(0, -offset);
1064 idGraphics.translate(0, alignmentDrawnHeight);
1065 getAlabels().drawComponent(idGraphics, idWidth);
1066 idGraphics.translate(0, -alignmentDrawnHeight);
1069 * draw the annotations starting at
1070 * (idOffset, alignmentHeight) from (0, scaleHeight)
1072 alignmentGraphics.translate(alignmentGraphicsOffset,
1073 alignmentDrawnHeight);
1074 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1075 alignmentGraphics, -1, startRes, endRes + 1);
1078 return Printable.PAGE_EXISTS;
1082 * Prints one page of an alignment in wrapped mode. Returns
1083 * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
1084 * no page could be drawn (page number out of range).
1094 * @throws PrinterException
1096 public int printWrappedAlignment(int pageWidth, int pageHeight,
1097 int pageNumber, Graphics g) throws PrinterException
1099 getSeqPanel().seqCanvas.calculateWrappedGeometry();
1100 int annotationHeight = 0;
1101 if (av.isShowAnnotation())
1103 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1106 int hgap = av.getCharHeight();
1107 if (av.getScaleAboveWrapped())
1109 hgap += av.getCharHeight();
1112 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1115 int idWidth = getVisibleIdWidth(false);
1117 int maxwidth = av.getAlignment().getVisibleWidth();
1119 int resWidth = getSeqPanel().seqCanvas
1120 .getWrappedCanvasWidth(pageWidth - idWidth);
1121 av.getRanges().setViewportStartAndWidth(0, resWidth);
1123 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1125 g.setColor(Color.white);
1126 g.fillRect(0, 0, pageWidth, pageHeight);
1127 g.setFont(av.getFont());
1128 g.setColor(Color.black);
1131 * method: print the whole wrapped alignment, but with a clip region that
1132 * is restricted to the requested page; this supports selective print of
1133 * single pages or ranges, (at the cost of repeated processing in the
1134 * 'normal' case, when all pages are printed)
1136 g.translate(0, -pageNumber * pageHeight);
1138 g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
1141 * draw sequence ids and annotation labels (if shown)
1143 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1144 idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
1146 g.translate(idWidth, 0);
1148 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
1149 pageWidth - idWidth, totalHeight, 0);
1151 if ((pageNumber * pageHeight) < totalHeight)
1153 return Printable.PAGE_EXISTS;
1157 return Printable.NO_SUCH_PAGE;
1162 * get current sequence ID panel width, or nominal value if panel were to be
1163 * displayed using default settings
1167 public int getVisibleIdWidth()
1169 return getVisibleIdWidth(true);
1173 * get current sequence ID panel width, or nominal value if panel were to be
1174 * displayed using default settings
1177 * indicate if the Id width for onscreen or offscreen display should
1181 protected int getVisibleIdWidth(boolean onscreen)
1183 // see if rendering offscreen - check preferences and calc width accordingly
1184 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1186 return calculateIdWidth(-1).width;
1188 Integer idwidth = onscreen ? null
1189 : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
1190 if (idwidth != null)
1192 return idwidth.intValue() + ID_WIDTH_PADDING;
1195 int w = getIdPanel().getWidth();
1196 return (w > 0 ? w : calculateIdWidth().width);
1200 * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
1201 * writes it to the specified file
1206 void makeAlignmentImage(ImageMaker.TYPE type, File file)
1208 final int borderBottomOffset = 5;
1210 AlignmentDimension aDimension = getAlignmentDimension();
1211 // todo use a lambda function in place of callback here?
