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 static jalview.util.ImageMaker.TYPE.EPS;
24 import static jalview.util.ImageMaker.TYPE.PNG;
25 import static jalview.util.ImageMaker.TYPE.SVG;
27 import jalview.analysis.AnnotationSorter;
28 import jalview.api.AlignViewportI;
29 import jalview.api.AlignmentViewPanel;
30 import jalview.bin.Cache;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.HiddenColumns;
33 import jalview.datamodel.SearchResultsI;
34 import jalview.datamodel.SequenceFeature;
35 import jalview.datamodel.SequenceGroup;
36 import jalview.datamodel.SequenceI;
37 import jalview.io.HTMLOutput;
38 import jalview.jbgui.GAlignmentPanel;
39 import jalview.math.AlignmentDimension;
40 import jalview.schemes.ResidueProperties;
41 import jalview.structure.StructureSelectionManager;
42 import jalview.util.Comparison;
43 import jalview.util.ImageMaker;
44 import jalview.util.MessageManager;
45 import jalview.viewmodel.ViewportListenerI;
46 import jalview.viewmodel.ViewportRanges;
48 import java.awt.BorderLayout;
49 import java.awt.Color;
50 import java.awt.Container;
51 import java.awt.Dimension;
53 import java.awt.FontMetrics;
54 import java.awt.Graphics;
55 import java.awt.Graphics2D;
56 import java.awt.event.AdjustmentEvent;
57 import java.awt.event.AdjustmentListener;
58 import java.awt.event.ComponentAdapter;
59 import java.awt.event.ComponentEvent;
60 import java.awt.print.PageFormat;
61 import java.awt.print.Printable;
62 import java.awt.print.PrinterException;
63 import java.beans.PropertyChangeEvent;
64 import java.beans.PropertyChangeListener;
66 import java.io.FileWriter;
67 import java.io.PrintWriter;
68 import java.util.List;
70 import javax.swing.SwingUtilities;
76 * @version $Revision: 1.161 $
78 public class AlignmentPanel extends GAlignmentPanel implements
79 AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
81 public AlignViewport av;
83 OverviewPanel overviewPanel;
85 private SeqPanel seqPanel;
87 private IdPanel idPanel;
89 private boolean headless;
91 IdwidthAdjuster idwidthAdjuster;
94 public AlignFrame alignFrame;
96 private ScalePanel scalePanel;
98 private AnnotationPanel annotationPanel;
100 private AnnotationLabels alabels;
102 private int hextent = 0;
104 private int vextent = 0;
107 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
108 * false, suppresses invoking the same method recursively.
110 private boolean scrollComplementaryPanel = true;
112 private PropertyChangeListener propertyChangeListener;
114 private CalculationChooser calculationDialog;
117 * Creates a new AlignmentPanel object.
122 public AlignmentPanel(AlignFrame af, final AlignViewport av)
126 setSeqPanel(new SeqPanel(av, this));
127 setIdPanel(new IdPanel(av, this));
129 setScalePanel(new ScalePanel(av, this));
131 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
132 idwidthAdjuster = new IdwidthAdjuster(this);
133 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
135 setAnnotationPanel(new AnnotationPanel(this));
136 setAlabels(new AnnotationLabels(this));
138 annotationScroller.setViewportView(getAnnotationPanel());
139 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
141 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
142 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
144 setScrollValues(0, 0);
146 hscroll.addAdjustmentListener(this);
147 vscroll.addAdjustmentListener(this);
149 addComponentListener(new ComponentAdapter()
152 public void componentResized(ComponentEvent evt)
154 // reset the viewport ranges when the alignment panel is resized
155 // in particular, this initialises the end residue value when Jalview
157 ViewportRanges ranges = av.getRanges();
158 if (av.getWrapAlignment())
160 int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
161 getSeqPanel().seqCanvas.getWidth());
162 ranges.setViewportWidth(widthInRes);
166 int widthInRes = getSeqPanel().seqCanvas.getWidth()
168 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
169 / av.getCharHeight();
171 ranges.setViewportWidth(widthInRes);
172 ranges.setViewportHeight(heightInSeq);
178 final AlignmentPanel ap = this;
179 propertyChangeListener = new PropertyChangeListener()
182 public void propertyChange(PropertyChangeEvent evt)
184 if (evt.getPropertyName().equals("alignment"))
186 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
191 av.addPropertyChangeListener(propertyChangeListener);
193 av.getRanges().addPropertyChangeListener(this);
195 adjustAnnotationHeight();
200 public AlignViewportI getAlignViewport()
205 public void alignmentChanged()
207 av.alignmentChanged(this);
209 if (getCalculationDialog() != null)
211 getCalculationDialog().validateCalcTypes();
214 alignFrame.updateEditMenuBar();
216 // no idea if we need to update structure
217 paintAlignment(true, true);
224 public void fontChanged()
226 // set idCanvas bufferedImage to null
227 // to prevent drawing old image
228 FontMetrics fm = getFontMetrics(av.getFont());
230 scalePanelHolder.setPreferredSize(
231 new Dimension(10, av.getCharHeight() + fm.getDescent()));
232 idSpaceFillerPanel1.setPreferredSize(
233 new Dimension(10, av.getCharHeight() + fm.getDescent()));
234 idwidthAdjuster.invalidate();
235 scalePanelHolder.invalidate();
236 getIdPanel().getIdCanvas().gg = null;
237 getSeqPanel().seqCanvas.img = null;
238 getAnnotationPanel().adjustPanelHeight();
240 Dimension d = calculateIdWidth();
242 d.setSize(d.width + 4, d.height);
243 getIdPanel().getIdCanvas().setPreferredSize(d);
244 hscrollFillerPanel.setPreferredSize(d);
250 * Calculate the width of the alignment labels based on the displayed names
251 * and any bounds on label width set in preferences.
