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.MessageManager;
38 import jalview.util.Platform;
39 import jalview.viewmodel.ViewportListenerI;
40 import jalview.viewmodel.ViewportRanges;
42 import java.awt.BorderLayout;
43 import java.awt.Color;
44 import java.awt.Container;
45 import java.awt.Dimension;
47 import java.awt.FontMetrics;
48 import java.awt.Graphics;
49 import java.awt.Insets;
50 import java.awt.event.AdjustmentEvent;
51 import java.awt.event.AdjustmentListener;
52 import java.awt.event.ComponentAdapter;
53 import java.awt.event.ComponentEvent;
54 import java.awt.print.PageFormat;
55 import java.awt.print.Printable;
56 import java.awt.print.PrinterException;
57 import java.beans.PropertyChangeEvent;
58 import java.beans.PropertyChangeListener;
60 import java.io.FileWriter;
61 import java.io.PrintWriter;
62 import java.util.List;
64 import javax.swing.SwingUtilities;
70 * @version $Revision: 1.161 $
72 public class AlignmentPanel extends GAlignmentPanel implements
73 AdjustmentListener, Printable, AlignmentViewPanel,
76 public AlignViewport av;
78 ViewportRanges vpRanges;
80 OverviewPanel overviewPanel;
82 private SeqPanel seqPanel;
84 private IdPanel idPanel;
86 private boolean headless;
88 IdwidthAdjuster idwidthAdjuster;
91 public AlignFrame alignFrame;
93 private ScalePanel scalePanel;
95 private AnnotationPanel annotationPanel;
97 private AnnotationLabels alabels;
99 // this value is set false when selection area being dragged
100 boolean fastPaint = true;
102 private int hextent = 0;
104 private int vextent = 0;
107 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
108 * false, suppresses invoking the same method recursively.
110 private boolean scrollComplementaryPanel = true;
112 private PropertyChangeListener propertyChangeListener;
114 private CalculationChooser calculationDialog;
117 * Creates a new AlignmentPanel object.
122 public AlignmentPanel(AlignFrame af, final AlignViewport av)
126 vpRanges = av.getRanges();
127 setSeqPanel(new SeqPanel(av, this));
128 setIdPanel(new IdPanel(av, this));
130 setScalePanel(new ScalePanel(av, this));
132 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
133 idwidthAdjuster = new IdwidthAdjuster(this);
134 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
136 setAnnotationPanel(new AnnotationPanel(this));
137 setAlabels(new AnnotationLabels(this));
139 annotationScroller.setViewportView(getAnnotationPanel());
140 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
142 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
143 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
145 setScrollValues(0, 0);
147 hscroll.addAdjustmentListener(this);
148 vscroll.addAdjustmentListener(this);
150 addComponentListener(new ComponentAdapter()
153 public void componentResized(ComponentEvent evt)
155 // reset the viewport ranges when the alignment panel is resized
156 // in particular, this initialises the end residue value when Jalview
158 if (av.getWrapAlignment())
160 int widthInRes = getSeqPanel().seqCanvas
161 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
162 vpRanges.setViewportWidth(widthInRes);
166 int widthInRes = getSeqPanel().seqCanvas.getWidth()
168 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
169 / av.getCharHeight();
171 vpRanges.setViewportWidth(widthInRes);
172 vpRanges.setViewportHeight(heightInSeq);
178 final AlignmentPanel ap = this;
179 propertyChangeListener = new PropertyChangeListener()
182 public void propertyChange(PropertyChangeEvent evt)
184 if (evt.getPropertyName().equals("alignment"))
186 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
191 av.addPropertyChangeListener(propertyChangeListener);
193 av.getRanges().addPropertyChangeListener(this);
195 adjustAnnotationHeight();
200 public AlignViewportI getAlignViewport()
205 public void alignmentChanged()
207 av.alignmentChanged(this);
209 if (getCalculationDialog() != null)
211 getCalculationDialog().validateCalcTypes();
214 alignFrame.updateEditMenuBar();
216 paintAlignment(true);
223 public void fontChanged()
225 // set idCanvas bufferedImage to null
226 // to prevent drawing old image
227 FontMetrics fm = getFontMetrics(av.getFont());
229 scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
231 idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
232 .getCharHeight() + fm.getDescent()));
234 getIdPanel().getIdCanvas().gg = null;
235 getSeqPanel().seqCanvas.img = null;
236 getAnnotationPanel().adjustPanelHeight();
238 Dimension d = calculateIdWidth();
240 d.setSize(d.width + 4, d.height);
241 getIdPanel().getIdCanvas().setPreferredSize(d);
242 hscrollFillerPanel.setPreferredSize(d);
244 if (this.alignFrame.getSplitViewContainer() != null)
246 ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
253 * Calculate the width of the alignment labels based on the displayed names
254 * and any bounds on label width set in preferences.