1212 ImageWriterI writer = new ImageWriterI()
1215 public void exportImage(Graphics graphics) throws Exception
1217 if (av.getWrapAlignment())
1219 printWrappedAlignment(aDimension.getWidth(),
1220 aDimension.getHeight() + borderBottomOffset, 0, graphics);
1224 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
1225 graphics, graphics);
1230 String fileTitle = alignFrame.getTitle();
1231 ImageExporter exporter = new ImageExporter(writer, alignFrame, type,
1233 int imageWidth = aDimension.getWidth();
1234 int imageHeight = aDimension.getHeight() + borderBottomOffset;
1235 String of = MessageManager.getString("label.alignment");
1236 exporter.doExport(file, this, imageWidth, imageHeight, of);
1240 * Calculates and returns a suitable width and height (in pixels) for an
1245 public AlignmentDimension getAlignmentDimension()
1247 int maxwidth = av.getAlignment().getVisibleWidth();
1249 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1250 + getScalePanel().getHeight();
1251 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1253 if (av.getWrapAlignment())
1255 height = getWrappedHeight();
1256 if (Jalview.isHeadlessMode())
1258 // need to obtain default alignment width and then add in any
1259 // additional allowance for id margin
1260 // this duplicates the calculation in getWrappedHeight but adjusts for
1262 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1263 - alignFrame.getInsets().left - alignFrame.getInsets().right
1264 - getVisibleIdWidth() + getVisibleIdWidth(false);
1268 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1272 else if (av.isShowAnnotation())
1274 height += getAnnotationPanel().adjustPanelHeight() + 3;
1276 return new AlignmentDimension(width, height);
1280 public void makePNGImageMap(File imgMapFile, String imageName)
1282 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1283 // ////////////////////////////////////////////
1284 int idWidth = getVisibleIdWidth(false);
1285 FontMetrics fm = getFontMetrics(av.getFont());
1286 int scaleHeight = av.getCharHeight() + fm.getDescent();
1289 // ////////////////////////////////
1290 if (imgMapFile != null)
1294 int sSize = av.getAlignment().getHeight();
1295 int alwidth = av.getAlignment().getWidth();
1296 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1297 out.println(HTMLOutput.getImageMapHTML());
1298 out.println("<img src=\"" + imageName
1299 + "\" border=\"0\" usemap=\"#Map\" >"
1300 + "<map name=\"Map\">");
1302 for (int s = 0; s < sSize; s++)
1304 int sy = s * av.getCharHeight() + scaleHeight;
1306 SequenceI seq = av.getAlignment().getSequenceAt(s);
1307 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1308 for (int column = 0; column < alwidth; column++)
1310 StringBuilder text = new StringBuilder(512);
1311 String triplet = null;
1312 if (av.getAlignment().isNucleotide())
1314 triplet = ResidueProperties.nucleotideName
1315 .get(seq.getCharAt(column) + "");
1319 triplet = ResidueProperties.aa2Triplet
1320 .get(seq.getCharAt(column) + "");
1323 if (triplet == null)
1328 int seqPos = seq.findPosition(column);
1329 int gSize = groups.length;
1330 for (int g = 0; g < gSize; g++)
1332 if (text.length() < 1)
1334 text.append("<area shape=\"rect\" coords=\"")
1335 .append((idWidth + column * av.getCharWidth()))
1336 .append(",").append(sy).append(",")
1338 + (column + 1) * av.getCharWidth()))
1339 .append(",").append((av.getCharHeight() + sy))
1340 .append("\"").append(" onMouseOver=\"toolTip('")
1341 .append(seqPos).append(" ").append(triplet);
1344 if (groups[g].getStartRes() < column
1345 && groups[g].getEndRes() > column)
1347 text.append("<br><em>").append(groups[g].getName())
1352 if (text.length() < 1)
1354 text.append("<area shape=\"rect\" coords=\"")
1355 .append((idWidth + column * av.getCharWidth()))
1356 .append(",").append(sy).append(",")
1357 .append((idWidth + (column + 1) * av.getCharWidth()))
1358 .append(",").append((av.getCharHeight() + sy))