253 * @return Dimension giving the maximum width of the alignment label panel
254 * that should be used.
256 public Dimension calculateIdWidth()
258 // calculate sensible default width when no preference is available
260 if (av.getIdWidth() < 0)
262 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
263 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
264 r = calculateIdWidth(maxwidth);
265 av.setIdWidth(r.width);
270 r.width = av.getIdWidth();
277 * Calculate the width of the alignment labels based on the displayed names
278 * and any bounds on label width set in preferences.
281 * -1 or maximum width allowed for IdWidth
282 * @return Dimension giving the maximum width of the alignment label panel
283 * that should be used.
285 public Dimension calculateIdWidth(int maxwidth)
287 Container c = new Container();
289 FontMetrics fm = c.getFontMetrics(
290 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
292 AlignmentI al = av.getAlignment();
297 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
299 SequenceI s = al.getSequenceAt(i);
301 id = s.getDisplayId(av.getShowJVSuffix());
303 if (fm.stringWidth(id) > idWidth)
305 idWidth = fm.stringWidth(id);
311 // Also check annotation label widths
314 if (al.getAlignmentAnnotation() != null)
316 fm = c.getFontMetrics(getAlabels().getFont());
318 while (i < al.getAlignmentAnnotation().length)
320 String label = al.getAlignmentAnnotation()[i].label;
322 if (fm.stringWidth(label) > idWidth)
324 idWidth = fm.stringWidth(label);
331 return new Dimension(
332 maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
336 * Highlight the given results on the alignment
339 public void highlightSearchResults(SearchResultsI results)
341 boolean scrolled = scrollToPosition(results, 0, false);
343 boolean noFastPaint = scrolled && av.getWrapAlignment();
345 getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint);
349 * Scroll the view to show the position of the highlighted region in results
352 * @param searchResults
355 public boolean scrollToPosition(SearchResultsI searchResults)
357 return scrollToPosition(searchResults, 0, false);
361 * Scrolls the view (if necessary) to show the position of the first
362 * highlighted region in results (if any). Answers true if the view was
363 * scrolled, or false if no matched region was found, or it is already
367 * @param verticalOffset
368 * if greater than zero, allows scrolling to a position below the
369 * first displayed sequence
371 * if true, try to centre the search results horizontally in the view
374 protected boolean scrollToPosition(SearchResultsI results,
375 int verticalOffset, boolean centre)
377 int startv, endv, starts, ends;
378 ViewportRanges ranges = av.getRanges();
380 if (results == null || results.isEmpty() || av == null
381 || av.getAlignment() == null)
385 int seqIndex = av.getAlignment().findIndex(results);
390 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
392 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
401 * To centre results, scroll to positions half the visible width
402 * left/right of the start/end positions
406 int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
407 start = Math.max(start - offset, 0);
408 end = end + offset - 1;
414 if (end == seq.getEnd())
419 if (av.hasHiddenColumns())
421 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
422 start = hidden.absoluteToVisibleColumn(start);
423 end = hidden.absoluteToVisibleColumn(end);
426 if (!hidden.isVisible(r[0]))
428 // don't scroll - position isn't visible
435 * allow for offset of target sequence (actually scroll to one above it)
437 seqIndex = Math.max(0, seqIndex - verticalOffset);
438 boolean scrollNeeded = true;
440 if (!av.getWrapAlignment())
442 if ((startv = ranges.getStartRes()) >= start)
445 * Scroll left to make start of search results visible
447 setScrollValues(start, seqIndex);
449 else if ((endv = ranges.getEndRes()) <= end)
452 * Scroll right to make end of search results visible
454 setScrollValues(startv + end - endv, seqIndex);
456 else if ((starts = ranges.getStartSeq()) > seqIndex)
459 * Scroll up to make start of search results visible
461 setScrollValues(ranges.getStartRes(), seqIndex);
463 else if ((ends = ranges.getEndSeq()) <= seqIndex)
466 * Scroll down to make end of search results visible
468 setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
472 * Else results are already visible - no need to scroll
474 scrollNeeded = false;
478 scrollNeeded = ranges.scrollToWrappedVisible(start);
481 paintAlignment(false, false);
489 * @return DOCUMENT ME!
