2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AnnotationSorter;
24 import jalview.api.AlignViewportI;
25 import jalview.api.AlignmentViewPanel;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SearchResultsI;
30 import jalview.datamodel.SequenceFeature;
31 import jalview.datamodel.SequenceGroup;
32 import jalview.datamodel.SequenceI;
33 import jalview.jbgui.GAlignmentPanel;
34 import jalview.math.AlignmentDimension;
35 import jalview.schemes.ResidueProperties;
36 import jalview.structure.StructureSelectionManager;
37 import jalview.util.MessageManager;
38 import jalview.util.Platform;
39 import jalview.viewmodel.ViewportListenerI;
40 import jalview.viewmodel.ViewportRanges;
42 import java.awt.BorderLayout;
43 import java.awt.Color;
44 import java.awt.Container;
45 import java.awt.Dimension;
47 import java.awt.FontMetrics;
48 import java.awt.Graphics;
49 import java.awt.Insets;
50 import java.awt.event.AdjustmentEvent;
51 import java.awt.event.AdjustmentListener;
52 import java.awt.event.ComponentAdapter;
53 import java.awt.event.ComponentEvent;
54 import java.awt.print.PageFormat;
55 import java.awt.print.Printable;
56 import java.awt.print.PrinterException;
57 import java.beans.PropertyChangeEvent;
58 import java.beans.PropertyChangeListener;
60 import java.io.FileWriter;
61 import java.io.PrintWriter;
62 import java.util.List;
64 import javax.swing.SwingUtilities;
70 * @version $Revision: 1.161 $
72 public class AlignmentPanel extends GAlignmentPanel implements
73 AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
75 public AlignViewport av;
77 ViewportRanges vpRanges;
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 // this value is set false when selection area being dragged
99 boolean fastPaint = true;
101 private int hextent = 0;
103 private int vextent = 0;
106 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
107 * false, suppresses invoking the same method recursively.
109 private boolean scrollComplementaryPanel = true;
111 private PropertyChangeListener propertyChangeListener;
113 private CalculationChooser calculationDialog;
116 * Creates a new AlignmentPanel object.
121 public AlignmentPanel(AlignFrame af, final AlignViewport av)
125 vpRanges = av.getRanges();
126 setSeqPanel(new SeqPanel(av, this));
127 setIdPanel(new IdPanel(av, this));
129 setScalePanel(new ScalePanel(av, this));
131 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
132 idwidthAdjuster = new IdwidthAdjuster(this);
133 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
135 setAnnotationPanel(new AnnotationPanel(this));
136 setAlabels(new AnnotationLabels(this));
138 annotationScroller.setViewportView(getAnnotationPanel());
139 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
141 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
142 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
144 setScrollValues(0, 0);
146 hscroll.addAdjustmentListener(this);
147 vscroll.addAdjustmentListener(this);
149 addComponentListener(new ComponentAdapter()
152 public void componentResized(ComponentEvent evt)
154 // reset the viewport ranges when the alignment panel is resized
155 // in particular, this initialises the end residue value when Jalview
157 if (av.getWrapAlignment())
159 int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
160 getSeqPanel().seqCanvas.getWidth());
161 vpRanges.setViewportWidth(widthInRes);
165 int widthInRes = getSeqPanel().seqCanvas.getWidth()
167 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
168 / av.getCharHeight();
170 vpRanges.setViewportWidth(widthInRes);
171 vpRanges.setViewportHeight(heightInSeq);
177 final AlignmentPanel ap = this;
178 propertyChangeListener = new PropertyChangeListener()
181 public void propertyChange(PropertyChangeEvent evt)
183 if (evt.getPropertyName().equals("alignment"))
185 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
190 av.addPropertyChangeListener(propertyChangeListener);
192 av.getRanges().addPropertyChangeListener(this);
194 adjustAnnotationHeight();
199 public AlignViewportI getAlignViewport()
204 public void alignmentChanged()
206 av.alignmentChanged(this);
208 if (getCalculationDialog() != null)
210 getCalculationDialog().validateCalcTypes();
213 alignFrame.updateEditMenuBar();
215 paintAlignment(true);
222 public void fontChanged()
224 // set idCanvas bufferedImage to null
225 // to prevent drawing old image
226 FontMetrics fm = getFontMetrics(av.getFont());
228 scalePanelHolder.setPreferredSize(
229 new Dimension(10, av.getCharHeight() + fm.getDescent()));
230 idSpaceFillerPanel1.setPreferredSize(
231 new Dimension(10, av.getCharHeight() + fm.getDescent()));
233 getIdPanel().getIdCanvas().gg = null;
234 getSeqPanel().seqCanvas.img = null;
235 getAnnotationPanel().adjustPanelHeight();
237 Dimension d = calculateIdWidth();
239 d.setSize(d.width + 4, d.height);
240 getIdPanel().getIdCanvas().setPreferredSize(d);
241 hscrollFillerPanel.setPreferredSize(d);
243 if (this.alignFrame.getSplitViewContainer() != null)
245 ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
252 * Calculate the width of the alignment labels based on the displayed names
253 * and any bounds on label width set in preferences.
