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. The calculated width is
260 * also set as a property of the viewport.
262 * @return Dimension giving the maximum width of the alignment label panel
263 * that should be used.
265 public Dimension calculateIdWidth()
267 int oldWidth = av.getIdWidth();
269 // calculate sensible default width when no preference is available
271 if (av.getIdWidth() < 0)
273 r = calculateDefaultAlignmentIdWidth();
274 av.setIdWidth(r.width);
279 r.width = av.getIdWidth();
284 * fudge: if desired width has changed, update layout
285 * (see also paintComponent - updates layout on a repaint)
287 if (r.width != oldWidth)
289 idPanelHolder.setPreferredSize(r);
295 public Dimension calculateDefaultAlignmentIdWidth()
297 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
298 int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
299 int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
300 return calculateIdWidth(-1, false, false);
304 * Calculate the width of the alignment labels based on the displayed names
305 * and any bounds on label width set in preferences. Also includes annotations
306 * not actually visible.
308 * FIXME JAL-244 JAL-4091 - doesn't include sequence associated annotation
309 * label decorators and only called during tests
312 * -1 or maximum width allowed for IdWidth
313 * @return Dimension giving the maximum width of the alignment label panel
314 * that should be used.
316 protected Dimension calculateIdWidth(int maxwidth)
318 return calculateIdWidth(maxwidth, true, false);
321 * Calculate the width of the alignment labels based on the displayed names
322 * and any bounds on label width set in preferences.
325 * -1 or maximum width allowed for IdWidth
326 * @param includeAnnotations - when true includes width of any additional marks in annotation id panel
327 * @param visibleOnly -
328 * @return Dimension giving the maximum width of the alignment label panel
329 * that should be used.
331 public Dimension calculateIdWidth(int maxwidth,
332 boolean includeAnnotations, boolean visibleOnly)
334 Container c = new Container();
336 FontMetrics fm = c.getFontMetrics(
337 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
339 AlignmentI al = av.getAlignment();
343 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
345 SequenceI s = al.getSequenceAt(i);
346 String id = s.getDisplayId(av.getShowJVSuffix());
347 int stringWidth = fm.stringWidth(id);
348 idWidth = Math.max(idWidth, stringWidth);
352 // Also check annotation label widths
353 if (includeAnnotations && al.getAlignmentAnnotation() != null)
355 if (Jalview.isHeadlessMode())
357 AnnotationLabels aal = getAlabels();
358 int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
360 idWidth = Math.max(idWidth, stringWidth);
364 fm = c.getFontMetrics(getAlabels().getFont());
366 for (i = 0; i < al.getAlignmentAnnotation().length; i++)
368 AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
369 if (visibleOnly && !aa.visible)
373 String label = aa.label;
374 int stringWidth = fm.stringWidth(label);
375 idWidth = Math.max(idWidth, stringWidth);
380 int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth);
381 w += ID_WIDTH_PADDING;
383 return new Dimension(w, 12);
387 * Highlight the given results on the alignment
390 public void highlightSearchResults(SearchResultsI results)
392 boolean scrolled = scrollToPosition(results, 0, false);
394 boolean fastPaint = !(scrolled && av.getWrapAlignment());
396 getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint);
400 * Scroll the view to show the position of the highlighted region in results
403 * @param searchResults
406 public boolean scrollToPosition(SearchResultsI searchResults)
408 return scrollToPosition(searchResults, 0, false);
412 * Scrolls the view (if necessary) to show the position of the first
413 * highlighted region in results (if any). Answers true if the view was
414 * scrolled, or false if no matched region was found, or it is already
418 * @param verticalOffset
419 * if greater than zero, allows scrolling to a position below the
420 * first displayed sequence
422 * if true, try to centre the search results horizontally in the view
425 protected boolean scrollToPosition(SearchResultsI results,
426 int verticalOffset, boolean centre)
428 int startv, endv, starts, ends;
429 ViewportRanges ranges = av.getRanges();
431 if (results == null || results.isEmpty() || av == null
432 || av.getAlignment() == null)
436 int seqIndex = av.getAlignment().findIndex(results);
441 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
443 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
452 * To centre results, scroll to positions half the visible width
453 * left/right of the start/end positions
457 int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
458 start = Math.max(start - offset, 0);
459 end = end + offset - 1;
