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.io.HTMLOutput;
34 import jalview.jbgui.GAlignmentPanel;
35 import jalview.math.AlignmentDimension;
36 import jalview.schemes.ResidueProperties;
37 import jalview.structure.StructureSelectionManager;
38 import jalview.util.Comparison;
39 import jalview.util.MessageManager;
40 import jalview.util.Platform;
41 import jalview.viewmodel.ViewportListenerI;
42 import jalview.viewmodel.ViewportRanges;
44 import java.awt.BorderLayout;
45 import java.awt.Color;
46 import java.awt.Container;
47 import java.awt.Dimension;
49 import java.awt.FontMetrics;
50 import java.awt.Graphics;
51 import java.awt.Insets;
52 import java.awt.event.AdjustmentEvent;
53 import java.awt.event.AdjustmentListener;
54 import java.awt.event.ComponentAdapter;
55 import java.awt.event.ComponentEvent;
56 import java.awt.print.PageFormat;
57 import java.awt.print.Printable;
58 import java.awt.print.PrinterException;
59 import java.beans.PropertyChangeEvent;
60 import java.beans.PropertyChangeListener;
62 import java.io.FileWriter;
63 import java.io.PrintWriter;
64 import java.util.List;
66 import javax.swing.SwingUtilities;
72 * @version $Revision: 1.161 $
74 public class AlignmentPanel extends GAlignmentPanel implements
75 AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
77 public AlignViewport av;
79 OverviewPanel overviewPanel;
81 private SeqPanel seqPanel;
83 private IdPanel idPanel;
85 private boolean headless;
87 IdwidthAdjuster idwidthAdjuster;
90 public AlignFrame alignFrame;
92 private ScalePanel scalePanel;
94 private AnnotationPanel annotationPanel;
96 private AnnotationLabels alabels;
98 private int hextent = 0;
100 private int vextent = 0;
103 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
104 * false, suppresses invoking the same method recursively.
106 private boolean scrollComplementaryPanel = true;
108 private PropertyChangeListener propertyChangeListener;
110 private CalculationChooser calculationDialog;
113 * Creates a new AlignmentPanel object.
118 public AlignmentPanel(AlignFrame af, final AlignViewport av)
122 setSeqPanel(new SeqPanel(av, this));
123 setIdPanel(new IdPanel(av, this));
125 setScalePanel(new ScalePanel(av, this));
127 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
128 idwidthAdjuster = new IdwidthAdjuster(this);
129 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
131 setAnnotationPanel(new AnnotationPanel(this));
132 setAlabels(new AnnotationLabels(this));
134 annotationScroller.setViewportView(getAnnotationPanel());
135 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
137 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
138 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
140 setScrollValues(0, 0);
142 hscroll.addAdjustmentListener(this);
143 vscroll.addAdjustmentListener(this);
145 addComponentListener(new ComponentAdapter()
148 public void componentResized(ComponentEvent evt)
150 // reset the viewport ranges when the alignment panel is resized
151 // in particular, this initialises the end residue value when Jalview
153 ViewportRanges ranges = av.getRanges();
154 if (av.getWrapAlignment())
156 int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
157 getSeqPanel().seqCanvas.getWidth());
158 ranges.setViewportWidth(widthInRes);
162 int widthInRes = getSeqPanel().seqCanvas.getWidth()
164 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
165 / av.getCharHeight();
167 ranges.setViewportWidth(widthInRes);
168 ranges.setViewportHeight(heightInSeq);
174 final AlignmentPanel ap = this;
175 propertyChangeListener = new PropertyChangeListener()
178 public void propertyChange(PropertyChangeEvent evt)
180 if (evt.getPropertyName().equals("alignment"))
182 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
187 av.addPropertyChangeListener(propertyChangeListener);
189 av.getRanges().addPropertyChangeListener(this);
191 adjustAnnotationHeight();
196 public AlignViewportI getAlignViewport()
201 public void alignmentChanged()
203 av.alignmentChanged(this);
205 if (getCalculationDialog() != null)
207 getCalculationDialog().validateCalcTypes();
210 alignFrame.updateEditMenuBar();
212 // no idea if we need to update structure
213 paintAlignment(true, true);
220 public void fontChanged()
222 // set idCanvas bufferedImage to null
223 // to prevent drawing old image
224 FontMetrics fm = getFontMetrics(av.getFont());
226 scalePanelHolder.setPreferredSize(
227 new Dimension(10, av.getCharHeight() + fm.getDescent()));
228 idSpaceFillerPanel1.setPreferredSize(
229 new Dimension(10, av.getCharHeight() + fm.getDescent()));
230 idwidthAdjuster.invalidate();
231 scalePanelHolder.invalidate();
232 getIdPanel().getIdCanvas().gg = null;
233 getSeqPanel().seqCanvas.img = null;
234 getAnnotationPanel().adjustPanelHeight();
236 Dimension d = calculateIdWidth();
238 d.setSize(d.width + 4, d.height);
239 getIdPanel().getIdCanvas().setPreferredSize(d);
240 hscrollFillerPanel.setPreferredSize(d);
246 * Calculate the width of the alignment labels based on the displayed names
247 * and any bounds on label width set in preferences.
