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.Console;
52 import jalview.bin.Jalview;
53 import jalview.datamodel.AlignmentAnnotation;
54 import jalview.datamodel.AlignmentI;
55 import jalview.datamodel.HiddenColumns;
56 import jalview.datamodel.SearchResultsI;
57 import jalview.datamodel.SequenceFeature;
58 import jalview.datamodel.SequenceGroup;
59 import jalview.datamodel.SequenceI;
60 import jalview.gui.ImageExporter.ImageWriterI;
61 import jalview.io.HTMLOutput;
62 import jalview.io.exceptions.ImageOutputException;
63 import jalview.jbgui.GAlignmentPanel;
64 import jalview.math.AlignmentDimension;
65 import jalview.schemes.ResidueProperties;
66 import jalview.structure.StructureSelectionManager;
67 import jalview.util.Comparison;
68 import jalview.util.ImageMaker;
69 import jalview.util.MessageManager;
70 import jalview.util.imagemaker.BitmapImageSizing;
71 import jalview.viewmodel.ViewportListenerI;
72 import jalview.viewmodel.ViewportRanges;
78 * @version $Revision: 1.161 $
80 @SuppressWarnings("serial")
81 public class AlignmentPanel extends GAlignmentPanel implements
82 AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
85 * spare space in pixels between sequence id and alignment panel
87 private static final int ID_WIDTH_PADDING = 4;
89 public AlignViewport av;
91 OverviewPanel overviewPanel;
93 private SeqPanel seqPanel;
95 private IdPanel idPanel;
97 IdwidthAdjuster idwidthAdjuster;
99 public AlignFrame alignFrame;
101 private ScalePanel scalePanel;
103 private AnnotationPanel annotationPanel;
105 private AnnotationLabels alabels;
107 private int hextent = 0;
109 private int vextent = 0;
112 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
113 * false, suppresses invoking the same method recursively.
115 private boolean scrollComplementaryPanel = true;
117 private PropertyChangeListener propertyChangeListener;
119 private CalculationChooser calculationDialog;
122 * Creates a new AlignmentPanel object.
127 public AlignmentPanel(AlignFrame af, final AlignViewport av)
129 // setBackground(Color.white); // BH 2019
132 setSeqPanel(new SeqPanel(av, this));
133 setIdPanel(new IdPanel(av, this));
135 setScalePanel(new ScalePanel(av, this));
137 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
138 idwidthAdjuster = new IdwidthAdjuster(this);
139 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
141 setAnnotationPanel(new AnnotationPanel(this));
142 setAlabels(new AnnotationLabels(this));
144 annotationScroller.setViewportView(getAnnotationPanel());
145 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
147 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
148 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
150 setScrollValues(0, 0);
152 hscroll.addAdjustmentListener(this);
153 vscroll.addAdjustmentListener(this);
155 addComponentListener(new ComponentAdapter()
158 public void componentResized(ComponentEvent evt)
160 // reset the viewport ranges when the alignment panel is resized
161 // in particular, this initialises the end residue value when Jalview
163 ViewportRanges ranges = av.getRanges();
164 if (av.getWrapAlignment())
166 int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
167 getSeqPanel().seqCanvas.getWidth());
168 ranges.setViewportWidth(widthInRes);
172 int widthInRes = getSeqPanel().seqCanvas.getWidth()
174 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
175 / av.getCharHeight();
177 ranges.setViewportWidth(widthInRes);
178 ranges.setViewportHeight(heightInSeq);
184 final AlignmentPanel ap = this;
185 propertyChangeListener = new PropertyChangeListener()
188 public void propertyChange(PropertyChangeEvent evt)
190 if (evt.getPropertyName().equals("alignment"))
192 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
197 av.addPropertyChangeListener(propertyChangeListener);
199 av.getRanges().addPropertyChangeListener(this);
201 adjustAnnotationHeight();
206 public AlignViewportI getAlignViewport()
211 public void alignmentChanged()
213 av.alignmentChanged(this);
215 if (getCalculationDialog() != null)
217 getCalculationDialog().validateCalcTypes();
220 alignFrame.updateEditMenuBar();
222 // no idea if we need to update structure
223 paintAlignment(true, true);
230 public void fontChanged()
232 // set idCanvas bufferedImage to null
233 // to prevent drawing old image
234 FontMetrics fm = getFontMetrics(av.getFont());
236 // update the flag controlling whether the grid is too small to render the
238 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
240 scalePanelHolder.setPreferredSize(
241 new Dimension(10, av.getCharHeight() + fm.getDescent()));
242 idSpaceFillerPanel1.setPreferredSize(
243 new Dimension(10, av.getCharHeight() + fm.getDescent()));
244 idwidthAdjuster.invalidate();
245 scalePanelHolder.invalidate();
246 // BH 2018 getIdPanel().getIdCanvas().gg = null;
247 getSeqPanel().seqCanvas.img = null;
248 getAnnotationPanel().adjustPanelHeight();
250 Dimension d = calculateIdWidth();
251 getIdPanel().getIdCanvas().setPreferredSize(d);
252 hscrollFillerPanel.setPreferredSize(d);
258 * Calculates the width of the alignment labels based on the displayed names
259 * and any bounds on label width set in preferences.