255 * @return Dimension giving the maximum width of the alignment label panel
256 * that should be used.
258 public Dimension calculateIdWidth()
260 // calculate sensible default width when no preference is available
262 if (av.getIdWidth() < 0)
264 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
265 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
266 r = calculateIdWidth(maxwidth);
267 av.setIdWidth(r.width);
272 r.width = av.getIdWidth();
279 * Calculate the width of the alignment labels based on the displayed names
280 * and any bounds on label width set in preferences.
283 * -1 or maximum width allowed for IdWidth
284 * @return Dimension giving the maximum width of the alignment label panel
285 * that should be used.
287 public Dimension calculateIdWidth(int maxwidth)
289 Container c = new Container();
291 FontMetrics fm = c.getFontMetrics(
292 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
294 AlignmentI al = av.getAlignment();
299 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
301 SequenceI s = al.getSequenceAt(i);
303 id = s.getDisplayId(av.getShowJVSuffix());
305 if (fm.stringWidth(id) > idWidth)
307 idWidth = fm.stringWidth(id);
313 // Also check annotation label widths
316 if (al.getAlignmentAnnotation() != null)
318 fm = c.getFontMetrics(getAlabels().getFont());
320 while (i < al.getAlignmentAnnotation().length)
322 String label = al.getAlignmentAnnotation()[i].label;
324 if (fm.stringWidth(label) > idWidth)
326 idWidth = fm.stringWidth(label);
333 return new Dimension(
334 maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
338 * Highlight the given results on the alignment.
341 public void highlightSearchResults(SearchResultsI results)
343 scrollToPosition(results);
344 getSeqPanel().seqCanvas.highlightSearchResults(results);
348 * Scroll the view to show the position of the highlighted region in results
349 * (if any) and redraw the overview
353 public boolean scrollToPosition(SearchResultsI results)
355 return scrollToPosition(results, 0, true, false);
359 * Scroll the view to show the position of the highlighted region in results
362 * @param searchResults
363 * @param redrawOverview
366 public boolean scrollToPosition(SearchResultsI searchResults,
367 boolean redrawOverview)
369 return scrollToPosition(searchResults, 0, redrawOverview, false);
373 * Scroll the view to show the position of the highlighted region in results
377 * @param verticalOffset
378 * if greater than zero, allows scrolling to a position below the
379 * first displayed sequence
380 * @param redrawOverview
381 * - when set, the overview will be recalculated (takes longer)
383 * if true, try to centre the search results horizontally in the view
384 * @return false if results were not found
386 public boolean scrollToPosition(SearchResultsI results,
387 int verticalOffset, boolean redrawOverview, boolean centre)
389 int startv, endv, starts, ends;
390 // TODO: properly locate search results in view when large numbers of hidden
391 // columns exist before highlighted region
392 // do we need to scroll the panel?
393 // TODO: tons of nullpointerexceptions raised here.
394 if (results != null && results.getSize() > 0 && av != null
395 && av.getAlignment() != null)
397 int seqIndex = av.getAlignment().findIndex(results);
402 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
404 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
413 * To centre results, scroll to positions half the visible width
414 * left/right of the start/end positions
418 int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
420 start = Math.max(start - offset, 0);
421 end = end + offset - 1;
427 if (end == seq.getEnd())
431 if (av.hasHiddenColumns())
433 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
434 start = hidden.findColumnPosition(start);
435 end = hidden.findColumnPosition(end);
438 if (!hidden.isVisible(r[0]))
440 // don't scroll - position isn't visible
447 * allow for offset of target sequence (actually scroll to one above it)
449 seqIndex = Math.max(0, seqIndex - verticalOffset);
451 if (!av.getWrapAlignment())
453 if ((startv = vpRanges.getStartRes()) >= start)
456 * Scroll left to make start of search results visible
458 setScrollValues(start, seqIndex);
460 else if ((endv = vpRanges.getEndRes()) <= end)
463 * Scroll right to make end of search results visible
465 setScrollValues(startv + end - endv, seqIndex);
467 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
470 * Scroll up to make start of search results visible
472 setScrollValues(vpRanges.getStartRes(), seqIndex);
474 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
477 * Scroll down to make end of search results visible
479 setScrollValues(vpRanges.getStartRes(),
480 starts + seqIndex - ends + 1);
483 * Else results are already visible - no need to scroll
488 vpRanges.scrollToWrappedVisible(start);
492 paintAlignment(redrawOverview);
499 * @return DOCUMENT ME!