465 if (end == seq.getEnd())
470 if (av.hasHiddenColumns())
472 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
473 start = hidden.absoluteToVisibleColumn(start);
474 end = hidden.absoluteToVisibleColumn(end);
477 if (!hidden.isVisible(r[0]))
479 // don't scroll - position isn't visible
486 * allow for offset of target sequence (actually scroll to one above it)
488 seqIndex = Math.max(0, seqIndex - verticalOffset);
489 boolean scrollNeeded = true;
491 if (!av.getWrapAlignment())
493 if ((startv = ranges.getStartRes()) >= start)
496 * Scroll left to make start of search results visible
498 setScrollValues(start, seqIndex);
500 else if ((endv = ranges.getEndRes()) <= end)
503 * Scroll right to make end of search results visible
505 setScrollValues(startv + end - endv, seqIndex);
507 else if ((starts = ranges.getStartSeq()) > seqIndex)
510 * Scroll up to make start of search results visible
512 setScrollValues(ranges.getStartRes(), seqIndex);
514 else if ((ends = ranges.getEndSeq()) <= seqIndex)
517 * Scroll down to make end of search results visible
519 setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
522 * Else results are already visible - no need to scroll
524 scrollNeeded = false;
528 scrollNeeded = ranges.scrollToWrappedVisible(start);
531 paintAlignment(false, false);
539 * @return DOCUMENT ME!
541 public OverviewPanel getOverviewPanel()
543 return overviewPanel;
552 public void setOverviewPanel(OverviewPanel op)
560 * Hide or show annotation panel
563 public void setAnnotationVisible(boolean b)
565 if (!av.getWrapAlignment())
567 annotationSpaceFillerHolder.setVisible(b);
568 annotationScroller.setVisible(b);
574 * automatically adjust annotation panel height for new annotation whilst
575 * ensuring the alignment is still visible.
578 public void adjustAnnotationHeight()
580 // TODO: display vertical annotation scrollbar if necessary
581 // this is called after loading new annotation onto alignment
582 if (alignFrame.getHeight() == 0)
584 jalview.bin.Console.outPrintln("NEEDS FIXING");
586 validateAnnotationDimensions(true);
588 // TODO: many places call this method and also paintAlignment with various
589 // different settings. this means multiple redraws are triggered...
590 paintAlignment(true, av.needToUpdateStructureViews());
594 * calculate the annotation dimensions and refresh slider values accordingly.
595 * need to do repaints/notifys afterwards.
597 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
599 // BH 2018.04.18 comment: addNotify() is not appropriate here. We
600 // are not changing ancestors, and keyboard action listeners do
601 // not need to be reset. addNotify() is a very expensive operation,
602 // requiring a full re-layout of all parents and children.
603 // Note in JComponent:
604 // This method is called by the toolkit internally and should
605 // not be called directly by programs.
606 // I note that addNotify() is called in several areas of Jalview.
608 AnnotationPanel ap = getAnnotationPanel();
609 int annotationHeight = ap.adjustPanelHeight();
610 annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight,
614 Dimension e = idPanel.getSize();
615 int idWidth = e.width;
616 boolean manuallyAdjusted = this.getIdPanel().getIdCanvas()
618 annotationScroller.setPreferredSize(new Dimension(
619 manuallyAdjusted ? idWidth : annotationScroller.getWidth(),
622 alabels.setPreferredSize(new Dimension(idWidth, annotationHeight));
624 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
625 manuallyAdjusted ? idWidth
626 : annotationSpaceFillerHolder.getWidth(),
628 annotationScroller.validate();
629 annotationScroller.addNotify();
634 * update alignment layout for viewport settings
639 public void updateLayout()
642 setAnnotationVisible(av.isShowAnnotation());
643 boolean wrap = av.getWrapAlignment();
644 ViewportRanges ranges = av.getRanges();
645 ranges.setStartSeq(0);
646 // scalePanelHolder.setVisible(!wrap);
647 hscroll.setVisible(!wrap);
648 // Allow idPanel width adjustment in wrap mode
649 idwidthAdjuster.setVisible(true);
653 annotationScroller.setVisible(false);
654 annotationSpaceFillerHolder.setVisible(false);
656 else if (av.isShowAnnotation())
658 annotationScroller.setVisible(true);
659 annotationSpaceFillerHolder.setVisible(true);
660 validateAnnotationDimensions(false);
663 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
665 { // may not yet be laid out
668 int widthInRes = getSeqPanel().seqCanvas
669 .getWrappedCanvasWidth(canvasWidth);
670 ranges.setViewportWidth(widthInRes);
674 int widthInRes = (canvasWidth / av.getCharWidth());
675 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
676 / av.getCharHeight());
678 ranges.setViewportWidth(widthInRes);
679 ranges.setViewportHeight(heightInSeq);
683 // idSpaceFillerPanel1.setVisible(!wrap);
689 * Adjust row/column scrollers to show a visible position in the alignment.
