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,
78 public AlignViewport av;
80 ViewportRanges vpRanges;
82 OverviewPanel overviewPanel;
84 private SeqPanel seqPanel;
86 private IdPanel idPanel;
88 private boolean headless;
90 IdwidthAdjuster idwidthAdjuster;
93 public AlignFrame alignFrame;
95 private ScalePanel scalePanel;
97 private AnnotationPanel annotationPanel;
99 private AnnotationLabels alabels;
101 // this value is set false when selection area being dragged
102 boolean fastPaint = true;
104 private int hextent = 0;
106 private int vextent = 0;
109 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
110 * false, suppresses invoking the same method recursively.
112 private boolean scrollComplementaryPanel = true;
114 private PropertyChangeListener propertyChangeListener;
116 private CalculationChooser calculationDialog;
119 * Creates a new AlignmentPanel object.
124 public AlignmentPanel(AlignFrame af, final AlignViewport av)
128 vpRanges = av.getRanges();
129 setSeqPanel(new SeqPanel(av, this));
130 setIdPanel(new IdPanel(av, this));
132 setScalePanel(new ScalePanel(av, this));
134 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
135 idwidthAdjuster = new IdwidthAdjuster(this);
136 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
138 setAnnotationPanel(new AnnotationPanel(this));
139 setAlabels(new AnnotationLabels(this));
141 annotationScroller.setViewportView(getAnnotationPanel());
142 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
144 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
145 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
147 setScrollValues(0, 0);
149 hscroll.addAdjustmentListener(this);
150 vscroll.addAdjustmentListener(this);
152 addComponentListener(new ComponentAdapter()
155 public void componentResized(ComponentEvent evt)
157 // reset the viewport ranges when the alignment panel is resized
158 // in particular, this initialises the end residue value when Jalview
160 if (av.getWrapAlignment())
162 int widthInRes = getSeqPanel().seqCanvas
163 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
164 vpRanges.setViewportWidth(widthInRes);
168 int widthInRes = getSeqPanel().seqCanvas.getWidth()
170 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
171 / av.getCharHeight();
173 vpRanges.setViewportWidth(widthInRes);
174 vpRanges.setViewportHeight(heightInSeq);
180 final AlignmentPanel ap = this;
181 propertyChangeListener = new PropertyChangeListener()
184 public void propertyChange(PropertyChangeEvent evt)
186 if (evt.getPropertyName().equals("alignment"))
188 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
193 av.addPropertyChangeListener(propertyChangeListener);
195 av.getRanges().addPropertyChangeListener(this);
197 adjustAnnotationHeight();
202 public AlignViewportI getAlignViewport()
207 public void alignmentChanged()
209 av.alignmentChanged(this);
211 if (getCalculationDialog() != null)
213 getCalculationDialog().validateCalcTypes();
216 alignFrame.updateEditMenuBar();
218 paintAlignment(true);
225 public void fontChanged()
227 // set idCanvas bufferedImage to null
228 // to prevent drawing old image
229 FontMetrics fm = getFontMetrics(av.getFont());
231 scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
233 idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
234 .getCharHeight() + fm.getDescent()));
236 getIdPanel().getIdCanvas().gg = null;
237 getSeqPanel().seqCanvas.img = null;
238 getAnnotationPanel().adjustPanelHeight();
240 Dimension d = calculateIdWidth();
242 d.setSize(d.width + 4, d.height);
243 getIdPanel().getIdCanvas().setPreferredSize(d);
244 hscrollFillerPanel.setPreferredSize(d);
246 if (this.alignFrame.getSplitViewContainer() != null)
248 ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
255 * Calculate the width of the alignment labels based on the displayed names
256 * and any bounds on label width set in preferences.
258 * @return Dimension giving the maximum width of the alignment label panel
259 * that should be used.
261 public Dimension calculateIdWidth()
263 // calculate sensible default width when no preference is available
265 if (av.getIdWidth() < 0)
267 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
268 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
269 r = calculateIdWidth(maxwidth);
270 av.setIdWidth(r.width);
275 r.width = av.getIdWidth();
282 * Calculate the width of the alignment labels based on the displayed names
283 * and any bounds on label width set in preferences.
286 * -1 or maximum width allowed for IdWidth
287 * @return Dimension giving the maximum width of the alignment label panel
288 * that should be used.
