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 jalview.analysis.AnnotationSorter;
24 import jalview.api.AlignViewportI;
25 import jalview.api.AlignmentViewPanel;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SearchResultsI;
30 import jalview.datamodel.SequenceFeature;
31 import jalview.datamodel.SequenceGroup;
32 import jalview.datamodel.SequenceI;
33 import jalview.jbgui.GAlignmentPanel;
34 import jalview.math.AlignmentDimension;
35 import jalview.schemes.ResidueProperties;
36 import jalview.structure.StructureSelectionManager;
37 import jalview.util.Comparison;
38 import jalview.util.MessageManager;
39 import jalview.util.Platform;
40 import jalview.viewmodel.ViewportListenerI;
41 import jalview.viewmodel.ViewportRanges;
43 import java.awt.BorderLayout;
44 import java.awt.Color;
45 import java.awt.Container;
46 import java.awt.Dimension;
48 import java.awt.FontMetrics;
49 import java.awt.Graphics;
50 import java.awt.Insets;
51 import java.awt.event.AdjustmentEvent;
52 import java.awt.event.AdjustmentListener;
53 import java.awt.event.ComponentAdapter;
54 import java.awt.event.ComponentEvent;
55 import java.awt.print.PageFormat;
56 import java.awt.print.Printable;
57 import java.awt.print.PrinterException;
58 import java.beans.PropertyChangeEvent;
59 import java.beans.PropertyChangeListener;
61 import java.io.FileWriter;
62 import java.io.PrintWriter;
63 import java.util.List;
65 import javax.swing.SwingUtilities;
71 * @version $Revision: 1.161 $
73 public class AlignmentPanel extends GAlignmentPanel implements
74 AdjustmentListener, Printable, AlignmentViewPanel,
77 public AlignViewport av;
79 ViewportRanges vpRanges;
81 OverviewPanel overviewPanel;
83 private SeqPanel seqPanel;
85 private IdPanel idPanel;
87 private boolean headless;
89 IdwidthAdjuster idwidthAdjuster;
92 public AlignFrame alignFrame;
94 private ScalePanel scalePanel;
96 private AnnotationPanel annotationPanel;
98 private AnnotationLabels alabels;
100 // this value is set false when selection area being dragged
101 boolean fastPaint = true;
103 private int hextent = 0;
105 private int vextent = 0;
108 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
109 * false, suppresses invoking the same method recursively.
111 private boolean scrollComplementaryPanel = true;
113 private PropertyChangeListener propertyChangeListener;
115 private CalculationChooser calculationDialog;
118 * Creates a new AlignmentPanel object.
123 public AlignmentPanel(AlignFrame af, final AlignViewport av)
127 vpRanges = av.getRanges();
128 setSeqPanel(new SeqPanel(av, this));
129 setIdPanel(new IdPanel(av, this));
131 setScalePanel(new ScalePanel(av, this));
133 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
134 idwidthAdjuster = new IdwidthAdjuster(this);
135 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
137 setAnnotationPanel(new AnnotationPanel(this));
138 setAlabels(new AnnotationLabels(this));
140 annotationScroller.setViewportView(getAnnotationPanel());
141 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
143 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
144 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
146 setScrollValues(0, 0);
148 hscroll.addAdjustmentListener(this);
149 vscroll.addAdjustmentListener(this);
151 addComponentListener(new ComponentAdapter()
154 public void componentResized(ComponentEvent evt)
156 // reset the viewport ranges when the alignment panel is resized
157 // in particular, this initialises the end residue value when Jalview
159 if (av.getWrapAlignment())
161 int widthInRes = getSeqPanel().seqCanvas
162 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
163 vpRanges.setViewportWidth(widthInRes);
167 int widthInRes = getSeqPanel().seqCanvas.getWidth()
169 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
170 / av.getCharHeight();
172 vpRanges.setViewportWidth(widthInRes);
173 vpRanges.setViewportHeight(heightInSeq);
179 final AlignmentPanel ap = this;
180 propertyChangeListener = new PropertyChangeListener()
183 public void propertyChange(PropertyChangeEvent evt)
185 if (evt.getPropertyName().equals("alignment"))
187 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
192 av.addPropertyChangeListener(propertyChangeListener);
194 av.getRanges().addPropertyChangeListener(this);
196 adjustAnnotationHeight();
201 public AlignViewportI getAlignViewport()
206 public void alignmentChanged()
208 av.alignmentChanged(this);
210 if (getCalculationDialog() != null)
212 getCalculationDialog().validateCalcTypes();
215 alignFrame.updateEditMenuBar();
217 paintAlignment(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(new Dimension(10, av.getCharHeight()
232 idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
233 .getCharHeight() + fm.getDescent()));
235 getIdPanel().getIdCanvas().gg = null;
236 getSeqPanel().seqCanvas.img = null;
237 getAnnotationPanel().adjustPanelHeight();
239 Dimension d = calculateIdWidth();
241 d.setSize(d.width + 4, d.height);
242 getIdPanel().getIdCanvas().setPreferredSize(d);
243 hscrollFillerPanel.setPreferredSize(d);
245 if (this.alignFrame.getSplitViewContainer() != null)
247 ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
254 * Calculate the width of the alignment labels based on the displayed names
255 * and any bounds on label width set in preferences.
