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() + 3;
976 pagesHigh /= pageHeight;
978 if (pageIndex >= (pagesWide * pagesHigh))
980 return Printable.NO_SUCH_PAGE;
982 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
985 * draw the Scale at horizontal offset, then reset to top left (0, 0)
987 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
988 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
989 pageWidth - idWidth, scaleHeight);
990 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
993 * Draw the sequence ids, offset for scale height,
994 * then reset to top left (0, 0)
996 idGraphics.translate(0, scaleHeight);
997 IdCanvas idCanvas = getIdPanel().getIdCanvas();
998 List<SequenceI> selection = av.getSelectionGroup() == null ? null
999 : av.getSelectionGroup().getSequences(null);
1000 idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
1003 idGraphics.setFont(av.getFont());
1004 idGraphics.translate(0, -scaleHeight);
1007 * draw the sequences, offset for scale height, and id width (if using a
1008 * single graphics context), then reset to (0, scale height)
1010 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1011 getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
1012 endRes, startSeq, endSeq - 1);
1013 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1015 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1018 * draw annotation labels; drawComponent() translates by
1019 * getScrollOffset(), so compensate for that first;
1020 * then reset to (0, scale height)
1022 int offset = getAlabels().getScrollOffset();
1023 idGraphics.translate(0, -offset);
1024 idGraphics.translate(0, alignmentDrawnHeight);
1025 getAlabels().drawComponent(idGraphics, idWidth);
1026 idGraphics.translate(0, -alignmentDrawnHeight);
1029 * draw the annotations starting at
1030 * (idOffset, alignmentHeight) from (0, scaleHeight)
1032 alignmentGraphics.translate(alignmentGraphicsOffset,
1033 alignmentDrawnHeight);
1034 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1035 alignmentGraphics, -1, startRes, endRes + 1);
1038 * reset to left margin
1040 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1043 return Printable.PAGE_EXISTS;
1047 * Prints one page of an alignment in wrapped mode. Returns
1048 * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
1049 * no page could be drawn (page number out of range).
1051 * The method is to write the whole alignment, but set a clip region such that
1052 * only the specified page is written. This allows specified page(s) to be
1053 * printed from the print dialog. The whole image may be written simply by
1054 * making the page size match the image size. In this case, parameter
1055 * {@code clipToPage} should be set to {@code false}, so that more output (for
1056 * example the second panel of a split frame) can be written if wanted.
1067 public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
1068 Graphics g, boolean clipToPage)
1070 int annotationHeight = 0;
1071 if (av.isShowAnnotation())
1073 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1076 int hgap = av.getCharHeight();
1077 if (av.getScaleAboveWrapped())
1079 hgap += av.getCharHeight();
1082 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1085 int idWidth = getVisibleIdWidth(false);
1087 int maxwidth = av.getAlignment().getVisibleWidth();
1089 int resWidth = getSeqPanel().seqCanvas
1090 .getWrappedCanvasWidth(pageWidth - idWidth);
1092 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1094 g.setColor(Color.white);
1095 g.fillRect(0, 0, pageWidth, pageHeight);
1096 g.setFont(av.getFont());
1097 g.setColor(Color.black);
1100 * method: print the whole wrapped alignment, but with a clip region that
1101 * is restricted to the requested page; this supports selective print of
1102 * single pages or ranges, (at the cost of some repeated processing in
1103 * the 'normal' case, when all pages are printed)
1105 g.translate(0, -pageNumber * pageHeight);
1109 g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
1113 * draw sequence ids and annotation labels (if shown)
1115 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1116 idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
1118 g.translate(idWidth, 0);
1119 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
1121 g.translate(-idWidth, 0);
1123 if ((pageNumber * pageHeight) < totalHeight)
1125 return Printable.PAGE_EXISTS;
1129 return Printable.NO_SUCH_PAGE;
1134 * get current sequence ID panel width, or nominal value if panel were to be
1135 * displayed using default settings
1139 public int getVisibleIdWidth()
1141 return getVisibleIdWidth(true);
1145 * get current sequence ID panel width, or nominal value if panel were to be
1146 * displayed using default settings
1149 * indicate if the Id width for onscreen or offscreen display should
1153 public int getVisibleIdWidth(boolean onscreen)
1155 // see if rendering offscreen - check preferences and calc width accordingly
1156 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1158 return calculateIdWidth(-1).width + 4;
1160 Integer idwidth = null;
1161 if (onscreen || (idwidth = Cache
1162 .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1164 int w = getIdPanel().getWidth();
1165 return (w > 0 ? w : calculateIdWidth().width + 4);
1167 return idwidth.intValue() + 4;
1171 * Generates an image of the alignment panel of the specified type. If
1172 * {@code type} is not null, the image is written to the file, otherwise the
1173 * user is prompted to specify the output file before writing to it.
