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.SearchResultsI;
29 import jalview.datamodel.SequenceFeature;
30 import jalview.datamodel.SequenceGroup;
31 import jalview.datamodel.SequenceI;
32 import jalview.jbgui.GAlignmentPanel;
33 import jalview.math.AlignmentDimension;
34 import jalview.schemes.ResidueProperties;
35 import jalview.structure.StructureSelectionManager;
36 import jalview.util.MessageManager;
37 import jalview.util.Platform;
38 import jalview.viewmodel.ViewportListenerI;
39 import jalview.viewmodel.ViewportRanges;
41 import java.awt.BorderLayout;
42 import java.awt.Color;
43 import java.awt.Container;
44 import java.awt.Dimension;
46 import java.awt.FontMetrics;
47 import java.awt.Graphics;
48 import java.awt.Insets;
49 import java.awt.event.AdjustmentEvent;
50 import java.awt.event.AdjustmentListener;
51 import java.awt.print.PageFormat;
52 import java.awt.print.Printable;
53 import java.awt.print.PrinterException;
54 import java.beans.PropertyChangeEvent;
55 import java.beans.PropertyChangeListener;
57 import java.io.FileWriter;
58 import java.io.PrintWriter;
59 import java.util.List;
61 import javax.swing.SwingUtilities;
67 * @version $Revision: 1.161 $
69 public class AlignmentPanel extends GAlignmentPanel implements
70 AdjustmentListener, Printable, AlignmentViewPanel,
73 public AlignViewport av;
75 ViewportRanges vpRanges;
77 OverviewPanel overviewPanel;
79 private SeqPanel seqPanel;
81 private IdPanel idPanel;
83 private boolean headless;
85 IdwidthAdjuster idwidthAdjuster;
88 public AlignFrame alignFrame;
90 private ScalePanel scalePanel;
92 private AnnotationPanel annotationPanel;
94 private AnnotationLabels alabels;
96 // this value is set false when selection area being dragged
97 boolean fastPaint = true;
99 private int hextent = 0;
101 private int vextent = 0;
104 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
105 * true, suppresses invoking the same method recursively.
107 private boolean dontScrollComplement;
109 private PropertyChangeListener propertyChangeListener;
112 * Creates a new AlignmentPanel object.
117 public AlignmentPanel(AlignFrame af, final AlignViewport av)
121 vpRanges = av.getRanges();
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 final AlignmentPanel ap = this;
146 propertyChangeListener = new PropertyChangeListener()
149 public void propertyChange(PropertyChangeEvent evt)
151 if (evt.getPropertyName().equals("alignment"))
153 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
158 av.addPropertyChangeListener(propertyChangeListener);
160 av.getRanges().addPropertyChangeListener(this);
162 adjustAnnotationHeight();
167 public AlignViewportI getAlignViewport()
172 public void alignmentChanged()
174 av.alignmentChanged(this);
176 alignFrame.updateEditMenuBar();
178 paintAlignment(true);
185 public void fontChanged()
187 // set idCanvas bufferedImage to null
188 // to prevent drawing old image
189 FontMetrics fm = getFontMetrics(av.getFont());
191 scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
193 idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
194 .getCharHeight() + fm.getDescent()));
196 getIdPanel().getIdCanvas().gg = null;
197 getSeqPanel().seqCanvas.img = null;
198 getAnnotationPanel().adjustPanelHeight();
200 Dimension d = calculateIdWidth();
202 d.setSize(d.width + 4, d.height);
203 getIdPanel().getIdCanvas().setPreferredSize(d);
204 hscrollFillerPanel.setPreferredSize(d);
206 if (overviewPanel != null)
208 overviewPanel.setBoxPosition();
210 if (this.alignFrame.getSplitViewContainer() != null)
212 ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
219 * Calculate the width of the alignment labels based on the displayed names
220 * and any bounds on label width set in preferences.
222 * @return Dimension giving the maximum width of the alignment label panel
223 * that should be used.
225 public Dimension calculateIdWidth()
227 // calculate sensible default width when no preference is available
229 if (av.getIdWidth() < 0)
231 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
232 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
233 r = calculateIdWidth(maxwidth);
234 av.setIdWidth(r.width);
239 r.width = av.getIdWidth();
246 * Calculate the width of the alignment labels based on the displayed names
247 * and any bounds on label width set in preferences.
250 * -1 or maximum width allowed for IdWidth
251 * @return Dimension giving the maximum width of the alignment label panel
252 * that should be used.
254 public Dimension calculateIdWidth(int maxwidth)
256 Container c = new Container();
258 FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
259 Font.ITALIC, av.font.getSize()));
261 AlignmentI al = av.getAlignment();
266 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
268 SequenceI s = al.getSequenceAt(i);
270 id = s.getDisplayId(av.getShowJVSuffix());
272 if (fm.stringWidth(id) > idWidth)
274 idWidth = fm.stringWidth(id);
280 // Also check annotation label widths
283 if (al.getAlignmentAnnotation() != null)
285 fm = c.getFontMetrics(getAlabels().getFont());
287 while (i < al.getAlignmentAnnotation().length)
289 String label = al.getAlignmentAnnotation()[i].label;
291 if (fm.stringWidth(label) > idWidth)
293 idWidth = fm.stringWidth(label);
300 return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
305 * Highlight the given results on the alignment.