257 * @return Dimension giving the maximum width of the alignment label panel
258 * that should be used.
260 public Dimension calculateIdWidth()
262 // calculate sensible default width when no preference is available
264 if (av.getIdWidth() < 0)
266 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
267 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
268 r = calculateIdWidth(maxwidth);
269 av.setIdWidth(r.width);
274 r.width = av.getIdWidth();
281 * Calculate the width of the alignment labels based on the displayed names
282 * and any bounds on label width set in preferences.
285 * -1 or maximum width allowed for IdWidth
286 * @return Dimension giving the maximum width of the alignment label panel
287 * that should be used.
289 public Dimension calculateIdWidth(int maxwidth)
291 Container c = new Container();
293 FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
294 Font.ITALIC, av.font.getSize()));
296 AlignmentI al = av.getAlignment();
301 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
303 SequenceI s = al.getSequenceAt(i);
305 id = s.getDisplayId(av.getShowJVSuffix());
307 if (fm.stringWidth(id) > idWidth)
309 idWidth = fm.stringWidth(id);
315 // Also check annotation label widths
318 if (al.getAlignmentAnnotation() != null)
320 fm = c.getFontMetrics(getAlabels().getFont());
322 while (i < al.getAlignmentAnnotation().length)
324 String label = al.getAlignmentAnnotation()[i].label;
326 if (fm.stringWidth(label) > idWidth)
328 idWidth = fm.stringWidth(label);
335 return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
340 * Highlight the given results on the alignment.
343 public void highlightSearchResults(SearchResultsI results)
345 scrollToPosition(results);
346 getSeqPanel().seqCanvas.highlightSearchResults(results);
350 * Scroll the view to show the position of the highlighted region in results
351 * (if any) and redraw the overview
355 public boolean scrollToPosition(SearchResultsI results)
357 return scrollToPosition(results, 0, true, false);
361 * Scroll the view to show the position of the highlighted region in results
364 * @param searchResults
365 * @param redrawOverview
368 public boolean scrollToPosition(SearchResultsI searchResults,
369 boolean redrawOverview)
371 return scrollToPosition(searchResults, 0, redrawOverview, false);
375 * Scroll the view to show the position of the highlighted region in results
379 * @param verticalOffset
380 * if greater than zero, allows scrolling to a position below the
381 * first displayed sequence
382 * @param redrawOverview
383 * - when set, the overview will be recalculated (takes longer)
385 * if true, try to centre the search results horizontally in the view
386 * @return false if results were not found
388 public boolean scrollToPosition(SearchResultsI results,
389 int verticalOffset, boolean redrawOverview, boolean centre)
391 int startv, endv, starts, ends;
392 // TODO: properly locate search results in view when large numbers of hidden
393 // columns exist before highlighted region
394 // do we need to scroll the panel?
395 // TODO: tons of nullpointerexceptions raised here.
396 if (results != null && results.getSize() > 0 && av != null
397 && av.getAlignment() != null)
399 int seqIndex = av.getAlignment().findIndex(results);
404 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
406 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
415 * To centre results, scroll to positions half the visible width
416 * left/right of the start/end positions
420 int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
421 start = Math.max(start - offset, 0);
422 end = end + offset - 1;
428 if (end == seq.getEnd())
432 if (av.hasHiddenColumns())
434 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
435 start = hidden.findColumnPosition(start);
436 end = hidden.findColumnPosition(end);
439 if (!hidden.isVisible(r[0]))
441 // don't scroll - position isn't visible
448 * allow for offset of target sequence (actually scroll to one above it)
450 seqIndex = Math.max(0, seqIndex - verticalOffset);
452 if (!av.getWrapAlignment())
454 if ((startv = vpRanges.getStartRes()) >= start)
457 * Scroll left to make start of search results visible
459 setScrollValues(start, seqIndex);
461 else if ((endv = vpRanges.getEndRes()) <= end)
464 * Scroll right to make end of search results visible
466 setScrollValues(startv + end - endv, seqIndex);
468 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
471 * Scroll up to make start of search results visible
473 setScrollValues(vpRanges.getStartRes(), seqIndex);
475 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
478 * Scroll down to make end of search results visible
480 setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
484 * Else results are already visible - no need to scroll
489 vpRanges.scrollToWrappedVisible(start);
493 paintAlignment(redrawOverview);
500 * @return DOCUMENT ME!