491 public OverviewPanel getOverviewPanel()
493 return overviewPanel;
502 public void setOverviewPanel(OverviewPanel op)
510 * Hide or show annotation panel
513 public void setAnnotationVisible(boolean b)
515 if (!av.getWrapAlignment())
517 annotationSpaceFillerHolder.setVisible(b);
518 annotationScroller.setVisible(b);
524 * automatically adjust annotation panel height for new annotation whilst
525 * ensuring the alignment is still visible.
528 public void adjustAnnotationHeight()
530 // TODO: display vertical annotation scrollbar if necessary
531 // this is called after loading new annotation onto alignment
532 if (alignFrame.getHeight() == 0)
534 System.out.println("NEEDS FIXING");
536 validateAnnotationDimensions(true);
538 // TODO: many places call this method and also paintAlignment with various
539 // different settings. this means multiple redraws are triggered...
540 paintAlignment(true, av.needToUpdateStructureViews());
544 * calculate the annotation dimensions and refresh slider values accordingly.
545 * need to do repaints/notifys afterwards.
547 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
549 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
550 annotationHeight = getAnnotationPanel()
551 .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
554 annotationScroller.setPreferredSize(
555 new Dimension(annotationScroller.getWidth(), annotationHeight));
557 Dimension e = idPanel.getSize();
558 alabels.setSize(new Dimension(e.width, annotationHeight));
560 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
561 annotationSpaceFillerHolder.getWidth(), annotationHeight));
562 annotationScroller.validate();
563 annotationScroller.addNotify();
567 * update alignment layout for viewport settings
572 public void updateLayout()
575 setAnnotationVisible(av.isShowAnnotation());
576 boolean wrap = av.getWrapAlignment();
577 ViewportRanges ranges = av.getRanges();
578 ranges.setStartSeq(0);
579 scalePanelHolder.setVisible(!wrap);
580 hscroll.setVisible(!wrap);
581 idwidthAdjuster.setVisible(!wrap);
585 annotationScroller.setVisible(false);
586 annotationSpaceFillerHolder.setVisible(false);
588 else if (av.isShowAnnotation())
590 annotationScroller.setVisible(true);
591 annotationSpaceFillerHolder.setVisible(true);
592 validateAnnotationDimensions(false);
595 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
597 { // may not yet be laid out
600 int widthInRes = getSeqPanel().seqCanvas
601 .getWrappedCanvasWidth(canvasWidth);
602 ranges.setViewportWidth(widthInRes);
606 int widthInRes = (canvasWidth / av.getCharWidth());
607 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
608 / av.getCharHeight());
610 ranges.setViewportWidth(widthInRes);
611 ranges.setViewportHeight(heightInSeq);
615 idSpaceFillerPanel1.setVisible(!wrap);
621 * Adjust row/column scrollers to show a visible position in the alignment.
624 * visible column to scroll to
626 * visible row to scroll to
629 public void setScrollValues(int xpos, int ypos)
634 if (av == null || av.getAlignment() == null)
639 if (av.getWrapAlignment())
641 setScrollingForWrappedPanel(x);
645 int width = av.getAlignment().getVisibleWidth();
646 int height = av.getAlignment().getHeight();
648 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
649 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
656 if (vextent > height)
661 if ((hextent + x) > width)
666 if ((vextent + y) > height)
668 y = height - vextent;
681 // update the scroll values
682 hscroll.setValues(x, hextent, 0, width);
683 vscroll.setValues(y, vextent, 0, height);
688 * Respond to adjustment event when horizontal or vertical scrollbar is
692 * adjustment event encoding whether hscroll or vscroll changed
695 public void adjustmentValueChanged(AdjustmentEvent evt)
697 if (av.getWrapAlignment())
699 adjustScrollingWrapped(evt);
703 ViewportRanges ranges = av.getRanges();
705 if (evt.getSource() == hscroll)
707 int oldX = ranges.getStartRes();
708 int oldwidth = ranges.getViewportWidth();
709 int x = hscroll.getValue();
710 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
712 // if we're scrolling to the position we're already at, stop
713 // this prevents infinite recursion of events when the scroll/viewport
714 // ranges values are the same
715 if ((x == oldX) && (width == oldwidth))
719 ranges.setViewportStartAndWidth(x, width);
721 else if (evt.getSource() == vscroll)
723 int oldY = ranges.getStartSeq();
724 int oldheight = ranges.getViewportHeight();
725 int y = vscroll.getValue();
726 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
728 // if we're scrolling to the position we're already at, stop
729 // this prevents infinite recursion of events when the scroll/viewport
730 // ranges values are the same
731 if ((y == oldY) && (height == oldheight))
735 ranges.setViewportStartAndHeight(y, height);
741 * Responds to a scroll change by setting the start position of the viewport.