290 public Dimension calculateIdWidth(int maxwidth)
292 Container c = new Container();
294 FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
295 Font.ITALIC, av.font.getSize()));
297 AlignmentI al = av.getAlignment();
302 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
304 SequenceI s = al.getSequenceAt(i);
306 id = s.getDisplayId(av.getShowJVSuffix());
308 if (fm.stringWidth(id) > idWidth)
310 idWidth = fm.stringWidth(id);
316 // Also check annotation label widths
319 if (al.getAlignmentAnnotation() != null)
321 fm = c.getFontMetrics(getAlabels().getFont());
323 while (i < al.getAlignmentAnnotation().length)
325 String label = al.getAlignmentAnnotation()[i].label;
327 if (fm.stringWidth(label) > idWidth)
329 idWidth = fm.stringWidth(label);
336 return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
341 * Highlight the given results on the alignment.
344 public void highlightSearchResults(SearchResultsI results)
346 boolean scrolled = scrollToPosition(results, 0, true, false);
348 boolean noFastPaint = scrolled && av.getWrapAlignment();
350 getSeqPanel().seqCanvas.highlightSearchResults(results, noFastPaint);
354 * Scroll the view to show the position of the highlighted region in results
357 * @param searchResults
358 * @param redrawOverview
361 public boolean scrollToPosition(SearchResultsI searchResults,
362 boolean redrawOverview)
364 return scrollToPosition(searchResults, 0, redrawOverview, false);
368 * Scrolls the view (if necessary) to show the position of the first
369 * highlighted region in results (if any). Answers true if the view was
370 * scrolled, or false if no matched region was found, or it is already
374 * @param verticalOffset
375 * if greater than zero, allows scrolling to a position below the
376 * first displayed sequence
377 * @param redrawOverview
378 * - when set, the overview will be recalculated (takes longer)
380 * if true, try to centre the search results horizontally in the view
383 protected boolean scrollToPosition(SearchResultsI results,
384 int verticalOffset, boolean redrawOverview, boolean centre)
386 int startv, endv, starts, ends;
388 if (results == null || results.isEmpty() || av == null
389 || av.getAlignment() == null)
393 int seqIndex = av.getAlignment().findIndex(results);
398 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
400 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
409 * To centre results, scroll to positions half the visible width
410 * left/right of the start/end positions
414 int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
415 start = Math.max(start - offset, 0);
416 end = end + offset - 1;
422 if (end == seq.getEnd())
427 if (av.hasHiddenColumns())
429 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
430 start = hidden.findColumnPosition(start);
431 end = hidden.findColumnPosition(end);
434 if (!hidden.isVisible(r[0]))
436 // don't scroll - position isn't visible
443 * allow for offset of target sequence (actually scroll to one above it)
445 seqIndex = Math.max(0, seqIndex - verticalOffset);
446 boolean scrollNeeded = true;
448 if (!av.getWrapAlignment())
450 if ((startv = vpRanges.getStartRes()) >= start)
453 * Scroll left to make start of search results visible
455 setScrollValues(start, seqIndex);
457 else if ((endv = vpRanges.getEndRes()) <= end)
460 * Scroll right to make end of search results visible
462 setScrollValues(startv + end - endv, seqIndex);
464 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
467 * Scroll up to make start of search results visible
469 setScrollValues(vpRanges.getStartRes(), seqIndex);
471 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
474 * Scroll down to make end of search results visible
476 setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
480 * Else results are already visible - no need to scroll
482 scrollNeeded = false;
486 scrollNeeded = vpRanges.scrollToWrappedVisible(start);
489 paintAlignment(redrawOverview);
497 * @return DOCUMENT ME!
499 public OverviewPanel getOverviewPanel()
501 return overviewPanel;
510 public void setOverviewPanel(OverviewPanel op)
518 * Hide or show annotation panel
521 public void setAnnotationVisible(boolean b)
523 if (!av.getWrapAlignment())
525 annotationSpaceFillerHolder.setVisible(b);
526 annotationScroller.setVisible(b);
532 * automatically adjust annotation panel height for new annotation whilst
533 * ensuring the alignment is still visible.
536 public void adjustAnnotationHeight()
538 // TODO: display vertical annotation scrollbar if necessary
539 // this is called after loading new annotation onto alignment
540 if (alignFrame.getHeight() == 0)
542 System.out.println("NEEDS FIXING");
544 validateAnnotationDimensions(true);
546 paintAlignment(true);
550 * calculate the annotation dimensions and refresh slider values accordingly.