261 * The calculated width is set as a property of the viewport and the layout is
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 r = calculateDefaultAlignmentIdWidth();
276 av.setIdWidth(r.width);
281 r.width = av.getIdWidth();
286 * fudge: if desired width has changed, update layout
287 * (see also paintComponent - updates layout on a repaint)
289 if (r.width != oldWidth)
291 idPanelHolder.setPreferredSize(r);
297 public Dimension calculateDefaultAlignmentIdWidth()
299 return calculateIdWidth(-1, false, false);
302 * pre 2.11.3 Id width calculation - used when importing old projects only
305 public int getLegacyIdWidth()
307 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
308 int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
309 int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
310 Dimension w = calculateIdWidthOrLegacy(true, maxwidth, false, false);
315 * Calculate the width of the alignment labels based on the displayed names
316 * and any bounds on label width set in preferences. Also includes annotations
317 * not actually visible.
319 * FIXME JAL-244 JAL-4091 - doesn't include sequence associated annotation
320 * label decorators and only called during tests
323 * -1 or maximum width allowed for IdWidth
324 * @return Dimension giving the maximum width of the alignment label panel
325 * that should be used.
327 protected Dimension calculateIdWidth(int maxwidth)
329 return calculateIdWidth(maxwidth, true, false);
332 * Calculate the width of the alignment labels based on the displayed names
333 * and any bounds on label width set in preferences.
336 * -1 or maximum width allowed for IdWidth
337 * @param includeAnnotations - when true includes width of any additional marks in annotation id panel
338 * @param visibleOnly - when true, ignore label widths for hidden annotation rows
339 * @return Dimension giving the maximum width of the alignment label panel
340 * that should be used.
342 public Dimension calculateIdWidth(int maxwidth,
343 boolean includeAnnotations, boolean visibleOnly)
345 return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations, visibleOnly);
349 * legacy mode or post 2.11.3 ID width calculation
350 * @param legacy - uses annotation labels, not rendered label width (excludes additional decorators)
352 * @param includeAnnotations
356 private Dimension calculateIdWidthOrLegacy(boolean legacy, int maxwidth,
357 boolean includeAnnotations, boolean visibleOnly)
359 Container c = new Container();
361 FontMetrics fm = c.getFontMetrics(
362 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
364 AlignmentI al = av.getAlignment();
368 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
370 SequenceI s = al.getSequenceAt(i);
371 String id = s.getDisplayId(av.getShowJVSuffix());
372 int stringWidth = fm.stringWidth(id);
373 idWidth = Math.max(idWidth, stringWidth);
377 // Also check annotation label widths
378 if (includeAnnotations && al.getAlignmentAnnotation() != null)
380 fm = c.getFontMetrics(getAlabels().getFont());
382 if (!legacy || Jalview.isHeadlessMode())
384 AnnotationLabels aal = getAlabels();
385 int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
387 idWidth = Math.max(idWidth, stringWidth);
391 for (i = 0; i < al.getAlignmentAnnotation().length; i++)
393 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
394 if (visibleOnly && !aa.visible)
398 String label = aa.label;
399 int stringWidth = fm.stringWidth(label);
400 idWidth = Math.max(idWidth, stringWidth);
405 int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth);
406 w += ID_WIDTH_PADDING;
408 return new Dimension(w, 12);
412 * Highlight the given results on the alignment
415 public void highlightSearchResults(SearchResultsI results)
417 boolean scrolled = scrollToPosition(results, 0, false);
419 boolean fastPaint = !(scrolled && av.getWrapAlignment());
421 getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint);
425 * Scroll the view to show the position of the highlighted region in results
428 * @param searchResults
431 public boolean scrollToPosition(SearchResultsI searchResults)
433 return scrollToPosition(searchResults, 0, false);
437 * Scrolls the view (if necessary) to show the position of the first
438 * highlighted region in results (if any). Answers true if the view was
439 * scrolled, or false if no matched region was found, or it is already
443 * @param verticalOffset
444 * if greater than zero, allows scrolling to a position below the
445 * first displayed sequence
447 * if true, try to centre the search results horizontally in the view
450 protected boolean scrollToPosition(SearchResultsI results,
451 int verticalOffset, boolean centre)
453 int startv, endv, starts, ends;
454 ViewportRanges ranges = av.getRanges();
456 if (results == null || results.isEmpty() || av == null
457 || av.getAlignment() == null)
461 int seqIndex = av.getAlignment().findIndex(results);
466 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
468 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
477 * To centre results, scroll to positions half the visible width
478 * left/right of the start/end positions
482 int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
483 start = Math.max(start - offset, 0);
484 end = end + offset - 1;
490 if (end == seq.getEnd())
495 if (av.hasHiddenColumns())
497 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
498 start = hidden.absoluteToVisibleColumn(start);
499 end = hidden.absoluteToVisibleColumn(end);
502 if (!hidden.isVisible(r[0]))
504 // don't scroll - position isn't visible
511 * allow for offset of target sequence (actually scroll to one above it)
513 seqIndex = Math.max(0, seqIndex - verticalOffset);
514 boolean scrollNeeded = true;
516 if (!av.getWrapAlignment())
518 if ((startv = ranges.getStartRes()) >= start)
521 * Scroll left to make start of search results visible
523 setScrollValues(start, seqIndex);
525 else if ((endv = ranges.getEndRes()) <= end)
528 * Scroll right to make end of search results visible
530 setScrollValues(startv + end - endv, seqIndex);
532 else if ((starts = ranges.getStartSeq()) > seqIndex)
535 * Scroll up to make start of search results visible
537 setScrollValues(ranges.getStartRes(), seqIndex);
539 else if ((ends = ranges.getEndSeq()) <= seqIndex)
542 * Scroll down to make end of search results visible
544 setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
547 * Else results are already visible - no need to scroll
549 scrollNeeded = false;
553 scrollNeeded = ranges.scrollToWrappedVisible(start);
556 paintAlignment(false, false);
564 * @return DOCUMENT ME!