1359 .append("\"").append(" onMouseOver=\"toolTip('")
1360 .append(seqPos).append(" ").append(triplet);
1362 if (!Comparison.isGap(seq.getCharAt(column)))
1364 List<SequenceFeature> features = seq.findFeatures(column,
1366 for (SequenceFeature sf : features)
1368 if (sf.isContactFeature())
1370 text.append("<br>").append(sf.getType()).append(" ")
1371 .append(sf.getBegin()).append(":")
1372 .append(sf.getEnd());
1376 text.append("<br>");
1377 text.append(sf.getType());
1378 String description = sf.getDescription();
1379 if (description != null
1380 && !sf.getType().equals(description))
1382 description = description.replace("\"", """);
1383 text.append(" ").append(description);
1386 String status = sf.getStatus();
1387 if (status != null && !"".equals(status))
1389 text.append(" (").append(status).append(")");
1392 if (text.length() > 1)
1394 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1395 out.println(text.toString());
1400 out.println("</map></body></html>");
1403 } catch (Exception ex)
1405 ex.printStackTrace();
1407 } // /////////END OF IMAGE MAP
1412 * Answers the height of the entire alignment in pixels, assuming it is in
1417 int getWrappedHeight()
1419 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1421 if (System.getProperty("java.awt.headless") != null
1422 && System.getProperty("java.awt.headless").equals("true"))
1424 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1425 - vscroll.getPreferredSize().width
1426 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1429 int chunkWidth = getSeqPanel().seqCanvas
1430 .getWrappedCanvasWidth(seqPanelWidth);
1432 int hgap = av.getCharHeight();
1433 if (av.getScaleAboveWrapped())
1435 hgap += av.getCharHeight();
1438 int annotationHeight = 0;
1439 if (av.isShowAnnotation())
1441 hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
1442 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1445 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1448 int maxwidth = av.getAlignment().getWidth();
1449 if (av.hasHiddenColumns())
1451 maxwidth = av.getAlignment().getHiddenColumns()
1452 .absoluteToVisibleColumn(maxwidth) - 1;
1455 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1461 * close the panel - deregisters all listeners and nulls any references to
1464 public void closePanel()
1466 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1467 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1468 PaintRefresher.RemoveComponent(this);
1473 * try to ensure references are nulled
1475 if (annotationPanel != null)
1477 annotationPanel.dispose();
1478 annotationPanel = null;
1483 av.removePropertyChangeListener(propertyChangeListener);
1484 propertyChangeListener = null;
1485 StructureSelectionManager ssm = av.getStructureSelectionManager();
1486 ssm.removeStructureViewerListener(getSeqPanel(), null);
1487 ssm.removeSelectionListener(getSeqPanel());
1488 ssm.removeCommandListener(av);
1489 ssm.removeStructureViewerListener(getSeqPanel(), null);
1490 ssm.removeSelectionListener(getSeqPanel());
1496 if (Cache.log.isDebugEnabled())
1498 Cache.log.warn("Closing alignment panel which is already closed.");
1504 * Close any open dialogs that would be orphaned when this one is closed
1506 protected void closeChildFrames()
1508 if (overviewPanel != null)
1510 overviewPanel.dispose();
1511 overviewPanel = null;
1513 if (calculationDialog != null)
1515 calculationDialog.closeFrame();
1516 calculationDialog = null;
1521 * hides or shows dynamic annotation rows based on groups and av state flags
1523 public void updateAnnotation()
1525 updateAnnotation(false, false);
1528 public void updateAnnotation(boolean applyGlobalSettings)
1530 updateAnnotation(applyGlobalSettings, false);
1533 public void updateAnnotation(boolean applyGlobalSettings,
1534 boolean preserveNewGroupSettings)
1536 av.updateGroupAnnotationSettings(applyGlobalSettings,
1537 preserveNewGroupSettings);
1538 adjustAnnotationHeight();
1542 public AlignmentI getAlignment()