551 * need to do repaints/notifys afterwards.
553 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
555 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
557 if (adjustPanelHeight)
559 int rowHeight = av.getCharHeight();
560 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
563 * Estimate available height in the AlignFrame for alignment +
564 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
565 * hscroll, status bar (as these are not laid out we can't inspect their
566 * actual heights). Insets gives frame borders.
568 int stuff = Platform.isAMac() ? 80 : 100;
569 Insets insets = alignFrame.getInsets();
570 int availableHeight = alignFrame.getHeight() - stuff - insets.top
574 * If not enough vertical space, maximize annotation height while keeping
575 * at least two rows of alignment visible
577 if (annotationHeight + alignmentHeight > availableHeight)
579 annotationHeight = Math.min(annotationHeight, availableHeight - 2
585 // maintain same window layout whilst updating sliders
586 annotationHeight = annotationScroller.getSize().height;
590 annotationScroller.setPreferredSize(new Dimension(annotationScroller
591 .getWidth(), annotationHeight));
593 Dimension e = idPanel.getSize();
594 alabels.setSize(new Dimension(e.width, annotationHeight));
596 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
597 annotationSpaceFillerHolder.getWidth(), annotationHeight));
598 annotationScroller.validate();
599 annotationScroller.addNotify();
603 * update alignment layout for viewport settings
608 public void updateLayout()
611 setAnnotationVisible(av.isShowAnnotation());
612 boolean wrap = av.getWrapAlignment();
613 vpRanges.setStartSeq(0);
614 scalePanelHolder.setVisible(!wrap);
615 hscroll.setVisible(!wrap);
616 idwidthAdjuster.setVisible(!wrap);
620 annotationScroller.setVisible(false);
621 annotationSpaceFillerHolder.setVisible(false);
623 else if (av.isShowAnnotation())
625 annotationScroller.setVisible(true);
626 annotationSpaceFillerHolder.setVisible(true);
629 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
631 { // may not yet be laid out
634 int widthInRes = getSeqPanel().seqCanvas
635 .getWrappedCanvasWidth(canvasWidth);
636 vpRanges.setViewportWidth(widthInRes);
640 int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
641 int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
642 .getCharHeight()) - 1;
644 vpRanges.setViewportWidth(widthInRes);
645 vpRanges.setViewportHeight(heightInSeq);
649 idSpaceFillerPanel1.setVisible(!wrap);
656 * Adjust row/column scrollers to show a visible position in the alignment.
659 * visible column to scroll to
661 * visible row to scroll to
664 public void setScrollValues(int xpos, int ypos)
669 if (av == null || av.getAlignment() == null)
674 if (av.getWrapAlignment())
676 setScrollingForWrappedPanel(x);
680 int width = av.getAlignment().getWidth();
681 int height = av.getAlignment().getHeight();
683 if (av.hasHiddenColumns())
685 // reset the width to exclude hidden columns
686 width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
689 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
690 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
697 if (vextent > height)
702 if ((hextent + x) > width)
707 if ((vextent + y) > height)
709 y = height - vextent;
722 // update the scroll values
723 hscroll.setValues(x, hextent, 0, width);
724 vscroll.setValues(y, vextent, 0, height);
729 * Respond to adjustment event when horizontal or vertical scrollbar is
733 * adjustment event encoding whether hscroll or vscroll changed
736 public void adjustmentValueChanged(AdjustmentEvent evt)
738 if (av.getWrapAlignment())
740 adjustScrollingWrapped(evt);
744 if (evt.getSource() == hscroll)
746 int oldX = vpRanges.getStartRes();
747 int oldwidth = vpRanges.getViewportWidth();
748 int x = hscroll.getValue();
749 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
751 // if we're scrolling to the position we're already at, stop
752 // this prevents infinite recursion of events when the scroll/viewport
753 // ranges values are the same
754 if ((x == oldX) && (width == oldwidth))
758 vpRanges.setViewportStartAndWidth(x, width);
760 else if (evt.getSource() == vscroll)
762 int oldY = vpRanges.getStartSeq();
763 int oldheight = vpRanges.getViewportHeight();
764 int y = vscroll.getValue();
765 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
767 // if we're scrolling to the position we're already at, stop
768 // this prevents infinite recursion of events when the scroll/viewport
769 // ranges values are the same
770 if ((y == oldY) && (height == oldheight))
774 vpRanges.setViewportStartAndHeight(y, height);
783 * Responds to a scroll change by setting the start position of the viewport.