249 * @return Dimension giving the maximum width of the alignment label panel
250 * that should be used.
252 public Dimension calculateIdWidth()
254 // calculate sensible default width when no preference is available
256 if (av.getIdWidth() < 0)
258 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
259 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
260 r = calculateIdWidth(maxwidth);
261 av.setIdWidth(r.width);
266 r.width = av.getIdWidth();
273 * Calculate the width of the alignment labels based on the displayed names
274 * and any bounds on label width set in preferences.
277 * -1 or maximum width allowed for IdWidth
278 * @return Dimension giving the maximum width of the alignment label panel
279 * that should be used.
281 public Dimension calculateIdWidth(int maxwidth)
283 Container c = new Container();
285 FontMetrics fm = c.getFontMetrics(
286 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
288 AlignmentI al = av.getAlignment();
293 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
295 SequenceI s = al.getSequenceAt(i);
297 id = s.getDisplayId(av.getShowJVSuffix());
299 if (fm.stringWidth(id) > idWidth)
301 idWidth = fm.stringWidth(id);
307 // Also check annotation label widths
310 if (al.getAlignmentAnnotation() != null)
312 fm = c.getFontMetrics(getAlabels().getFont());
314 while (i < al.getAlignmentAnnotation().length)
316 String label = al.getAlignmentAnnotation()[i].label;
318 if (fm.stringWidth(label) > idWidth)
320 idWidth = fm.stringWidth(label);
327 return new Dimension(
328 maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
332 * Highlight the given results on the alignment.
335 public void highlightSearchResults(SearchResultsI results)
337 boolean scrolled = scrollToPosition(results, 0, true, false);
339 boolean noFastPaint = scrolled && av.getWrapAlignment();
341 getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint);
345 * Scroll the view to show the position of the highlighted region in results
348 * @param searchResults
349 * @param redrawOverview
352 public boolean scrollToPosition(SearchResultsI searchResults,
353 boolean redrawOverview)
355 return scrollToPosition(searchResults, 0, redrawOverview, false);
359 * Scrolls the view (if necessary) to show the position of the first
360 * highlighted region in results (if any). Answers true if the view was
361 * scrolled, or false if no matched region was found, or it is already
365 * @param verticalOffset
366 * if greater than zero, allows scrolling to a position below the
367 * first displayed sequence
368 * @param redrawOverview
369 * - when set, the overview will be recalculated (takes longer)
371 * if true, try to centre the search results horizontally in the view
374 protected boolean scrollToPosition(SearchResultsI results,
375 int verticalOffset, boolean redrawOverview, boolean centre)
377 int startv, endv, starts, ends;
378 ViewportRanges ranges = av.getRanges();
380 if (results == null || results.isEmpty() || av == null
381 || av.getAlignment() == null)
385 int seqIndex = av.getAlignment().findIndex(results);
390 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
392 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
401 * To centre results, scroll to positions half the visible width
402 * left/right of the start/end positions
406 int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
407 start = Math.max(start - offset, 0);
408 end = end + offset - 1;
414 if (end == seq.getEnd())
419 if (av.hasHiddenColumns())
421 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
422 start = hidden.findColumnPosition(start);
423 end = hidden.findColumnPosition(end);
426 if (!hidden.isVisible(r[0]))
428 // don't scroll - position isn't visible
435 * allow for offset of target sequence (actually scroll to one above it)
437 seqIndex = Math.max(0, seqIndex - verticalOffset);
438 boolean scrollNeeded = true;
440 if (!av.getWrapAlignment())
442 if ((startv = ranges.getStartRes()) >= start)
445 * Scroll left to make start of search results visible
447 setScrollValues(start, seqIndex);
449 else if ((endv = ranges.getEndRes()) <= end)
452 * Scroll right to make end of search results visible
454 setScrollValues(startv + end - endv, seqIndex);
456 else if ((starts = ranges.getStartSeq()) > seqIndex)
459 * Scroll up to make start of search results visible
461 setScrollValues(ranges.getStartRes(), seqIndex);
463 else if ((ends = ranges.getEndSeq()) <= seqIndex)
466 * Scroll down to make end of search results visible
468 setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
472 * Else results are already visible - no need to scroll
474 scrollNeeded = false;
478 scrollNeeded = ranges.scrollToWrappedVisible(start);
481 paintAlignment(redrawOverview, false);
489 * @return DOCUMENT ME!
