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.ImageMaker;
40 import jalview.util.MessageManager;
41 import jalview.util.Platform;
42 import jalview.viewmodel.ViewportListenerI;
43 import jalview.viewmodel.ViewportRanges;
45 import java.awt.BorderLayout;
46 import java.awt.Color;
47 import java.awt.Container;
48 import java.awt.Dimension;
50 import java.awt.FontMetrics;
51 import java.awt.Graphics;
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 fastPaint = !(scrolled && av.getWrapAlignment());
341 getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint);
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.absoluteToVisibleColumn(start);
423 end = hidden.absoluteToVisibleColumn(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, insets.
561 int stuff = Platform.isAMac() ? 120 : 140;
562 int availableHeight = alignFrame.getHeight() - stuff;
565 * If not enough vertical space, maximize annotation height while keeping
566 * at least two rows of alignment visible
568 if (annotationHeight + alignmentHeight > availableHeight)
570 annotationHeight = Math.min(annotationHeight,
571 availableHeight - 2 * rowHeight);
576 // maintain same window layout whilst updating sliders
577 annotationHeight = annotationScroller.getSize().height;
581 annotationScroller.setPreferredSize(
582 new Dimension(annotationScroller.getWidth(), annotationHeight));
584 Dimension e = idPanel.getSize();
585 alabels.setSize(new Dimension(e.width, annotationHeight));
587 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
588 annotationSpaceFillerHolder.getWidth(), annotationHeight));
589 annotationScroller.validate();
590 annotationScroller.addNotify();
594 * update alignment layout for viewport settings
599 public void updateLayout()
602 setAnnotationVisible(av.isShowAnnotation());
603 boolean wrap = av.getWrapAlignment();
604 ViewportRanges ranges = av.getRanges();
605 ranges.setStartSeq(0);
606 scalePanelHolder.setVisible(!wrap);
607 hscroll.setVisible(!wrap);
608 idwidthAdjuster.setVisible(!wrap);
612 annotationScroller.setVisible(false);
613 annotationSpaceFillerHolder.setVisible(false);
615 else if (av.isShowAnnotation())
617 annotationScroller.setVisible(true);
618 annotationSpaceFillerHolder.setVisible(true);
621 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
623 { // may not yet be laid out
626 int widthInRes = getSeqPanel().seqCanvas
627 .getWrappedCanvasWidth(canvasWidth);
628 ranges.setViewportWidth(widthInRes);
632 int widthInRes = (canvasWidth / av.getCharWidth());
633 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
634 / av.getCharHeight());
636 ranges.setViewportWidth(widthInRes);
637 ranges.setViewportHeight(heightInSeq);
641 idSpaceFillerPanel1.setVisible(!wrap);
647 * Adjust row/column scrollers to show a visible position in the alignment.
650 * visible column to scroll to
652 * visible row to scroll to
655 public void setScrollValues(int xpos, int ypos)
660 if (av == null || av.getAlignment() == null)
665 if (av.getWrapAlignment())
667 setScrollingForWrappedPanel(x);
671 int width = av.getAlignment().getWidth();
672 int height = av.getAlignment().getHeight();
674 if (av.hasHiddenColumns())
676 // reset the width to exclude hidden columns
677 width = av.getAlignment().getHiddenColumns()
678 .absoluteToVisibleColumn(width);
681 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
682 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
689 if (vextent > height)
694 if ((hextent + x) > width)
699 if ((vextent + y) > height)
701 y = height - vextent;
714 // update the scroll values
715 hscroll.setValues(x, hextent, 0, width);
716 vscroll.setValues(y, vextent, 0, height);
721 * Respond to adjustment event when horizontal or vertical scrollbar is
725 * adjustment event encoding whether hscroll or vscroll changed
728 public void adjustmentValueChanged(AdjustmentEvent evt)
730 if (av.getWrapAlignment())
732 adjustScrollingWrapped(evt);
736 ViewportRanges ranges = av.getRanges();
738 if (evt.getSource() == hscroll)
740 int oldX = ranges.getStartRes();
741 int oldwidth = ranges.getViewportWidth();
742 int x = hscroll.getValue();
743 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
745 // if we're scrolling to the position we're already at, stop
746 // this prevents infinite recursion of events when the scroll/viewport
747 // ranges values are the same
748 if ((x == oldX) && (width == oldwidth))
752 ranges.setViewportStartAndWidth(x, width);
754 else if (evt.getSource() == vscroll)
756 int oldY = ranges.getStartSeq();
757 int oldheight = ranges.getViewportHeight();
758 int y = vscroll.getValue();
759 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
761 // if we're scrolling to the position we're already at, stop
762 // this prevents infinite recursion of events when the scroll/viewport
763 // ranges values are the same
764 if ((y == oldY) && (height == oldheight))
768 ranges.setViewportStartAndHeight(y, height);
774 * Responds to a scroll change by setting the start position of the viewport.