746 protected void adjustScrollingWrapped(AdjustmentEvent evt)
748 if (evt.getSource() == hscroll)
750 return; // no horizontal scroll when wrapped
752 final ViewportRanges ranges = av.getRanges();
754 if (evt.getSource() == vscroll)
756 int newY = vscroll.getValue();
759 * if we're scrolling to the position we're already at, stop
760 * this prevents infinite recursion of events when the scroll/viewport
761 * ranges values are the same
763 int oldX = ranges.getStartRes();
764 int oldY = ranges.getWrappedScrollPosition(oldX);
772 * limit page up/down to one width's worth of positions
774 int rowSize = ranges.getViewportWidth();
775 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
776 ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
781 // This is only called if file loaded is a jar file that
782 // was wrapped when saved and user has wrap alignment true
783 // as preference setting
784 SwingUtilities.invokeLater(new Runnable()
789 // When updating scrolling to use ViewportChange events, this code
790 // could not be validated and it is not clear if it is now being
791 // called. Log warning here in case it is called and unforeseen
794 "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
796 // scroll to start of panel
797 ranges.setStartRes(0);
798 ranges.setStartSeq(0);
806 * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
809 public void paintAlignment(boolean updateOverview,
810 boolean updateStructures)
812 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
813 av.isShowAutocalculatedAbove());
814 sorter.sort(getAlignment().getAlignmentAnnotation(),
815 av.getSortAnnotationsBy());
818 if (updateStructures)
820 av.getStructureSelectionManager().sequenceColoursChanged(this);
825 if (overviewPanel != null)
827 overviewPanel.updateOverviewImage();
839 public void paintComponent(Graphics g)
841 invalidate(); // needed so that the id width adjuster works correctly
843 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
844 idPanelHolder.setPreferredSize(d);
845 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
847 validate(); // needed so that the id width adjuster works correctly
850 * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
851 * though I still think this call should be elsewhere.
853 ViewportRanges ranges = av.getRanges();
854 setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
858 * Set vertical scroll bar position, and number of increments, for wrapped
861 * @param topLeftColumn
862 * the column position at top left (0..)
864 private void setScrollingForWrappedPanel(int topLeftColumn)
866 ViewportRanges ranges = av.getRanges();
867 int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
868 int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
871 * a scrollbar's value can be set to at most (maximum-extent)
872 * so we add extent (1) to the maxScroll value
874 vscroll.setUnitIncrement(1);
875 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
879 * Provides the implementation of Printable.print
888 * @return DOCUMENT ME!
890 * @throws PrinterException
893 public int print(Graphics pg, PageFormat pf, int pi)
894 throws PrinterException
896 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
898 int pwidth = (int) pf.getImageableWidth();
899 int pheight = (int) pf.getImageableHeight();
901 if (av.getWrapAlignment())
903 return printWrappedAlignment(pwidth, pheight, pi, pg, true);
907 return printUnwrapped(pwidth, pheight, pi, pg, pg);
912 * Draws the alignment image, including sequence ids, sequences, and
913 * annotation labels and annotations if shown, on either one or two Graphics
923 * the graphics context for sequence ids and annotation labels
924 * @param alignmentGraphics
925 * the graphics context for sequences and annotations (may or may not
926 * be the same context as idGraphics)
928 * @throws PrinterException
930 public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
931 Graphics idGraphics, Graphics alignmentGraphics)
932 throws PrinterException
934 final int idWidth = getVisibleIdWidth(false);
937 * Get the horizontal offset to where we draw the sequences.
938 * This is idWidth if using a single Graphics context, else zero.
940 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
943 FontMetrics fm = getFontMetrics(av.getFont());
944 final int charHeight = av.getCharHeight();
945 final int scaleHeight = charHeight + fm.getDescent();
947 idGraphics.setColor(Color.white);
948 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
949 idGraphics.setFont(av.getFont());
952 * How many sequences and residues can we fit on a printable page?
954 final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
956 final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
958 final int alignmentWidth = av.getAlignment().getVisibleWidth();
959 int pagesWide = (alignmentWidth / totalRes) + 1;
961 final int startRes = (pageIndex % pagesWide) * totalRes;
962 final int endRes = Math.min(startRes + totalRes - 1,
965 final int startSeq = (pageIndex / pagesWide) * totalSeq;
966 final int alignmentHeight = av.getAlignment().getHeight();
967 final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
969 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
971 if (av.isShowAnnotation())
973 pagesHigh += getAnnotationPanel().adjustPanelHeight()
974 + SeqCanvas.SEQS_ANNOTATION_GAP;
977 pagesHigh /= pageHeight;
979 if (pageIndex >= (pagesWide * pagesHigh))
981 return Printable.NO_SUCH_PAGE;
983 final int alignmentDrawnHeight = (endSeq - startSeq + 1) * charHeight;
986 * draw the Scale at horizontal offset, then reset to top left (0, 0)
988 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
989 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
990 pageWidth - idWidth, scaleHeight);
991 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
994 * Draw the sequence ids, offset for scale height,
995 * then reset to top left (0, 0)
997 idGraphics.translate(0, scaleHeight);
998 IdCanvas idCanvas = getIdPanel().getIdCanvas();
999 List<SequenceI> selection = av.getSelectionGroup() == null ? null
1000 : av.getSelectionGroup().getSequences(null);
1001 idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
1004 idGraphics.setFont(av.getFont());
1005 idGraphics.translate(0, -scaleHeight);
1008 * draw the sequences, offset for scale height, and id width (if using a
1009 * single graphics context), then reset to (0, scale height)
1011 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1012 getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
1013 endRes, startSeq, endSeq - 1);
1014 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1016 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1019 * draw annotation labels; drawComponent() translates by
1020 * getScrollOffset(), so compensate for that first;
1021 * then reset to (0, scale height)
1023 int offset = getAlabels().getScrollOffset();
1024 int yShift = alignmentDrawnHeight + SeqCanvas.SEQS_ANNOTATION_GAP;
1025 idGraphics.translate(0, -offset);
1026 idGraphics.translate(0, yShift);
1027 getAlabels().drawComponent(idGraphics, idWidth);
1028 idGraphics.translate(0, -yShift);
1031 * draw the annotations starting at
1032 * (idOffset, alignmentHeight) from (0, scaleHeight)
1034 alignmentGraphics.translate(alignmentGraphicsOffset,
1036 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1037 alignmentGraphics, -1, startRes, endRes + 1);
1040 * reset to left margin below annotation
1042 int justDrawn = getAnnotationPanel().renderer.getLastDrawnHeight();
1043 alignmentGraphics.translate(-alignmentGraphicsOffset, justDrawn);
1048 * shift graphics to position after drawn sequences
1050 alignmentGraphics.translate(0, alignmentDrawnHeight);
1053 return Printable.PAGE_EXISTS;
1057 * Prints one page of an alignment in wrapped mode. Returns
1058 * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
1059 * no page could be drawn (page number out of range).