256 * @return Dimension giving the maximum width of the alignment label panel
257 * that should be used.
259 public Dimension calculateIdWidth()
261 // calculate sensible default width when no preference is available
263 if (av.getIdWidth() < 0)
265 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
266 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
267 r = calculateIdWidth(maxwidth);
268 av.setIdWidth(r.width);
273 r.width = av.getIdWidth();
280 * Calculate the width of the alignment labels based on the displayed names
281 * and any bounds on label width set in preferences.
284 * -1 or maximum width allowed for IdWidth
285 * @return Dimension giving the maximum width of the alignment label panel
286 * that should be used.
288 public Dimension calculateIdWidth(int maxwidth)
290 Container c = new Container();
292 FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
293 Font.ITALIC, av.font.getSize()));
295 AlignmentI al = av.getAlignment();
300 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
302 SequenceI s = al.getSequenceAt(i);
304 id = s.getDisplayId(av.getShowJVSuffix());
306 if (fm.stringWidth(id) > idWidth)
308 idWidth = fm.stringWidth(id);
314 // Also check annotation label widths
317 if (al.getAlignmentAnnotation() != null)
319 fm = c.getFontMetrics(getAlabels().getFont());
321 while (i < al.getAlignmentAnnotation().length)
323 String label = al.getAlignmentAnnotation()[i].label;
325 if (fm.stringWidth(label) > idWidth)
327 idWidth = fm.stringWidth(label);
334 return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
339 * Highlight the given results on the alignment.
342 public void highlightSearchResults(SearchResultsI results)
344 scrollToPosition(results);
345 getSeqPanel().seqCanvas.highlightSearchResults(results);
349 * Scroll the view to show the position of the highlighted region in results
350 * (if any) and redraw the overview
354 public boolean scrollToPosition(SearchResultsI results)
356 return scrollToPosition(results, 0, true, false);
360 * Scroll the view to show the position of the highlighted region in results
363 * @param searchResults
364 * @param redrawOverview
367 public boolean scrollToPosition(SearchResultsI searchResults,
368 boolean redrawOverview)
370 return scrollToPosition(searchResults, 0, redrawOverview, false);
374 * Scroll the view to show the position of the highlighted region in results
378 * @param verticalOffset
379 * if greater than zero, allows scrolling to a position below the
380 * first displayed sequence
381 * @param redrawOverview
382 * - when set, the overview will be recalculated (takes longer)
384 * if true, try to centre the search results horizontally in the view
385 * @return false if results were not found
387 public boolean scrollToPosition(SearchResultsI results,
388 int verticalOffset, boolean redrawOverview, boolean centre)
390 int startv, endv, starts, ends;
391 // TODO: properly locate search results in view when large numbers of hidden
392 // columns exist before highlighted region
393 // do we need to scroll the panel?
394 // TODO: tons of nullpointerexceptions raised here.
395 if (results != null && results.getSize() > 0 && av != null
396 && av.getAlignment() != null)
398 int seqIndex = av.getAlignment().findIndex(results);
403 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
405 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
414 * To centre results, scroll to positions half the visible width
415 * left/right of the start/end positions
419 int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
420 start = Math.max(start - offset, 0);
421 end = end + offset - 1;
427 if (end == seq.getEnd())
431 if (av.hasHiddenColumns())
433 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
434 start = hidden.findColumnPosition(start);
435 end = hidden.findColumnPosition(end);
438 if (!hidden.isVisible(r[0]))
440 // don't scroll - position isn't visible
447 * allow for offset of target sequence (actually scroll to one above it)
449 seqIndex = Math.max(0, seqIndex - verticalOffset);
451 if (!av.getWrapAlignment())
453 if ((startv = vpRanges.getStartRes()) >= start)
456 * Scroll left to make start of search results visible
458 setScrollValues(start, seqIndex);
460 else if ((endv = vpRanges.getEndRes()) <= end)
463 * Scroll right to make end of search results visible
465 setScrollValues(startv + end - endv, seqIndex);
467 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
470 * Scroll up to make start of search results visible
472 setScrollValues(vpRanges.getStartRes(), seqIndex);
474 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
477 * Scroll down to make end of search results visible
479 setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
483 * Else results are already visible - no need to scroll
488 vpRanges.scrollToWrappedVisible(start);
492 paintAlignment(redrawOverview);
499 * @return DOCUMENT ME!