1177 * @param forSplitFrame
1179 void makeAlignmentImage(ImageMaker.TYPE type, File file,
1180 boolean forSplitFrame)
1182 int borderBottomOffset = 5;
1183 long pSessionId = System.currentTimeMillis();
1184 headless = (System.getProperty("java.awt.headless") != null
1185 && System.getProperty("java.awt.headless").equals("true"));
1186 if (alignFrame != null && !headless)
1190 alignFrame.setProgressBar(MessageManager
1191 .formatMessage("status.saving_file", new Object[]
1192 { type.getLabel() }), pSessionId);
1198 * if exporting a split frame image, the graphics object has
1199 * width: maximum of the top and bottom image widths
1200 * height: sum of the top and bottom image heights
1202 AlignmentPanel comp = null;
1203 AlignmentDimension dim1 = getAlignmentDimension();
1204 AlignmentDimension dim2 = new AlignmentDimension(0, 0);
1207 comp = ((AlignViewport) av.getCodingComplement())
1209 dim2 = comp.getAlignmentDimension();
1211 final int graphicsHeight = dim1.height + dim2.height
1212 + borderBottomOffset;
1213 final int graphicsWidth = Math.max(dim1.width, dim2.width);
1215 final String dialogTitle = MessageManager
1216 .formatMessage("label.make_alignment_image", type.getName());
1217 String imageTitle = type == PNG ? null : alignFrame.getTitle();
1219 ImageMaker im = new ImageMaker(this, type, dialogTitle,
1220 graphicsWidth, graphicsHeight, file,
1221 imageTitle, alignFrame, pSessionId, headless);
1222 Graphics graphics = im.getGraphics();
1223 if (graphics == null)
1227 graphics.setColor(Color.white);
1228 graphics.fillRect(0, 0, graphicsWidth, graphicsHeight);
1229 if (av.getWrapAlignment())
1231 printWrappedAlignment(dim1.width, dim1.height + borderBottomOffset,
1232 0, graphics, false);
1236 printUnwrapped(dim1.width, dim1.height, 0, graphics, graphics);
1242 * append coding complement image
1244 boolean test = true;
1248 * debug location of next write to Graphics
1250 graphics.setColor(Color.red);
1251 graphics.drawString("Hello world", 0, 0);
1252 graphics.setColor(Color.black);
1254 if (av.getCodingComplement().getWrapAlignment())
1256 comp.printWrappedAlignment(dim2.width,
1257 dim2.height + borderBottomOffset, 0, graphics, false);
1261 comp.printUnwrapped(dim2.width, dim2.height, 0, graphics,
1267 } catch (OutOfMemoryError err)
1270 System.out.println("########################\n" + "OUT OF MEMORY "
1271 + file + "\n" + "########################");
1272 new OOMWarning("Creating Image for " + file, err);
1273 // System.out.println("Create IMAGE: " + err);
1274 } catch (Exception ex)
1276 ex.printStackTrace();
1281 * Computes and answers the width and height of the alignment in pixels,
1284 * <li>sequence ids</li>
1285 * <li>scale above, left or right if shown</li>
1286 * <li>sequences</li>
1287 * <li>annotations, if shown</li>
1289 * The alignment may be in wrapped or unwrapped mode.