1061 * The method is to write the whole alignment, but set a clip region such that
1062 * only the specified page is written. This allows specified page(s) to be
1063 * printed from the print dialog. The whole image may be written simply by
1064 * making the page size match the image size. In this case, parameter
1065 * {@code clipToPage} should be set to {@code false}, so that more output (for
1066 * example the second panel of a split frame) can be written if wanted.
1077 public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
1078 Graphics g, boolean clipToPage)
1080 getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
1082 int annotationHeight = 0;
1083 if (av.isShowAnnotation())
1085 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1088 int hgap = av.getCharHeight();
1089 if (av.getScaleAboveWrapped())
1091 hgap += av.getCharHeight();
1094 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1097 int idWidth = getVisibleIdWidth(false);
1099 int maxwidth = av.getAlignment().getVisibleWidth();
1101 int resWidth = getSeqPanel().seqCanvas
1102 .getWrappedCanvasWidth(pageWidth - idWidth);
1103 av.getRanges().setViewportStartAndWidth(0, resWidth);
1105 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1107 g.setColor(Color.white);
1108 g.fillRect(0, 0, pageWidth, pageHeight);
1109 g.setFont(av.getFont());
1110 g.setColor(Color.black);
1113 * method: print the whole wrapped alignment, but with a clip region that
1114 * is restricted to the requested page; this supports selective print of
1115 * single pages or ranges, (at the cost of repeated processing in the
1116 * 'normal' case, when all pages are printed)
1118 g.translate(0, -pageNumber * pageHeight);
1122 g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
1126 * draw sequence ids and annotation labels (if shown)
1128 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1129 idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
1131 g.translate(idWidth, 0);
1132 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
1134 g.translate(-idWidth, 0);
1136 if ((pageNumber * pageHeight) < totalHeight)
1138 return Printable.PAGE_EXISTS;
1142 return Printable.NO_SUCH_PAGE;
1147 * get current sequence ID panel width, or nominal value if panel were to be
1148 * displayed using default settings
1152 public int getVisibleIdWidth()
1154 return getVisibleIdWidth(true);
1158 * get current sequence ID panel width, or nominal value if panel were to be
1159 * displayed using default settings
1162 * indicate if the Id width for onscreen or offscreen display should
1166 public int getVisibleIdWidth(boolean onscreen)
1168 // see if rendering offscreen - check preferences and calc width accordingly
1169 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1171 return calculateIdWidth(-1).width + 4;
1173 Integer idwidth = null;
1174 if (onscreen || (idwidth = Cache
1175 .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1177 int w = getIdPanel().getWidth();
1178 return (w > 0 ? w : calculateIdWidth().width + 4);
1180 return idwidth.intValue() + 4;
1184 * Generates an image of the alignment panel of the specified type. If
1185 * {@code type} is not null, the image is written to the file, otherwise the
1186 * user is prompted to specify the output file before writing to it.