502 public OverviewPanel getOverviewPanel()
504 return overviewPanel;
513 public void setOverviewPanel(OverviewPanel op)
521 * Hide or show annotation panel
524 public void setAnnotationVisible(boolean b)
526 if (!av.getWrapAlignment())
528 annotationSpaceFillerHolder.setVisible(b);
529 annotationScroller.setVisible(b);
535 * automatically adjust annotation panel height for new annotation whilst
536 * ensuring the alignment is still visible.
539 public void adjustAnnotationHeight()
541 // TODO: display vertical annotation scrollbar if necessary
542 // this is called after loading new annotation onto alignment
543 if (alignFrame.getHeight() == 0)
545 System.out.println("NEEDS FIXING");
547 validateAnnotationDimensions(true);
549 paintAlignment(true);
553 * calculate the annotation dimensions and refresh slider values accordingly.
554 * need to do repaints/notifys afterwards.
556 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
558 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
560 if (adjustPanelHeight)
562 int rowHeight = av.getCharHeight();
563 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
566 * Estimate available height in the AlignFrame for alignment +
567 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
568 * hscroll, status bar (as these are not laid out we can't inspect their
569 * actual heights). Insets gives frame borders.
571 int stuff = Platform.isAMac() ? 80 : 100;
572 Insets insets = alignFrame.getInsets();
573 int availableHeight = alignFrame.getHeight() - stuff - insets.top
577 * If not enough vertical space, maximize annotation height while keeping
578 * at least two rows of alignment visible
580 if (annotationHeight + alignmentHeight > availableHeight)
582 annotationHeight = Math.min(annotationHeight, availableHeight - 2
588 // maintain same window layout whilst updating sliders
589 annotationHeight = annotationScroller.getSize().height;
593 annotationScroller.setPreferredSize(new Dimension(annotationScroller
594 .getWidth(), annotationHeight));
596 Dimension e = idPanel.getSize();
597 alabels.setSize(new Dimension(e.width, annotationHeight));
599 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
600 annotationSpaceFillerHolder.getWidth(), annotationHeight));
601 annotationScroller.validate();
602 annotationScroller.addNotify();
606 * update alignment layout for viewport settings
611 public void updateLayout()
614 setAnnotationVisible(av.isShowAnnotation());
615 boolean wrap = av.getWrapAlignment();
616 vpRanges.setStartSeq(0);
617 scalePanelHolder.setVisible(!wrap);
618 hscroll.setVisible(!wrap);
619 idwidthAdjuster.setVisible(!wrap);
623 annotationScroller.setVisible(false);
624 annotationSpaceFillerHolder.setVisible(false);
626 else if (av.isShowAnnotation())
628 annotationScroller.setVisible(true);
629 annotationSpaceFillerHolder.setVisible(true);
634 int widthInRes = getSeqPanel().seqCanvas
635 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
636 vpRanges.setViewportWidth(widthInRes);
640 int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
641 .getCharWidth()) - 1;
642 int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
643 .getCharHeight()) - 1;
645 vpRanges.setViewportWidth(widthInRes);
646 vpRanges.setViewportHeight(heightInSeq);
649 idSpaceFillerPanel1.setVisible(!wrap);
656 * Adjust row/column scrollers to show a visible position in the alignment.