501 public OverviewPanel getOverviewPanel()
503 return overviewPanel;
512 public void setOverviewPanel(OverviewPanel op)
520 * Hide or show annotation panel
523 public void setAnnotationVisible(boolean b)
525 if (!av.getWrapAlignment())
527 annotationSpaceFillerHolder.setVisible(b);
528 annotationScroller.setVisible(b);
534 * automatically adjust annotation panel height for new annotation whilst
535 * ensuring the alignment is still visible.
538 public void adjustAnnotationHeight()
540 // TODO: display vertical annotation scrollbar if necessary
541 // this is called after loading new annotation onto alignment
542 if (alignFrame.getHeight() == 0)
544 System.out.println("NEEDS FIXING");
546 validateAnnotationDimensions(true);
548 paintAlignment(true);
552 * calculate the annotation dimensions and refresh slider values accordingly.
553 * need to do repaints/notifys afterwards.
555 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
557 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
559 if (adjustPanelHeight)
561 int rowHeight = av.getCharHeight();
562 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
565 * Estimate available height in the AlignFrame for alignment +
566 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
567 * hscroll, status bar (as these are not laid out we can't inspect their
568 * actual heights). Insets gives frame borders.
570 int stuff = Platform.isAMac() ? 80 : 100;
571 Insets insets = alignFrame.getInsets();
572 int availableHeight = alignFrame.getHeight() - stuff - insets.top
576 * If not enough vertical space, maximize annotation height while keeping
577 * at least two rows of alignment visible
579 if (annotationHeight + alignmentHeight > availableHeight)
581 annotationHeight = Math.min(annotationHeight,
582 availableHeight - 2 * rowHeight);
587 // maintain same window layout whilst updating sliders
588 annotationHeight = annotationScroller.getSize().height;
592 annotationScroller.setPreferredSize(
593 new Dimension(annotationScroller.getWidth(), annotationHeight));
595 Dimension e = idPanel.getSize();
596 alabels.setSize(new Dimension(e.width, annotationHeight));
598 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
599 annotationSpaceFillerHolder.getWidth(), annotationHeight));
600 annotationScroller.validate();
601 annotationScroller.addNotify();
605 * update alignment layout for viewport settings
610 public void updateLayout()
613 setAnnotationVisible(av.isShowAnnotation());
614 boolean wrap = av.getWrapAlignment();
615 vpRanges.setStartSeq(0);
616 scalePanelHolder.setVisible(!wrap);
617 hscroll.setVisible(!wrap);
618 idwidthAdjuster.setVisible(!wrap);
622 annotationScroller.setVisible(false);
623 annotationSpaceFillerHolder.setVisible(false);
625 else if (av.isShowAnnotation())
627 annotationScroller.setVisible(true);
628 annotationSpaceFillerHolder.setVisible(true);
631 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
633 { // may not yet be laid out
636 int widthInRes = getSeqPanel().seqCanvas
637 .getWrappedCanvasWidth(canvasWidth);
638 vpRanges.setViewportWidth(widthInRes);
642 int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
643 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
644 / av.getCharHeight()) - 1;
646 vpRanges.setViewportWidth(widthInRes);
647 vpRanges.setViewportHeight(heightInSeq);
651 idSpaceFillerPanel1.setVisible(!wrap);
657 * Adjust row/column scrollers to show a visible position in the alignment.