1190 * @param forSplitFrame
1192 void makeAlignmentImage(ImageMaker.TYPE type, File file,
1193 boolean forSplitFrame)
1195 int borderBottomOffset = 5;
1196 long pSessionId = System.currentTimeMillis();
1197 headless = (System.getProperty("java.awt.headless") != null
1198 && System.getProperty("java.awt.headless").equals("true"));
1199 if (alignFrame != null && !headless)
1203 alignFrame.setProgressBar(MessageManager
1204 .formatMessage("status.saving_file", new Object[]
1205 { type.getLabel() }), pSessionId);
1210 * cache preferences in case we need to fudge them for export of
1211 * split frame with 'protein scaled to codons' and 'auto id width'
1214 final String autoIdWidth = Cache.getProperty("FIGURE_AUTOIDWIDTH");
1215 final Integer fixedIdWidth = Cache
1216 .getIntegerProperty("FIGURE_FIXEDIDWIDTH");
1221 * if exporting a split frame image, the graphics object has
1222 * width: maximum of the top and bottom image widths
1223 * height: sum of the top and bottom image heights
1224 * if 'protein scaled to codons' and 'auto id width', fudge
1225 * to a fixed width (and restore preferences afterwards)
1227 AlignmentPanel complement = null;
1228 AlignmentDimension dim1 = getAlignmentDimension();
1229 AlignmentDimension dim2 = new AlignmentDimension(0, 0);
1233 complement = ((AlignViewport) av.getCodingComplement())
1235 dim2 = complement.getAlignmentDimension();
1236 if (Boolean.valueOf(autoIdWidth) && av.isScaleProteinAsCdna())
1238 int w1 = this.getVisibleIdWidth(false);
1239 int w2 = complement.getVisibleIdWidth(false);
1240 Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.FALSE.toString());
1241 Cache.setProperty("FIGURE_FIXEDIDWIDTH",
1242 String.valueOf(Math.max(w1, w2)));
1245 final int graphicsHeight = dim1.height + dim2.height
1246 + borderBottomOffset;
1247 final int graphicsWidth = Math.max(dim1.width, dim2.width);
1249 final String dialogTitle = MessageManager
1250 .formatMessage("label.make_alignment_image", type.getName());
1251 String imageTitle = type == PNG ? null : alignFrame.getTitle();
1253 ImageMaker im = new ImageMaker(this, type, dialogTitle,
1254 graphicsWidth, graphicsHeight, file,
1255 imageTitle, alignFrame, pSessionId, headless);
1256 Graphics graphics = im.getGraphics();
1257 if (graphics == null)
1261 graphics.setColor(Color.white);
1262 graphics.fillRect(0, 0, graphicsWidth, graphicsHeight);
1263 if (av.getWrapAlignment())
1265 printWrappedAlignment(dim1.width, dim1.height + borderBottomOffset,
1266 0, graphics, false);
1270 printUnwrapped(dim1.width, dim1.height, 0, graphics, graphics);
1276 * append coding complement image
1278 // to debug location of next write to Graphics:
1279 // graphics.drawString("Hello world", 0, 0);
1280 if (av.getCodingComplement().getWrapAlignment())
1282 complement.printWrappedAlignment(dim2.width,
1283 dim2.height + borderBottomOffset, 0, graphics, false);
1287 complement.printUnwrapped(dim2.width, dim2.height, 0, graphics,
1293 } catch (OutOfMemoryError err)
1296 System.out.println("########################\n" + "OUT OF MEMORY "
1297 + file + "\n" + "########################");
1298 new OOMWarning("Creating Image for " + file, err);
1299 // System.out.println("Create IMAGE: " + err);
1300 } catch (Exception ex)
1302 ex.printStackTrace();
1306 * restore preference settings in case they were fudged
1308 if (autoIdWidth == null)
1310 Cache.removeProperty("FIGURE_AUTOIDWIDTH");
1314 Cache.setProperty("FIGURE_AUTOIDWIDTH", autoIdWidth);
1316 if (fixedIdWidth == null)
1318 Cache.removeProperty("FIGURE_FIXEDIDWIDTH");
1322 Cache.setProperty("FIGURE_FIXEDIDWIDTH",
1323 String.valueOf(fixedIdWidth));
1329 * Computes and answers the width and height of the alignment in pixels,
1332 * <li>sequence ids</li>
1333 * <li>scale above, left or right if shown</li>
1334 * <li>sequence rows, plus one spacer line</li>
1335 * <li>annotations, if shown</li>
1337 * The alignment may be in wrapped or unwrapped mode.
1342 public AlignmentDimension getAlignmentDimension()
1344 int maxwidth = av.getAlignment().getVisibleWidth();
1346 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1347 + getScalePanel().getHeight();
1348 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1350 if (av.getWrapAlignment())
1352 height = getWrappedHeight();
1355 // need to obtain default alignment width and then add in any
1356 // additional allowance for id margin
1357 // this duplicates the calculation in getWrappedHeight but adjusts for
1359 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1360 - alignFrame.getInsets().left - alignFrame.getInsets().right
1361 - getVisibleIdWidth() + getVisibleIdWidth(false);
1365 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1369 else if (av.isShowAnnotation())
1371 height += getAnnotationPanel().adjustPanelHeight() + 3;
1374 return new AlignmentDimension(width, height);
1378 * Creates and writes an EPS image of the alignment, to the given file if
1379 * specified, else after prompting for the output file
1382 * @param forSplitFrame
1384 public void makeEPS(File epsFile, boolean forSplitFrame)
1386 makeAlignmentImage(EPS, epsFile, forSplitFrame);
1390 * Creates and writes a PNG image of the alignment, to the given file if
1391 * specified, else after prompting for the output file
1394 * @param forSplitFrame
1396 public void makePNG(File pngFile, boolean forSplitFrame)