1294 public AlignmentDimension getAlignmentDimension()
1296 int maxwidth = av.getAlignment().getVisibleWidth();
1298 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1299 + getScalePanel().getHeight();
1300 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1302 if (av.getWrapAlignment())
1304 height = getWrappedHeight();
1307 // need to obtain default alignment width and then add in any
1308 // additional allowance for id margin
1309 // this duplicates the calculation in getWrappedHeight but adjusts for
1311 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1312 - alignFrame.getInsets().left - alignFrame.getInsets().right
1313 - getVisibleIdWidth() + getVisibleIdWidth(false);
1317 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1321 else if (av.isShowAnnotation())
1323 height += getAnnotationPanel().adjustPanelHeight() + 3;
1326 return new AlignmentDimension(width, height);
1330 * Creates and writes an EPS image of the alignment, to the given file if
1331 * specified, else after prompting for the output file
1334 * @param forSplitFrame
1336 public void makeEPS(File epsFile, boolean forSplitFrame)
1338 makeAlignmentImage(EPS, epsFile, forSplitFrame);
1342 * Creates and writes a PNG image of the alignment, to the given file if
1343 * specified, else after prompting for the output file
1346 * @param forSplitFrame
1348 public void makePNG(File pngFile, boolean forSplitFrame)
1350 makeAlignmentImage(PNG, pngFile, forSplitFrame);
1354 * Creates and writes an SVG image of the alignment, to the given file if
1355 * specified, else after prompting for the output file
1358 * @param forSplitFrame
1360 public void makeSVG(File svgFile, boolean forSplitFrame)
1362 makeAlignmentImage(SVG, svgFile, forSplitFrame);
1365 public void makePNGImageMap(File imgMapFile, String imageName)
1367 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1368 // ////////////////////////////////////////////
1369 int idWidth = getVisibleIdWidth(false);
1370 FontMetrics fm = getFontMetrics(av.getFont());
1371 int scaleHeight = av.getCharHeight() + fm.getDescent();
1374 // ////////////////////////////////
1375 if (imgMapFile != null)
1379 int sSize = av.getAlignment().getHeight();
1380 int alwidth = av.getAlignment().getWidth();
1381 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1382 out.println(HTMLOutput.getImageMapHTML());
1383 out.println("<img src=\"" + imageName
1384 + "\" border=\"0\" usemap=\"#Map\" >"
1385 + "<map name=\"Map\">");
1387 for (int s = 0; s < sSize; s++)
1389 int sy = s * av.getCharHeight() + scaleHeight;
1391 SequenceI seq = av.getAlignment().getSequenceAt(s);
1392 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1393 for (int column = 0; column < alwidth; column++)
1395 StringBuilder text = new StringBuilder(512);
1396 String triplet = null;
1397 if (av.getAlignment().isNucleotide())
1399 triplet = ResidueProperties.nucleotideName.get(seq
1400 .getCharAt(column) + "");
1404 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
1408 if (triplet == null)
1413 int seqPos = seq.findPosition(column);
1414 int gSize = groups.length;
1415 for (int g = 0; g < gSize; g++)
1417 if (text.length() < 1)
1419 text.append("<area shape=\"rect\" coords=\"")
1420 .append((idWidth + column * av.getCharWidth()))
1421 .append(",").append(sy).append(",")
1422 .append((idWidth + (column + 1) * av.getCharWidth()))
1423 .append(",").append((av.getCharHeight() + sy))
1424 .append("\"").append(" onMouseOver=\"toolTip('")
1425 .append(seqPos).append(" ").append(triplet);
1428 if (groups[g].getStartRes() < column
1429 && groups[g].getEndRes() > column)
1431 text.append("<br><em>").append(groups[g].getName())
1436 if (text.length() < 1)
1438 text.append("<area shape=\"rect\" coords=\"")
1439 .append((idWidth + column * av.getCharWidth()))
1440 .append(",").append(sy).append(",")
1441 .append((idWidth + (column + 1) * av.getCharWidth()))
1442 .append(",").append((av.getCharHeight() + sy))
1443 .append("\"").append(" onMouseOver=\"toolTip('")