566 public OverviewPanel getOverviewPanel()
568 return overviewPanel;
577 public void setOverviewPanel(OverviewPanel op)
585 * Hide or show annotation panel
588 public void setAnnotationVisible(boolean b)
590 if (!av.getWrapAlignment())
592 annotationSpaceFillerHolder.setVisible(b);
593 annotationScroller.setVisible(b);
599 * automatically adjust annotation panel height for new annotation whilst
600 * ensuring the alignment is still visible.
603 public void adjustAnnotationHeight()
605 // TODO: display vertical annotation scrollbar if necessary
606 // this is called after loading new annotation onto alignment
607 if (alignFrame.getHeight() == 0)
609 jalview.bin.Console.error("adjustAnnotationHeight called with zero height alignment window");
611 validateAnnotationDimensions(true);
613 // TODO: many places call this method and also paintAlignment with various
614 // different settings. this means multiple redraws are triggered...
615 paintAlignment(true, av.needToUpdateStructureViews());
619 * calculate the annotation dimensions and refresh slider values accordingly.
620 * need to do repaints/notifys afterwards.
622 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
624 // BH 2018.04.18 comment: addNotify() is not appropriate here. We
625 // are not changing ancestors, and keyboard action listeners do
626 // not need to be reset. addNotify() is a very expensive operation,
627 // requiring a full re-layout of all parents and children.
628 // Note in JComponent:
629 // This method is called by the toolkit internally and should
630 // not be called directly by programs.
631 // I note that addNotify() is called in several areas of Jalview.
633 AnnotationPanel ap = getAnnotationPanel();
634 int annotationHeight = ap.adjustPanelHeight();
635 annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight,
639 Dimension e = idPanel.getSize();
640 int idWidth = e.width;
641 boolean manuallyAdjusted = this.getIdPanel().getIdCanvas()
642 .isManuallyAdjusted();
643 annotationScroller.setPreferredSize(new Dimension(
644 manuallyAdjusted ? idWidth : annotationScroller.getWidth(),
647 alabels.setPreferredSize(new Dimension(idWidth, annotationHeight));
649 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
650 manuallyAdjusted ? idWidth
651 : annotationSpaceFillerHolder.getWidth(),
653 annotationScroller.validate();
654 annotationScroller.addNotify();
659 * update alignment layout for viewport settings
664 public void updateLayout()
667 setAnnotationVisible(av.isShowAnnotation());
668 boolean wrap = av.getWrapAlignment();
669 ViewportRanges ranges = av.getRanges();
670 ranges.setStartSeq(0);
671 // scalePanelHolder.setVisible(!wrap);
672 hscroll.setVisible(!wrap);
673 // Allow idPanel width adjustment in wrap mode
674 idwidthAdjuster.setVisible(true);
678 annotationScroller.setVisible(false);
679 annotationSpaceFillerHolder.setVisible(false);
681 else if (av.isShowAnnotation())
683 annotationScroller.setVisible(true);
684 annotationSpaceFillerHolder.setVisible(true);
685 validateAnnotationDimensions(false);
688 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
690 { // may not yet be laid out
693 int widthInRes = getSeqPanel().seqCanvas
694 .getWrappedCanvasWidth(canvasWidth);
695 ranges.setViewportWidth(widthInRes);
699 int widthInRes = (canvasWidth / av.getCharWidth());
700 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
701 / av.getCharHeight());
703 ranges.setViewportWidth(widthInRes);
704 ranges.setViewportHeight(heightInSeq);
708 // idSpaceFillerPanel1.setVisible(!wrap);
714 * Adjust row/column scrollers to show a visible position in the alignment.