491 public OverviewPanel getOverviewPanel()
493 return overviewPanel;
502 public void setOverviewPanel(OverviewPanel op)
510 * Hide or show annotation panel
513 public void setAnnotationVisible(boolean b)
515 if (!av.getWrapAlignment())
517 annotationSpaceFillerHolder.setVisible(b);
518 annotationScroller.setVisible(b);
524 * automatically adjust annotation panel height for new annotation whilst
525 * ensuring the alignment is still visible.
528 public void adjustAnnotationHeight()
530 // TODO: display vertical annotation scrollbar if necessary
531 // this is called after loading new annotation onto alignment
532 if (alignFrame.getHeight() == 0)
534 System.out.println("NEEDS FIXING");
536 validateAnnotationDimensions(true);
538 // TODO: many places call this method and also paintAlignment with various
539 // different settings. this means multiple redraws are triggered...
540 paintAlignment(true, false);
544 * calculate the annotation dimensions and refresh slider values accordingly.
545 * need to do repaints/notifys afterwards.
547 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
549 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
551 if (adjustPanelHeight)
553 int rowHeight = av.getCharHeight();
554 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
557 * Estimate available height in the AlignFrame for alignment +
558 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
559 * hscroll, status bar (as these are not laid out we can't inspect their
560 * actual heights). Insets gives frame borders.
562 int stuff = Platform.isAMac() ? 80 : 100;
563 Insets insets = alignFrame.getInsets();
564 int availableHeight = alignFrame.getHeight() - stuff - insets.top
568 * If not enough vertical space, maximize annotation height while keeping
569 * at least two rows of alignment visible
571 if (annotationHeight + alignmentHeight > availableHeight)
573 annotationHeight = Math.min(annotationHeight,
574 availableHeight - 2 * rowHeight);
579 // maintain same window layout whilst updating sliders
580 annotationHeight = annotationScroller.getSize().height;
584 annotationScroller.setPreferredSize(
585 new Dimension(annotationScroller.getWidth(), annotationHeight));
587 Dimension e = idPanel.getSize();
588 alabels.setSize(new Dimension(e.width, annotationHeight));
590 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
591 annotationSpaceFillerHolder.getWidth(), annotationHeight));
592 annotationScroller.validate();
593 annotationScroller.addNotify();
597 * update alignment layout for viewport settings
602 public void updateLayout()
605 setAnnotationVisible(av.isShowAnnotation());
606 boolean wrap = av.getWrapAlignment();
607 ViewportRanges ranges = av.getRanges();
608 ranges.setStartSeq(0);
609 scalePanelHolder.setVisible(!wrap);
610 hscroll.setVisible(!wrap);
611 idwidthAdjuster.setVisible(!wrap);
615 annotationScroller.setVisible(false);
616 annotationSpaceFillerHolder.setVisible(false);
618 else if (av.isShowAnnotation())
620 annotationScroller.setVisible(true);
621 annotationSpaceFillerHolder.setVisible(true);
624 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
626 { // may not yet be laid out
629 int widthInRes = getSeqPanel().seqCanvas
630 .getWrappedCanvasWidth(canvasWidth);
631 ranges.setViewportWidth(widthInRes);
635 int widthInRes = (canvasWidth / av.getCharWidth());
636 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
637 / av.getCharHeight());
639 ranges.setViewportWidth(widthInRes);
640 ranges.setViewportHeight(heightInSeq);
644 idSpaceFillerPanel1.setVisible(!wrap);
650 * Adjust row/column scrollers to show a visible position in the alignment.
653 * visible column to scroll to
655 * visible row to scroll to
658 public void setScrollValues(int xpos, int ypos)
663 if (av == null || av.getAlignment() == null)
668 if (av.getWrapAlignment())
670 setScrollingForWrappedPanel(x);
674 int width = av.getAlignment().getWidth();
675 int height = av.getAlignment().getHeight();
677 if (av.hasHiddenColumns())
679 // reset the width to exclude hidden columns
680 width = av.getAlignment().getHiddenColumns()
681 .findColumnPosition(width);
684 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
685 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
692 if (vextent > height)
697 if ((hextent + x) > width)
702 if ((vextent + y) > height)
704 y = height - vextent;
717 // update the scroll values
718 hscroll.setValues(x, hextent, 0, width);
719 vscroll.setValues(y, vextent, 0, height);
724 * Respond to adjustment event when horizontal or vertical scrollbar is
728 * adjustment event encoding whether hscroll or vscroll changed
731 public void adjustmentValueChanged(AdjustmentEvent evt)
733 if (av.getWrapAlignment())
735 adjustScrollingWrapped(evt);
739 ViewportRanges ranges = av.getRanges();
741 if (evt.getSource() == hscroll)
743 int oldX = ranges.getStartRes();
744 int oldwidth = ranges.getViewportWidth();
745 int x = hscroll.getValue();
746 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
748 // if we're scrolling to the position we're already at, stop
749 // this prevents infinite recursion of events when the scroll/viewport
750 // ranges values are the same
751 if ((x == oldX) && (width == oldwidth))
755 ranges.setViewportStartAndWidth(x, width);
757 else if (evt.getSource() == vscroll)
759 int oldY = ranges.getStartSeq();
760 int oldheight = ranges.getViewportHeight();
761 int y = vscroll.getValue();
762 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
764 // if we're scrolling to the position we're already at, stop
765 // this prevents infinite recursion of events when the scroll/viewport
766 // ranges values are the same
767 if ((y == oldY) && (height == oldheight))
771 ranges.setViewportStartAndHeight(y, height);
777 * Responds to a scroll change by setting the start position of the viewport.