501 public OverviewPanel getOverviewPanel()
503 return overviewPanel;
512 public void setOverviewPanel(OverviewPanel op)
520 * Hide or show annotation panel
523 public void setAnnotationVisible(boolean b)
525 if (!av.getWrapAlignment())
527 annotationSpaceFillerHolder.setVisible(b);
528 annotationScroller.setVisible(b);
534 * automatically adjust annotation panel height for new annotation whilst
535 * ensuring the alignment is still visible.
538 public void adjustAnnotationHeight()
540 // TODO: display vertical annotation scrollbar if necessary
541 // this is called after loading new annotation onto alignment
542 if (alignFrame.getHeight() == 0)
544 System.out.println("NEEDS FIXING");
546 validateAnnotationDimensions(true);
548 paintAlignment(true);
552 * calculate the annotation dimensions and refresh slider values accordingly.
553 * need to do repaints/notifys afterwards.
555 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
557 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
559 if (adjustPanelHeight)
561 int rowHeight = av.getCharHeight();
562 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
565 * Estimate available height in the AlignFrame for alignment +
566 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
567 * hscroll, status bar (as these are not laid out we can't inspect their
568 * actual heights). Insets gives frame borders.
570 int stuff = Platform.isAMac() ? 80 : 100;
571 Insets insets = alignFrame.getInsets();
572 int availableHeight = alignFrame.getHeight() - stuff - insets.top
576 * If not enough vertical space, maximize annotation height while keeping
577 * at least two rows of alignment visible
579 if (annotationHeight + alignmentHeight > availableHeight)
581 annotationHeight = Math.min(annotationHeight, availableHeight - 2
587 // maintain same window layout whilst updating sliders
588 annotationHeight = annotationScroller.getSize().height;
592 annotationScroller.setPreferredSize(new Dimension(annotationScroller
593 .getWidth(), annotationHeight));
595 Dimension e = idPanel.getSize();
596 alabels.setSize(new Dimension(e.width, annotationHeight));
598 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
599 annotationSpaceFillerHolder.getWidth(), annotationHeight));
600 annotationScroller.validate();
601 annotationScroller.addNotify();
605 * update alignment layout for viewport settings
610 public void updateLayout()
613 setAnnotationVisible(av.isShowAnnotation());
614 boolean wrap = av.getWrapAlignment();
615 vpRanges.setStartSeq(0);
616 scalePanelHolder.setVisible(!wrap);
617 hscroll.setVisible(!wrap);
618 idwidthAdjuster.setVisible(!wrap);
622 annotationScroller.setVisible(false);
623 annotationSpaceFillerHolder.setVisible(false);
625 else if (av.isShowAnnotation())
627 annotationScroller.setVisible(true);
628 annotationSpaceFillerHolder.setVisible(true);
633 int widthInRes = getSeqPanel().seqCanvas
634 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
635 vpRanges.setViewportWidth(widthInRes);
639 int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
640 .getCharWidth()) - 1;
641 int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
642 .getCharHeight()) - 1;
644 vpRanges.setViewportWidth(widthInRes);
645 vpRanges.setViewportHeight(heightInSeq);
648 idSpaceFillerPanel1.setVisible(!wrap);
655 * Adjust row/column scrollers to show a visible position in the alignment.