717 * visible column to scroll to
719 * visible row to scroll to
722 public void setScrollValues(int xpos, int ypos)
727 if (av == null || av.getAlignment() == null)
732 if (av.getWrapAlignment())
734 setScrollingForWrappedPanel(x);
738 int width = av.getAlignment().getVisibleWidth();
739 int height = av.getAlignment().getHeight();
741 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
742 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
749 if (vextent > height)
754 if ((hextent + x) > width)
759 if ((vextent + y) > height)
761 y = height - vextent;
774 // update the scroll values
775 hscroll.setValues(x, hextent, 0, width);
776 vscroll.setValues(y, vextent, 0, height);
781 * Respond to adjustment event when horizontal or vertical scrollbar is
785 * adjustment event encoding whether hscroll or vscroll changed
788 public void adjustmentValueChanged(AdjustmentEvent evt)
790 if (av.getWrapAlignment())
792 adjustScrollingWrapped(evt);
796 ViewportRanges ranges = av.getRanges();
798 if (evt.getSource() == hscroll)
800 int oldX = ranges.getStartRes();
801 int oldwidth = ranges.getViewportWidth();
802 int x = hscroll.getValue();
803 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
805 // if we're scrolling to the position we're already at, stop
806 // this prevents infinite recursion of events when the scroll/viewport
807 // ranges values are the same
808 if ((x == oldX) && (width == oldwidth))
812 ranges.setViewportStartAndWidth(x, width);
814 else if (evt.getSource() == vscroll)
816 int oldY = ranges.getStartSeq();
817 int oldheight = ranges.getViewportHeight();
818 int y = vscroll.getValue();
819 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
821 // if we're scrolling to the position we're already at, stop
822 // this prevents infinite recursion of events when the scroll/viewport
823 // ranges values are the same
824 if ((y == oldY) && (height == oldheight))
828 ranges.setViewportStartAndHeight(y, height);
834 * Responds to a scroll change by setting the start position of the viewport.
839 protected void adjustScrollingWrapped(AdjustmentEvent evt)
841 if (evt.getSource() == hscroll)
843 return; // no horizontal scroll when wrapped
845 final ViewportRanges ranges = av.getRanges();
847 if (evt.getSource() == vscroll)
849 int newY = vscroll.getValue();
852 * if we're scrolling to the position we're already at, stop
853 * this prevents infinite recursion of events when the scroll/viewport
854 * ranges values are the same
856 int oldX = ranges.getStartRes();
857 int oldY = ranges.getWrappedScrollPosition(oldX);
865 * limit page up/down to one width's worth of positions
867 int rowSize = ranges.getViewportWidth();
868 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
869 ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
874 // This is only called if file loaded is a jar file that
875 // was wrapped when saved and user has wrap alignment true
876 // as preference setting
877 SwingUtilities.invokeLater(new Runnable()
882 // When updating scrolling to use ViewportChange events, this code
883 // could not be validated and it is not clear if it is now being
884 // called. Log warning here in case it is called and unforeseen
887 "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
889 // scroll to start of panel
890 ranges.setStartRes(0);
891 ranges.setStartSeq(0);
899 * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
902 public void paintAlignment(boolean updateOverview,
903 boolean updateStructures)
905 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
906 av.isShowAutocalculatedAbove());
907 sorter.sort(getAlignment().getAlignmentAnnotation(),
908 av.getSortAnnotationsBy());
911 if (updateStructures)
913 av.getStructureSelectionManager().sequenceColoursChanged(this);
918 if (overviewPanel != null)
920 overviewPanel.updateOverviewImage();
926 public void paintComponent(Graphics g)
928 invalidate(); // needed so that the id width adjuster works correctly
929 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
930 int idWidth = d.width;
932 // check wrapped alignment as at least 1 residue width
933 if (av.getWrapAlignment())
935 SeqCanvas sc = this.getSeqPanel().seqCanvas;
936 if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth())
938 // need to make some adjustments
939 idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth());
940 av.setIdWidth(idWidth);
941 av.getAlignPanel().getIdPanel().getIdCanvas()
942 .setManuallyAdjusted(true);
944 validateAnnotationDimensions(false);
948 idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height));
949 hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
951 validate(); // needed so that the id width adjuster works correctly
954 * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
955 * though I still think this call should be elsewhere.
957 ViewportRanges ranges = av.getRanges();
958 setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
959 super.paintComponent(g);
963 * Set vertical scroll bar position, and number of increments, for wrapped
966 * @param topLeftColumn
967 * the column position at top left (0..)
969 private void setScrollingForWrappedPanel(int topLeftColumn)
971 ViewportRanges ranges = av.getRanges();
972 int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
973 int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
976 * a scrollbar's value can be set to at most (maximum-extent)
977 * so we add extent (1) to the maxScroll value
979 vscroll.setUnitIncrement(1);
980 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
993 * @return DOCUMENT ME!