782 protected void adjustScrollingWrapped(AdjustmentEvent evt)
784 if (evt.getSource() == hscroll)
786 return; // no horizontal scroll when wrapped
788 final ViewportRanges ranges = av.getRanges();
790 if (evt.getSource() == vscroll)
792 int newY = vscroll.getValue();
795 * if we're scrolling to the position we're already at, stop
796 * this prevents infinite recursion of events when the scroll/viewport
797 * ranges values are the same
799 int oldX = ranges.getStartRes();
800 int oldY = ranges.getWrappedScrollPosition(oldX);
808 * limit page up/down to one width's worth of positions
810 int rowSize = ranges.getViewportWidth();
811 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
812 ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
817 // This is only called if file loaded is a jar file that
818 // was wrapped when saved and user has wrap alignment true
819 // as preference setting
820 SwingUtilities.invokeLater(new Runnable()
825 // When updating scrolling to use ViewportChange events, this code
826 // could not be validated and it is not clear if it is now being
827 // called. Log warning here in case it is called and unforeseen
830 "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
832 // scroll to start of panel
833 ranges.setStartRes(0);
834 ranges.setStartSeq(0);
842 * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
845 public void paintAlignment(boolean updateOverview,
846 boolean updateStructures)
848 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
849 av.isShowAutocalculatedAbove());
850 sorter.sort(getAlignment().getAlignmentAnnotation(),
851 av.getSortAnnotationsBy());
854 if (updateStructures)
856 av.getStructureSelectionManager().sequenceColoursChanged(this);
861 if (overviewPanel != null)
863 overviewPanel.updateOverviewImage();
875 public void paintComponent(Graphics g)
877 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
878 idPanelHolder.setPreferredSize(d);
879 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
883 * Set vertical scroll bar position, and number of increments, for wrapped
886 * @param topLeftColumn
887 * the column position at top left (0..)
889 private void setScrollingForWrappedPanel(int topLeftColumn)
891 ViewportRanges ranges = av.getRanges();
892 int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
893 int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
896 * a scrollbar's value can be set to at most (maximum-extent)
897 * so we add extent (1) to the maxScroll value
899 vscroll.setUnitIncrement(1);
900 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
913 * @return DOCUMENT ME!
915 * @throws PrinterException
919 public int print(Graphics pg, PageFormat pf, int pi)
920 throws PrinterException
922 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
924 int pwidth = (int) pf.getImageableWidth();
925 int pheight = (int) pf.getImageableHeight();
927 if (av.getWrapAlignment())
929 return printWrappedAlignment(pwidth, pheight, pi, pg);
933 return printUnwrapped(pwidth, pheight, pi, pg, pg);
949 * @return DOCUMENT ME!
951 * @throws PrinterException
955 * Draws the alignment image, including sequence ids, sequences, and
956 * annotation labels and annotations if shown, on either one or two Graphics
963 * the graphics context for sequence ids and annotation labels
964 * @param alignmentGraphics
965 * the graphics context for sequences and annotations (may or may not
966 * be the same context as idGraphics)
968 * @throws PrinterException
970 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
971 Graphics idGraphics, Graphics alignmentGraphics)
972 throws PrinterException
974 final int idWidth = getVisibleIdWidth(false);
977 * Get the horizontal offset to where we draw the sequences.
978 * This is idWidth if using a single Graphics context, else zero.
980 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
983 FontMetrics fm = getFontMetrics(av.getFont());
984 int charHeight = av.getCharHeight();
985 int scaleHeight = charHeight + fm.getDescent();
987 idGraphics.setColor(Color.white);
988 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
989 idGraphics.setFont(av.getFont());
992 * How many sequences and residues can we fit on a printable page?