1544 return av == null ? null : av.getAlignment();
1548 public String getViewName()
1550 return av.getViewName();
1554 * Make/Unmake this alignment panel the current input focus
1558 public void setSelected(boolean b)
1562 if (alignFrame.getSplitViewContainer() != null)
1565 * bring enclosing SplitFrame to front first if there is one
1567 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1569 alignFrame.setSelected(b);
1570 } catch (Exception ex)
1576 alignFrame.setDisplayedView(this);
1581 public StructureSelectionManager getStructureSelectionManager()
1583 return av.getStructureSelectionManager();
1587 public void raiseOOMWarning(String string, OutOfMemoryError error)
1589 new OOMWarning(string, error, this);
1593 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1596 return new FeatureRenderer(this);
1600 public jalview.api.FeatureRenderer getFeatureRenderer()
1602 return seqPanel.seqCanvas.getFeatureRenderer();
1605 public void updateFeatureRenderer(
1606 jalview.renderer.seqfeatures.FeatureRenderer fr)
1608 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1611 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1613 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1615 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1619 public ScalePanel getScalePanel()
1624 public void setScalePanel(ScalePanel scalePanel)
1626 this.scalePanel = scalePanel;
1629 public SeqPanel getSeqPanel()
1634 public void setSeqPanel(SeqPanel seqPanel)
1636 this.seqPanel = seqPanel;
1639 public AnnotationPanel getAnnotationPanel()
1641 return annotationPanel;
1644 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1646 this.annotationPanel = annotationPanel;
1649 public AnnotationLabels getAlabels()
1654 public void setAlabels(AnnotationLabels alabels)
1656 this.alabels = alabels;
1659 public IdPanel getIdPanel()
1664 public void setIdPanel(IdPanel idPanel)
1666 this.idPanel = idPanel;
1670 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1671 * The aim is to keep the two alignments 'lined up' on their centre columns.
1674 * holds mapped region(s) of this alignment that we are scrolling
1675 * 'to'; may be modified for sequence offset by this method
1676 * @param verticalOffset
1677 * the number of visible sequences to show above the mapped region
1679 protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1681 scrollToPosition(sr, verticalOffset, true);
1685 * Set a flag to say do not scroll any (cDNA/protein) complement.
1689 protected void setToScrollComplementPanel(boolean b)
1691 this.scrollComplementaryPanel = b;
1695 * Get whether to scroll complement panel
1697 * @return true if cDNA/protein complement panels should be scrolled
1699 protected boolean isSetToScrollComplementPanel()
1701 return this.scrollComplementaryPanel;
1707 * @adjustHeight if true, try to recalculate panel height for visible
1710 protected void refresh(boolean adjustHeight)
1712 validateAnnotationDimensions(adjustHeight);
1716 // sort, repaint, update overview
1717 paintAlignment(true, false);
1721 // lightweight repaint
1728 * Property change event fired when a change is made to the viewport ranges
1729 * object associated with this alignment panel's viewport
1731 public void propertyChange(PropertyChangeEvent evt)
1733 // update this panel's scroll values based on the new viewport ranges values
1734 updateScrollBarsFromRanges();
1736 // now update any complementary alignment (its viewport ranges object
1737 // is different so does not get automatically updated)
1738 if (isSetToScrollComplementPanel())
1740 setToScrollComplementPanel(false);
1741 av.scrollComplementaryAlignment();
1742 setToScrollComplementPanel(true);
1746 void updateScrollBarsFromRanges()
1748 ViewportRanges ranges = av.getRanges();
1749 setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
1753 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1754 * reference should be nulled when the dialog is closed.