995 * @throws PrinterException
999 public int print(Graphics pg, PageFormat pf, int pi)
1000 throws PrinterException
1002 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
1004 int pwidth = (int) pf.getImageableWidth();
1005 int pheight = (int) pf.getImageableHeight();
1007 if (av.getWrapAlignment())
1009 return printWrappedAlignment(pwidth, pheight, pi, pg);
1013 return printUnwrapped(pwidth, pheight, pi, pg, pg);
1018 * Draws the alignment image, including sequence ids, sequences, and
1019 * annotation labels and annotations if shown, on either one or two Graphics
1029 * the graphics context for sequence ids and annotation labels
1030 * @param alignmentGraphics
1031 * the graphics context for sequences and annotations (may or may not
1032 * be the same context as idGraphics)
1034 * @throws PrinterException
1036 public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
1037 Graphics idGraphics, Graphics alignmentGraphics)
1038 throws PrinterException
1040 final int idWidth, idWidthForGui;
1041 // otherwise calculate it
1042 idWidth = getVisibleIdWidth(false);
1043 // if (getIdPanel()!=null && getIdPanel().getWidth()>0)
1045 // // use the current IdPanel's width, if its set and non-zero
1046 // idWidthForGui = getIdPanel().getWidth();
1051 * Get the horizontal offset to where we draw the sequences.
1052 * This is idWidth if using a single Graphics context, else zero.
1054 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
1057 FontMetrics fm = getFontMetrics(av.getFont());
1058 final int charHeight = av.getCharHeight();
1059 final int scaleHeight = charHeight + fm.getDescent();
1061 idGraphics.setColor(Color.white);
1062 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
1063 idGraphics.setFont(av.getFont());
1066 * How many sequences and residues can we fit on a printable page?
1068 final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1070 final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1072 final int alignmentWidth = av.getAlignment().getVisibleWidth();
1073 int pagesWide = (alignmentWidth / totalRes) + 1;
1075 final int startRes = (pageIndex % pagesWide) * totalRes;
1076 final int endRes = Math.min(startRes + totalRes - 1,
1077 alignmentWidth - 1);
1079 final int startSeq = (pageIndex / pagesWide) * totalSeq;
1080 final int alignmentHeight = av.getAlignment().getHeight();
1081 final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
1083 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
1085 if (av.isShowAnnotation())
1087 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1090 pagesHigh /= pageHeight;
1092 if (pageIndex >= (pagesWide * pagesHigh))
1094 return Printable.NO_SUCH_PAGE;
1096 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
1098 alignmentGraphics.setColor(Color.white);
1099 alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight+scaleHeight);
1102 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1104 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1105 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1106 pageWidth - idWidth, scaleHeight);
1107 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1110 * Draw the sequence ids, offset for scale height,
1111 * then reset to top left (0, 0)
1113 idGraphics.translate(0, scaleHeight);
1114 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1115 List<SequenceI> selection = av.getSelectionGroup() == null ? null
1116 : av.getSelectionGroup().getSequences(null);
1118 idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
1119 selection, false,idWidth);
1121 idGraphics.setFont(av.getFont());
1122 idGraphics.translate(0, -scaleHeight);
1125 * draw the sequences, offset for scale height, and id width (if using a
1126 * single graphics context), then reset to (0, scale height)
1128 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1129 getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
1130 startRes, endRes, startSeq, endSeq - 1);
1131 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1133 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1136 * draw annotation labels; drawComponent() translates by
1137 * getScrollOffset(), so compensate for that first;
1138 * then reset to (0, scale height)
1140 int offset = getAlabels().getScrollOffset();
1141 idGraphics.translate(0, -offset);
1142 idGraphics.translate(0, alignmentDrawnHeight);
1143 getAlabels().drawComponentNotGUI(idGraphics, idWidth);
1144 idGraphics.translate(0, -alignmentDrawnHeight);
1147 * draw the annotations starting at
1148 * (idOffset, alignmentHeight) from (0, scaleHeight)
1150 alignmentGraphics.translate(alignmentGraphicsOffset,
1151 alignmentDrawnHeight);
1153 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1154 alignmentGraphics, -1, startRes, endRes + 1);
1157 return Printable.PAGE_EXISTS;
1161 * Prints one page of an alignment in wrapped mode. Returns
1162 * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
1163 * no page could be drawn (page number out of range).