994 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
996 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
998 int alignmentWidth = av.getAlignment().getWidth();
999 int pagesWide = (alignmentWidth / totalRes) + 1;
1001 final int startRes = (pi % pagesWide) * totalRes;
1002 int endRes = (startRes + totalRes) - 1;
1004 if (endRes > (alignmentWidth - 1))
1006 endRes = alignmentWidth - 1;
1009 final int startSeq = (pi / pagesWide) * totalSeq;
1010 int endSeq = startSeq + totalSeq;
1012 int alignmentHeight = av.getAlignment().getHeight();
1013 if (endSeq > alignmentHeight)
1015 endSeq = alignmentHeight;
1018 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
1020 if (av.isShowAnnotation())
1022 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1025 pagesHigh /= pageHeight;
1027 if (pi >= (pagesWide * pagesHigh))
1029 return Printable.NO_SUCH_PAGE;
1031 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
1034 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1036 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1037 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1038 pageWidth - idWidth, scaleHeight);
1039 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1042 * Draw the sequence ids, offset for scale height,
1043 * then reset to top left (0, 0)
1045 idGraphics.translate(0, scaleHeight);
1046 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1047 Color currentColor = null;
1048 Color currentTextColor = null;
1051 for (int i = startSeq; i < endSeq; i++)
1053 seq = av.getAlignment().getSequenceAt(i);
1054 if ((av.getSelectionGroup() != null)
1055 && av.getSelectionGroup().getSequences(null).contains(seq))
1058 * gray out ids of sequences in selection group (if any)
1060 currentColor = Color.gray;
1061 currentTextColor = Color.black;
1065 currentColor = av.getSequenceColour(seq);
1066 currentTextColor = Color.black;
1069 idGraphics.setColor(currentColor);
1070 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1073 idGraphics.setColor(currentTextColor);
1076 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1077 if (av.isRightAlignIds())
1079 fm = idGraphics.getFontMetrics();
1080 xPos = idWidth - fm.stringWidth(displayId) - 4;
1083 idGraphics.drawString(displayId, xPos,
1084 (((i - startSeq) * charHeight) + charHeight)
1085 - (charHeight / 5));
1087 idGraphics.setFont(av.getFont());
1088 idGraphics.translate(0, -scaleHeight);
1091 * draw the sequences, offset for scale height, and id width (if using a
1092 * single graphics context), then reset to (0, scale height)
1094 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1095 getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
1096 endRes, startSeq, endSeq);
1097 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1099 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1102 * draw annotation labels; drawComponent() translates by
1103 * getScrollOffset(), so compensate for that first;
1104 * then reset to (0, scale height)
1106 int offset = getAlabels().getScrollOffset();
1107 idGraphics.translate(0, -offset);
1108 idGraphics.translate(0, alignmentDrawnHeight);
1109 getAlabels().drawComponent(idGraphics, idWidth);
1110 idGraphics.translate(0, -alignmentDrawnHeight);
1113 * draw the annotations starting at
1114 * (idOffset, alignmentHeight) from (0, scaleHeight)
1116 alignmentGraphics.translate(alignmentGraphicsOffset,
1117 alignmentDrawnHeight);
1118 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1119 alignmentGraphics, -1, startRes, endRes + 1);
1122 return Printable.PAGE_EXISTS;
1137 * @return DOCUMENT ME!
1139 * @throws PrinterException
1142 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1143 Graphics pg) throws PrinterException
1145 int annotationHeight = 0;
1146 AnnotationLabels labels = null;
1147 if (av.isShowAnnotation())
1149 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1150 labels = new AnnotationLabels(av);
1153 int hgap = av.getCharHeight();
1154 if (av.getScaleAboveWrapped())
1156 hgap += av.getCharHeight();
1159 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1162 int idWidth = getVisibleIdWidth(false);
1164 int maxwidth = av.getAlignment().getWidth();
1165 if (av.hasHiddenColumns())
1167 maxwidth = av.getAlignment().getHiddenColumns()
1168 .findColumnPosition(maxwidth) - 1;
1171 int resWidth = getSeqPanel().seqCanvas
1172 .getWrappedCanvasWidth(pwidth - idWidth);
1174 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1176 pg.setColor(Color.white);
1177 pg.fillRect(0, 0, pwidth, pheight);
1178 pg.setFont(av.getFont());
1182 pg.setColor(Color.black);
1184 pg.translate(0, -pi * pheight);
1186 pg.setClip(0, pi * pheight, pwidth, pheight);
1192 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1194 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1195 SequenceI s = av.getAlignment().getSequenceAt(i);
1196 String string = s.getDisplayId(av.getShowJVSuffix());
1198 if (av.isRightAlignIds())
1200 FontMetrics fm = pg.getFontMetrics();
1201 xPos = idWidth - fm.stringWidth(string) - 4;
1203 pg.drawString(string, xPos,
1204 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1205 - (av.getCharHeight() / 5));