659 * visible column to scroll to
661 * visible row to scroll to
664 public void setScrollValues(int xpos, int ypos)
669 if (av == null || av.getAlignment() == null)
674 if (av.getWrapAlignment())
676 setScrollingForWrappedPanel(x);
680 int width = av.getAlignment().getWidth();
681 int height = av.getAlignment().getHeight();
683 if (av.hasHiddenColumns())
685 // reset the width to exclude hidden columns
686 width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
689 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
690 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
697 if (vextent > height)
702 if ((hextent + x) > width)
707 if ((vextent + y) > height)
709 y = height - vextent;
722 // update the scroll values
723 hscroll.setValues(x, hextent, 0, width);
724 vscroll.setValues(y, vextent, 0, height);
729 * Respond to adjustment event when horizontal or vertical scrollbar is
733 * adjustment event encoding whether hscroll or vscroll changed
736 public void adjustmentValueChanged(AdjustmentEvent evt)
738 int oldX = vpRanges.getStartRes();
739 int oldwidth = vpRanges.getViewportWidth();
740 int oldY = vpRanges.getStartSeq();
741 int oldheight = vpRanges.getViewportHeight();
743 if (av.getWrapAlignment())
745 if (evt.getSource() == hscroll)
747 return; // no horizontal scroll when wrapped
749 else if (evt.getSource() == vscroll)
751 int offy = vscroll.getValue();
752 int rowSize = getSeqPanel().seqCanvas
753 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
755 // if we're scrolling to the position we're already at, stop
756 // this prevents infinite recursion of events when the scroll/viewport
757 // ranges values are the same
758 if ((offy * rowSize == oldX) && (oldwidth == rowSize))
764 vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
769 // This is only called if file loaded is a jar file that
770 // was wrapped when saved and user has wrap alignment true
771 // as preference setting
772 SwingUtilities.invokeLater(new Runnable()
777 // When updating scrolling to use ViewportChange events, this code
778 // could not be validated and it is not clear if it is now being
779 // called. Log warning here in case it is called and unforeseen
782 .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
784 // scroll to start of panel
785 vpRanges.setStartRes(0);
786 vpRanges.setStartSeq(0);
795 if (evt.getSource() == hscroll)
797 int x = hscroll.getValue();
798 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
800 // if we're scrolling to the position we're already at, stop
801 // this prevents infinite recursion of events when the scroll/viewport
802 // ranges values are the same
803 if ((x == oldX) && (width == oldwidth))
807 vpRanges.setViewportStartAndWidth(x, width);
809 else if (evt.getSource() == vscroll)
811 int y = vscroll.getValue();
812 int height = getSeqPanel().seqCanvas.getHeight()
813 / av.getCharHeight();
815 // if we're scrolling to the position we're already at, stop
816 // this prevents infinite recursion of events when the scroll/viewport
817 // ranges values are the same
818 if ((y == oldY) && (height == oldheight))
822 vpRanges.setViewportStartAndHeight(y, height);
832 * Repaint the alignment including the annotations and overview panels (if
836 public void paintAlignment(boolean updateOverview)
838 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
839 av.isShowAutocalculatedAbove());
840 sorter.sort(getAlignment().getAlignmentAnnotation(),
841 av.getSortAnnotationsBy());
846 // TODO: determine if this paintAlignment changed structure colours
847 av.getStructureSelectionManager().sequenceColoursChanged(this);
849 if (overviewPanel != null)
851 overviewPanel.updateOverviewImage();
863 public void paintComponent(Graphics g)
867 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
868 idPanelHolder.setPreferredSize(d);
869 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
873 * set scroll bar positions
875 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
879 * Set vertical scroll bar parameters for wrapped panel
881 * the residue to scroll to
883 private void setScrollingForWrappedPanel(int res)
885 // get the width of the alignment in residues
886 int maxwidth = av.getAlignment().getWidth();
887 if (av.hasHiddenColumns())
889 maxwidth = av.getAlignment().getHiddenColumns()
890 .findColumnPosition(maxwidth) - 1;
893 // get the width of the canvas in residues
894 int canvasWidth = getSeqPanel().seqCanvas
895 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
898 // position we want to scroll to is number of canvasWidth's to get there
899 int current = res / canvasWidth;
901 // max scroll position: add one because extent is 1 and scrollbar value
902 // can only be set to at most max - extent
903 int max = maxwidth / canvasWidth + 1;
904 vscroll.setUnitIncrement(1);
905 vscroll.setValues(current, 1, 0, max);
919 * @return DOCUMENT ME!
921 * @throws PrinterException
925 public int print(Graphics pg, PageFormat pf, int pi)
926 throws PrinterException
928 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
930 int pwidth = (int) pf.getImageableWidth();
931 int pheight = (int) pf.getImageableHeight();
933 if (av.getWrapAlignment())
935 return printWrappedAlignment(pwidth, pheight, pi, pg);
939 return printUnwrapped(pwidth, pheight, pi, pg, pg);
955 * @return DOCUMENT ME!
957 * @throws PrinterException
961 * Draws the alignment image, including sequence ids, sequences, and
962 * annotation labels and annotations if shown, on either one or two Graphics
969 * the graphics context for sequence ids and annotation labels
970 * @param alignmentGraphics
971 * the graphics context for sequences and annotations (may or may not
972 * be the same context as idGraphics)
974 * @throws PrinterException
976 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
977 Graphics idGraphics, Graphics alignmentGraphics)
978 throws PrinterException
980 final int idWidth = getVisibleIdWidth(false);
983 * Get the horizontal offset to where we draw the sequences.
984 * This is idWidth if using a single Graphics context, else zero.
986 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
988 FontMetrics fm = getFontMetrics(av.getFont());
989 int charHeight = av.getCharHeight();
990 int scaleHeight = charHeight + fm.getDescent();
992 idGraphics.setColor(Color.white);
993 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
994 idGraphics.setFont(av.getFont());
997 * How many sequences and residues can we fit on a printable page?