1173 * @throws PrinterException
1175 public int printWrappedAlignment(int pageWidth, int pageHeight,
1176 int pageNumber, Graphics g) throws PrinterException
1178 getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
1180 int annotationHeight = 0;
1181 if (av.isShowAnnotation())
1183 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1186 int hgap = av.getCharHeight();
1187 if (av.getScaleAboveWrapped())
1189 hgap += av.getCharHeight();
1192 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1195 int idWidth = getVisibleIdWidth(false);
1197 int maxwidth = av.getAlignment().getVisibleWidth();
1199 int resWidth = getSeqPanel().seqCanvas
1200 .getWrappedCanvasWidth(pageWidth - idWidth);
1201 av.getRanges().setViewportStartAndWidth(0, resWidth);
1203 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1205 g.setColor(Color.white);
1206 g.fillRect(0, 0, pageWidth, pageHeight);
1207 g.setFont(av.getFont());
1208 g.setColor(Color.black);
1211 * method: print the whole wrapped alignment, but with a clip region that
1212 * is restricted to the requested page; this supports selective print of
1213 * single pages or ranges, (at the cost of repeated processing in the
1214 * 'normal' case, when all pages are printed)
1216 g.translate(0, -pageNumber * pageHeight);
1218 g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
1221 * draw sequence ids and annotation labels (if shown)
1223 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1224 idCanvas.drawIdsWrappedNoGUI((Graphics2D) g, av, 0, totalHeight);
1226 g.translate(idWidth, 0);
1228 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
1229 pageWidth - idWidth, totalHeight, 0);
1231 if ((pageNumber * pageHeight) < totalHeight)
1233 return Printable.PAGE_EXISTS;
1237 return Printable.NO_SUCH_PAGE;
1242 * get current sequence ID panel width, or nominal value if panel were to be
1243 * displayed using default settings
1247 public int getVisibleIdWidth()
1249 return getVisibleIdWidth(true);
1253 * get current sequence ID panel width, or nominal value if panel were to be
1254 * displayed using default settings
1257 * indicate if the Id width for onscreen or offscreen display should
1261 protected int getVisibleIdWidth(boolean onscreen)
1263 // see if rendering offscreen - check preferences and calc width accordingly
1264 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1266 return calculateIdWidth(-1,true,true).width;
1268 Integer idwidth = onscreen ? null
1269 : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
1270 if (idwidth != null)
1272 return idwidth.intValue() + ID_WIDTH_PADDING;
1275 int w = getIdPanel().getWidth();
1276 w = calculateIdWidth(-1, true, true).width;
1277 return (w > 0 ? w : calculateIdWidth().width);
1280 void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
1281 throws ImageOutputException
1283 makeAlignmentImage(type, file, renderer,
1284 BitmapImageSizing.defaultBitmapImageSizing());
1288 * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
1289 * writes it to the specified file
1293 * @param textrenderer
1294 * @param bitmapscale
1296 void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer,
1297 BitmapImageSizing userBis) throws ImageOutputException
1299 final int borderBottomOffset = 5;
1301 AlignmentDimension aDimension = getAlignmentDimension();
1303 // todo use a lambda function in place of callback here?
1304 ImageWriterI writer = new ImageWriterI()
1307 public void exportImage(Graphics graphics) throws Exception
1309 if (av.getWrapAlignment())
1311 printWrappedAlignment(aDimension.getWidth(),
1312 aDimension.getHeight() + borderBottomOffset, 0, graphics);
1316 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
1317 graphics, graphics);
1322 String fileTitle = alignFrame.getTitle();
1323 ImageExporter exporter = new ImageExporter(writer, alignFrame, type,
1325 int imageWidth = aDimension.getWidth();
1326 int imageHeight = aDimension.getHeight() + borderBottomOffset;
1327 String of = MessageManager.getString("label.alignment");
1328 exporter.doExport(file, this, imageWidth, imageHeight, of, renderer,
1333 * Calculates and returns a suitable width and height (in pixels) for an
1338 public AlignmentDimension getAlignmentDimension()
1340 int maxwidth = av.getAlignment().getVisibleWidth();
1342 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1343 + getScalePanel().getHeight();
1344 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1346 if (av.getWrapAlignment())
1348 height = getWrappedHeight();
1349 if (Jalview.isHeadlessMode())
1351 // need to obtain default alignment width and then add in any
1352 // additional allowance for id margin
1353 // this duplicates the calculation in getWrappedHeight but adjusts for
1355 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1356 - alignFrame.getInsets().left - alignFrame.getInsets().right
1357 - getVisibleIdWidth() + getVisibleIdWidth(false);
1361 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1365 else if (av.isShowAnnotation())
1367 height += getAnnotationPanel().adjustPanelHeight() + 3;
1369 return new AlignmentDimension(width, height);
1373 public void makePNGImageMap(File imgMapFile, String imageName)
1374 throws ImageOutputException
1376 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1377 // ////////////////////////////////////////////
1378 int idWidth = getVisibleIdWidth(false);
1379 FontMetrics fm = getFontMetrics(av.getFont());
1380 int scaleHeight = av.getCharHeight() + fm.getDescent();