692 * visible column to scroll to
694 * visible row to scroll to
697 public void setScrollValues(int xpos, int ypos)
702 if (av == null || av.getAlignment() == null)
707 if (av.getWrapAlignment())
709 setScrollingForWrappedPanel(x);
713 int width = av.getAlignment().getVisibleWidth();
714 int height = av.getAlignment().getHeight();
716 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
717 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
724 if (vextent > height)
729 if ((hextent + x) > width)
734 if ((vextent + y) > height)
736 y = height - vextent;
749 // update the scroll values
750 hscroll.setValues(x, hextent, 0, width);
751 vscroll.setValues(y, vextent, 0, height);
756 * Respond to adjustment event when horizontal or vertical scrollbar is
760 * adjustment event encoding whether hscroll or vscroll changed
763 public void adjustmentValueChanged(AdjustmentEvent evt)
765 if (av.getWrapAlignment())
767 adjustScrollingWrapped(evt);
771 ViewportRanges ranges = av.getRanges();
773 if (evt.getSource() == hscroll)
775 int oldX = ranges.getStartRes();
776 int oldwidth = ranges.getViewportWidth();
777 int x = hscroll.getValue();
778 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
780 // if we're scrolling to the position we're already at, stop
781 // this prevents infinite recursion of events when the scroll/viewport
782 // ranges values are the same
783 if ((x == oldX) && (width == oldwidth))
787 ranges.setViewportStartAndWidth(x, width);
789 else if (evt.getSource() == vscroll)
791 int oldY = ranges.getStartSeq();
792 int oldheight = ranges.getViewportHeight();
793 int y = vscroll.getValue();
794 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
796 // if we're scrolling to the position we're already at, stop
797 // this prevents infinite recursion of events when the scroll/viewport
798 // ranges values are the same
799 if ((y == oldY) && (height == oldheight))
803 ranges.setViewportStartAndHeight(y, height);
809 * Responds to a scroll change by setting the start position of the viewport.
814 protected void adjustScrollingWrapped(AdjustmentEvent evt)
816 if (evt.getSource() == hscroll)
818 return; // no horizontal scroll when wrapped
820 final ViewportRanges ranges = av.getRanges();
822 if (evt.getSource() == vscroll)
824 int newY = vscroll.getValue();
827 * if we're scrolling to the position we're already at, stop
828 * this prevents infinite recursion of events when the scroll/viewport
829 * ranges values are the same
831 int oldX = ranges.getStartRes();
832 int oldY = ranges.getWrappedScrollPosition(oldX);
840 * limit page up/down to one width's worth of positions
842 int rowSize = ranges.getViewportWidth();
843 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
844 ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
849 // This is only called if file loaded is a jar file that
850 // was wrapped when saved and user has wrap alignment true
851 // as preference setting
852 SwingUtilities.invokeLater(new Runnable()
857 // When updating scrolling to use ViewportChange events, this code
858 // could not be validated and it is not clear if it is now being
859 // called. Log warning here in case it is called and unforeseen
862 "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
864 // scroll to start of panel
865 ranges.setStartRes(0);
866 ranges.setStartSeq(0);
874 * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
877 public void paintAlignment(boolean updateOverview,
878 boolean updateStructures)
880 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
881 av.isShowAutocalculatedAbove());
882 sorter.sort(getAlignment().getAlignmentAnnotation(),
883 av.getSortAnnotationsBy());
886 if (updateStructures)
888 av.getStructureSelectionManager().sequenceColoursChanged(this);
893 if (overviewPanel != null)
895 overviewPanel.updateOverviewImage();
901 public void paintComponent(Graphics g)
903 invalidate(); // needed so that the id width adjuster works correctly
904 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
905 int idWidth = d.width;
907 // check wrapped alignment as at least 1 residue width
908 if (av.getWrapAlignment())
910 SeqCanvas sc = this.getSeqPanel().seqCanvas;
911 if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth())
913 // need to make some adjustments
914 idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth());
915 av.setIdWidth(idWidth);
916 av.getAlignPanel().getIdPanel().getIdCanvas()
917 .setManuallyAdjusted(true);
919 validateAnnotationDimensions(false);
923 idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height));
924 hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
926 validate(); // needed so that the id width adjuster works correctly
929 * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
930 * though I still think this call should be elsewhere.