1398 makeAlignmentImage(PNG, pngFile, forSplitFrame);
1402 * Creates and writes an SVG image of the alignment, to the given file if
1403 * specified, else after prompting for the output file
1406 * @param forSplitFrame
1408 public void makeSVG(File svgFile, boolean forSplitFrame)
1410 makeAlignmentImage(SVG, svgFile, forSplitFrame);
1413 public void makePNGImageMap(File imgMapFile, String imageName)
1415 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1416 // ////////////////////////////////////////////
1417 int idWidth = getVisibleIdWidth(false);
1418 FontMetrics fm = getFontMetrics(av.getFont());
1419 int scaleHeight = av.getCharHeight() + fm.getDescent();
1422 // ////////////////////////////////
1423 if (imgMapFile != null)
1427 int sSize = av.getAlignment().getHeight();
1428 int alwidth = av.getAlignment().getWidth();
1429 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1430 out.println(HTMLOutput.getImageMapHTML());
1431 out.println("<img src=\"" + imageName
1432 + "\" border=\"0\" usemap=\"#Map\" >"
1433 + "<map name=\"Map\">");
1435 for (int s = 0; s < sSize; s++)
1437 int sy = s * av.getCharHeight() + scaleHeight;
1439 SequenceI seq = av.getAlignment().getSequenceAt(s);
1440 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1441 for (int column = 0; column < alwidth; column++)
1443 StringBuilder text = new StringBuilder(512);
1444 String triplet = null;
1445 if (av.getAlignment().isNucleotide())
1447 triplet = ResidueProperties.nucleotideName.get(seq
1448 .getCharAt(column) + "");
1452 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
1456 if (triplet == null)
1461 int seqPos = seq.findPosition(column);
1462 int gSize = groups.length;
1463 for (int g = 0; g < gSize; g++)
1465 if (text.length() < 1)
1467 text.append("<area shape=\"rect\" coords=\"")
1468 .append((idWidth + column * av.getCharWidth()))
1469 .append(",").append(sy).append(",")
1470 .append((idWidth + (column + 1) * av.getCharWidth()))
1471 .append(",").append((av.getCharHeight() + sy))
1472 .append("\"").append(" onMouseOver=\"toolTip('")
1473 .append(seqPos).append(" ").append(triplet);
1476 if (groups[g].getStartRes() < column
1477 && groups[g].getEndRes() > column)
1479 text.append("<br><em>").append(groups[g].getName())
1484 if (text.length() < 1)
1486 text.append("<area shape=\"rect\" coords=\"")
1487 .append((idWidth + column * av.getCharWidth()))
1488 .append(",").append(sy).append(",")
1489 .append((idWidth + (column + 1) * av.getCharWidth()))
1490 .append(",").append((av.getCharHeight() + sy))
1491 .append("\"").append(" onMouseOver=\"toolTip('")
1492 .append(seqPos).append(" ").append(triplet);
1494 if (!Comparison.isGap(seq.getCharAt(column)))
1496 List<SequenceFeature> features = seq.findFeatures(column, column);
1497 for (SequenceFeature sf : features)
1499 if (sf.isContactFeature())
1501 text.append("<br>").append(sf.getType()).append(" ")
1502 .append(sf.getBegin()).append(":")
1503 .append(sf.getEnd());
1507 text.append("<br>");
1508 text.append(sf.getType());
1509 String description = sf.getDescription();
1510 if (description != null
1511 && !sf.getType().equals(description))
1513 description = description.replace("\"", """);
1514 text.append(" ").append(description);
1517 String status = sf.getStatus();
1518 if (status != null && !"".equals(status))
1520 text.append(" (").append(status).append(")");
1523 if (text.length() > 1)
1525 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1526 out.println(text.toString());
1531 out.println("</map></body></html>");
1534 } catch (Exception ex)
1536 ex.printStackTrace();
1538 } // /////////END OF IMAGE MAP
1543 * Answers the height of the entire alignment in pixels, assuming it is in
1548 int getWrappedHeight()
1550 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1552 if (System.getProperty("java.awt.headless") != null
1553 && System.getProperty("java.awt.headless").equals("true"))
1555 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1556 - vscroll.getPreferredSize().width
1557 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1560 int chunkWidth = getSeqPanel().seqCanvas
1561 .getWrappedCanvasWidth(seqPanelWidth);
1563 int hgap = av.getCharHeight();
1564 if (av.getScaleAboveWrapped())
1566 hgap += av.getCharHeight();
1569 int annotationHeight = 0;
1570 if (av.isShowAnnotation())
1572 hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
1573 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1576 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1579 int maxwidth = av.getAlignment().getWidth();
1580 if (av.hasHiddenColumns())
1582 maxwidth = av.getAlignment().getHiddenColumns()
1583 .absoluteToVisibleColumn(maxwidth) - 1;
1586 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1592 * close the panel - deregisters all listeners and nulls any references to
1595 public void closePanel()
1597 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1598 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1599 PaintRefresher.RemoveComponent(this);
1604 * try to ensure references are nulled
1606 if (annotationPanel != null)
1608 annotationPanel.dispose();
1609 annotationPanel = null;
1614 av.removePropertyChangeListener(propertyChangeListener);
1615 propertyChangeListener = null;
1616 StructureSelectionManager ssm = av.getStructureSelectionManager();
1617 ssm.removeStructureViewerListener(getSeqPanel(), null);