660 * visible column to scroll to
662 * visible row to scroll to
665 public void setScrollValues(int xpos, int ypos)
670 if (av == null || av.getAlignment() == null)
675 if (av.getWrapAlignment())
677 setScrollingForWrappedPanel(x);
681 int width = av.getAlignment().getWidth();
682 int height = av.getAlignment().getHeight();
684 if (av.hasHiddenColumns())
686 // reset the width to exclude hidden columns
687 width = av.getAlignment().getHiddenColumns()
688 .findColumnPosition(width);
691 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
692 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
699 if (vextent > height)
704 if ((hextent + x) > width)
709 if ((vextent + y) > height)
711 y = height - vextent;
724 // update the scroll values
725 hscroll.setValues(x, hextent, 0, width);
726 vscroll.setValues(y, vextent, 0, height);
731 * Respond to adjustment event when horizontal or vertical scrollbar is
735 * adjustment event encoding whether hscroll or vscroll changed
738 public void adjustmentValueChanged(AdjustmentEvent evt)
740 if (av.getWrapAlignment())
742 adjustScrollingWrapped(evt);
746 if (evt.getSource() == hscroll)
748 int oldX = vpRanges.getStartRes();
749 int oldwidth = vpRanges.getViewportWidth();
750 int x = hscroll.getValue();
751 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
753 // if we're scrolling to the position we're already at, stop
754 // this prevents infinite recursion of events when the scroll/viewport
755 // ranges values are the same
756 if ((x == oldX) && (width == oldwidth))
760 vpRanges.setViewportStartAndWidth(x, width);
762 else if (evt.getSource() == vscroll)
764 int oldY = vpRanges.getStartSeq();
765 int oldheight = vpRanges.getViewportHeight();
766 int y = vscroll.getValue();
767 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
769 // if we're scrolling to the position we're already at, stop
770 // this prevents infinite recursion of events when the scroll/viewport
771 // ranges values are the same
772 if ((y == oldY) && (height == oldheight))
776 vpRanges.setViewportStartAndHeight(y, height);
785 * Responds to a scroll change by setting the start position of the viewport.
790 protected void adjustScrollingWrapped(AdjustmentEvent evt)
792 if (evt.getSource() == hscroll)
794 return; // no horizontal scroll when wrapped
796 if (evt.getSource() == vscroll)
798 int newY = vscroll.getValue();
801 * if we're scrolling to the position we're already at, stop
802 * this prevents infinite recursion of events when the scroll/viewport
803 * ranges values are the same
805 int oldX = vpRanges.getStartRes();
806 int oldY = vpRanges.getWrappedScrollPosition(oldX);
814 * limit page up/down to one width's worth of positions
816 int rowSize = vpRanges.getViewportWidth();
817 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
818 vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
823 // This is only called if file loaded is a jar file that
824 // was wrapped when saved and user has wrap alignment true
825 // as preference setting
826 SwingUtilities.invokeLater(new Runnable()
831 // When updating scrolling to use ViewportChange events, this code
832 // could not be validated and it is not clear if it is now being
833 // called. Log warning here in case it is called and unforeseen
836 "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
838 // scroll to start of panel
839 vpRanges.setStartRes(0);
840 vpRanges.setStartSeq(0);
848 * Repaint the alignment including the annotations and overview panels (if
852 public void paintAlignment(boolean updateOverview)
854 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
855 av.isShowAutocalculatedAbove());
856 sorter.sort(getAlignment().getAlignmentAnnotation(),
857 av.getSortAnnotationsBy());
862 // TODO: determine if this paintAlignment changed structure colours
863 av.getStructureSelectionManager().sequenceColoursChanged(this);
865 if (overviewPanel != null)
867 overviewPanel.updateOverviewImage();
879 public void paintComponent(Graphics g)
883 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
884 idPanelHolder.setPreferredSize(d);
885 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
889 * set scroll bar positions
891 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
895 * Set vertical scroll bar position, and number of increments, for wrapped
898 * @param topLeftColumn
899 * the column position at top left (0..)
901 private void setScrollingForWrappedPanel(int topLeftColumn)
903 int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
904 int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
907 * a scrollbar's value can be set to at most (maximum-extent)
908 * so we add extent (1) to the maxScroll value
910 vscroll.setUnitIncrement(1);
911 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
924 * @return DOCUMENT ME!
926 * @throws PrinterException
930 public int print(Graphics pg, PageFormat pf, int pi)
931 throws PrinterException
933 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
935 int pwidth = (int) pf.getImageableWidth();
936 int pheight = (int) pf.getImageableHeight();
938 if (av.getWrapAlignment())
940 return printWrappedAlignment(pwidth, pheight, pi, pg);
944 return printUnwrapped(pwidth, pheight, pi, pg, pg);
960 * @return DOCUMENT ME!
962 * @throws PrinterException
966 * Draws the alignment image, including sequence ids, sequences, and
967 * annotation labels and annotations if shown, on either one or two Graphics
974 * the graphics context for sequence ids and annotation labels
975 * @param alignmentGraphics
976 * the graphics context for sequences and annotations (may or may not
977 * be the same context as idGraphics)
979 * @throws PrinterException
981 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
982 Graphics idGraphics, Graphics alignmentGraphics)
983 throws PrinterException
985 final int idWidth = getVisibleIdWidth(false);
988 * Get the horizontal offset to where we draw the sequences.
989 * This is idWidth if using a single Graphics context, else zero.