779 protected void adjustScrollingWrapped(AdjustmentEvent evt)
781 if (evt.getSource() == hscroll)
783 return; // no horizontal scroll when wrapped
785 final ViewportRanges ranges = av.getRanges();
787 if (evt.getSource() == vscroll)
789 int newY = vscroll.getValue();
792 * if we're scrolling to the position we're already at, stop
793 * this prevents infinite recursion of events when the scroll/viewport
794 * ranges values are the same
796 int oldX = ranges.getStartRes();
797 int oldY = ranges.getWrappedScrollPosition(oldX);
805 * limit page up/down to one width's worth of positions
807 int rowSize = ranges.getViewportWidth();
808 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
809 ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
814 // This is only called if file loaded is a jar file that
815 // was wrapped when saved and user has wrap alignment true
816 // as preference setting
817 SwingUtilities.invokeLater(new Runnable()
822 // When updating scrolling to use ViewportChange events, this code
823 // could not be validated and it is not clear if it is now being
824 // called. Log warning here in case it is called and unforeseen
827 "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
829 // scroll to start of panel
830 ranges.setStartRes(0);
831 ranges.setStartSeq(0);
839 * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
842 public void paintAlignment(boolean updateOverview,
843 boolean updateStructures)
845 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
846 av.isShowAutocalculatedAbove());
847 sorter.sort(getAlignment().getAlignmentAnnotation(),
848 av.getSortAnnotationsBy());
851 if (updateStructures)
853 av.getStructureSelectionManager().sequenceColoursChanged(this);
858 if (overviewPanel != null)
860 overviewPanel.updateOverviewImage();
872 public void paintComponent(Graphics g)
874 invalidate(); // needed so that the id width adjuster works correctly
876 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
877 idPanelHolder.setPreferredSize(d);
878 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
880 validate(); // needed so that the id width adjuster works correctly
883 * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
884 * though I still think this call should be elsewhere.
886 ViewportRanges ranges = av.getRanges();
887 setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
891 * Set vertical scroll bar position, and number of increments, for wrapped
894 * @param topLeftColumn
895 * the column position at top left (0..)
897 private void setScrollingForWrappedPanel(int topLeftColumn)
899 ViewportRanges ranges = av.getRanges();
900 int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
901 int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
904 * a scrollbar's value can be set to at most (maximum-extent)
905 * so we add extent (1) to the maxScroll value
907 vscroll.setUnitIncrement(1);
908 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
921 * @return DOCUMENT ME!
923 * @throws PrinterException
927 public int print(Graphics pg, PageFormat pf, int pi)
928 throws PrinterException
930 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
932 int pwidth = (int) pf.getImageableWidth();
933 int pheight = (int) pf.getImageableHeight();
935 if (av.getWrapAlignment())
937 return printWrappedAlignment(pwidth, pheight, pi, pg);
941 return printUnwrapped(pwidth, pheight, pi, pg, pg);
957 * @return DOCUMENT ME!
959 * @throws PrinterException
963 * Draws the alignment image, including sequence ids, sequences, and
964 * annotation labels and annotations if shown, on either one or two Graphics
971 * the graphics context for sequence ids and annotation labels
972 * @param alignmentGraphics
973 * the graphics context for sequences and annotations (may or may not
974 * be the same context as idGraphics)
976 * @throws PrinterException
978 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
979 Graphics idGraphics, Graphics alignmentGraphics)
980 throws PrinterException
982 final int idWidth = getVisibleIdWidth(false);
985 * Get the horizontal offset to where we draw the sequences.