932 ViewportRanges ranges = av.getRanges();
933 setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
934 super.paintComponent(g);
938 * Set vertical scroll bar position, and number of increments, for wrapped
941 * @param topLeftColumn
942 * the column position at top left (0..)
944 private void setScrollingForWrappedPanel(int topLeftColumn)
946 ViewportRanges ranges = av.getRanges();
947 int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
948 int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
951 * a scrollbar's value can be set to at most (maximum-extent)
952 * so we add extent (1) to the maxScroll value
954 vscroll.setUnitIncrement(1);
955 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
968 * @return DOCUMENT ME!
970 * @throws PrinterException
974 public int print(Graphics pg, PageFormat pf, int pi)
975 throws PrinterException
977 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
979 int pwidth = (int) pf.getImageableWidth();
980 int pheight = (int) pf.getImageableHeight();
982 if (av.getWrapAlignment())
984 return printWrappedAlignment(pwidth, pheight, pi, pg);
988 return printUnwrapped(pwidth, pheight, pi, pg, pg);
993 * Draws the alignment image, including sequence ids, sequences, and
994 * annotation labels and annotations if shown, on either one or two Graphics
1004 * the graphics context for sequence ids and annotation labels
1005 * @param alignmentGraphics
1006 * the graphics context for sequences and annotations (may or may not
1007 * be the same context as idGraphics)
1009 * @throws PrinterException
1011 public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
1012 Graphics idGraphics, Graphics alignmentGraphics)
1013 throws PrinterException
1016 if (getIdPanel()!=null && getIdPanel().getWidth()>0)
1018 // use the current IdPanel's width, if its set and non-zero
1019 idWidth = getIdPanel().getWidth();
1021 // otherwise calculate it
1022 idWidth = getVisibleIdWidth(false);
1026 * Get the horizontal offset to where we draw the sequences.
1027 * This is idWidth if using a single Graphics context, else zero.
1029 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
1032 FontMetrics fm = getFontMetrics(av.getFont());
1033 final int charHeight = av.getCharHeight();
1034 final int scaleHeight = charHeight + fm.getDescent();
1036 idGraphics.setColor(Color.white);
1037 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
1038 idGraphics.setFont(av.getFont());
1041 * How many sequences and residues can we fit on a printable page?