999 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1001 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1003 int alignmentWidth = av.getAlignment().getWidth();
1004 int pagesWide = (alignmentWidth / totalRes) + 1;
1006 final int startRes = (pi % pagesWide) * totalRes;
1007 int endRes = (startRes + totalRes) - 1;
1009 if (endRes > (alignmentWidth - 1))
1011 endRes = alignmentWidth - 1;
1014 final int startSeq = (pi / pagesWide) * totalSeq;
1015 int endSeq = startSeq + totalSeq;
1017 int alignmentHeight = av.getAlignment().getHeight();
1018 if (endSeq > alignmentHeight)
1020 endSeq = alignmentHeight;
1023 int pagesHigh = ((alignmentHeight / totalSeq) + 1)
1026 if (av.isShowAnnotation())
1028 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1031 pagesHigh /= pageHeight;
1033 if (pi >= (pagesWide * pagesHigh))
1035 return Printable.NO_SUCH_PAGE;
1037 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
1041 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1043 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1044 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1045 pageWidth - idWidth, scaleHeight);
1046 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1049 * Draw the sequence ids, offset for scale height,
1050 * then reset to top left (0, 0)
1052 idGraphics.translate(0, scaleHeight);
1053 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1054 Color currentColor = null;
1055 Color currentTextColor = null;
1058 for (int i = startSeq; i < endSeq; i++)
1060 seq = av.getAlignment().getSequenceAt(i);
1061 if ((av.getSelectionGroup() != null)
1062 && av.getSelectionGroup().getSequences(null).contains(seq))
1065 * gray out ids of sequences in selection group (if any)
1067 currentColor = Color.gray;
1068 currentTextColor = Color.black;
1072 currentColor = av.getSequenceColour(seq);
1073 currentTextColor = Color.black;
1076 idGraphics.setColor(currentColor);
1077 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1080 idGraphics.setColor(currentTextColor);
1083 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1084 if (av.isRightAlignIds())
1086 fm = idGraphics.getFontMetrics();
1088 - fm.stringWidth(displayId)
1092 idGraphics.drawString(displayId, xPos,
1093 (((i - startSeq) * charHeight) + charHeight)
1094 - (charHeight / 5));
1096 idGraphics.setFont(av.getFont());
1097 idGraphics.translate(0, -scaleHeight);
1100 * draw the sequences, offset for scale height, and id width (if using a
1101 * single graphics context), then reset to (0, scale height)
1103 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1104 getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
1105 startSeq, endSeq, 0);
1106 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1108 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1111 * draw annotation labels; drawComponent() translates by
1112 * getScrollOffset(), so compensate for that first;
1113 * then reset to (0, scale height)
1115 int offset = getAlabels().getScrollOffset();
1116 idGraphics.translate(0, -offset);
1117 idGraphics.translate(0, alignmentDrawnHeight);
1118 getAlabels().drawComponent(idGraphics, idWidth);
1119 idGraphics.translate(0, -alignmentDrawnHeight);
1122 * draw the annotations starting at
1123 * (idOffset, alignmentHeight) from (0, scaleHeight)
1125 alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
1126 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1127 alignmentGraphics, -1, startRes, endRes + 1);
1130 return Printable.PAGE_EXISTS;
1145 * @return DOCUMENT ME!
1147 * @throws PrinterException
1150 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1151 Graphics pg) throws PrinterException
1153 int annotationHeight = 0;
1154 AnnotationLabels labels = null;
1155 if (av.isShowAnnotation())
1157 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1158 labels = new AnnotationLabels(av);
1161 int hgap = av.getCharHeight();
1162 if (av.getScaleAboveWrapped())
1164 hgap += av.getCharHeight();
1167 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1170 int idWidth = getVisibleIdWidth(false);
1172 int maxwidth = av.getAlignment().getWidth();
1173 if (av.hasHiddenColumns())
1175 maxwidth = av.getAlignment().getHiddenColumns()
1176 .findColumnPosition(maxwidth) - 1;
1179 int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
1182 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1184 pg.setColor(Color.white);
1185 pg.fillRect(0, 0, pwidth, pheight);
1186 pg.setFont(av.getFont());
1190 pg.setColor(Color.black);
1192 pg.translate(0, -pi * pheight);
1194 pg.setClip(0, pi * pheight, pwidth, pheight);
1200 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1202 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1203 SequenceI s = av.getAlignment().getSequenceAt(i);
1204 String string = s.getDisplayId(av.getShowJVSuffix());
1206 if (av.isRightAlignIds())
1208 FontMetrics fm = pg.getFontMetrics();
1209 xPos = idWidth - fm.stringWidth(string) - 4;
1211 pg.drawString(string, xPos,