991 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
994 FontMetrics fm = getFontMetrics(av.getFont());
995 int charHeight = av.getCharHeight();
996 int scaleHeight = charHeight + fm.getDescent();
998 idGraphics.setColor(Color.white);
999 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
1000 idGraphics.setFont(av.getFont());
1003 * How many sequences and residues can we fit on a printable page?
1005 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1007 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1009 int alignmentWidth = av.getAlignment().getWidth();
1010 int pagesWide = (alignmentWidth / totalRes) + 1;
1012 final int startRes = (pi % pagesWide) * totalRes;
1013 int endRes = (startRes + totalRes) - 1;
1015 if (endRes > (alignmentWidth - 1))
1017 endRes = alignmentWidth - 1;
1020 final int startSeq = (pi / pagesWide) * totalSeq;
1021 int endSeq = startSeq + totalSeq;
1023 int alignmentHeight = av.getAlignment().getHeight();
1024 if (endSeq > alignmentHeight)
1026 endSeq = alignmentHeight;
1029 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
1031 if (av.isShowAnnotation())
1033 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1036 pagesHigh /= pageHeight;
1038 if (pi >= (pagesWide * pagesHigh))
1040 return Printable.NO_SUCH_PAGE;
1042 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
1045 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1047 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1048 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1049 pageWidth - idWidth, scaleHeight);
1050 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1053 * Draw the sequence ids, offset for scale height,
1054 * then reset to top left (0, 0)
1056 idGraphics.translate(0, scaleHeight);
1057 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1058 Color currentColor = null;
1059 Color currentTextColor = null;
1062 for (int i = startSeq; i < endSeq; i++)
1064 seq = av.getAlignment().getSequenceAt(i);
1065 if ((av.getSelectionGroup() != null)
1066 && av.getSelectionGroup().getSequences(null).contains(seq))
1069 * gray out ids of sequences in selection group (if any)
1071 currentColor = Color.gray;
1072 currentTextColor = Color.black;
1076 currentColor = av.getSequenceColour(seq);
1077 currentTextColor = Color.black;
1080 idGraphics.setColor(currentColor);
1081 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1084 idGraphics.setColor(currentTextColor);
1087 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1088 if (av.isRightAlignIds())
1090 fm = idGraphics.getFontMetrics();
1091 xPos = idWidth - fm.stringWidth(displayId) - 4;
1094 idGraphics.drawString(displayId, xPos,
1095 (((i - startSeq) * charHeight) + charHeight)
1096 - (charHeight / 5));
1098 idGraphics.setFont(av.getFont());
1099 idGraphics.translate(0, -scaleHeight);
1102 * draw the sequences, offset for scale height, and id width (if using a
1103 * single graphics context), then reset to (0, scale height)
1105 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1106 getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
1107 startSeq, endSeq, 0);
1108 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1110 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1113 * draw annotation labels; drawComponent() translates by
1114 * getScrollOffset(), so compensate for that first;
1115 * then reset to (0, scale height)
1117 int offset = getAlabels().getScrollOffset();
1118 idGraphics.translate(0, -offset);
1119 idGraphics.translate(0, alignmentDrawnHeight);
1120 getAlabels().drawComponent(idGraphics, idWidth);
1121 idGraphics.translate(0, -alignmentDrawnHeight);
1124 * draw the annotations starting at
1125 * (idOffset, alignmentHeight) from (0, scaleHeight)
1127 alignmentGraphics.translate(alignmentGraphicsOffset,
1128 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
1183 .getWrappedCanvasWidth(pwidth - idWidth);
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));
1220 pg.translate(-3, ypos
1221 + (av.getAlignment().getHeight() * av.getCharHeight()));
1223 pg.setFont(av.getFont());
1224 labels.drawComponent(pg, idWidth);
1225 pg.translate(+3, -ypos
1226 - (av.getAlignment().getHeight() * av.getCharHeight()));
1230 } while (ypos < totalHeight);
1232 pg.translate(idWidth, 0);
1234 getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
1237 if ((pi * pheight) < totalHeight)
1239 return Printable.PAGE_EXISTS;
1244 return Printable.NO_SUCH_PAGE;
1249 * get current sequence ID panel width, or nominal value if panel were to be
1250 * displayed using default settings
1254 public int getVisibleIdWidth()
1256 return getVisibleIdWidth(true);
1260 * get current sequence ID panel width, or nominal value if panel were to be
1261 * displayed using default settings
1264 * indicate if the Id width for onscreen or offscreen display should