986 * This is idWidth if using a single Graphics context, else zero.
988 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
991 FontMetrics fm = getFontMetrics(av.getFont());
992 int charHeight = av.getCharHeight();
993 int scaleHeight = charHeight + fm.getDescent();
995 idGraphics.setColor(Color.white);
996 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
997 idGraphics.setFont(av.getFont());
1000 * How many sequences and residues can we fit on a printable page?
1002 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1004 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1006 int alignmentWidth = av.getAlignment().getWidth();
1007 int pagesWide = (alignmentWidth / totalRes) + 1;
1009 final int startRes = (pi % pagesWide) * totalRes;
1010 int endRes = (startRes + totalRes) - 1;
1012 if (endRes > (alignmentWidth - 1))
1014 endRes = alignmentWidth - 1;
1017 final int startSeq = (pi / pagesWide) * totalSeq;
1018 int endSeq = startSeq + totalSeq;
1020 int alignmentHeight = av.getAlignment().getHeight();
1021 if (endSeq > alignmentHeight)
1023 endSeq = alignmentHeight;
1026 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
1028 if (av.isShowAnnotation())
1030 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1033 pagesHigh /= pageHeight;
1035 if (pi >= (pagesWide * pagesHigh))
1037 return Printable.NO_SUCH_PAGE;
1039 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
1042 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1044 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1045 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1046 pageWidth - idWidth, scaleHeight);
1047 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1050 * Draw the sequence ids, offset for scale height,
1051 * then reset to top left (0, 0)
1053 idGraphics.translate(0, scaleHeight);
1054 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1055 Color currentColor = null;
1056 Color currentTextColor = null;
1059 for (int i = startSeq; i < endSeq; i++)
1061 seq = av.getAlignment().getSequenceAt(i);
1062 if ((av.getSelectionGroup() != null)
1063 && av.getSelectionGroup().getSequences(null).contains(seq))
1066 * gray out ids of sequences in selection group (if any)
1068 currentColor = Color.gray;
1069 currentTextColor = Color.black;
1073 currentColor = av.getSequenceColour(seq);
1074 currentTextColor = Color.black;
1077 idGraphics.setColor(currentColor);
1078 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1081 idGraphics.setColor(currentTextColor);
1084 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1085 if (av.isRightAlignIds())
1087 fm = idGraphics.getFontMetrics();
1088 xPos = idWidth - fm.stringWidth(displayId) - 4;
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.drawPanelForPrinting(alignmentGraphics, startRes,
1104 endRes, startSeq, endSeq);
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,
1125 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 .absoluteToVisibleColumn(maxwidth) - 1;
1179 int resWidth = getSeqPanel().seqCanvas
1180 .getWrappedCanvasWidth(pwidth - idWidth);
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));
1217 pg.translate(-3, ypos
1218 + (av.getAlignment().getHeight() * av.getCharHeight()));
1220 pg.setFont(av.getFont());
1221 labels.drawComponent(pg, idWidth);
1222 pg.translate(+3, -ypos
1223 - (av.getAlignment().getHeight() * av.getCharHeight()));
1227 } while (ypos < totalHeight);
1229 pg.translate(idWidth, 0);
1231 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth,
1234 if ((pi * pheight) < totalHeight)
1236 return Printable.PAGE_EXISTS;
1241 return Printable.NO_SUCH_PAGE;
1246 * get current sequence ID panel width, or nominal value if panel were to be
1247 * displayed using default settings
1251 public int getVisibleIdWidth()
1253 return getVisibleIdWidth(true);
1257 * get current sequence ID panel width, or nominal value if panel were to be
1258 * displayed using default settings
1261 * indicate if the Id width for onscreen or offscreen display should
1265 public int getVisibleIdWidth(boolean onscreen)
1267 // see if rendering offscreen - check preferences and calc width accordingly
1268 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1270 return calculateIdWidth(-1).width + 4;
1272 Integer idwidth = null;
1273 if (onscreen || (idwidth = Cache