1212 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1213 - (av.getCharHeight() / 5));
1218 ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
1220 pg.setFont(av.getFont());
1221 labels.drawComponent(pg, idWidth);
1225 - (av.getAlignment().getHeight() * av
1230 } while (ypos < totalHeight);
1232 pg.translate(idWidth, 0);
1234 getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
1237 if ((pi * pheight) < totalHeight)
1239 return Printable.PAGE_EXISTS;
1244 return Printable.NO_SUCH_PAGE;
1249 * get current sequence ID panel width, or nominal value if panel were to be
1250 * displayed using default settings
1254 public int getVisibleIdWidth()
1256 return getVisibleIdWidth(true);
1260 * get current sequence ID panel width, or nominal value if panel were to be
1261 * displayed using default settings
1264 * indicate if the Id width for onscreen or offscreen display should
1268 public int getVisibleIdWidth(boolean onscreen)
1270 // see if rendering offscreen - check preferences and calc width accordingly
1271 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1273 return calculateIdWidth(-1).width + 4;
1275 Integer idwidth = null;
1277 || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1279 int w = getIdPanel().getWidth();
1280 return (w > 0 ? w : calculateIdWidth().width + 4);
1282 return idwidth.intValue() + 4;
1285 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1287 int boarderBottomOffset = 5;
1288 long pSessionId = System.currentTimeMillis();
1289 headless = (System.getProperty("java.awt.headless") != null && System
1290 .getProperty("java.awt.headless").equals("true"));
1291 if (alignFrame != null && !headless)
1295 alignFrame.setProgressBar(MessageManager.formatMessage(
1296 "status.saving_file", new Object[] { type.getLabel() }),
1302 AlignmentDimension aDimension = getAlignmentDimension();
1305 jalview.util.ImageMaker im;
1306 final String imageAction, imageTitle;
1307 if (type == jalview.util.ImageMaker.TYPE.PNG)
1309 imageAction = "Create PNG image from alignment";
1312 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1314 imageAction = "Create EPS file from alignment";
1315 imageTitle = alignFrame.getTitle();
1319 imageAction = "Create SVG file from alignment";
1320 imageTitle = alignFrame.getTitle();
1323 im = new jalview.util.ImageMaker(this, type, imageAction,
1324 aDimension.getWidth(), aDimension.getHeight()
1325 + boarderBottomOffset, file, imageTitle,
1326 alignFrame, pSessionId, headless);
1327 Graphics graphics = im.getGraphics();
1328 if (av.getWrapAlignment())
1330 if (graphics != null)
1332 printWrappedAlignment(aDimension.getWidth(),
1333 aDimension.getHeight() + boarderBottomOffset, 0,
1340 if (graphics != null)
1342 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
1343 0, graphics, graphics);
1348 } catch (OutOfMemoryError err)
1351 System.out.println("########################\n" + "OUT OF MEMORY "
1352 + file + "\n" + "########################");
1353 new OOMWarning("Creating Image for " + file, err);
1354 // System.out.println("Create IMAGE: " + err);
1355 } catch (Exception ex)
1357 ex.printStackTrace();
1365 public AlignmentDimension getAlignmentDimension()
1367 int maxwidth = av.getAlignment().getWidth();
1368 if (av.hasHiddenColumns())
1370 maxwidth = av.getAlignment().getHiddenColumns()
1371 .findColumnPosition(maxwidth);
1374 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1375 + getScalePanel().getHeight();
1376 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1378 if (av.getWrapAlignment())
1380 height = getWrappedHeight();
1383 // need to obtain default alignment width and then add in any
1384 // additional allowance for id margin
1385 // this duplicates the calculation in getWrappedHeight but adjusts for
1387 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1388 - alignFrame.getInsets().left
1389 - alignFrame.getInsets().right - getVisibleIdWidth()
1390 + getVisibleIdWidth(false);
1394 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1398 else if (av.isShowAnnotation())
1400 height += getAnnotationPanel().adjustPanelHeight() + 3;
1402 return new AlignmentDimension(width, height);
1409 public void makeEPS(File epsFile)
1411 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1417 public void makePNG(File pngFile)
1419 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1422 public void makeSVG(File svgFile)
1424 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1427 public void makePNGImageMap(File imgMapFile, String imageName)
1429 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1430 // ////////////////////////////////////////////
1431 int idWidth = getVisibleIdWidth(false);
1432 FontMetrics fm = getFontMetrics(av.getFont());
1433 int scaleHeight = av.getCharHeight() + fm.getDescent();
1436 // ////////////////////////////////
1437 if (imgMapFile != null)
1441 int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
1442 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