308 public void highlightSearchResults(SearchResultsI results)
310 scrollToPosition(results);
311 getSeqPanel().seqCanvas.highlightSearchResults(results);
315 * Scroll the view to show the position of the highlighted region in results
316 * (if any) and redraw the overview
320 public boolean scrollToPosition(SearchResultsI results)
322 return scrollToPosition(results, 0, true, false);
326 * Scroll the view to show the position of the highlighted region in results
329 * @param searchResults
330 * @param redrawOverview
333 public boolean scrollToPosition(SearchResultsI searchResults,
334 boolean redrawOverview)
336 return scrollToPosition(searchResults, 0, redrawOverview, false);
340 * Scroll the view to show the position of the highlighted region in results
344 * @param verticalOffset
345 * if greater than zero, allows scrolling to a position below the
346 * first displayed sequence
347 * @param redrawOverview
348 * - when set, the overview will be recalculated (takes longer)
350 * if true, try to centre the search results horizontally in the view
351 * @return false if results were not found
353 public boolean scrollToPosition(SearchResultsI results,
354 int verticalOffset, boolean redrawOverview, boolean centre)
356 int startv, endv, starts, ends;
357 // TODO: properly locate search results in view when large numbers of hidden
358 // columns exist before highlighted region
359 // do we need to scroll the panel?
360 // TODO: tons of nullpointerexceptions raised here.
361 if (results != null && results.getSize() > 0 && av != null
362 && av.getAlignment() != null)
364 int seqIndex = av.getAlignment().findIndex(results);
369 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
371 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
379 // System.err.println(this.av.viewName + " Seq : " + seqIndex
380 // + " Scroll to " + start + "," + end);
383 * To centre results, scroll to positions half the visible width
384 * left/right of the start/end positions
388 int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
389 start = Math.max(start - offset, 0);
390 end = end + offset - 1;
396 if (end == seq.getEnd())
400 if (av.hasHiddenColumns())
402 start = av.getColumnSelection().findColumnPosition(start);
403 end = av.getColumnSelection().findColumnPosition(end);
406 if (!av.getColumnSelection().isVisible(r[0]))
408 // don't scroll - position isn't visible
415 * allow for offset of target sequence (actually scroll to one above it)
417 seqIndex = Math.max(0, seqIndex - verticalOffset);
419 // System.out.println("start=" + start + ", end=" + end + ", startv="
420 // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
421 // + av.getStartSeq() + ", ends=" + av.getEndSeq());
422 if (!av.getWrapAlignment())
424 if ((startv = vpRanges.getStartRes()) >= start)
427 * Scroll left to make start of search results visible
429 // setScrollValues(start - 1, seqIndex); // plus one residue
430 setScrollValues(start, seqIndex);
432 else if ((endv = vpRanges.getEndRes()) <= end)
435 * Scroll right to make end of search results visible
437 // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
438 setScrollValues(startv + end - endv, seqIndex);
440 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
443 * Scroll up to make start of search results visible
445 setScrollValues(vpRanges.getStartRes(), seqIndex);
447 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
450 * Scroll down to make end of search results visible
452 setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
456 * Else results are already visible - no need to scroll
461 scrollToWrappedVisible(start);
464 if (redrawOverview && overviewPanel != null)
466 overviewPanel.setBoxPosition();
468 paintAlignment(redrawOverview);
472 void scrollToWrappedVisible(int res)
474 int cwidth = getSeqPanel().seqCanvas
475 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
476 if (res < vpRanges.getStartRes()
477 || res >= (vpRanges.getStartRes() + cwidth))
479 vscroll.setValue((res / cwidth));
480 // vpRanges.setStartRes(vscroll.getValue() * cwidth);
488 * @return DOCUMENT ME!
490 public OverviewPanel getOverviewPanel()
492 return overviewPanel;
501 public void setOverviewPanel(OverviewPanel op)
509 * Hide or show annotation panel
512 public void setAnnotationVisible(boolean b)
514 if (!av.getWrapAlignment())
516 annotationSpaceFillerHolder.setVisible(b);
517 annotationScroller.setVisible(b);
523 * automatically adjust annotation panel height for new annotation whilst
524 * ensuring the alignment is still visible.
527 public void adjustAnnotationHeight()
529 // TODO: display vertical annotation scrollbar if necessary
530 // this is called after loading new annotation onto alignment
531 if (alignFrame.getHeight() == 0)
533 System.out.println("NEEDS FIXING");
535 validateAnnotationDimensions(true);
537 paintAlignment(true);
541 * calculate the annotation dimensions and refresh slider values accordingly.
542 * need to do repaints/notifys afterwards.