658 * visible column to scroll to
660 * visible row to scroll to
663 public void setScrollValues(int xpos, int ypos)
668 if (av == null || av.getAlignment() == null)
673 if (av.getWrapAlignment())
675 setScrollingForWrappedPanel(x);
679 int width = av.getAlignment().getWidth();
680 int height = av.getAlignment().getHeight();
682 if (av.hasHiddenColumns())
684 // reset the width to exclude hidden columns
685 width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
688 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
689 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
696 if (vextent > height)
701 if ((hextent + x) > width)
706 if ((vextent + y) > height)
708 y = height - vextent;
721 // update the scroll values
722 hscroll.setValues(x, hextent, 0, width);
723 vscroll.setValues(y, vextent, 0, height);
728 * Respond to adjustment event when horizontal or vertical scrollbar is
732 * adjustment event encoding whether hscroll or vscroll changed
735 public void adjustmentValueChanged(AdjustmentEvent evt)
737 int oldX = vpRanges.getStartRes();
738 int oldwidth = vpRanges.getViewportWidth();
739 int oldY = vpRanges.getStartSeq();
740 int oldheight = vpRanges.getViewportHeight();
742 if (av.getWrapAlignment())
744 if (evt.getSource() == hscroll)
746 return; // no horizontal scroll when wrapped
748 else if (evt.getSource() == vscroll)
750 int offy = vscroll.getValue();
751 int rowSize = getSeqPanel().seqCanvas
752 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
754 // if we're scrolling to the position we're already at, stop
755 // this prevents infinite recursion of events when the scroll/viewport
756 // ranges values are the same
757 if ((offy * rowSize == oldX) && (oldwidth == rowSize))
763 vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
768 // This is only called if file loaded is a jar file that
769 // was wrapped when saved and user has wrap alignment true
770 // as preference setting
771 SwingUtilities.invokeLater(new Runnable()
776 // When updating scrolling to use ViewportChange events, this code
777 // could not be validated and it is not clear if it is now being
778 // called. Log warning here in case it is called and unforeseen
781 .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
783 // scroll to start of panel
784 vpRanges.setStartRes(0);
785 vpRanges.setStartSeq(0);
794 if (evt.getSource() == hscroll)
796 int x = hscroll.getValue();
797 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
799 // if we're scrolling to the position we're already at, stop
800 // this prevents infinite recursion of events when the scroll/viewport
801 // ranges values are the same
802 if ((x == oldX) && (width == oldwidth))
806 vpRanges.setViewportStartAndWidth(x, width);
808 else if (evt.getSource() == vscroll)
810 int y = vscroll.getValue();
811 int height = getSeqPanel().seqCanvas.getHeight()
812 / av.getCharHeight();
814 // if we're scrolling to the position we're already at, stop
815 // this prevents infinite recursion of events when the scroll/viewport
816 // ranges values are the same
817 if ((y == oldY) && (height == oldheight))
821 vpRanges.setViewportStartAndHeight(y, height);
831 * Repaint the alignment including the annotations and overview panels (if
835 public void paintAlignment(boolean updateOverview)
837 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
838 av.isShowAutocalculatedAbove());
839 sorter.sort(getAlignment().getAlignmentAnnotation(),
840 av.getSortAnnotationsBy());
845 // TODO: determine if this paintAlignment changed structure colours
846 av.getStructureSelectionManager().sequenceColoursChanged(this);
848 if (overviewPanel != null)
850 overviewPanel.updateOverviewImage();
862 public void paintComponent(Graphics g)
866 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
867 idPanelHolder.setPreferredSize(d);
868 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
872 * set scroll bar positions
874 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
878 * Set vertical scroll bar parameters for wrapped panel
880 * the residue to scroll to
882 private void setScrollingForWrappedPanel(int res)
884 // get the width of the alignment in residues
885 int maxwidth = av.getAlignment().getWidth();
886 if (av.hasHiddenColumns())
888 maxwidth = av.getAlignment().getHiddenColumns()
889 .findColumnPosition(maxwidth) - 1;
892 // get the width of the canvas in residues
893 int canvasWidth = getSeqPanel().seqCanvas
894 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
897 // position we want to scroll to is number of canvasWidth's to get there
898 int current = res / canvasWidth;
900 // max scroll position: add one because extent is 1 and scrollbar value
901 // can only be set to at most max - extent
902 int max = maxwidth / canvasWidth + 1;
903 vscroll.setUnitIncrement(1);
904 vscroll.setValues(current, 1, 0, max);
918 * @return DOCUMENT ME!
920 * @throws PrinterException
924 public int print(Graphics pg, PageFormat pf, int pi)
925 throws PrinterException
927 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
929 int pwidth = (int) pf.getImageableWidth();
930 int pheight = (int) pf.getImageableHeight();
932 if (av.getWrapAlignment())
934 return printWrappedAlignment(pwidth, pheight, pi, pg);
938 return printUnwrapped(pwidth, pheight, pi, pg, pg);
954 * @return DOCUMENT ME!
956 * @throws PrinterException
960 * Draws the alignment image, including sequence ids, sequences, and
961 * annotation labels and annotations if shown, on either one or two Graphics
968 * the graphics context for sequence ids and annotation labels
969 * @param alignmentGraphics
970 * the graphics context for sequences and annotations (may or may not
971 * be the same context as idGraphics)
973 * @throws PrinterException
975 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
976 Graphics idGraphics, Graphics alignmentGraphics)
977 throws PrinterException
979 final int idWidth = getVisibleIdWidth(false);
982 * Get the horizontal offset to where we draw the sequences.
983 * This is idWidth if using a single Graphics context, else zero.
985 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
987 FontMetrics fm = getFontMetrics(av.getFont());
988 int charHeight = av.getCharHeight();
989 int scaleHeight = charHeight + fm.getDescent();
991 idGraphics.setColor(Color.white);
992 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
993 idGraphics.setFont(av.getFont());
996 * How many sequences and residues can we fit on a printable page?