1444 .append(seqPos).append(" ").append(triplet);
1446 if (!Comparison.isGap(seq.getCharAt(column)))
1448 List<SequenceFeature> features = seq.findFeatures(column, column);
1449 for (SequenceFeature sf : features)
1451 if (sf.isContactFeature())
1453 text.append("<br>").append(sf.getType()).append(" ")
1454 .append(sf.getBegin()).append(":")
1455 .append(sf.getEnd());
1459 text.append("<br>");
1460 text.append(sf.getType());
1461 String description = sf.getDescription();
1462 if (description != null
1463 && !sf.getType().equals(description))
1465 description = description.replace("\"", """);
1466 text.append(" ").append(description);
1469 String status = sf.getStatus();
1470 if (status != null && !"".equals(status))
1472 text.append(" (").append(status).append(")");
1475 if (text.length() > 1)
1477 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1478 out.println(text.toString());
1483 out.println("</map></body></html>");
1486 } catch (Exception ex)
1488 ex.printStackTrace();
1490 } // /////////END OF IMAGE MAP
1494 int getWrappedHeight()
1496 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1498 if (System.getProperty("java.awt.headless") != null
1499 && System.getProperty("java.awt.headless").equals("true"))
1501 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1502 - vscroll.getPreferredSize().width
1503 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1506 int chunkWidth = getSeqPanel().seqCanvas
1507 .getWrappedCanvasWidth(seqPanelWidth);
1509 int hgap = av.getCharHeight();
1510 if (av.getScaleAboveWrapped())
1512 hgap += av.getCharHeight();
1515 int annotationHeight = 0;
1516 if (av.isShowAnnotation())
1518 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1521 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1524 int maxwidth = av.getAlignment().getWidth();
1525 if (av.hasHiddenColumns())
1527 maxwidth = av.getAlignment().getHiddenColumns()
1528 .absoluteToVisibleColumn(maxwidth) - 1;
1531 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1537 * close the panel - deregisters all listeners and nulls any references to
1540 public void closePanel()
1542 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1543 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1544 PaintRefresher.RemoveComponent(this);
1549 * try to ensure references are nulled
1551 if (annotationPanel != null)
1553 annotationPanel.dispose();
1554 annotationPanel = null;
1559 av.removePropertyChangeListener(propertyChangeListener);
1560 propertyChangeListener = null;
1561 StructureSelectionManager ssm = av.getStructureSelectionManager();
1562 ssm.removeStructureViewerListener(getSeqPanel(), null);
1563 ssm.removeSelectionListener(getSeqPanel());
1564 ssm.removeCommandListener(av);
1565 ssm.removeStructureViewerListener(getSeqPanel(), null);
1566 ssm.removeSelectionListener(getSeqPanel());
1572 if (Cache.log.isDebugEnabled())
1574 Cache.log.warn("Closing alignment panel which is already closed.");
1580 * Close any open dialogs that would be orphaned when this one is closed
1582 protected void closeChildFrames()
1584 if (overviewPanel != null)
1586 overviewPanel.dispose();
1587 overviewPanel = null;
1589 if (calculationDialog != null)
1591 calculationDialog.closeFrame();
1592 calculationDialog = null;
1597 * hides or shows dynamic annotation rows based on groups and av state flags
1599 public void updateAnnotation()
1601 updateAnnotation(false, false);
1604 public void updateAnnotation(boolean applyGlobalSettings)
1606 updateAnnotation(applyGlobalSettings, false);
1609 public void updateAnnotation(boolean applyGlobalSettings,
1610 boolean preserveNewGroupSettings)
1612 av.updateGroupAnnotationSettings(applyGlobalSettings,
1613 preserveNewGroupSettings);
1614 adjustAnnotationHeight();
1618 public AlignmentI getAlignment()
1620 return av == null ? null : av.getAlignment();
1624 public String getViewName()
1626 return av.getViewName();
1630 * Make/Unmake this alignment panel the current input focus
1634 public void setSelected(boolean b)