1209 pg.translate(-3, ypos
1210 + (av.getAlignment().getHeight() * av.getCharHeight()));
1212 pg.setFont(av.getFont());
1213 labels.drawComponent(pg, idWidth);
1214 pg.translate(+3, -ypos
1215 - (av.getAlignment().getHeight() * av.getCharHeight()));
1219 } while (ypos < totalHeight);
1221 pg.translate(idWidth, 0);
1223 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth,
1226 if ((pi * pheight) < totalHeight)
1228 return Printable.PAGE_EXISTS;
1233 return Printable.NO_SUCH_PAGE;
1238 * get current sequence ID panel width, or nominal value if panel were to be
1239 * displayed using default settings
1243 public int getVisibleIdWidth()
1245 return getVisibleIdWidth(true);
1249 * get current sequence ID panel width, or nominal value if panel were to be
1250 * displayed using default settings
1253 * indicate if the Id width for onscreen or offscreen display should
1257 public int getVisibleIdWidth(boolean onscreen)
1259 // see if rendering offscreen - check preferences and calc width accordingly
1260 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1262 return calculateIdWidth(-1).width + 4;
1264 Integer idwidth = null;
1265 if (onscreen || (idwidth = Cache
1266 .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1268 int w = getIdPanel().getWidth();
1269 return (w > 0 ? w : calculateIdWidth().width + 4);
1271 return idwidth.intValue() + 4;
1274 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1276 int boarderBottomOffset = 5;
1277 long pSessionId = System.currentTimeMillis();
1278 headless = (System.getProperty("java.awt.headless") != null
1279 && System.getProperty("java.awt.headless").equals("true"));
1280 if (alignFrame != null && !headless)
1284 alignFrame.setProgressBar(MessageManager
1285 .formatMessage("status.saving_file", new Object[]
1286 { type.getLabel() }), pSessionId);
1291 AlignmentDimension aDimension = getAlignmentDimension();
1294 jalview.util.ImageMaker im;
1295 final String imageAction, imageTitle;
1296 if (type == jalview.util.ImageMaker.TYPE.PNG)
1298 imageAction = "Create PNG image from alignment";
1301 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1303 imageAction = "Create EPS file from alignment";
1304 imageTitle = alignFrame.getTitle();
1308 imageAction = "Create SVG file from alignment";
1309 imageTitle = alignFrame.getTitle();
1312 im = new jalview.util.ImageMaker(this, type, imageAction,
1313 aDimension.getWidth(),
1314 aDimension.getHeight() + boarderBottomOffset, file,
1315 imageTitle, alignFrame, pSessionId, headless);
1316 Graphics graphics = im.getGraphics();
1317 if (av.getWrapAlignment())
1319 if (graphics != null)
1321 printWrappedAlignment(aDimension.getWidth(),
1322 aDimension.getHeight() + boarderBottomOffset, 0,
1329 if (graphics != null)
1331 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
1332 graphics, graphics);
1337 } catch (OutOfMemoryError err)
1340 System.out.println("########################\n" + "OUT OF MEMORY "
1341 + file + "\n" + "########################");
1342 new OOMWarning("Creating Image for " + file, err);
1343 // System.out.println("Create IMAGE: " + err);
1344 } catch (Exception ex)
1346 ex.printStackTrace();
1354 public AlignmentDimension getAlignmentDimension()
1356 int maxwidth = av.getAlignment().getWidth();
1357 if (av.hasHiddenColumns())
1359 maxwidth = av.getAlignment().getHiddenColumns()
1360 .findColumnPosition(maxwidth);
1363 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1364 + getScalePanel().getHeight();
1365 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1367 if (av.getWrapAlignment())
1369 height = getWrappedHeight();
1372 // need to obtain default alignment width and then add in any
1373 // additional allowance for id margin
1374 // this duplicates the calculation in getWrappedHeight but adjusts for
1376 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1377 - alignFrame.getInsets().left - alignFrame.getInsets().right
1378 - getVisibleIdWidth() + getVisibleIdWidth(false);
1382 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1386 else if (av.isShowAnnotation())
1388 height += getAnnotationPanel().adjustPanelHeight() + 3;
1390 return new AlignmentDimension(width, height);
1397 public void makeEPS(File epsFile)
1399 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1405 public void makePNG(File pngFile)
1407 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1410 public void makeSVG(File svgFile)
1412 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1415 public void makePNGImageMap(File imgMapFile, String imageName)
1417 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1418 // ////////////////////////////////////////////
1419 int idWidth = getVisibleIdWidth(false);
1420 FontMetrics fm = getFontMetrics(av.getFont());
1421 int scaleHeight = av.getCharHeight() + fm.getDescent();
1424 // ////////////////////////////////
1425 if (imgMapFile != null)
1429 int sSize = av.getAlignment().getHeight();
1430 int alwidth = av.getAlignment().getWidth();
1431 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1432 out.println(HTMLOutput.getImageMapHTML());