1274 .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1276 int w = getIdPanel().getWidth();
1277 return (w > 0 ? w : calculateIdWidth().width + 4);
1279 return idwidth.intValue() + 4;
1283 * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
1284 * writes it to the specified file
1289 void makeAlignmentImage(ImageMaker.TYPE type, File file)
1291 int borderBottomOffset = 5;
1292 long pSessionId = System.currentTimeMillis();
1293 headless = (System.getProperty("java.awt.headless") != null
1294 && System.getProperty("java.awt.headless").equals("true"));
1295 if (alignFrame != null && !headless)
1299 alignFrame.setProgressBar(MessageManager
1300 .formatMessage("status.saving_file", new Object[]
1301 { type.getLabel() }), pSessionId);
1306 AlignmentDimension aDimension = getAlignmentDimension();
1307 String imageAction = "Create " + type.getName()
1308 + " image from alignment";
1309 String imageTitle = alignFrame.getTitle();
1311 ImageMaker im = new ImageMaker(this, type, imageAction,
1312 aDimension.getWidth(),
1313 aDimension.getHeight() + borderBottomOffset, file, imageTitle,
1314 alignFrame, pSessionId, headless);
1315 Graphics graphics = im.getGraphics();
1316 if (graphics != null)
1318 if (av.getWrapAlignment())
1320 printWrappedAlignment(aDimension.getWidth(),
1321 aDimension.getHeight() + borderBottomOffset, 0, graphics);
1325 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
1326 graphics, graphics);
1330 } catch (OutOfMemoryError err)
1333 System.out.println("########################\n" + "OUT OF MEMORY "
1334 + file + "\n" + "########################");
1335 new OOMWarning("Creating Image for " + file, err);
1336 // System.out.println("Create IMAGE: " + err);
1337 } catch (Exception ex)
1339 ex.printStackTrace();
1343 public AlignmentDimension getAlignmentDimension()
1345 int maxwidth = av.getAlignment().getWidth();
1346 if (av.hasHiddenColumns())
1348 maxwidth = av.getAlignment().getHiddenColumns()
1349 .absoluteToVisibleColumn(maxwidth);
1352 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1353 + getScalePanel().getHeight();
1354 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1356 if (av.getWrapAlignment())
1358 height = getWrappedHeight();
1361 // need to obtain default alignment width and then add in any
1362 // additional allowance for id margin
1363 // this duplicates the calculation in getWrappedHeight but adjusts for
1365 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1366 - alignFrame.getInsets().left - alignFrame.getInsets().right
1367 - getVisibleIdWidth() + getVisibleIdWidth(false);
1371 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1375 else if (av.isShowAnnotation())
1377 height += getAnnotationPanel().adjustPanelHeight() + 3;
1379 return new AlignmentDimension(width, height);
1383 public void makePNGImageMap(File imgMapFile, String imageName)
1385 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1386 // ////////////////////////////////////////////
1387 int idWidth = getVisibleIdWidth(false);
1388 FontMetrics fm = getFontMetrics(av.getFont());
1389 int scaleHeight = av.getCharHeight() + fm.getDescent();
1392 // ////////////////////////////////
1393 if (imgMapFile != null)
1397 int sSize = av.getAlignment().getHeight();
1398 int alwidth = av.getAlignment().getWidth();
1399 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1400 out.println(HTMLOutput.getImageMapHTML());
1401 out.println("<img src=\"" + imageName
1402 + "\" border=\"0\" usemap=\"#Map\" >"
1403 + "<map name=\"Map\">");
1405 for (int s = 0; s < sSize; s++)
1407 int sy = s * av.getCharHeight() + scaleHeight;
1409 SequenceI seq = av.getAlignment().getSequenceAt(s);
1410 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1411 for (int column = 0; column < alwidth; column++)
1413 StringBuilder text = new StringBuilder(512);
1414 String triplet = null;
1415 if (av.getAlignment().isNucleotide())
1417 triplet = ResidueProperties.nucleotideName.get(seq
1418 .getCharAt(column) + "");
1422 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
1426 if (triplet == null)
1431 int seqPos = seq.findPosition(column);
1432 int gSize = groups.length;
1433 for (int g = 0; g < gSize; g++)
1435 if (text.length() < 1)
1437 text.append("<area shape=\"rect\" coords=\"")
1438 .append((idWidth + column * av.getCharWidth()))
1439 .append(",").append(sy).append(",")