1268 public int getVisibleIdWidth(boolean onscreen)
1270 // see if rendering offscreen - check preferences and calc width accordingly
1271 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1273 return calculateIdWidth(-1).width + 4;
1275 Integer idwidth = null;
1276 if (onscreen || (idwidth = Cache
1277 .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1279 int w = getIdPanel().getWidth();
1280 return (w > 0 ? w : calculateIdWidth().width + 4);
1282 return idwidth.intValue() + 4;
1285 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1287 int boarderBottomOffset = 5;
1288 long pSessionId = System.currentTimeMillis();
1289 headless = (System.getProperty("java.awt.headless") != null
1290 && System.getProperty("java.awt.headless").equals("true"));
1291 if (alignFrame != null && !headless)
1295 alignFrame.setProgressBar(MessageManager
1296 .formatMessage("status.saving_file", new Object[]
1297 { type.getLabel() }), pSessionId);
1302 AlignmentDimension aDimension = getAlignmentDimension();
1305 jalview.util.ImageMaker im;
1306 final String imageAction, imageTitle;
1307 if (type == jalview.util.ImageMaker.TYPE.PNG)
1309 imageAction = "Create PNG image from alignment";
1312 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1314 imageAction = "Create EPS file from alignment";
1315 imageTitle = alignFrame.getTitle();
1319 imageAction = "Create SVG file from alignment";
1320 imageTitle = alignFrame.getTitle();
1323 im = new jalview.util.ImageMaker(this, type, imageAction,
1324 aDimension.getWidth(),
1325 aDimension.getHeight() + boarderBottomOffset, file,
1326 imageTitle, alignFrame, pSessionId, headless);
1327 Graphics graphics = im.getGraphics();
1328 if (av.getWrapAlignment())
1330 if (graphics != null)
1332 printWrappedAlignment(aDimension.getWidth(),
1333 aDimension.getHeight() + boarderBottomOffset, 0,
1340 if (graphics != null)
1342 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
1343 graphics, graphics);
1348 } catch (OutOfMemoryError err)
1351 System.out.println("########################\n" + "OUT OF MEMORY "
1352 + file + "\n" + "########################");
1353 new OOMWarning("Creating Image for " + file, err);
1354 // System.out.println("Create IMAGE: " + err);
1355 } catch (Exception ex)
1357 ex.printStackTrace();
1365 public AlignmentDimension getAlignmentDimension()
1367 int maxwidth = av.getAlignment().getWidth();
1368 if (av.hasHiddenColumns())
1370 maxwidth = av.getAlignment().getHiddenColumns()
1371 .findColumnPosition(maxwidth);
1374 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1375 + getScalePanel().getHeight();
1376 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1378 if (av.getWrapAlignment())
1380 height = getWrappedHeight();
1383 // need to obtain default alignment width and then add in any
1384 // additional allowance for id margin
1385 // this duplicates the calculation in getWrappedHeight but adjusts for
1387 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1388 - alignFrame.getInsets().left - alignFrame.getInsets().right
1389 - getVisibleIdWidth() + getVisibleIdWidth(false);
1393 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1397 else if (av.isShowAnnotation())
1399 height += getAnnotationPanel().adjustPanelHeight() + 3;
1401 return new AlignmentDimension(width, height);
1408 public void makeEPS(File epsFile)
1410 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1416 public void makePNG(File pngFile)
1418 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1421 public void makeSVG(File svgFile)
1423 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1426 public void makePNGImageMap(File imgMapFile, String imageName)
1428 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1429 // ////////////////////////////////////////////
1430 int idWidth = getVisibleIdWidth(false);
1431 FontMetrics fm = getFontMetrics(av.getFont());
1432 int scaleHeight = av.getCharHeight() + fm.getDescent();
1435 // ////////////////////////////////
1436 if (imgMapFile != null)
1440 int s, sSize = av.getAlignment().getHeight(), res,
1441 alwidth = av.getAlignment().getWidth(), g, gSize, f, fSize,
1443 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1444 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1445 out.println("<img src=\"" + imageName
1446 + "\" border=\"0\" usemap=\"#Map\" >"
1447 + "<map name=\"Map\">");
1449 for (s = 0; s < sSize; s++)
1451 sy = s * av.getCharHeight() + scaleHeight;
1453 SequenceI seq = av.getAlignment().getSequenceAt(s);
1454 SequenceFeature[] features = seq.getSequenceFeatures();
1455 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1456 for (res = 0; res < alwidth; res++)
1458 StringBuilder text = new StringBuilder();
1459 String triplet = null;
1460 if (av.getAlignment().isNucleotide())