788 protected void adjustScrollingWrapped(AdjustmentEvent evt)
790 if (evt.getSource() == hscroll)
792 return; // no horizontal scroll when wrapped
794 if (evt.getSource() == vscroll)
796 int newY = vscroll.getValue();
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
803 int oldX = vpRanges.getStartRes();
804 int oldY = vpRanges.getWrappedScrollPosition(oldX);
812 * limit page up/down to one width's worth of positions
814 int rowSize = vpRanges.getViewportWidth();
815 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
816 vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
821 // This is only called if file loaded is a jar file that
822 // was wrapped when saved and user has wrap alignment true
823 // as preference setting
824 SwingUtilities.invokeLater(new Runnable()
829 // When updating scrolling to use ViewportChange events, this code
830 // could not be validated and it is not clear if it is now being
831 // called. Log warning here in case it is called and unforeseen
834 .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
836 // scroll to start of panel
837 vpRanges.setStartRes(0);
838 vpRanges.setStartSeq(0);
846 * Repaint the alignment including the annotations and overview panels (if
850 public void paintAlignment(boolean updateOverview)
852 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
853 av.isShowAutocalculatedAbove());
854 sorter.sort(getAlignment().getAlignmentAnnotation(),
855 av.getSortAnnotationsBy());
860 // TODO: determine if this paintAlignment changed structure colours
861 av.getStructureSelectionManager().sequenceColoursChanged(this);
863 if (overviewPanel != null)
865 overviewPanel.updateOverviewImage();
877 public void paintComponent(Graphics g)
881 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
882 idPanelHolder.setPreferredSize(d);
883 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
887 * set scroll bar positions
889 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
893 * Set vertical scroll bar position, and number of increments, for wrapped
896 * @param topLeftColumn
897 * the column position at top left (0..)
899 private void setScrollingForWrappedPanel(int topLeftColumn)
901 int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
902 int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
905 * a scrollbar's value can be set to at most (maximum-extent)
906 * so we add extent (1) to the maxScroll value
908 vscroll.setUnitIncrement(1);
909 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
922 * @return DOCUMENT ME!
924 * @throws PrinterException
928 public int print(Graphics pg, PageFormat pf, int pi)
929 throws PrinterException
931 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
933 int pwidth = (int) pf.getImageableWidth();
934 int pheight = (int) pf.getImageableHeight();
936 if (av.getWrapAlignment())
938 return printWrappedAlignment(pwidth, pheight, pi, pg);
942 return printUnwrapped(pwidth, pheight, pi, pg, pg);
958 * @return DOCUMENT ME!
960 * @throws PrinterException
964 * Draws the alignment image, including sequence ids, sequences, and
965 * annotation labels and annotations if shown, on either one or two Graphics
972 * the graphics context for sequence ids and annotation labels
973 * @param alignmentGraphics
974 * the graphics context for sequences and annotations (may or may not
975 * be the same context as idGraphics)
977 * @throws PrinterException
979 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
980 Graphics idGraphics, Graphics alignmentGraphics)
981 throws PrinterException
983 final int idWidth = getVisibleIdWidth(false);
986 * Get the horizontal offset to where we draw the sequences.
987 * This is idWidth if using a single Graphics context, else zero.