1433 out.println("<img src=\"" + imageName
1434 + "\" border=\"0\" usemap=\"#Map\" >"
1435 + "<map name=\"Map\">");
1437 for (int s = 0; s < sSize; s++)
1439 int sy = s * av.getCharHeight() + scaleHeight;
1441 SequenceI seq = av.getAlignment().getSequenceAt(s);
1442 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1443 for (int column = 0; column < alwidth; column++)
1445 StringBuilder text = new StringBuilder(512);
1446 String triplet = null;
1447 if (av.getAlignment().isNucleotide())
1449 triplet = ResidueProperties.nucleotideName.get(seq
1450 .getCharAt(column) + "");
1454 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
1458 if (triplet == null)
1463 int seqPos = seq.findPosition(column);
1464 int gSize = groups.length;
1465 for (int g = 0; g < gSize; g++)
1467 if (text.length() < 1)
1469 text.append("<area shape=\"rect\" coords=\"")
1470 .append((idWidth + column * av.getCharWidth()))
1471 .append(",").append(sy).append(",")
1472 .append((idWidth + (column + 1) * av.getCharWidth()))
1473 .append(",").append((av.getCharHeight() + sy))
1474 .append("\"").append(" onMouseOver=\"toolTip('")
1475 .append(seqPos).append(" ").append(triplet);
1478 if (groups[g].getStartRes() < column
1479 && groups[g].getEndRes() > column)
1481 text.append("<br><em>").append(groups[g].getName())
1486 if (text.length() < 1)
1488 text.append("<area shape=\"rect\" coords=\"")
1489 .append((idWidth + column * av.getCharWidth()))
1490 .append(",").append(sy).append(",")
1491 .append((idWidth + (column + 1) * av.getCharWidth()))
1492 .append(",").append((av.getCharHeight() + sy))
1493 .append("\"").append(" onMouseOver=\"toolTip('")
1494 .append(seqPos).append(" ").append(triplet);
1496 if (!Comparison.isGap(seq.getCharAt(column)))
1498 List<SequenceFeature> features = seq.findFeatures(column, column);
1499 for (SequenceFeature sf : features)
1501 if (sf.isContactFeature())
1503 text.append("<br>").append(sf.getType()).append(" ")
1504 .append(sf.getBegin()).append(":")
1505 .append(sf.getEnd());
1509 text.append("<br>");
1510 text.append(sf.getType());
1511 String description = sf.getDescription();
1512 if (description != null
1513 && !sf.getType().equals(description))
1515 description = description.replace("\"", """);
1516 text.append(" ").append(description);
1519 String status = sf.getStatus();
1520 if (status != null && !"".equals(status))
1522 text.append(" (").append(status).append(")");
1525 if (text.length() > 1)
1527 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1528 out.println(text.toString());
1533 out.println("</map></body></html>");
1536 } catch (Exception ex)
1538 ex.printStackTrace();
1540 } // /////////END OF IMAGE MAP
1544 int getWrappedHeight()
1546 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1548 if (System.getProperty("java.awt.headless") != null
1549 && System.getProperty("java.awt.headless").equals("true"))
1551 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1552 - vscroll.getPreferredSize().width
1553 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1556 int chunkWidth = getSeqPanel().seqCanvas
1557 .getWrappedCanvasWidth(seqPanelWidth);
1559 int hgap = av.getCharHeight();
1560 if (av.getScaleAboveWrapped())
1562 hgap += av.getCharHeight();
1565 int annotationHeight = 0;
1566 if (av.isShowAnnotation())
1568 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1571 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1574 int maxwidth = av.getAlignment().getWidth();
1575 if (av.hasHiddenColumns())
1577 maxwidth = av.getAlignment().getHiddenColumns()
1578 .findColumnPosition(maxwidth) - 1;
1581 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1587 * close the panel - deregisters all listeners and nulls any references to
1590 public void closePanel()
1592 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1593 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1594 PaintRefresher.RemoveComponent(this);
1599 * try to ensure references are nulled
1601 if (annotationPanel != null)
1603 annotationPanel.dispose();
1604 annotationPanel = null;
1609 av.removePropertyChangeListener(propertyChangeListener);
1610 propertyChangeListener = null;
1611 StructureSelectionManager ssm = av.getStructureSelectionManager();
1612 ssm.removeStructureViewerListener(getSeqPanel(), null);
1613 ssm.removeSelectionListener(getSeqPanel());
1614 ssm.removeCommandListener(av);
1615 ssm.removeStructureViewerListener(getSeqPanel(), null);
1616 ssm.removeSelectionListener(getSeqPanel());
1622 if (Cache.log.isDebugEnabled())
1624 Cache.log.warn("Closing alignment panel which is already closed.");
1630 * Close any open dialogs that would be orphaned when this one is closed
1632 protected void closeChildFrames()
1634 if (overviewPanel != null)
1636 overviewPanel.dispose();
1637 overviewPanel = null;
1639 if (calculationDialog != null)
1641 calculationDialog.closeFrame();
1642 calculationDialog = null;
1647 * hides or shows dynamic annotation rows based on groups and av state flags
1649 public void updateAnnotation()
1651 updateAnnotation(false, false);
1654 public void updateAnnotation(boolean applyGlobalSettings)