1462 triplet = ResidueProperties.nucleotideName
1463 .get(seq.getCharAt(res) + "");
1467 triplet = ResidueProperties.aa2Triplet
1468 .get(seq.getCharAt(res) + "");
1471 if (triplet == null)
1476 int alIndex = seq.findPosition(res);
1477 gSize = groups.length;
1478 for (g = 0; g < gSize; g++)
1480 if (text.length() < 1)
1482 text.append("<area shape=\"rect\" coords=\"")
1483 .append((idWidth + res * av.getCharWidth()))
1484 .append(",").append(sy).append(",")
1485 .append((idWidth + (res + 1) * av.getCharWidth()))
1486 .append(",").append((av.getCharHeight() + sy))
1487 .append("\"").append(" onMouseOver=\"toolTip('")
1488 .append(alIndex).append(" ").append(triplet);
1491 if (groups[g].getStartRes() < res
1492 && groups[g].getEndRes() > res)
1494 text.append("<br><em>").append(groups[g].getName())
1499 if (features != null)
1501 if (text.length() < 1)
1503 text.append("<area shape=\"rect\" coords=\"")
1504 .append((idWidth + res * av.getCharWidth()))
1505 .append(",").append(sy).append(",")
1506 .append((idWidth + (res + 1) * av.getCharWidth()))
1507 .append(",").append((av.getCharHeight() + sy))
1508 .append("\"").append(" onMouseOver=\"toolTip('")
1509 .append(alIndex).append(" ").append(triplet);
1511 fSize = features.length;
1512 for (f = 0; f < fSize; f++)
1515 if ((features[f].getBegin() <= seq.findPosition(res))
1516 && (features[f].getEnd() >= seq.findPosition(res)))
1518 if (features[f].isContactFeature())
1520 if (features[f].getBegin() == seq.findPosition(res)
1521 || features[f].getEnd() == seq
1524 text.append("<br>").append(features[f].getType())
1525 .append(" ").append(features[f].getBegin())
1526 .append(":").append(features[f].getEnd());
1531 text.append("<br>");
1532 text.append(features[f].getType());
1533 if (features[f].getDescription() != null && !features[f]
1534 .getType().equals(features[f].getDescription()))
1536 text.append(" ").append(features[f].getDescription());
1539 if (features[f].getValue("status") != null)
1542 .append(features[f].getValue("status"))
1550 if (text.length() > 1)
1552 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1553 out.println(text.toString());
1557 out.println("</map></body></html>");
1560 } catch (Exception ex)
1562 ex.printStackTrace();
1564 } // /////////END OF IMAGE MAP
1568 int getWrappedHeight()
1570 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1572 if (System.getProperty("java.awt.headless") != null
1573 && System.getProperty("java.awt.headless").equals("true"))
1575 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1576 - vscroll.getPreferredSize().width
1577 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1580 int chunkWidth = getSeqPanel().seqCanvas
1581 .getWrappedCanvasWidth(seqPanelWidth);
1583 int hgap = av.getCharHeight();
1584 if (av.getScaleAboveWrapped())
1586 hgap += av.getCharHeight();
1589 int annotationHeight = 0;
1590 if (av.isShowAnnotation())
1592 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1595 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1598 int maxwidth = av.getAlignment().getWidth();
1599 if (av.hasHiddenColumns())
1601 maxwidth = av.getAlignment().getHiddenColumns()
1602 .findColumnPosition(maxwidth) - 1;
1605 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1611 * close the panel - deregisters all listeners and nulls any references to
1614 public void closePanel()
1616 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1617 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1618 PaintRefresher.RemoveComponent(this);
1623 * try to ensure references are nulled
1625 if (annotationPanel != null)
1627 annotationPanel.dispose();
1632 av.removePropertyChangeListener(propertyChangeListener);
1633 jalview.structure.StructureSelectionManager ssm = av
1634 .getStructureSelectionManager();
1635 ssm.removeStructureViewerListener(getSeqPanel(), null);
1636 ssm.removeSelectionListener(getSeqPanel());
1637 ssm.removeCommandListener(av);
1638 ssm.removeStructureViewerListener(getSeqPanel(), null);
1639 ssm.removeSelectionListener(getSeqPanel());
1645 if (Cache.log.isDebugEnabled())
1647 Cache.log.warn("Closing alignment panel which is already closed.");
1653 * Close any open dialogs that would be orphaned when this one is closed
1655 protected void closeChildFrames()
1657 if (calculationDialog != null)
1659 calculationDialog.closeFrame();
1664 * hides or shows dynamic annotation rows based on groups and av state flags
1666 public void updateAnnotation()
1668 updateAnnotation(false, false);
1671 public void updateAnnotation(boolean applyGlobalSettings)
1673 updateAnnotation(applyGlobalSettings, false);
1676 public void updateAnnotation(boolean applyGlobalSettings,
1677 boolean preserveNewGroupSettings)
1679 av.updateGroupAnnotationSettings(applyGlobalSettings,
1680 preserveNewGroupSettings);