1443 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1444 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1445 out.println("<img src=\"" + imageName
1446 + "\" border=\"0\" usemap=\"#Map\" >"
1447 + "<map name=\"Map\">");
1449 for (s = 0; s < sSize; s++)
1451 sy = s * av.getCharHeight() + scaleHeight;
1453 SequenceI seq = av.getAlignment().getSequenceAt(s);
1454 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1455 for (res = 0; res < alwidth; res++)
1457 StringBuilder text = new StringBuilder(512);
1458 String triplet = null;
1459 if (av.getAlignment().isNucleotide())
1461 triplet = ResidueProperties.nucleotideName.get(seq
1462 .getCharAt(res) + "");
1466 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
1470 if (triplet == null)
1475 int seqPos = seq.findPosition(res);
1476 gSize = groups.length;
1477 for (g = 0; g < gSize; g++)
1479 if (text.length() < 1)
1481 text.append("<area shape=\"rect\" coords=\"")
1482 .append((idWidth + res * av.getCharWidth()))
1483 .append(",").append(sy).append(",")
1484 .append((idWidth + (res + 1) * av.getCharWidth()))
1485 .append(",").append((av.getCharHeight() + sy))
1486 .append("\"").append(" onMouseOver=\"toolTip('")
1487 .append(seqPos).append(" ").append(triplet);
1490 if (groups[g].getStartRes() < res
1491 && groups[g].getEndRes() > res)
1493 text.append("<br><em>").append(groups[g].getName())
1498 if (text.length() < 1)
1500 text.append("<area shape=\"rect\" coords=\"")
1501 .append((idWidth + res * av.getCharWidth()))
1502 .append(",").append(sy).append(",")
1503 .append((idWidth + (res + 1) * av.getCharWidth()))
1504 .append(",").append((av.getCharHeight() + sy))
1505 .append("\"").append(" onMouseOver=\"toolTip('")
1506 .append(seqPos).append(" ").append(triplet);
1508 if (!Comparison.isGap(seq.getCharAt(res)))
1510 List<SequenceFeature> features = seq.getFeatures()
1511 .findFeatures(seqPos, seqPos);
1512 for (SequenceFeature sf : features)
1514 if (sf.isContactFeature())
1516 text.append("<br>").append(sf.getType()).append(" ")
1517 .append(sf.getBegin()).append(":")
1518 .append(sf.getEnd());
1522 text.append("<br>");
1523 text.append(sf.getType());
1524 String description = sf.getDescription();
1525 if (description != null
1526 && !sf.getType().equals(description))
1528 description = description.replace("\"", """);
1529 text.append(" ").append(description);
1532 String status = sf.getStatus();
1533 if (status != null && !"".equals(status))
1535 text.append(" (").append(status).append(")");
1538 if (text.length() > 1)
1540 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1541 out.println(text.toString());
1546 out.println("</map></body></html>");
1549 } catch (Exception ex)
1551 ex.printStackTrace();
1553 } // /////////END OF IMAGE MAP
1557 int getWrappedHeight()
1559 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1561 if (System.getProperty("java.awt.headless") != null
1562 && System.getProperty("java.awt.headless").equals("true"))
1564 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1565 - vscroll.getPreferredSize().width
1566 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1569 int chunkWidth = getSeqPanel().seqCanvas
1570 .getWrappedCanvasWidth(seqPanelWidth);
1572 int hgap = av.getCharHeight();
1573 if (av.getScaleAboveWrapped())
1575 hgap += av.getCharHeight();
1578 int annotationHeight = 0;
1579 if (av.isShowAnnotation())
1581 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1584 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1587 int maxwidth = av.getAlignment().getWidth();
1588 if (av.hasHiddenColumns())
1590 maxwidth = av.getAlignment().getHiddenColumns()
1591 .findColumnPosition(maxwidth) - 1;
1594 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1600 * close the panel - deregisters all listeners and nulls any references to
1603 public void closePanel()
1605 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1606 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1607 PaintRefresher.RemoveComponent(this);
1612 * try to ensure references are nulled
1614 if (annotationPanel != null)
1616 annotationPanel.dispose();
1621 av.removePropertyChangeListener(propertyChangeListener);
1622 jalview.structure.StructureSelectionManager ssm = av
1623 .getStructureSelectionManager();
1624 ssm.removeStructureViewerListener(getSeqPanel(), null);
1625 ssm.removeSelectionListener(getSeqPanel());
1626 ssm.removeCommandListener(av);
1627 ssm.removeStructureViewerListener(getSeqPanel(), null);
1628 ssm.removeSelectionListener(getSeqPanel());
1634 if (Cache.log.isDebugEnabled())
1636 Cache.log.warn("Closing alignment panel which is already closed.");
1642 * Close any open dialogs that would be orphaned when this one is closed
1644 protected void closeChildFrames()
1646 if (calculationDialog != null)
1648 calculationDialog.closeFrame();
1653 * hides or shows dynamic annotation rows based on groups and av state flags
1655 public void updateAnnotation()
1657 updateAnnotation(false, false);
1660 public void updateAnnotation(boolean applyGlobalSettings)
1662 updateAnnotation(applyGlobalSettings, false);