1656 updateAnnotation(applyGlobalSettings, false);
1659 public void updateAnnotation(boolean applyGlobalSettings,
1660 boolean preserveNewGroupSettings)
1662 av.updateGroupAnnotationSettings(applyGlobalSettings,
1663 preserveNewGroupSettings);
1664 adjustAnnotationHeight();
1668 public AlignmentI getAlignment()
1670 return av == null ? null : av.getAlignment();
1674 public String getViewName()
1680 * Make/Unmake this alignment panel the current input focus
1684 public void setSelected(boolean b)
1688 if (alignFrame.getSplitViewContainer() != null)
1691 * bring enclosing SplitFrame to front first if there is one
1693 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1695 alignFrame.setSelected(b);
1696 } catch (Exception ex)
1702 alignFrame.setDisplayedView(this);
1707 public StructureSelectionManager getStructureSelectionManager()
1709 return av.getStructureSelectionManager();
1713 public void raiseOOMWarning(String string, OutOfMemoryError error)
1715 new OOMWarning(string, error, this);
1719 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1722 return new FeatureRenderer(this);
1726 public jalview.api.FeatureRenderer getFeatureRenderer()
1728 return seqPanel.seqCanvas.getFeatureRenderer();
1731 public void updateFeatureRenderer(
1732 jalview.renderer.seqfeatures.FeatureRenderer fr)
1734 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1737 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1739 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1741 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1745 public ScalePanel getScalePanel()
1750 public void setScalePanel(ScalePanel scalePanel)
1752 this.scalePanel = scalePanel;
1755 public SeqPanel getSeqPanel()
1760 public void setSeqPanel(SeqPanel seqPanel)
1762 this.seqPanel = seqPanel;
1765 public AnnotationPanel getAnnotationPanel()
1767 return annotationPanel;
1770 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1772 this.annotationPanel = annotationPanel;
1775 public AnnotationLabels getAlabels()
1780 public void setAlabels(AnnotationLabels alabels)
1782 this.alabels = alabels;
1785 public IdPanel getIdPanel()
1790 public void setIdPanel(IdPanel idPanel)
1792 this.idPanel = idPanel;
1796 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1797 * The aim is to keep the two alignments 'lined up' on their centre columns.
1800 * holds mapped region(s) of this alignment that we are scrolling
1801 * 'to'; may be modified for sequence offset by this method
1802 * @param verticalOffset
1803 * the number of visible sequences to show above the mapped region
1805 protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1808 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1809 * mapped), we can make the scroll-to location a sequence above the one
1812 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1813 List<SequenceI> seqs = av.getAlignment().getSequences();
1816 * This is like AlignmentI.findIndex(seq) but here we are matching the
1817 * dataset sequence not the aligned sequence
1819 boolean matched = false;
1820 for (SequenceI seq : seqs)
1822 if (mappedTo == seq.getDatasetSequence())
1830 return; // failsafe, shouldn't happen
1834 * Scroll to position but centring the target residue.
1836 scrollToPosition(sr, verticalOffset, true, true);
1840 * Set a flag to say do not scroll any (cDNA/protein) complement.
1844 protected void setToScrollComplementPanel(boolean b)
1846 this.scrollComplementaryPanel = b;
1850 * Get whether to scroll complement panel
1852 * @return true if cDNA/protein complement panels should be scrolled
1854 protected boolean isSetToScrollComplementPanel()
1856 return this.scrollComplementaryPanel;
1862 * @adjustHeight if true, try to recalculate panel height for visible
1865 protected void refresh(boolean adjustHeight)
1867 validateAnnotationDimensions(adjustHeight);
1871 // sort, repaint, update overview
1872 paintAlignment(true, false);
1876 // lightweight repaint
1883 * Property change event fired when a change is made to the viewport ranges
1884 * object associated with this alignment panel's viewport
1886 public void propertyChange(PropertyChangeEvent evt)
1888 // update this panel's scroll values based on the new viewport ranges values
1889 ViewportRanges ranges = av.getRanges();
1890 int x = ranges.getStartRes();
1891 int y = ranges.getStartSeq();
1892 setScrollValues(x, y);
1894 // now update any complementary alignment (its viewport ranges object
1895 // is different so does not get automatically updated)
1896 if (isSetToScrollComplementPanel())
1898 setToScrollComplementPanel(false);
1899 av.scrollComplementaryAlignment();
1900 setToScrollComplementPanel(true);
1905 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1906 * reference should be nulled when the dialog is closed.
1908 * @param calculationChooser
1910 public void setCalculationDialog(CalculationChooser calculationChooser)
1912 calculationDialog = calculationChooser;
1916 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1919 public CalculationChooser getCalculationDialog()
1921 return calculationDialog;