1440 .append((idWidth + (column + 1) * av.getCharWidth()))
1441 .append(",").append((av.getCharHeight() + sy))
1442 .append("\"").append(" onMouseOver=\"toolTip('")
1443 .append(seqPos).append(" ").append(triplet);
1446 if (groups[g].getStartRes() < column
1447 && groups[g].getEndRes() > column)
1449 text.append("<br><em>").append(groups[g].getName())
1454 if (text.length() < 1)
1456 text.append("<area shape=\"rect\" coords=\"")
1457 .append((idWidth + column * av.getCharWidth()))
1458 .append(",").append(sy).append(",")
1459 .append((idWidth + (column + 1) * av.getCharWidth()))
1460 .append(",").append((av.getCharHeight() + sy))
1461 .append("\"").append(" onMouseOver=\"toolTip('")
1462 .append(seqPos).append(" ").append(triplet);
1464 if (!Comparison.isGap(seq.getCharAt(column)))
1466 List<SequenceFeature> features = seq.findFeatures(column, column);
1467 for (SequenceFeature sf : features)
1469 if (sf.isContactFeature())
1471 text.append("<br>").append(sf.getType()).append(" ")
1472 .append(sf.getBegin()).append(":")
1473 .append(sf.getEnd());
1477 text.append("<br>");
1478 text.append(sf.getType());
1479 String description = sf.getDescription();
1480 if (description != null
1481 && !sf.getType().equals(description))
1483 description = description.replace("\"", """);
1484 text.append(" ").append(description);
1487 String status = sf.getStatus();
1488 if (status != null && !"".equals(status))
1490 text.append(" (").append(status).append(")");
1493 if (text.length() > 1)
1495 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1496 out.println(text.toString());
1501 out.println("</map></body></html>");
1504 } catch (Exception ex)
1506 ex.printStackTrace();
1508 } // /////////END OF IMAGE MAP
1512 int getWrappedHeight()
1514 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1516 if (System.getProperty("java.awt.headless") != null
1517 && System.getProperty("java.awt.headless").equals("true"))
1519 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1520 - vscroll.getPreferredSize().width
1521 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1524 int chunkWidth = getSeqPanel().seqCanvas
1525 .getWrappedCanvasWidth(seqPanelWidth);
1527 int hgap = av.getCharHeight();
1528 if (av.getScaleAboveWrapped())
1530 hgap += av.getCharHeight();
1533 int annotationHeight = 0;
1534 if (av.isShowAnnotation())
1536 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1539 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1542 int maxwidth = av.getAlignment().getWidth();
1543 if (av.hasHiddenColumns())
1545 maxwidth = av.getAlignment().getHiddenColumns()
1546 .absoluteToVisibleColumn(maxwidth) - 1;
1549 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1555 * close the panel - deregisters all listeners and nulls any references to
1558 public void closePanel()
1560 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1561 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1562 PaintRefresher.RemoveComponent(this);
1567 * try to ensure references are nulled
1569 if (annotationPanel != null)
1571 annotationPanel.dispose();
1572 annotationPanel = null;
1577 av.removePropertyChangeListener(propertyChangeListener);
1578 propertyChangeListener = null;
1579 StructureSelectionManager ssm = av.getStructureSelectionManager();
1580 ssm.removeStructureViewerListener(getSeqPanel(), null);
1581 ssm.removeSelectionListener(getSeqPanel());
1582 ssm.removeCommandListener(av);
1583 ssm.removeStructureViewerListener(getSeqPanel(), null);
1584 ssm.removeSelectionListener(getSeqPanel());
1590 if (Cache.log.isDebugEnabled())
1592 Cache.log.warn("Closing alignment panel which is already closed.");
1598 * Close any open dialogs that would be orphaned when this one is closed
1600 protected void closeChildFrames()
1602 if (overviewPanel != null)
1604 overviewPanel.dispose();
1605 overviewPanel = null;
1607 if (calculationDialog != null)
1609 calculationDialog.closeFrame();
1610 calculationDialog = null;
1615 * hides or shows dynamic annotation rows based on groups and av state flags
1617 public void updateAnnotation()
1619 updateAnnotation(false, false);
1622 public void updateAnnotation(boolean applyGlobalSettings)
1624 updateAnnotation(applyGlobalSettings, false);
1627 public void updateAnnotation(boolean applyGlobalSettings,
1628 boolean preserveNewGroupSettings)