1665 public void updateAnnotation(boolean applyGlobalSettings,
1666 boolean preserveNewGroupSettings)
1668 av.updateGroupAnnotationSettings(applyGlobalSettings,
1669 preserveNewGroupSettings);
1670 adjustAnnotationHeight();
1674 public AlignmentI getAlignment()
1676 return av == null ? null : av.getAlignment();
1680 public String getViewName()
1686 * Make/Unmake this alignment panel the current input focus
1690 public void setSelected(boolean b)
1694 if (alignFrame.getSplitViewContainer() != null)
1697 * bring enclosing SplitFrame to front first if there is one
1699 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1701 alignFrame.setSelected(b);
1702 } catch (Exception ex)
1708 alignFrame.setDisplayedView(this);
1713 public StructureSelectionManager getStructureSelectionManager()
1715 return av.getStructureSelectionManager();
1719 public void raiseOOMWarning(String string, OutOfMemoryError error)
1721 new OOMWarning(string, error, this);
1725 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1728 return new FeatureRenderer(this);
1732 public jalview.api.FeatureRenderer getFeatureRenderer()
1734 return seqPanel.seqCanvas.getFeatureRenderer();
1737 public void updateFeatureRenderer(
1738 jalview.renderer.seqfeatures.FeatureRenderer fr)
1740 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1743 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1745 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1747 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1751 public ScalePanel getScalePanel()
1756 public void setScalePanel(ScalePanel scalePanel)
1758 this.scalePanel = scalePanel;
1761 public SeqPanel getSeqPanel()
1766 public void setSeqPanel(SeqPanel seqPanel)
1768 this.seqPanel = seqPanel;
1771 public AnnotationPanel getAnnotationPanel()
1773 return annotationPanel;
1776 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1778 this.annotationPanel = annotationPanel;
1781 public AnnotationLabels getAlabels()
1786 public void setAlabels(AnnotationLabels alabels)
1788 this.alabels = alabels;
1791 public IdPanel getIdPanel()
1796 public void setIdPanel(IdPanel idPanel)
1798 this.idPanel = idPanel;
1802 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1803 * The aim is to keep the two alignments 'lined up' on their centre columns.
1806 * holds mapped region(s) of this alignment that we are scrolling
1807 * 'to'; may be modified for sequence offset by this method
1808 * @param verticalOffset
1809 * the number of visible sequences to show above the mapped region
1811 public void scrollToCentre(SearchResultsI sr, int verticalOffset)
1814 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1815 * mapped), we can make the scroll-to location a sequence above the one
1818 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1819 List<SequenceI> seqs = av.getAlignment().getSequences();
1822 * This is like AlignmentI.findIndex(seq) but here we are matching the
1823 * dataset sequence not the aligned sequence
1825 boolean matched = false;
1826 for (SequenceI seq : seqs)
1828 if (mappedTo == seq.getDatasetSequence())
1836 return; // failsafe, shouldn't happen
1840 * Scroll to position but centring the target residue.
1842 scrollToPosition(sr, verticalOffset, true, true);
1846 * Set a flag to say do not scroll any (cDNA/protein) complement.
1850 protected void setToScrollComplementPanel(boolean b)
1852 this.scrollComplementaryPanel = b;
1856 * Get whether to scroll complement panel
1858 * @return true if cDNA/protein complement panels should be scrolled
1860 protected boolean isSetToScrollComplementPanel()
1862 return this.scrollComplementaryPanel;
1868 * @adjustHeight if true, try to recalculate panel height for visible
1871 protected void refresh(boolean adjustHeight)
1873 validateAnnotationDimensions(adjustHeight);
1877 // sort, repaint, update overview
1878 paintAlignment(true);
1882 // lightweight repaint
1889 * Property change event fired when a change is made to the viewport ranges
1890 * object associated with this alignment panel's viewport
1892 public void propertyChange(PropertyChangeEvent evt)
1894 // update this panel's scroll values based on the new viewport ranges values
1895 int x = vpRanges.getStartRes();
1896 int y = vpRanges.getStartSeq();
1897 setScrollValues(x, y);
1899 // now update any complementary alignment (its viewport ranges object
1900 // is different so does not get automatically updated)
1901 if (isSetToScrollComplementPanel())
1903 setToScrollComplementPanel(false);
1904 av.scrollComplementaryAlignment();
1905 setToScrollComplementPanel(true);
1910 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1911 * reference should be nulled when the dialog is closed.
1913 * @param calculationChooser
1915 public void setCalculationDialog(CalculationChooser calculationChooser)
1917 calculationDialog = calculationChooser;
1921 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1924 public CalculationChooser getCalculationDialog()
1926 return calculationDialog;