989 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
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)
1029 if (av.isShowAnnotation())
1031 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1034 pagesHigh /= pageHeight;
1036 if (pi >= (pagesWide * pagesHigh))
1038 return Printable.NO_SUCH_PAGE;
1040 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
1044 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1046 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1047 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1048 pageWidth - idWidth, scaleHeight);
1049 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1052 * Draw the sequence ids, offset for scale height,
1053 * then reset to top left (0, 0)
1055 idGraphics.translate(0, scaleHeight);
1056 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1057 Color currentColor = null;
1058 Color currentTextColor = null;
1061 for (int i = startSeq; i < endSeq; i++)
1063 seq = av.getAlignment().getSequenceAt(i);
1064 if ((av.getSelectionGroup() != null)
1065 && av.getSelectionGroup().getSequences(null).contains(seq))
1068 * gray out ids of sequences in selection group (if any)
1070 currentColor = Color.gray;
1071 currentTextColor = Color.black;
1075 currentColor = av.getSequenceColour(seq);
1076 currentTextColor = Color.black;
1079 idGraphics.setColor(currentColor);
1080 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1083 idGraphics.setColor(currentTextColor);
1086 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1087 if (av.isRightAlignIds())
1089 fm = idGraphics.getFontMetrics();
1091 - fm.stringWidth(displayId)
1095 idGraphics.drawString(displayId, xPos,
1096 (((i - startSeq) * charHeight) + charHeight)
1097 - (charHeight / 5));
1099 idGraphics.setFont(av.getFont());
1100 idGraphics.translate(0, -scaleHeight);
1103 * draw the sequences, offset for scale height, and id width (if using a
1104 * single graphics context), then reset to (0, scale height)
1106 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1107 getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
1108 startSeq, endSeq, 0);
1109 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1111 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1114 * draw annotation labels; drawComponent() translates by
1115 * getScrollOffset(), so compensate for that first;
1116 * then reset to (0, scale height)
1118 int offset = getAlabels().getScrollOffset();
1119 idGraphics.translate(0, -offset);
1120 idGraphics.translate(0, alignmentDrawnHeight);
1121 getAlabels().drawComponent(idGraphics, idWidth);
1122 idGraphics.translate(0, -alignmentDrawnHeight);
1125 * draw the annotations starting at
1126 * (idOffset, alignmentHeight) from (0, scaleHeight)
1128 alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
1129 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1130 alignmentGraphics, -1, startRes, endRes + 1);
1133 return Printable.PAGE_EXISTS;
1148 * @return DOCUMENT ME!
1150 * @throws PrinterException
1153 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1154 Graphics pg) throws PrinterException
1156 int annotationHeight = 0;
1157 AnnotationLabels labels = null;
1158 if (av.isShowAnnotation())
1160 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1161 labels = new AnnotationLabels(av);
1164 int hgap = av.getCharHeight();
1165 if (av.getScaleAboveWrapped())
1167 hgap += av.getCharHeight();
1170 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1173 int idWidth = getVisibleIdWidth(false);
1175 int maxwidth = av.getAlignment().getWidth();
1176 if (av.hasHiddenColumns())
1178 maxwidth = av.getAlignment().getHiddenColumns()
1179 .findColumnPosition(maxwidth) - 1;
1182 int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
1185 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1187 pg.setColor(Color.white);
1188 pg.fillRect(0, 0, pwidth, pheight);
1189 pg.setFont(av.getFont());
1193 pg.setColor(Color.black);
1195 pg.translate(0, -pi * pheight);
1197 pg.setClip(0, pi * pheight, pwidth, pheight);
1203 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1205 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1206 SequenceI s = av.getAlignment().getSequenceAt(i);
1207 String string = s.getDisplayId(av.getShowJVSuffix());
1209 if (av.isRightAlignIds())
1211 FontMetrics fm = pg.getFontMetrics();
1212 xPos = idWidth - fm.stringWidth(string) - 4;
1214 pg.drawString(string, xPos,
1215 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1216 - (av.getCharHeight() / 5));
1221 ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
1223 pg.setFont(av.getFont());
1224 labels.drawComponent(pg, idWidth);
1228 - (av.getAlignment().getHeight() * av
1233 } while (ypos < totalHeight);
1235 pg.translate(idWidth, 0);
1237 getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
1240 if ((pi * pheight) < totalHeight)
1242 return Printable.PAGE_EXISTS;