1681 adjustAnnotationHeight();
1685 public AlignmentI getAlignment()
1687 return av == null ? null : av.getAlignment();
1691 public String getViewName()
1697 * Make/Unmake this alignment panel the current input focus
1701 public void setSelected(boolean b)
1705 if (alignFrame.getSplitViewContainer() != null)
1708 * bring enclosing SplitFrame to front first if there is one
1710 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1712 alignFrame.setSelected(b);
1713 } catch (Exception ex)
1719 alignFrame.setDisplayedView(this);
1724 public StructureSelectionManager getStructureSelectionManager()
1726 return av.getStructureSelectionManager();
1730 public void raiseOOMWarning(String string, OutOfMemoryError error)
1732 new OOMWarning(string, error, this);
1736 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1739 return new FeatureRenderer(this);
1743 public jalview.api.FeatureRenderer getFeatureRenderer()
1745 return seqPanel.seqCanvas.getFeatureRenderer();
1748 public void updateFeatureRenderer(
1749 jalview.renderer.seqfeatures.FeatureRenderer fr)
1751 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1754 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1756 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1758 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1762 public ScalePanel getScalePanel()
1767 public void setScalePanel(ScalePanel scalePanel)
1769 this.scalePanel = scalePanel;
1772 public SeqPanel getSeqPanel()
1777 public void setSeqPanel(SeqPanel seqPanel)
1779 this.seqPanel = seqPanel;
1782 public AnnotationPanel getAnnotationPanel()
1784 return annotationPanel;
1787 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1789 this.annotationPanel = annotationPanel;
1792 public AnnotationLabels getAlabels()
1797 public void setAlabels(AnnotationLabels alabels)
1799 this.alabels = alabels;
1802 public IdPanel getIdPanel()
1807 public void setIdPanel(IdPanel idPanel)
1809 this.idPanel = idPanel;
1813 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1814 * The aim is to keep the two alignments 'lined up' on their centre columns.
1817 * holds mapped region(s) of this alignment that we are scrolling
1818 * 'to'; may be modified for sequence offset by this method
1819 * @param verticalOffset
1820 * the number of visible sequences to show above the mapped region
1822 public void scrollToCentre(SearchResultsI sr, int verticalOffset)
1825 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1826 * mapped), we can make the scroll-to location a sequence above the one
1829 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1830 List<SequenceI> seqs = av.getAlignment().getSequences();
1833 * This is like AlignmentI.findIndex(seq) but here we are matching the
1834 * dataset sequence not the aligned sequence
1836 boolean matched = false;
1837 for (SequenceI seq : seqs)
1839 if (mappedTo == seq.getDatasetSequence())
1847 return; // failsafe, shouldn't happen
1851 * Scroll to position but centring the target residue.
1853 scrollToPosition(sr, verticalOffset, true, true);
1857 * Set a flag to say do not scroll any (cDNA/protein) complement.
1861 protected void setToScrollComplementPanel(boolean b)
1863 this.scrollComplementaryPanel = b;
1867 * Get whether to scroll complement panel
1869 * @return true if cDNA/protein complement panels should be scrolled
1871 protected boolean isSetToScrollComplementPanel()
1873 return this.scrollComplementaryPanel;
1879 * @adjustHeight if true, try to recalculate panel height for visible
1882 protected void refresh(boolean adjustHeight)
1884 validateAnnotationDimensions(adjustHeight);
1888 // sort, repaint, update overview
1889 paintAlignment(true);
1893 // lightweight repaint
1900 * Property change event fired when a change is made to the viewport ranges
1901 * object associated with this alignment panel's viewport
1903 public void propertyChange(PropertyChangeEvent evt)
1905 // update this panel's scroll values based on the new viewport ranges values
1906 int x = vpRanges.getStartRes();
1907 int y = vpRanges.getStartSeq();
1908 setScrollValues(x, y);
1910 // now update any complementary alignment (its viewport ranges object
1911 // is different so does not get automatically updated)
1912 if (isSetToScrollComplementPanel())
1914 setToScrollComplementPanel(false);
1915 av.scrollComplementaryAlignment();
1916 setToScrollComplementPanel(true);
1921 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1922 * reference should be nulled when the dialog is closed.
1924 * @param calculationChooser
1926 public void setCalculationDialog(CalculationChooser calculationChooser)
1928 calculationDialog = calculationChooser;
1932 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1935 public CalculationChooser getCalculationDialog()
1937 return calculationDialog;