1043 final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1045 final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1047 final int alignmentWidth = av.getAlignment().getVisibleWidth();
1048 int pagesWide = (alignmentWidth / totalRes) + 1;
1050 final int startRes = (pageIndex % pagesWide) * totalRes;
1051 final int endRes = Math.min(startRes + totalRes - 1,
1052 alignmentWidth - 1);
1054 final int startSeq = (pageIndex / pagesWide) * totalSeq;
1055 final int alignmentHeight = av.getAlignment().getHeight();
1056 final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
1058 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
1060 if (av.isShowAnnotation())
1062 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1065 pagesHigh /= pageHeight;
1067 if (pageIndex >= (pagesWide * pagesHigh))
1069 return Printable.NO_SUCH_PAGE;
1071 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
1074 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1076 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1077 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1078 pageWidth - idWidth, scaleHeight);
1079 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1082 * Draw the sequence ids, offset for scale height,
1083 * then reset to top left (0, 0)
1085 idGraphics.translate(0, scaleHeight);
1086 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1087 List<SequenceI> selection = av.getSelectionGroup() == null ? null
1088 : av.getSelectionGroup().getSequences(null);
1089 idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
1092 idGraphics.setFont(av.getFont());
1093 idGraphics.translate(0, -scaleHeight);
1096 * draw the sequences, offset for scale height, and id width (if using a
1097 * single graphics context), then reset to (0, scale height)
1099 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1100 getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
1101 startRes, endRes, startSeq, endSeq - 1);
1102 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1104 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1107 * draw annotation labels; drawComponent() translates by
1108 * getScrollOffset(), so compensate for that first;
1109 * then reset to (0, scale height)
1111 int offset = getAlabels().getScrollOffset();
1112 idGraphics.translate(0, -offset);
1113 idGraphics.translate(0, alignmentDrawnHeight);
1114 getAlabels().drawComponentNotGUI(idGraphics, idWidth);
1115 idGraphics.translate(0, -alignmentDrawnHeight);
1118 * draw the annotations starting at
1119 * (idOffset, alignmentHeight) from (0, scaleHeight)
1121 alignmentGraphics.translate(alignmentGraphicsOffset,
1122 alignmentDrawnHeight);
1124 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1125 alignmentGraphics, -1, startRes, endRes + 1);
1128 return Printable.PAGE_EXISTS;
1132 * Prints one page of an alignment in wrapped mode. Returns
1133 * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
1134 * no page could be drawn (page number out of range).
1144 * @throws PrinterException
1146 public int printWrappedAlignment(int pageWidth, int pageHeight,
1147 int pageNumber, Graphics g) throws PrinterException
1149 getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
1151 int annotationHeight = 0;
1152 if (av.isShowAnnotation())
1154 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1157 int hgap = av.getCharHeight();
1158 if (av.getScaleAboveWrapped())
1160 hgap += av.getCharHeight();
1163 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1166 int idWidth = getVisibleIdWidth(false);
1168 int maxwidth = av.getAlignment().getVisibleWidth();
1170 int resWidth = getSeqPanel().seqCanvas
1171 .getWrappedCanvasWidth(pageWidth - idWidth);
1172 av.getRanges().setViewportStartAndWidth(0, resWidth);
1174 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1176 g.setColor(Color.white);
1177 g.fillRect(0, 0, pageWidth, pageHeight);
1178 g.setFont(av.getFont());
1179 g.setColor(Color.black);
1182 * method: print the whole wrapped alignment, but with a clip region that
1183 * is restricted to the requested page; this supports selective print of
1184 * single pages or ranges, (at the cost of repeated processing in the
1185 * 'normal' case, when all pages are printed)
1187 g.translate(0, -pageNumber * pageHeight);
1189 g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
1192 * draw sequence ids and annotation labels (if shown)
1194 IdCanvas idCanvas = getIdPanel().getIdCanvas();
1195 idCanvas.drawIdsWrappedNoGUI((Graphics2D) g, av, 0, totalHeight);
1197 g.translate(idWidth, 0);
1199 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
1200 pageWidth - idWidth, totalHeight, 0);
1202 if ((pageNumber * pageHeight) < totalHeight)
1204 return Printable.PAGE_EXISTS;
1208 return Printable.NO_SUCH_PAGE;
1213 * get current sequence ID panel width, or nominal value if panel were to be
1214 * displayed using default settings
1218 public int getVisibleIdWidth()
1220 return getVisibleIdWidth(true);
1224 * get current sequence ID panel width, or nominal value if panel were to be
1225 * displayed using default settings
1228 * indicate if the Id width for onscreen or offscreen display should
1232 protected int getVisibleIdWidth(boolean onscreen)
1234 // see if rendering offscreen - check preferences and calc width accordingly
1235 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1237 return calculateIdWidth(-1).width;
1239 Integer idwidth = onscreen ? null
1240 : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
1241 if (idwidth != null)
1243 return idwidth.intValue() + ID_WIDTH_PADDING;
1246 int w = getIdPanel().getWidth();
1247 w = this.calculateIdWidth(-1, true, true).width;
1248 return (w > 0 ? w : calculateIdWidth().width);
1251 void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
1252 throws ImageOutputException
1254 makeAlignmentImage(type, file, renderer,
1255 BitmapImageSizing.defaultBitmapImageSizing());
1259 * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
1260 * writes it to the specified file
1264 * @param textrenderer
1265 * @param bitmapscale
1267 void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer,
1268 BitmapImageSizing userBis) throws ImageOutputException
1270 final int borderBottomOffset = 5;
1272 AlignmentDimension aDimension = getAlignmentDimension();
1274 // todo use a lambda function in place of callback here?