1247 return Printable.NO_SUCH_PAGE;
1252 * get current sequence ID panel width, or nominal value if panel were to be
1253 * displayed using default settings
1257 public int getVisibleIdWidth()
1259 return getVisibleIdWidth(true);
1263 * get current sequence ID panel width, or nominal value if panel were to be
1264 * displayed using default settings
1267 * indicate if the Id width for onscreen or offscreen display should
1271 public int getVisibleIdWidth(boolean onscreen)
1273 // see if rendering offscreen - check preferences and calc width accordingly
1274 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1276 return calculateIdWidth(-1).width + 4;
1278 Integer idwidth = null;
1280 || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1282 int w = getIdPanel().getWidth();
1283 return (w > 0 ? w : calculateIdWidth().width + 4);
1285 return idwidth.intValue() + 4;
1288 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1290 int boarderBottomOffset = 5;
1291 long pSessionId = System.currentTimeMillis();
1292 headless = (System.getProperty("java.awt.headless") != null && System
1293 .getProperty("java.awt.headless").equals("true"));
1294 if (alignFrame != null && !headless)
1298 alignFrame.setProgressBar(MessageManager.formatMessage(
1299 "status.saving_file", new Object[] { type.getLabel() }),
1305 AlignmentDimension aDimension = getAlignmentDimension();
1308 jalview.util.ImageMaker im;
1309 final String imageAction, imageTitle;
1310 if (type == jalview.util.ImageMaker.TYPE.PNG)
1312 imageAction = "Create PNG image from alignment";
1315 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1317 imageAction = "Create EPS file from alignment";
1318 imageTitle = alignFrame.getTitle();
1322 imageAction = "Create SVG file from alignment";
1323 imageTitle = alignFrame.getTitle();
1326 im = new jalview.util.ImageMaker(this, type, imageAction,
1327 aDimension.getWidth(), aDimension.getHeight()
1328 + boarderBottomOffset, file, imageTitle,
1329 alignFrame, pSessionId, headless);
1330 Graphics graphics = im.getGraphics();
1331 if (av.getWrapAlignment())
1333 if (graphics != null)
1335 printWrappedAlignment(aDimension.getWidth(),
1336 aDimension.getHeight() + boarderBottomOffset, 0,
1343 if (graphics != null)
1345 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
1346 0, graphics, graphics);
1351 } catch (OutOfMemoryError err)
1354 System.out.println("########################\n" + "OUT OF MEMORY "
1355 + file + "\n" + "########################");
1356 new OOMWarning("Creating Image for " + file, err);
1357 // System.out.println("Create IMAGE: " + err);
1358 } catch (Exception ex)
1360 ex.printStackTrace();
1368 public AlignmentDimension getAlignmentDimension()
1370 int maxwidth = av.getAlignment().getWidth();
1371 if (av.hasHiddenColumns())
1373 maxwidth = av.getAlignment().getHiddenColumns()
1374 .findColumnPosition(maxwidth);
1377 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1378 + getScalePanel().getHeight();
1379 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1381 if (av.getWrapAlignment())
1383 height = getWrappedHeight();
1386 // need to obtain default alignment width and then add in any
1387 // additional allowance for id margin
1388 // this duplicates the calculation in getWrappedHeight but adjusts for
1390 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1391 - alignFrame.getInsets().left
1392 - alignFrame.getInsets().right - getVisibleIdWidth()
1393 + getVisibleIdWidth(false);
1397 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1401 else if (av.isShowAnnotation())
1403 height += getAnnotationPanel().adjustPanelHeight() + 3;
1405 return new AlignmentDimension(width, height);
1412 public void makeEPS(File epsFile)
1414 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1420 public void makePNG(File pngFile)
1422 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1425 public void makeSVG(File svgFile)
1427 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1430 public void makePNGImageMap(File imgMapFile, String imageName)
1432 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1433 // ////////////////////////////////////////////
1434 int idWidth = getVisibleIdWidth(false);
1435 FontMetrics fm = getFontMetrics(av.getFont());
1436 int scaleHeight = av.getCharHeight() + fm.getDescent();
1439 // ////////////////////////////////
1440 if (imgMapFile != null)
1444 int sSize = av.getAlignment().getHeight();
1445 int alwidth = av.getAlignment().getWidth();
1446 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1447 out.println(HTMLOutput.getImageMapHTML());
1448 out.println("<img src=\"" + imageName
1449 + "\" border=\"0\" usemap=\"#Map\" >"
1450 + "<map name=\"Map\">");
1452 for (int s = 0; s < sSize; s++)
1454 int sy = s * av.getCharHeight() + scaleHeight;
1456 SequenceI seq = av.getAlignment().getSequenceAt(s);