998 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1000 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1002 int alignmentWidth = av.getAlignment().getWidth();
1003 int pagesWide = (alignmentWidth / totalRes) + 1;
1005 final int startRes = (pi % pagesWide) * totalRes;
1006 int endRes = (startRes + totalRes) - 1;
1008 if (endRes > (alignmentWidth - 1))
1010 endRes = alignmentWidth - 1;
1013 final int startSeq = (pi / pagesWide) * totalSeq;
1014 int endSeq = startSeq + totalSeq;
1016 int alignmentHeight = av.getAlignment().getHeight();
1017 if (endSeq > alignmentHeight)
1019 endSeq = alignmentHeight;
1022 int pagesHigh = ((alignmentHeight / totalSeq) + 1)
1025 if (av.isShowAnnotation())
1027 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1030 pagesHigh /= pageHeight;
1032 if (pi >= (pagesWide * pagesHigh))
1034 return Printable.NO_SUCH_PAGE;
1036 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
1040 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1042 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1043 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1044 pageWidth - idWidth, scaleHeight);
1045 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1048 * Draw the sequence ids, offset for scale height,
1049 * then reset to top left (0, 0)
1051 idGraphics.translate(0, scaleHeight);
1052 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1053 Color currentColor = null;
1054 Color currentTextColor = null;
1057 for (int i = startSeq; i < endSeq; i++)
1059 seq = av.getAlignment().getSequenceAt(i);
1060 if ((av.getSelectionGroup() != null)
1061 && av.getSelectionGroup().getSequences(null).contains(seq))
1064 * gray out ids of sequences in selection group (if any)
1066 currentColor = Color.gray;
1067 currentTextColor = Color.black;
1071 currentColor = av.getSequenceColour(seq);
1072 currentTextColor = Color.black;
1075 idGraphics.setColor(currentColor);
1076 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1079 idGraphics.setColor(currentTextColor);
1082 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1083 if (av.isRightAlignIds())
1085 fm = idGraphics.getFontMetrics();
1087 - fm.stringWidth(displayId)
1091 idGraphics.drawString(displayId, xPos,
1092 (((i - startSeq) * charHeight) + charHeight)
1093 - (charHeight / 5));
1095 idGraphics.setFont(av.getFont());
1096 idGraphics.translate(0, -scaleHeight);
1099 * draw the sequences, offset for scale height, and id width (if using a
1100 * single graphics context), then reset to (0, scale height)
1102 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1103 getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
1104 startSeq, endSeq, 0);
1105 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1107 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1110 * draw annotation labels; drawComponent() translates by
1111 * getScrollOffset(), so compensate for that first;
1112 * then reset to (0, scale height)
1114 int offset = getAlabels().getScrollOffset();
1115 idGraphics.translate(0, -offset);
1116 idGraphics.translate(0, alignmentDrawnHeight);
1117 getAlabels().drawComponent(idGraphics, idWidth);
1118 idGraphics.translate(0, -alignmentDrawnHeight);
1121 * draw the annotations starting at
1122 * (idOffset, alignmentHeight) from (0, scaleHeight)
1124 alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
1125 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1126 alignmentGraphics, -1, startRes, endRes + 1);
1129 return Printable.PAGE_EXISTS;
1144 * @return DOCUMENT ME!