1275 ImageWriterI writer = new ImageWriterI()
1278 public void exportImage(Graphics graphics) throws Exception
1280 if (av.getWrapAlignment())
1282 printWrappedAlignment(aDimension.getWidth(),
1283 aDimension.getHeight() + borderBottomOffset, 0, graphics);
1287 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
1288 graphics, graphics);
1293 String fileTitle = alignFrame.getTitle();
1294 ImageExporter exporter = new ImageExporter(writer, alignFrame, type,
1296 int imageWidth = aDimension.getWidth();
1297 int imageHeight = aDimension.getHeight() + borderBottomOffset;
1298 String of = MessageManager.getString("label.alignment");
1299 exporter.doExport(file, this, imageWidth, imageHeight, of, renderer,
1304 * Calculates and returns a suitable width and height (in pixels) for an
1309 public AlignmentDimension getAlignmentDimension()
1311 int maxwidth = av.getAlignment().getVisibleWidth();
1313 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1314 + getScalePanel().getHeight();
1315 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1317 if (av.getWrapAlignment())
1319 height = getWrappedHeight();
1320 if (Jalview.isHeadlessMode())
1322 // need to obtain default alignment width and then add in any
1323 // additional allowance for id margin
1324 // this duplicates the calculation in getWrappedHeight but adjusts for
1326 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1327 - alignFrame.getInsets().left - alignFrame.getInsets().right
1328 - getVisibleIdWidth() + getVisibleIdWidth(false);
1332 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1336 else if (av.isShowAnnotation())
1338 height += getAnnotationPanel().adjustPanelHeight() + 3;
1340 return new AlignmentDimension(width, height);
1344 public void makePNGImageMap(File imgMapFile, String imageName)
1345 throws ImageOutputException
1347 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1348 // ////////////////////////////////////////////
1349 int idWidth = getVisibleIdWidth(false);
1350 FontMetrics fm = getFontMetrics(av.getFont());
1351 int scaleHeight = av.getCharHeight() + fm.getDescent();
1354 // ////////////////////////////////
1355 if (imgMapFile != null)
1359 int sSize = av.getAlignment().getHeight();
1360 int alwidth = av.getAlignment().getWidth();
1361 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1362 out.println(HTMLOutput.getImageMapHTML());
1363 out.println("<img src=\"" + imageName
1364 + "\" border=\"0\" usemap=\"#Map\" >"
1365 + "<map name=\"Map\">");
1367 for (int s = 0; s < sSize; s++)
1369 int sy = s * av.getCharHeight() + scaleHeight;
1371 SequenceI seq = av.getAlignment().getSequenceAt(s);
1372 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1373 for (int column = 0; column < alwidth; column++)
1375 StringBuilder text = new StringBuilder(512);
1376 String triplet = null;
1377 if (av.getAlignment().isNucleotide())
1379 triplet = ResidueProperties.nucleotideName
1380 .get(seq.getCharAt(column) + "");
1384 triplet = ResidueProperties.aa2Triplet
1385 .get(seq.getCharAt(column) + "");
1388 if (triplet == null)
1393 int seqPos = seq.findPosition(column);
1394 int gSize = groups.length;
1395 for (int g = 0; g < gSize; g++)
1397 if (text.length() < 1)
1399 text.append("<area shape=\"rect\" coords=\"")
1400 .append((idWidth + column * av.getCharWidth()))
1401 .append(",").append(sy).append(",")
1403 + (column + 1) * av.getCharWidth()))
1404 .append(",").append((av.getCharHeight() + sy))
1405 .append("\"").append(" onMouseOver=\"toolTip('")
1406 .append(seqPos).append(" ").append(triplet);
1409 if (groups[g].getStartRes() < column
1410 && groups[g].getEndRes() > column)
1412 text.append("<br><em>").append(groups[g].getName())
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);
1427 if (!Comparison.isGap(seq.getCharAt(column)))
1429 List<SequenceFeature> features = seq.findFeatures(column,
1431 for (SequenceFeature sf : features)
1433 if (sf.isContactFeature())
1435 text.append("<br>").append(sf.getType()).append(" ")
1436 .append(sf.getBegin()).append(":")
1437 .append(sf.getEnd());
1441 text.append("<br>");
1442 text.append(sf.getType());
1443 String description = sf.getDescription();
1444 if (description != null
1445 && !sf.getType().equals(description))