1630 av.updateGroupAnnotationSettings(applyGlobalSettings,
1631 preserveNewGroupSettings);
1632 adjustAnnotationHeight();
1636 public AlignmentI getAlignment()
1638 return av == null ? null : av.getAlignment();
1642 public String getViewName()
1648 * Make/Unmake this alignment panel the current input focus
1652 public void setSelected(boolean b)
1656 if (alignFrame.getSplitViewContainer() != null)
1659 * bring enclosing SplitFrame to front first if there is one
1661 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1663 alignFrame.setSelected(b);
1664 } catch (Exception ex)
1670 alignFrame.setDisplayedView(this);
1675 public StructureSelectionManager getStructureSelectionManager()
1677 return av.getStructureSelectionManager();
1681 public void raiseOOMWarning(String string, OutOfMemoryError error)
1683 new OOMWarning(string, error, this);
1687 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1690 return new FeatureRenderer(this);
1694 public jalview.api.FeatureRenderer getFeatureRenderer()
1696 return seqPanel.seqCanvas.getFeatureRenderer();
1699 public void updateFeatureRenderer(
1700 jalview.renderer.seqfeatures.FeatureRenderer fr)
1702 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1705 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1707 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1709 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1713 public ScalePanel getScalePanel()
1718 public void setScalePanel(ScalePanel scalePanel)
1720 this.scalePanel = scalePanel;
1723 public SeqPanel getSeqPanel()
1728 public void setSeqPanel(SeqPanel seqPanel)
1730 this.seqPanel = seqPanel;
1733 public AnnotationPanel getAnnotationPanel()
1735 return annotationPanel;
1738 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1740 this.annotationPanel = annotationPanel;
1743 public AnnotationLabels getAlabels()
1748 public void setAlabels(AnnotationLabels alabels)
1750 this.alabels = alabels;
1753 public IdPanel getIdPanel()
1758 public void setIdPanel(IdPanel idPanel)
1760 this.idPanel = idPanel;
1764 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1765 * The aim is to keep the two alignments 'lined up' on their centre columns.
1768 * holds mapped region(s) of this alignment that we are scrolling
1769 * 'to'; may be modified for sequence offset by this method
1770 * @param verticalOffset
1771 * the number of visible sequences to show above the mapped region
1773 protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1775 scrollToPosition(sr, verticalOffset, true, true);
1779 * Set a flag to say do not scroll any (cDNA/protein) complement.
1783 protected void setToScrollComplementPanel(boolean b)
1785 this.scrollComplementaryPanel = b;
1789 * Get whether to scroll complement panel
1791 * @return true if cDNA/protein complement panels should be scrolled
1793 protected boolean isSetToScrollComplementPanel()
1795 return this.scrollComplementaryPanel;
1801 * @adjustHeight if true, try to recalculate panel height for visible
1804 protected void refresh(boolean adjustHeight)
1806 validateAnnotationDimensions(adjustHeight);
1810 // sort, repaint, update overview
1811 paintAlignment(true, false);
1815 // lightweight repaint
1822 * Property change event fired when a change is made to the viewport ranges
1823 * object associated with this alignment panel's viewport
1825 public void propertyChange(PropertyChangeEvent evt)
1827 // update this panel's scroll values based on the new viewport ranges values
1828 ViewportRanges ranges = av.getRanges();
1829 int x = ranges.getStartRes();
1830 int y = ranges.getStartSeq();
1831 setScrollValues(x, y);
1833 // now update any complementary alignment (its viewport ranges object
1834 // is different so does not get automatically updated)
1835 if (isSetToScrollComplementPanel())
1837 setToScrollComplementPanel(false);
1838 av.scrollComplementaryAlignment();
1839 setToScrollComplementPanel(true);
1844 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1845 * reference should be nulled when the dialog is closed.
1847 * @param calculationChooser
1849 public void setCalculationDialog(CalculationChooser calculationChooser)
1851 calculationDialog = calculationChooser;
1855 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1858 public CalculationChooser getCalculationDialog()
1860 return calculationDialog;