1383 // ////////////////////////////////
1384 if (imgMapFile != null)
1388 int sSize = av.getAlignment().getHeight();
1389 int alwidth = av.getAlignment().getWidth();
1390 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1391 out.println(HTMLOutput.getImageMapHTML());
1392 out.println("<img src=\"" + imageName
1393 + "\" border=\"0\" usemap=\"#Map\" >"
1394 + "<map name=\"Map\">");
1396 for (int s = 0; s < sSize; s++)
1398 int sy = s * av.getCharHeight() + scaleHeight;
1400 SequenceI seq = av.getAlignment().getSequenceAt(s);
1401 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1402 for (int column = 0; column < alwidth; column++)
1404 StringBuilder text = new StringBuilder(512);
1405 String triplet = null;
1406 if (av.getAlignment().isNucleotide())
1408 triplet = ResidueProperties.nucleotideName
1409 .get(seq.getCharAt(column) + "");
1413 triplet = ResidueProperties.aa2Triplet
1414 .get(seq.getCharAt(column) + "");
1417 if (triplet == null)
1422 int seqPos = seq.findPosition(column);
1423 int gSize = groups.length;
1424 for (int g = 0; g < gSize; g++)
1426 if (text.length() < 1)
1428 text.append("<area shape=\"rect\" coords=\"")
1429 .append((idWidth + column * av.getCharWidth()))
1430 .append(",").append(sy).append(",")
1432 + (column + 1) * av.getCharWidth()))
1433 .append(",").append((av.getCharHeight() + sy))
1434 .append("\"").append(" onMouseOver=\"toolTip('")
1435 .append(seqPos).append(" ").append(triplet);
1438 if (groups[g].getStartRes() < column
1439 && groups[g].getEndRes() > column)
1441 text.append("<br><em>").append(groups[g].getName())
1446 if (text.length() < 1)
1448 text.append("<area shape=\"rect\" coords=\"")
1449 .append((idWidth + column * av.getCharWidth()))
1450 .append(",").append(sy).append(",")
1451 .append((idWidth + (column + 1) * av.getCharWidth()))
1452 .append(",").append((av.getCharHeight() + sy))
1453 .append("\"").append(" onMouseOver=\"toolTip('")
1454 .append(seqPos).append(" ").append(triplet);
1456 if (!Comparison.isGap(seq.getCharAt(column)))
1458 List<SequenceFeature> features = seq.findFeatures(column,
1460 for (SequenceFeature sf : features)
1462 if (sf.isContactFeature())
1464 text.append("<br>").append(sf.getType()).append(" ")
1465 .append(sf.getBegin()).append(":")
1466 .append(sf.getEnd());
1470 text.append("<br>");
1471 text.append(sf.getType());
1472 String description = sf.getDescription();
1473 if (description != null
1474 && !sf.getType().equals(description))
1476 description = description.replace("\"", """);
1477 text.append(" ").append(description);
1480 String status = sf.getStatus();
1481 if (status != null && !"".equals(status))
1483 text.append(" (").append(status).append(")");
1486 if (text.length() > 1)
1488 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1489 out.println(text.toString());
1494 out.println("</map></body></html>");
1497 } catch (Exception ex)
1499 throw new ImageOutputException(
1500 "couldn't write ImageMap due to unexpected error", ex);
1502 } // /////////END OF IMAGE MAP
1507 * Answers the height of the entire alignment in pixels, assuming it is in
1512 int getWrappedHeight()
1514 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1516 if (Jalview.isHeadlessMode())
1518 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1519 - vscroll.getPreferredSize().width
1520 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1523 int chunkWidth = getSeqPanel().seqCanvas
1524 .getWrappedCanvasWidth(seqPanelWidth);
1526 int hgap = av.getCharHeight();
1527 if (av.getScaleAboveWrapped())
1529 hgap += av.getCharHeight();
1532 int annotationHeight = 0;
1533 if (av.isShowAnnotation())
1535 hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
1536 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1539 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1542 int maxwidth = av.getAlignment().getWidth();
1543 if (av.hasHiddenColumns())
1545 maxwidth = av.getAlignment().getHiddenColumns()
1546 .absoluteToVisibleColumn(maxwidth) - 1;
1549 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1555 * close the panel - deregisters all listeners and nulls any references to
1558 public void closePanel()
1560 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1561 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1562 PaintRefresher.RemoveComponent(this);
1567 * try to ensure references are nulled
1569 if (annotationPanel != null)
1571 annotationPanel.dispose();
1572 annotationPanel = null;
1577 av.removePropertyChangeListener(propertyChangeListener);
1578 propertyChangeListener = null;
1579 StructureSelectionManager ssm = av.getStructureSelectionManager();
1580 ssm.removeStructureViewerListener(getSeqPanel(), null);
1581 ssm.removeSelectionListener(getSeqPanel());
1582 ssm.removeCommandListener(av);
1583 ssm.removeStructureViewerListener(getSeqPanel(), null);
1584 ssm.removeSelectionListener(getSeqPanel());
1590 if (Console.isDebugEnabled())
1592 Console.warn("Closing alignment panel which is already closed.");
1598 * Close any open dialogs that would be orphaned when this one is closed
1600 protected void closeChildFrames()
1602 if (overviewPanel != null)
1604 overviewPanel.dispose();
1605 overviewPanel = null;
1607 if (calculationDialog != null)
1609 calculationDialog.closeFrame();
1610 calculationDialog = null;
1615 * hides or shows dynamic annotation rows based on groups and av state flags
1617 public void updateAnnotation()
1619 updateAnnotation(false, false);