1447 description = description.replace("\"", """);
1448 text.append(" ").append(description);
1451 String status = sf.getStatus();
1452 if (status != null && !"".equals(status))
1454 text.append(" (").append(status).append(")");
1457 if (text.length() > 1)
1459 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1460 out.println(text.toString());
1465 out.println("</map></body></html>");
1468 } catch (Exception ex)
1470 throw new ImageOutputException(
1471 "couldn't write ImageMap due to unexpected error", ex);
1473 } // /////////END OF IMAGE MAP
1478 * Answers the height of the entire alignment in pixels, assuming it is in
1483 int getWrappedHeight()
1485 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1487 if (Jalview.isHeadlessMode())
1489 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1490 - vscroll.getPreferredSize().width
1491 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1494 int chunkWidth = getSeqPanel().seqCanvas
1495 .getWrappedCanvasWidth(seqPanelWidth);
1497 int hgap = av.getCharHeight();
1498 if (av.getScaleAboveWrapped())
1500 hgap += av.getCharHeight();
1503 int annotationHeight = 0;
1504 if (av.isShowAnnotation())
1506 hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
1507 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1510 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1513 int maxwidth = av.getAlignment().getWidth();
1514 if (av.hasHiddenColumns())
1516 maxwidth = av.getAlignment().getHiddenColumns()
1517 .absoluteToVisibleColumn(maxwidth) - 1;
1520 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1526 * close the panel - deregisters all listeners and nulls any references to
1529 public void closePanel()
1531 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1532 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1533 PaintRefresher.RemoveComponent(this);
1538 * try to ensure references are nulled
1540 if (annotationPanel != null)
1542 annotationPanel.dispose();
1543 annotationPanel = null;
1548 av.removePropertyChangeListener(propertyChangeListener);
1549 propertyChangeListener = null;
1550 StructureSelectionManager ssm = av.getStructureSelectionManager();
1551 ssm.removeStructureViewerListener(getSeqPanel(), null);
1552 ssm.removeSelectionListener(getSeqPanel());
1553 ssm.removeCommandListener(av);
1554 ssm.removeStructureViewerListener(getSeqPanel(), null);
1555 ssm.removeSelectionListener(getSeqPanel());
1561 if (Console.isDebugEnabled())
1563 Console.warn("Closing alignment panel which is already closed.");
1569 * Close any open dialogs that would be orphaned when this one is closed
1571 protected void closeChildFrames()
1573 if (overviewPanel != null)
1575 overviewPanel.dispose();
1576 overviewPanel = null;
1578 if (calculationDialog != null)
1580 calculationDialog.closeFrame();
1581 calculationDialog = null;
1586 * hides or shows dynamic annotation rows based on groups and av state flags
1588 public void updateAnnotation()
1590 updateAnnotation(false, false);
1593 public void updateAnnotation(boolean applyGlobalSettings)
1595 updateAnnotation(applyGlobalSettings, false);
1598 public void updateAnnotation(boolean applyGlobalSettings,
1599 boolean preserveNewGroupSettings)
1601 av.updateGroupAnnotationSettings(applyGlobalSettings,
1602 preserveNewGroupSettings);
1603 adjustAnnotationHeight();
1607 public AlignmentI getAlignment()
1609 return av == null ? null : av.getAlignment();
1613 public String getViewName()
1615 return av.getViewName();
1619 * Make/Unmake this alignment panel the current input focus
1623 public void setSelected(boolean b)
1627 if (alignFrame.getSplitViewContainer() != null)
1630 * bring enclosing SplitFrame to front first if there is one
1632 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1634 alignFrame.setSelected(b);
1635 } catch (Exception ex)
1640 setAlignFrameView();
1644 public void setAlignFrameView()
1646 alignFrame.setDisplayedView(this);
1650 public StructureSelectionManager getStructureSelectionManager()
1652 return av.getStructureSelectionManager();
1656 public void raiseOOMWarning(String string, OutOfMemoryError error)
1658 new OOMWarning(string, error, this);
1662 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1665 return new FeatureRenderer(this);