1618 ssm.removeSelectionListener(getSeqPanel());
1619 ssm.removeCommandListener(av);
1620 ssm.removeStructureViewerListener(getSeqPanel(), null);
1621 ssm.removeSelectionListener(getSeqPanel());
1627 if (Cache.log.isDebugEnabled())
1629 Cache.log.warn("Closing alignment panel which is already closed.");
1635 * Close any open dialogs that would be orphaned when this one is closed
1637 protected void closeChildFrames()
1639 if (overviewPanel != null)
1641 overviewPanel.dispose();
1642 overviewPanel = null;
1644 if (calculationDialog != null)
1646 calculationDialog.closeFrame();
1647 calculationDialog = null;
1652 * hides or shows dynamic annotation rows based on groups and av state flags
1654 public void updateAnnotation()
1656 updateAnnotation(false, false);
1659 public void updateAnnotation(boolean applyGlobalSettings)
1661 updateAnnotation(applyGlobalSettings, false);
1664 public void updateAnnotation(boolean applyGlobalSettings,
1665 boolean preserveNewGroupSettings)
1667 av.updateGroupAnnotationSettings(applyGlobalSettings,
1668 preserveNewGroupSettings);
1669 adjustAnnotationHeight();
1673 public AlignmentI getAlignment()
1675 return av == null ? null : av.getAlignment();
1679 public String getViewName()
1681 return av.getViewName();
1685 * Make/Unmake this alignment panel the current input focus
1689 public void setSelected(boolean b)
1693 if (alignFrame.getSplitViewContainer() != null)
1696 * bring enclosing SplitFrame to front first if there is one
1698 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1700 alignFrame.setSelected(b);
1701 } catch (Exception ex)
1707 alignFrame.setDisplayedView(this);
1712 public StructureSelectionManager getStructureSelectionManager()
1714 return av.getStructureSelectionManager();
1718 public void raiseOOMWarning(String string, OutOfMemoryError error)
1720 new OOMWarning(string, error, this);
1724 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1727 return new FeatureRenderer(this);
1731 public jalview.api.FeatureRenderer getFeatureRenderer()
1733 return seqPanel.seqCanvas.getFeatureRenderer();
1736 public void updateFeatureRenderer(
1737 jalview.renderer.seqfeatures.FeatureRenderer fr)
1739 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1742 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1744 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1746 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1750 public ScalePanel getScalePanel()
1755 public void setScalePanel(ScalePanel scalePanel)
1757 this.scalePanel = scalePanel;
1760 public SeqPanel getSeqPanel()
1765 public void setSeqPanel(SeqPanel seqPanel)
1767 this.seqPanel = seqPanel;
1770 public AnnotationPanel getAnnotationPanel()
1772 return annotationPanel;
1775 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1777 this.annotationPanel = annotationPanel;
1780 public AnnotationLabels getAlabels()
1785 public void setAlabels(AnnotationLabels alabels)
1787 this.alabels = alabels;
1790 public IdPanel getIdPanel()
1795 public void setIdPanel(IdPanel idPanel)
1797 this.idPanel = idPanel;
1801 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1802 * The aim is to keep the two alignments 'lined up' on their centre columns.
1805 * holds mapped region(s) of this alignment that we are scrolling
1806 * 'to'; may be modified for sequence offset by this method
1807 * @param verticalOffset
1808 * the number of visible sequences to show above the mapped region
1810 protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1812 scrollToPosition(sr, verticalOffset, true);
1816 * Set a flag to say do not scroll any (cDNA/protein) complement.
1820 protected void setToScrollComplementPanel(boolean b)
1822 this.scrollComplementaryPanel = b;
1826 * Get whether to scroll complement panel
1828 * @return true if cDNA/protein complement panels should be scrolled
1830 protected boolean isSetToScrollComplementPanel()
1832 return this.scrollComplementaryPanel;
1838 * @adjustHeight if true, try to recalculate panel height for visible
1841 protected void refresh(boolean adjustHeight)
1843 validateAnnotationDimensions(adjustHeight);
1847 // sort, repaint, update overview
1848 paintAlignment(true, false);
1852 // lightweight repaint
1859 * Property change event fired when a change is made to the viewport ranges
1860 * object associated with this alignment panel's viewport
1862 public void propertyChange(PropertyChangeEvent evt)
1864 // update this panel's scroll values based on the new viewport ranges values
1865 ViewportRanges ranges = av.getRanges();
1866 int x = ranges.getStartRes();
1867 int y = ranges.getStartSeq();
1868 setScrollValues(x, y);
1870 // now update any complementary alignment (its viewport ranges object
1871 // is different so does not get automatically updated)
1872 if (isSetToScrollComplementPanel())
1874 setToScrollComplementPanel(false);
1875 av.scrollComplementaryAlignment();
1876 setToScrollComplementPanel(true);
1881 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1882 * reference should be nulled when the dialog is closed.
1884 * @param calculationChooser
1886 public void setCalculationDialog(CalculationChooser calculationChooser)
1888 calculationDialog = calculationChooser;
1892 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1895 public CalculationChooser getCalculationDialog()
1897 return calculationDialog;