1146 * @throws PrinterException
1149 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1150 Graphics pg) throws PrinterException
1152 int annotationHeight = 0;
1153 AnnotationLabels labels = null;
1154 if (av.isShowAnnotation())
1156 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1157 labels = new AnnotationLabels(av);
1160 int hgap = av.getCharHeight();
1161 if (av.getScaleAboveWrapped())
1163 hgap += av.getCharHeight();
1166 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1169 int idWidth = getVisibleIdWidth(false);
1171 int maxwidth = av.getAlignment().getWidth();
1172 if (av.hasHiddenColumns())
1174 maxwidth = av.getAlignment().getHiddenColumns()
1175 .findColumnPosition(maxwidth) - 1;
1178 int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
1181 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1183 pg.setColor(Color.white);
1184 pg.fillRect(0, 0, pwidth, pheight);
1185 pg.setFont(av.getFont());
1189 pg.setColor(Color.black);
1191 pg.translate(0, -pi * pheight);
1193 pg.setClip(0, pi * pheight, pwidth, pheight);
1199 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1201 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1202 SequenceI s = av.getAlignment().getSequenceAt(i);
1203 String string = s.getDisplayId(av.getShowJVSuffix());
1205 if (av.isRightAlignIds())
1207 FontMetrics fm = pg.getFontMetrics();
1208 xPos = idWidth - fm.stringWidth(string) - 4;
1210 pg.drawString(string, xPos,
1211 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1212 - (av.getCharHeight() / 5));
1217 ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
1219 pg.setFont(av.getFont());
1220 labels.drawComponent(pg, idWidth);
1224 - (av.getAlignment().getHeight() * av
1229 } while (ypos < totalHeight);
1231 pg.translate(idWidth, 0);
1233 getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
1236 if ((pi * pheight) < totalHeight)
1238 return Printable.PAGE_EXISTS;
1243 return Printable.NO_SUCH_PAGE;
1248 * get current sequence ID panel width, or nominal value if panel were to be
1249 * displayed using default settings
1253 public int getVisibleIdWidth()
1255 return getVisibleIdWidth(true);
1259 * get current sequence ID panel width, or nominal value if panel were to be
1260 * displayed using default settings
1263 * indicate if the Id width for onscreen or offscreen display should
1267 public int getVisibleIdWidth(boolean onscreen)
1269 // see if rendering offscreen - check preferences and calc width accordingly
1270 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1272 return calculateIdWidth(-1).width + 4;
1274 Integer idwidth = null;
1276 || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1278 int w = getIdPanel().getWidth();
1279 return (w > 0 ? w : calculateIdWidth().width + 4);
1281 return idwidth.intValue() + 4;
1284 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1286 int boarderBottomOffset = 5;
1287 long pSessionId = System.currentTimeMillis();
1288 headless = (System.getProperty("java.awt.headless") != null && System
1289 .getProperty("java.awt.headless").equals("true"));
1290 if (alignFrame != null && !headless)
1294 alignFrame.setProgressBar(MessageManager.formatMessage(
1295 "status.saving_file", new Object[] { type.getLabel() }),
1301 AlignmentDimension aDimension = getAlignmentDimension();
1304 jalview.util.ImageMaker im;
1305 final String imageAction, imageTitle;
1306 if (type == jalview.util.ImageMaker.TYPE.PNG)
1308 imageAction = "Create PNG image from alignment";
1311 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1313 imageAction = "Create EPS file from alignment";
1314 imageTitle = alignFrame.getTitle();
1318 imageAction = "Create SVG file from alignment";
1319 imageTitle = alignFrame.getTitle();
1322 im = new jalview.util.ImageMaker(this, type, imageAction,
1323 aDimension.getWidth(), aDimension.getHeight()
1324 + boarderBottomOffset, file, imageTitle,
1325 alignFrame, pSessionId, headless);
1326 Graphics graphics = im.getGraphics();
1327 if (av.getWrapAlignment())
1329 if (graphics != null)
1331 printWrappedAlignment(aDimension.getWidth(),
1332 aDimension.getHeight() + boarderBottomOffset, 0,
1339 if (graphics != null)
1341 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
1342 0, graphics, graphics);
1347 } catch (OutOfMemoryError err)
1350 System.out.println("########################\n" + "OUT OF MEMORY "
1351 + file + "\n" + "########################");
1352 new OOMWarning("Creating Image for " + file, err);
1353 // System.out.println("Create IMAGE: " + err);
1354 } catch (Exception ex)
1356 ex.printStackTrace();
1364 public AlignmentDimension getAlignmentDimension()
1366 int maxwidth = av.getAlignment().getWidth();
1367 if (av.hasHiddenColumns())
1369 maxwidth = av.getAlignment().getHiddenColumns()
1370 .findColumnPosition(maxwidth);
1373 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1374 + getScalePanel().getHeight();
1375 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1377 if (av.getWrapAlignment())
1379 height = getWrappedHeight();
1382 // need to obtain default alignment width and then add in any
1383 // additional allowance for id margin
1384 // this duplicates the calculation in getWrappedHeight but adjusts for
1386 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1387 - alignFrame.getInsets().left
1388 - alignFrame.getInsets().right - getVisibleIdWidth()