1457 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1458 for (int column = 0; column < alwidth; column++)
1460 StringBuilder text = new StringBuilder(512);
1461 String triplet = null;
1462 if (av.getAlignment().isNucleotide())
1464 triplet = ResidueProperties.nucleotideName.get(seq
1465 .getCharAt(column) + "");
1469 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
1473 if (triplet == null)
1478 int seqPos = seq.findPosition(column);
1479 int gSize = groups.length;
1480 for (int g = 0; g < gSize; g++)
1482 if (text.length() < 1)
1484 text.append("<area shape=\"rect\" coords=\"")
1485 .append((idWidth + column * av.getCharWidth()))
1486 .append(",").append(sy).append(",")
1487 .append((idWidth + (column + 1) * av.getCharWidth()))
1488 .append(",").append((av.getCharHeight() + sy))
1489 .append("\"").append(" onMouseOver=\"toolTip('")
1490 .append(seqPos).append(" ").append(triplet);
1493 if (groups[g].getStartRes() < column
1494 && groups[g].getEndRes() > column)
1496 text.append("<br><em>").append(groups[g].getName())
1501 if (text.length() < 1)
1503 text.append("<area shape=\"rect\" coords=\"")
1504 .append((idWidth + column * av.getCharWidth()))
1505 .append(",").append(sy).append(",")
1506 .append((idWidth + (column + 1) * av.getCharWidth()))
1507 .append(",").append((av.getCharHeight() + sy))
1508 .append("\"").append(" onMouseOver=\"toolTip('")
1509 .append(seqPos).append(" ").append(triplet);
1511 if (!Comparison.isGap(seq.getCharAt(column)))
1513 List<SequenceFeature> features = seq.findFeatures(column, column);
1514 for (SequenceFeature sf : features)
1516 if (sf.isContactFeature())
1518 text.append("<br>").append(sf.getType()).append(" ")
1519 .append(sf.getBegin()).append(":")
1520 .append(sf.getEnd());
1524 text.append("<br>");
1525 text.append(sf.getType());
1526 String description = sf.getDescription();
1527 if (description != null
1528 && !sf.getType().equals(description))
1530 description = description.replace("\"", """);
1531 text.append(" ").append(description);
1534 String status = sf.getStatus();
1535 if (status != null && !"".equals(status))
1537 text.append(" (").append(status).append(")");
1540 if (text.length() > 1)
1542 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1543 out.println(text.toString());
1548 out.println("</map></body></html>");
1551 } catch (Exception ex)
1553 ex.printStackTrace();
1555 } // /////////END OF IMAGE MAP
1559 int getWrappedHeight()
1561 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1563 if (System.getProperty("java.awt.headless") != null
1564 && System.getProperty("java.awt.headless").equals("true"))
1566 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1567 - vscroll.getPreferredSize().width
1568 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1571 int chunkWidth = getSeqPanel().seqCanvas
1572 .getWrappedCanvasWidth(seqPanelWidth);
1574 int hgap = av.getCharHeight();
1575 if (av.getScaleAboveWrapped())
1577 hgap += av.getCharHeight();
1580 int annotationHeight = 0;
1581 if (av.isShowAnnotation())
1583 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1586 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1589 int maxwidth = av.getAlignment().getWidth();
1590 if (av.hasHiddenColumns())
1592 maxwidth = av.getAlignment().getHiddenColumns()
1593 .findColumnPosition(maxwidth) - 1;
1596 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1602 * close the panel - deregisters all listeners and nulls any references to
1605 public void closePanel()
1607 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1608 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1609 PaintRefresher.RemoveComponent(this);
1614 * try to ensure references are nulled
1616 if (annotationPanel != null)
1618 annotationPanel.dispose();
1623 av.removePropertyChangeListener(propertyChangeListener);
1624 jalview.structure.StructureSelectionManager ssm = av
1625 .getStructureSelectionManager();
1626 ssm.removeStructureViewerListener(getSeqPanel(), null);
1627 ssm.removeSelectionListener(getSeqPanel());
1628 ssm.removeCommandListener(av);
1629 ssm.removeStructureViewerListener(getSeqPanel(), null);
1630 ssm.removeSelectionListener(getSeqPanel());
1636 if (Cache.log.isDebugEnabled())
1638 Cache.log.warn("Closing alignment panel which is already closed.");
1644 * Close any open dialogs that would be orphaned when this one is closed
1646 protected void closeChildFrames()
1648 if (calculationDialog != null)
1650 calculationDialog.closeFrame();
1655 * hides or shows dynamic annotation rows based on groups and av state flags
1657 public void updateAnnotation()
1659 updateAnnotation(false, false);
1662 public void updateAnnotation(boolean applyGlobalSettings)
1664 updateAnnotation(applyGlobalSettings, false);
1667 public void updateAnnotation(boolean applyGlobalSettings,
1668 boolean preserveNewGroupSettings)