1669 public jalview.api.FeatureRenderer getFeatureRenderer()
1671 return seqPanel.seqCanvas.getFeatureRenderer();
1674 public void updateFeatureRenderer(
1675 jalview.renderer.seqfeatures.FeatureRenderer fr)
1677 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1680 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1682 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1684 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1688 public ScalePanel getScalePanel()
1693 public void setScalePanel(ScalePanel scalePanel)
1695 this.scalePanel = scalePanel;
1698 public SeqPanel getSeqPanel()
1703 public void setSeqPanel(SeqPanel seqPanel)
1705 this.seqPanel = seqPanel;
1708 public AnnotationPanel getAnnotationPanel()
1710 return annotationPanel;
1713 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1715 this.annotationPanel = annotationPanel;
1718 public AnnotationLabels getAlabels()
1723 public void setAlabels(AnnotationLabels alabels)
1725 this.alabels = alabels;
1728 public IdPanel getIdPanel()
1733 public void setIdPanel(IdPanel idPanel)
1735 this.idPanel = idPanel;
1739 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1740 * The aim is to keep the two alignments 'lined up' on their centre columns.
1743 * holds mapped region(s) of this alignment that we are scrolling
1744 * 'to'; may be modified for sequence offset by this method
1745 * @param verticalOffset
1746 * the number of visible sequences to show above the mapped region
1748 protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1750 scrollToPosition(sr, verticalOffset, true);
1754 * Set a flag to say do not scroll any (cDNA/protein) complement.
1758 protected void setToScrollComplementPanel(boolean b)
1760 this.scrollComplementaryPanel = b;
1764 * Get whether to scroll complement panel
1766 * @return true if cDNA/protein complement panels should be scrolled
1768 protected boolean isSetToScrollComplementPanel()
1770 return this.scrollComplementaryPanel;
1776 * @adjustHeight if true, try to recalculate panel height for visible
1779 protected void refresh(boolean adjustHeight)
1781 validateAnnotationDimensions(adjustHeight);
1785 // sort, repaint, update overview
1786 paintAlignment(true, false);
1790 // lightweight repaint
1797 * Property change event fired when a change is made to the viewport ranges
1798 * object associated with this alignment panel's viewport
1800 public void propertyChange(PropertyChangeEvent evt)
1802 // update this panel's scroll values based on the new viewport ranges values
1803 ViewportRanges ranges = av.getRanges();
1804 int x = ranges.getStartRes();
1805 int y = ranges.getStartSeq();
1806 setScrollValues(x, y);
1808 // now update any complementary alignment (its viewport ranges object
1809 // is different so does not get automatically updated)
1810 if (isSetToScrollComplementPanel())
1812 setToScrollComplementPanel(false);
1813 av.scrollComplementaryAlignment();
1814 setToScrollComplementPanel(true);
1819 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1820 * reference should be nulled when the dialog is closed.
1822 * @param calculationChooser
1824 public void setCalculationDialog(CalculationChooser calculationChooser)
1826 calculationDialog = calculationChooser;
1830 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1833 public CalculationChooser getCalculationDialog()
1835 return calculationDialog;
1839 * Constructs and sets the title for the Overview window (if there is one),
1840 * including the align frame's title, and view name (if applicable). Returns
1841 * the title, or null if this panel has no Overview window open.
1846 public String setOverviewTitle(AlignFrame alignFrame)
1848 if (this.overviewPanel == null)
1852 String overviewTitle = MessageManager
1853 .formatMessage("label.overview_params", new Object[]
1854 { alignFrame.getTitle() });
1855 String viewName = getViewName();
1856 if (viewName != null)
1858 overviewTitle += (" " + viewName);
1860 overviewPanel.setTitle(overviewTitle);
1861 return overviewTitle;
1865 * If this alignment panel has an Overview panel open, closes it
1867 public void closeOverviewPanel()
1869 if (overviewPanel != null)
1871 overviewPanel.close();
1872 overviewPanel = null;