1389 + getVisibleIdWidth(false);
1393 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1397 else if (av.isShowAnnotation())
1399 height += getAnnotationPanel().adjustPanelHeight() + 3;
1401 return new AlignmentDimension(width, height);
1408 public void makeEPS(File epsFile)
1410 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1416 public void makePNG(File pngFile)
1418 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1421 public void makeSVG(File svgFile)
1423 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1426 public void makePNGImageMap(File imgMapFile, String imageName)
1428 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1429 // ////////////////////////////////////////////
1430 int idWidth = getVisibleIdWidth(false);
1431 FontMetrics fm = getFontMetrics(av.getFont());
1432 int scaleHeight = av.getCharHeight() + fm.getDescent();
1435 // ////////////////////////////////
1436 if (imgMapFile != null)
1440 int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
1441 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
1442 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1443 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1444 out.println("<img src=\"" + imageName
1445 + "\" border=\"0\" usemap=\"#Map\" >"
1446 + "<map name=\"Map\">");
1448 for (s = 0; s < sSize; s++)
1450 sy = s * av.getCharHeight() + scaleHeight;
1452 SequenceI seq = av.getAlignment().getSequenceAt(s);
1453 SequenceFeature[] features = seq.getSequenceFeatures();
1454 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1455 for (res = 0; res < alwidth; res++)
1457 StringBuilder text = new StringBuilder();
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 alIndex = 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(alIndex).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 (features != null)
1500 if (text.length() < 1)
1502 text.append("<area shape=\"rect\" coords=\"")
1503 .append((idWidth + res * av.getCharWidth()))
1504 .append(",").append(sy).append(",")
1505 .append((idWidth + (res + 1) * av.getCharWidth()))
1506 .append(",").append((av.getCharHeight() + sy))
1507 .append("\"").append(" onMouseOver=\"toolTip('")
1508 .append(alIndex).append(" ").append(triplet);
1510 fSize = features.length;
1511 for (f = 0; f < fSize; f++)
1514 if ((features[f].getBegin() <= seq.findPosition(res))
1515 && (features[f].getEnd() >= seq.findPosition(res)))
1517 if (features[f].isContactFeature())
1519 if (features[f].getBegin() == seq.findPosition(res)
1520 || features[f].getEnd() == seq
1523 text.append("<br>").append(features[f].getType())
1524 .append(" ").append(features[f].getBegin())
1525 .append(":").append(features[f].getEnd());
1530 text.append("<br>");
1531 text.append(features[f].getType());
1532 if (features[f].getDescription() != null
1533 && !features[f].getType().equals(
1534 features[f].getDescription()))
1536 text.append(" ").append(features[f].getDescription());
1539 if (features[f].getValue("status") != null)
1541 text.append(" (").append(features[f].getValue("status"))
1549 if (text.length() > 1)
1551 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1552 out.println(text.toString());
1556 out.println("</map></body></html>");
1559 } catch (Exception ex)
1561 ex.printStackTrace();
1563 } // /////////END OF IMAGE MAP
1567 int getWrappedHeight()
1569 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1571 if (System.getProperty("java.awt.headless") != null
1572 && System.getProperty("java.awt.headless").equals("true"))
1574 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1575 - vscroll.getPreferredSize().width
1576 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1579 int chunkWidth = getSeqPanel().seqCanvas
1580 .getWrappedCanvasWidth(seqPanelWidth);
1582 int hgap = av.getCharHeight();
1583 if (av.getScaleAboveWrapped())
1585 hgap += av.getCharHeight();
1588 int annotationHeight = 0;
1589 if (av.isShowAnnotation())
1591 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1594 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1597 int maxwidth = av.getAlignment().getWidth();
1598 if (av.hasHiddenColumns())
1600 maxwidth = av.getAlignment().getHiddenColumns()
1601 .findColumnPosition(maxwidth) - 1;
1604 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1610 * close the panel - deregisters all listeners and nulls any references to
1613 public void closePanel()
1615 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1616 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1617 PaintRefresher.RemoveComponent(this);
1622 * try to ensure references are nulled
1624 if (annotationPanel != null)
1626 annotationPanel.dispose();
1631 av.removePropertyChangeListener(propertyChangeListener);
1632 jalview.structure.StructureSelectionManager ssm = av
1633 .getStructureSelectionManager();
1634 ssm.removeStructureViewerListener(getSeqPanel(), null);
1635 ssm.removeSelectionListener(getSeqPanel());
1636 ssm.removeCommandListener(av);
1637 ssm.removeStructureViewerListener(getSeqPanel(), null);
1638 ssm.removeSelectionListener(getSeqPanel());
1644 if (Cache.log.isDebugEnabled())
1646 Cache.log.warn("Closing alignment panel which is already closed.");
1652 * Close any open dialogs that would be orphaned when this one is closed
1654 protected void closeChildFrames()