1670 av.updateGroupAnnotationSettings(applyGlobalSettings,
1671 preserveNewGroupSettings);
1672 adjustAnnotationHeight();
1676 public AlignmentI getAlignment()
1678 return av == null ? null : av.getAlignment();
1682 public String getViewName()
1688 * Make/Unmake this alignment panel the current input focus
1692 public void setSelected(boolean b)
1696 if (alignFrame.getSplitViewContainer() != null)
1699 * bring enclosing SplitFrame to front first if there is one
1701 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1703 alignFrame.setSelected(b);
1704 } catch (Exception ex)
1710 alignFrame.setDisplayedView(this);
1715 public StructureSelectionManager getStructureSelectionManager()
1717 return av.getStructureSelectionManager();
1721 public void raiseOOMWarning(String string, OutOfMemoryError error)
1723 new OOMWarning(string, error, this);
1727 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1730 return new FeatureRenderer(this);
1734 public jalview.api.FeatureRenderer getFeatureRenderer()
1736 return seqPanel.seqCanvas.getFeatureRenderer();
1739 public void updateFeatureRenderer(
1740 jalview.renderer.seqfeatures.FeatureRenderer fr)
1742 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1745 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1747 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1749 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1753 public ScalePanel getScalePanel()
1758 public void setScalePanel(ScalePanel scalePanel)
1760 this.scalePanel = scalePanel;
1763 public SeqPanel getSeqPanel()
1768 public void setSeqPanel(SeqPanel seqPanel)
1770 this.seqPanel = seqPanel;
1773 public AnnotationPanel getAnnotationPanel()
1775 return annotationPanel;
1778 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1780 this.annotationPanel = annotationPanel;
1783 public AnnotationLabels getAlabels()
1788 public void setAlabels(AnnotationLabels alabels)
1790 this.alabels = alabels;
1793 public IdPanel getIdPanel()
1798 public void setIdPanel(IdPanel idPanel)
1800 this.idPanel = idPanel;
1804 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1805 * The aim is to keep the two alignments 'lined up' on their centre columns.
1808 * holds mapped region(s) of this alignment that we are scrolling
1809 * 'to'; may be modified for sequence offset by this method
1810 * @param verticalOffset
1811 * the number of visible sequences to show above the mapped region
1813 protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
1816 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1817 * mapped), we can make the scroll-to location a sequence above the one
1820 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1821 List<SequenceI> seqs = av.getAlignment().getSequences();
1824 * This is like AlignmentI.findIndex(seq) but here we are matching the
1825 * dataset sequence not the aligned sequence
1827 boolean matched = false;
1828 for (SequenceI seq : seqs)
1830 if (mappedTo == seq.getDatasetSequence())
1838 return; // failsafe, shouldn't happen
1842 * Scroll to position but centring the target residue.
1844 scrollToPosition(sr, verticalOffset, true, true);
1848 * Set a flag to say do not scroll any (cDNA/protein) complement.
1852 protected void setToScrollComplementPanel(boolean b)
1854 this.scrollComplementaryPanel = b;
1858 * Get whether to scroll complement panel
1860 * @return true if cDNA/protein complement panels should be scrolled
1862 protected boolean isSetToScrollComplementPanel()
1864 return this.scrollComplementaryPanel;
1870 * @adjustHeight if true, try to recalculate panel height for visible
1873 protected void refresh(boolean adjustHeight)
1875 validateAnnotationDimensions(adjustHeight);
1879 // sort, repaint, update overview
1880 paintAlignment(true);
1884 // lightweight repaint
1891 * Property change event fired when a change is made to the viewport ranges
1892 * object associated with this alignment panel's viewport
1894 public void propertyChange(PropertyChangeEvent evt)
1896 // update this panel's scroll values based on the new viewport ranges values
1897 int x = vpRanges.getStartRes();
1898 int y = vpRanges.getStartSeq();
1899 setScrollValues(x, y);
1901 // now update any complementary alignment (its viewport ranges object
1902 // is different so does not get automatically updated)
1903 if (isSetToScrollComplementPanel())
1905 setToScrollComplementPanel(false);
1906 av.scrollComplementaryAlignment();
1907 setToScrollComplementPanel(true);
1912 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1913 * reference should be nulled when the dialog is closed.
1915 * @param calculationChooser
1917 public void setCalculationDialog(CalculationChooser calculationChooser)
1919 calculationDialog = calculationChooser;
1923 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1926 public CalculationChooser getCalculationDialog()
1928 return calculationDialog;