1622 public void updateAnnotation(boolean applyGlobalSettings)
1624 updateAnnotation(applyGlobalSettings, false);
1627 public void updateAnnotation(boolean applyGlobalSettings,
1628 boolean preserveNewGroupSettings)
1630 av.updateGroupAnnotationSettings(applyGlobalSettings,
1631 preserveNewGroupSettings);
1632 adjustAnnotationHeight();
1636 public AlignmentI getAlignment()
1638 return av == null ? null : av.getAlignment();
1642 public String getViewName()
1644 return av.getViewName();
1648 * Make/Unmake this alignment panel the current input focus
1652 public void setSelected(boolean b)
1656 if (alignFrame.getSplitViewContainer() != null)
1659 * bring enclosing SplitFrame to front first if there is one
1661 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1663 alignFrame.setSelected(b);
1664 } catch (Exception ex)
1669 setAlignFrameView();
1673 public void setAlignFrameView()
1675 alignFrame.setDisplayedView(this);
1679 public StructureSelectionManager getStructureSelectionManager()
1681 return av.getStructureSelectionManager();
1685 public void raiseOOMWarning(String string, OutOfMemoryError error)
1687 new OOMWarning(string, error, this);
1691 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1694 return new FeatureRenderer(this);
1698 public jalview.api.FeatureRenderer getFeatureRenderer()
1700 return seqPanel.seqCanvas.getFeatureRenderer();
1703 public void updateFeatureRenderer(
1704 jalview.renderer.seqfeatures.FeatureRenderer fr)
1706 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1709 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1711 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1713 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1717 public ScalePanel getScalePanel()
1722 public void setScalePanel(ScalePanel scalePanel)
1724 this.scalePanel = scalePanel;
1727 public SeqPanel getSeqPanel()
1732 public void setSeqPanel(SeqPanel seqPanel)
1734 this.seqPanel = seqPanel;
1737 public AnnotationPanel getAnnotationPanel()
1739 return annotationPanel;
1742 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1744 this.annotationPanel = annotationPanel;
1747 public AnnotationLabels getAlabels()
1752 public void setAlabels(AnnotationLabels alabels)
1754 this.alabels = alabels;
1757 public IdPanel getIdPanel()
1762 public void setIdPanel(IdPanel idPanel)
1764 this.idPanel = idPanel;
1768 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1769 * The aim is to keep the two alignments 'lined up' on their centre columns.
1772 * holds mapped region(s) of this alignment that we are scrolling
1773 * 'to'; may be modified for sequence offset by this method
1774 * @param verticalOffset
1775 * the number of visible sequences to show above the mapped region
1777 protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1779 scrollToPosition(sr, verticalOffset, true);
1783 * Set a flag to say do not scroll any (cDNA/protein) complement.
1787 protected void setToScrollComplementPanel(boolean b)
1789 this.scrollComplementaryPanel = b;
1793 * Get whether to scroll complement panel
1795 * @return true if cDNA/protein complement panels should be scrolled
1797 protected boolean isSetToScrollComplementPanel()
1799 return this.scrollComplementaryPanel;
1805 * @adjustHeight if true, try to recalculate panel height for visible
1808 protected void refresh(boolean adjustHeight)
1810 validateAnnotationDimensions(adjustHeight);
1814 // sort, repaint, update overview
1815 paintAlignment(true, false);
1819 // lightweight repaint
1826 * Property change event fired when a change is made to the viewport ranges
1827 * object associated with this alignment panel's viewport
1829 public void propertyChange(PropertyChangeEvent evt)
1831 // update this panel's scroll values based on the new viewport ranges values
1832 ViewportRanges ranges = av.getRanges();
1833 int x = ranges.getStartRes();
1834 int y = ranges.getStartSeq();
1835 setScrollValues(x, y);
1837 // now update any complementary alignment (its viewport ranges object
1838 // is different so does not get automatically updated)
1839 if (isSetToScrollComplementPanel())
1841 setToScrollComplementPanel(false);
1842 av.scrollComplementaryAlignment();
1843 setToScrollComplementPanel(true);
1848 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1849 * reference should be nulled when the dialog is closed.
1851 * @param calculationChooser
1853 public void setCalculationDialog(CalculationChooser calculationChooser)
1855 calculationDialog = calculationChooser;
1859 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1862 public CalculationChooser getCalculationDialog()
1864 return calculationDialog;
1868 * Constructs and sets the title for the Overview window (if there is one),
1869 * including the align frame's title, and view name (if applicable). Returns
1870 * the title, or null if this panel has no Overview window open.
1875 public String setOverviewTitle(AlignFrame alignFrame)
1877 if (this.overviewPanel == null)
1881 String overviewTitle = MessageManager
1882 .formatMessage("label.overview_params", new Object[]
1883 { alignFrame.getTitle() });
1884 String viewName = getViewName();
1885 if (viewName != null)
1887 overviewTitle += (" " + viewName);
1889 overviewPanel.setTitle(overviewTitle);
1890 return overviewTitle;
1894 * If this alignment panel has an Overview panel open, closes it
1896 public void closeOverviewPanel()
1898 if (overviewPanel != null)
1900 overviewPanel.close();
1901 overviewPanel = null;