1656 if (calculationDialog != null)
1658 calculationDialog.closeFrame();
1663 * hides or shows dynamic annotation rows based on groups and av state flags
1665 public void updateAnnotation()
1667 updateAnnotation(false, false);
1670 public void updateAnnotation(boolean applyGlobalSettings)
1672 updateAnnotation(applyGlobalSettings, false);
1675 public void updateAnnotation(boolean applyGlobalSettings,
1676 boolean preserveNewGroupSettings)
1678 av.updateGroupAnnotationSettings(applyGlobalSettings,
1679 preserveNewGroupSettings);
1680 adjustAnnotationHeight();
1684 public AlignmentI getAlignment()
1686 return av == null ? null : av.getAlignment();
1690 public String getViewName()
1696 * Make/Unmake this alignment panel the current input focus
1700 public void setSelected(boolean b)
1704 if (alignFrame.getSplitViewContainer() != null)
1707 * bring enclosing SplitFrame to front first if there is one
1709 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1711 alignFrame.setSelected(b);
1712 } catch (Exception ex)
1718 alignFrame.setDisplayedView(this);
1723 public StructureSelectionManager getStructureSelectionManager()
1725 return av.getStructureSelectionManager();
1729 public void raiseOOMWarning(String string, OutOfMemoryError error)
1731 new OOMWarning(string, error, this);
1735 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1738 return new FeatureRenderer(this);
1742 public jalview.api.FeatureRenderer getFeatureRenderer()
1744 return seqPanel.seqCanvas.getFeatureRenderer();
1747 public void updateFeatureRenderer(
1748 jalview.renderer.seqfeatures.FeatureRenderer fr)
1750 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1753 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1755 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1757 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1761 public ScalePanel getScalePanel()
1766 public void setScalePanel(ScalePanel scalePanel)
1768 this.scalePanel = scalePanel;
1771 public SeqPanel getSeqPanel()
1776 public void setSeqPanel(SeqPanel seqPanel)
1778 this.seqPanel = seqPanel;
1781 public AnnotationPanel getAnnotationPanel()
1783 return annotationPanel;
1786 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1788 this.annotationPanel = annotationPanel;
1791 public AnnotationLabels getAlabels()
1796 public void setAlabels(AnnotationLabels alabels)
1798 this.alabels = alabels;
1801 public IdPanel getIdPanel()
1806 public void setIdPanel(IdPanel idPanel)
1808 this.idPanel = idPanel;
1812 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1813 * The aim is to keep the two alignments 'lined up' on their centre columns.
1816 * holds mapped region(s) of this alignment that we are scrolling
1817 * 'to'; may be modified for sequence offset by this method
1818 * @param verticalOffset
1819 * the number of visible sequences to show above the mapped region
1821 public void scrollToCentre(SearchResultsI sr, int verticalOffset)
1824 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1825 * mapped), we can make the scroll-to location a sequence above the one
1828 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1829 List<SequenceI> seqs = av.getAlignment().getSequences();
1832 * This is like AlignmentI.findIndex(seq) but here we are matching the
1833 * dataset sequence not the aligned sequence
1835 boolean matched = false;
1836 for (SequenceI seq : seqs)
1838 if (mappedTo == seq.getDatasetSequence())
1846 return; // failsafe, shouldn't happen
1850 * Scroll to position but centring the target residue.
1852 scrollToPosition(sr, verticalOffset, true, true);
1856 * Set a flag to say do not scroll any (cDNA/protein) complement.
1860 protected void setToScrollComplementPanel(boolean b)
1862 this.scrollComplementaryPanel = b;
1866 * Get whether to scroll complement panel
1868 * @return true if cDNA/protein complement panels should be scrolled
1870 protected boolean isSetToScrollComplementPanel()
1872 return this.scrollComplementaryPanel;
1878 * @adjustHeight if true, try to recalculate panel height for visible
1881 protected void refresh(boolean adjustHeight)
1883 validateAnnotationDimensions(adjustHeight);
1887 // sort, repaint, update overview
1888 paintAlignment(true);
1892 // lightweight repaint
1899 * Property change event fired when a change is made to the viewport ranges
1900 * object associated with this alignment panel's viewport
1902 public void propertyChange(PropertyChangeEvent evt)
1904 // update this panel's scroll values based on the new viewport ranges values
1905 int x = vpRanges.getStartRes();
1906 int y = vpRanges.getStartSeq();
1907 setScrollValues(x, y);
1909 // now update any complementary alignment (its viewport ranges object
1910 // is different so does not get automatically updated)
1911 if (isSetToScrollComplementPanel())
1913 setToScrollComplementPanel(false);
1914 av.scrollComplementaryAlignment();
1915 setToScrollComplementPanel(true);
1920 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1921 * reference should be nulled when the dialog is closed.
1923 * @param calculationChooser
1925 public void setCalculationDialog(CalculationChooser calculationChooser)
1927 calculationDialog = calculationChooser;
1931 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1934 public CalculationChooser getCalculationDialog()
1936 return calculationDialog;