1756 * @param calculationChooser
1758 public void setCalculationDialog(CalculationChooser calculationChooser)
1760 calculationDialog = calculationChooser;
1764 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1767 public CalculationChooser getCalculationDialog()
1769 return calculationDialog;
1773 * From appletgui, for JalviewJS JavaScript interface
1775 * preliminary - untested
1780 * @param scrollToNearest
1781 * @param redrawOverview
1784 public boolean scrollTo(int ostart, int end, int seqIndex,
1785 boolean scrollToNearest, boolean redrawOverview)
1787 int startv, endv, starts, ends;// , width;
1790 if (av.hasHiddenColumns())
1792 AlignmentI al = av.getAlignment();
1793 start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
1794 end = al.getHiddenColumns().absoluteToVisibleColumn(end);
1797 if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
1799 // don't scroll - position isn't visible
1809 ViewportRanges ranges = av.getRanges();
1810 if (!av.getWrapAlignment())
1813 * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
1814 * av.getStartRes()) >= start) { spos=start-1; // seqIn //
1815 * setScrollValues(start - 1, seqIndex); } else if ((endv =
1816 * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
1817 * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
1818 * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
1819 * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
1820 * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
1823 // below is scrolling logic up to Jalview 2.8.2
1824 // if ((av.getStartRes() > end)
1825 // || (av.getEndRes() < start)
1826 // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
1828 // if (start > av.getAlignment().getWidth() - hextent)
1830 // start = av.getAlignment().getWidth() - hextent;
1837 // if (seqIndex > av.getAlignment().getHeight() - vextent)
1839 // seqIndex = av.getAlignment().getHeight() - vextent;
1840 // if (seqIndex < 0)
1845 // setScrollValues(start, seqIndex);
1847 // logic copied from jalview.gui.AlignmentPanel:
1848 if ((startv = ranges.getStartRes()) >= start)
1851 * Scroll left to make start of search results visible
1853 setScrollValues(start - 1, seqIndex);
1855 else if ((endv = ranges.getEndRes()) <= end)
1858 * Scroll right to make end of search results visible
1860 setScrollValues(startv + 1 + end - endv, seqIndex);
1862 else if ((starts = ranges.getStartSeq()) > seqIndex)
1865 * Scroll up to make start of search results visible
1867 setScrollValues(ranges.getStartRes(), seqIndex);
1869 else if ((ends = ranges.getEndSeq()) <= seqIndex)
1872 * Scroll down to make end of search results visible
1874 setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
1877 * Else results are already visible - no need to scroll
1882 ranges.scrollToWrappedVisible(start);
1885 paintAlignment(redrawOverview, false);
1889 private boolean holdRepaint = false;
1892 * Called by IdCanvas and SeqPanel to defer painting until after JVP loading.
1894 * @return true if holding
1896 public boolean getHoldRepaint()
1902 * Called by Jalview2xml while loading
1906 public void setHoldRepaint(boolean tf)
1908 if (holdRepaint == tf)
1920 public void repaint()
1924 // System.out.println("AP repaint holding");
1925 // Platform.stackTrace();
1931 public void selectAllSequences()
1933 selectSequences(av.getAlignment().getSequences());
1936 public void deselectAllSequences()
1940 getSeqPanel().keyboardNo1 = null;
1941 getSeqPanel().keyboardNo2 = null;
1943 av.setSelectionGroup(null);
1944 av.getColumnSelection().clear();
1945 av.setSearchResults(null);
1946 getIdPanel().getIdCanvas().searchResults = null;
1948 // JAL-2034 - should delegate to
1949 // alignPanel to decide if overview needs
1951 paintAlignment(false, false);
1952 PaintRefresher.Refresh(this, av.getSequenceSetId());
1955 public void selectSequences(List<SequenceI> seqs)
1957 SequenceGroup sg = new SequenceGroup(seqs);
1958 sg.setEndRes(av.getAlignment().getWidth() - 1);
1959 av.setSelectionGroup(sg);
1960 av.isSelectionGroupChanged(true);
1962 // JAL-2034 - should delegate to
1963 // alignPanel to decide if overview needs
1965 paintAlignment(false, false);
1966 PaintRefresher.Refresh(this, av.getSequenceSetId());