1638 if (alignFrame.getSplitViewContainer() != null)
1641 * bring enclosing SplitFrame to front first if there is one
1643 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1645 alignFrame.setSelected(b);
1646 } catch (Exception ex)
1652 alignFrame.setDisplayedView(this);
1657 public StructureSelectionManager getStructureSelectionManager()
1659 return av.getStructureSelectionManager();
1663 public void raiseOOMWarning(String string, OutOfMemoryError error)
1665 new OOMWarning(string, error, this);
1669 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1672 return new FeatureRenderer(this);
1676 public jalview.api.FeatureRenderer getFeatureRenderer()
1678 return seqPanel.seqCanvas.getFeatureRenderer();
1681 public void updateFeatureRenderer(
1682 jalview.renderer.seqfeatures.FeatureRenderer fr)
1684 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1687 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1689 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1691 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1695 public ScalePanel getScalePanel()
1700 public void setScalePanel(ScalePanel scalePanel)
1702 this.scalePanel = scalePanel;
1705 public SeqPanel getSeqPanel()
1710 public void setSeqPanel(SeqPanel seqPanel)
1712 this.seqPanel = seqPanel;
1715 public AnnotationPanel getAnnotationPanel()
1717 return annotationPanel;
1720 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1722 this.annotationPanel = annotationPanel;
1725 public AnnotationLabels getAlabels()
1730 public void setAlabels(AnnotationLabels alabels)
1732 this.alabels = alabels;
1735 public IdPanel getIdPanel()
1740 public void setIdPanel(IdPanel idPanel)
1742 this.idPanel = idPanel;
1746 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1747 * The aim is to keep the two alignments 'lined up' on their centre columns.
1750 * holds mapped region(s) of this alignment that we are scrolling
1751 * 'to'; may be modified for sequence offset by this method
1752 * @param verticalOffset
1753 * the number of visible sequences to show above the mapped region
1755 protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1757 scrollToPosition(sr, verticalOffset, true);
1761 * Set a flag to say do not scroll any (cDNA/protein) complement.
1765 protected void setToScrollComplementPanel(boolean b)
1767 this.scrollComplementaryPanel = b;
1771 * Get whether to scroll complement panel
1773 * @return true if cDNA/protein complement panels should be scrolled
1775 protected boolean isSetToScrollComplementPanel()
1777 return this.scrollComplementaryPanel;
1783 * @adjustHeight if true, try to recalculate panel height for visible
1786 protected void refresh(boolean adjustHeight)
1788 validateAnnotationDimensions(adjustHeight);
1792 // sort, repaint, update overview
1793 paintAlignment(true, false);
1797 // lightweight repaint
1804 * Property change event fired when a change is made to the viewport ranges
1805 * object associated with this alignment panel's viewport
1807 public void propertyChange(PropertyChangeEvent evt)
1809 // update this panel's scroll values based on the new viewport ranges values
1810 ViewportRanges ranges = av.getRanges();
1811 int x = ranges.getStartRes();
1812 int y = ranges.getStartSeq();
1813 setScrollValues(x, y);
1815 // now update any complementary alignment (its viewport ranges object
1816 // is different so does not get automatically updated)
1817 if (isSetToScrollComplementPanel())
1819 setToScrollComplementPanel(false);
1820 av.scrollComplementaryAlignment();
1821 setToScrollComplementPanel(true);
1826 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1827 * reference should be nulled when the dialog is closed.
1829 * @param calculationChooser
1831 public void setCalculationDialog(CalculationChooser calculationChooser)
1833 calculationDialog = calculationChooser;
1837 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1840 public CalculationChooser getCalculationDialog()
1842 return calculationDialog;