544 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
546 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
548 if (adjustPanelHeight)
550 int rowHeight = av.getCharHeight();
551 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
554 * Estimate available height in the AlignFrame for alignment +
555 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
556 * hscroll, status bar (as these are not laid out we can't inspect their
557 * actual heights). Insets gives frame borders.
559 int stuff = Platform.isAMac() ? 80 : 100;
560 Insets insets = alignFrame.getInsets();
561 int availableHeight = alignFrame.getHeight() - stuff - insets.top
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, availableHeight - 2
576 // maintain same window layout whilst updating sliders
577 annotationHeight = annotationScroller.getSize().height;
581 annotationScroller.setPreferredSize(new Dimension(annotationScroller
582 .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 vpRanges.setStartSeq(0);
605 scalePanelHolder.setVisible(!wrap);
606 hscroll.setVisible(!wrap);
607 idwidthAdjuster.setVisible(!wrap);
611 annotationScroller.setVisible(false);
612 annotationSpaceFillerHolder.setVisible(false);
614 else if (av.isShowAnnotation())
616 annotationScroller.setVisible(true);
617 annotationSpaceFillerHolder.setVisible(true);
620 idSpaceFillerPanel1.setVisible(!wrap);
625 // return value is true if the scroll is valid
626 public boolean scrollUp(boolean up)
630 if (vscroll.getValue() < 1)
636 vscroll.setValue(vscroll.getValue() - 1);
640 if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
646 vscroll.setValue(vscroll.getValue() + 1);
660 * @return DOCUMENT ME!
662 public boolean scrollRight(boolean right)
666 if (hscroll.getValue() < 1)
672 hscroll.setValue(hscroll.getValue() - 1);
676 if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
682 hscroll.setValue(hscroll.getValue() + 1);
691 * Adjust row/column scrollers to show a visible position in the alignment.
694 * visible column to scroll to
696 * visible row to scroll to
699 public void setScrollValues(int x, int y)
701 if (av == null || av.getAlignment() == null)
705 int width = av.getAlignment().getWidth();
706 int height = av.getAlignment().getHeight();
708 if (av.hasHiddenColumns())
710 // reset the width to exclude hidden columns
711 width = av.getColumnSelection().findColumnPosition(width);
714 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
715 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
722 if (vextent > height)
727 if ((hextent + x) > width)
732 if ((vextent + y) > height)
734 y = height - vextent;
747 // update endRes after x has (possibly) been adjusted
748 vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
749 .getCharWidth())) - 1);
752 * each scroll adjustment triggers adjustmentValueChanged, which resets the
753 * 'do not scroll complement' flag; ensure it is the same for both
756 // boolean flag = isDontScrollComplement();
757 hscroll.setValues(x, hextent, 0, width);
758 // setDontScrollComplement(flag);
759 vscroll.setValues(y, vextent, 0, height);
769 public void adjustmentValueChanged(AdjustmentEvent evt)
771 int oldX = vpRanges.getStartRes();
772 int oldY = vpRanges.getStartSeq();
774 if (evt.getSource() == hscroll)
776 int x = hscroll.getValue();
781 // vpRanges.setStartRes(x);
782 // vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
783 // .getCharWidth())) - 1);
784 vpRanges.setStartEndRes(
786 (x + (getSeqPanel().seqCanvas.getWidth() / av
787 .getCharWidth())) - 1);
790 if (evt.getSource() == vscroll)
792 int offy = vscroll.getValue();
794 if (av.getWrapAlignment())
802 int rowSize = getSeqPanel().seqCanvas
803 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
804 vpRanges.setStartEndRes(offy * rowSize, (offy + 1) * rowSize);
805 // vpRanges.setStartRes(offy * rowSize);
806 // vpRanges.setEndRes((offy + 1) * rowSize);
811 // This is only called if file loaded is a jar file that
812 // was wrapped when saved and user has wrap alignment true
813 // as preference setting
814 SwingUtilities.invokeLater(new Runnable()
819 setScrollValues(vpRanges.getStartRes(),
820 vpRanges.getStartSeq());
831 // vpRanges.setStartSeq(offy);
832 // vpRanges.setEndSeq(offy
833 // + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
835 vpRanges.setStartEndSeq(
838 + (getSeqPanel().seqCanvas.getHeight() / av
839 .getCharHeight()) - 1);
843 /*if (overviewPanel != null)
845 overviewPanel.setBoxPosition();
848 // int scrollX = vpRanges.getStartRes() - oldX;
849 // int scrollY = vpRanges.getStartSeq() - oldY;
851 if (av.getWrapAlignment() || !fastPaint)
857 // Make sure we're not trying to draw a panel
858 // larger than the visible window
859 if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
861 scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
863 else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
865 scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
868 if (scrollX != 0 || scrollY != 0)
870 getIdPanel().getIdCanvas().fastPaint(scrollY);
871 getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
872 getScalePanel().repaint();
874 if (av.isShowAnnotation() && scrollX != 0)
876 getAnnotationPanel().fastPaint(scrollX);
881 * If there is one, scroll the (Protein/cDNA) complementary alignment to
882 * match, unless we are ourselves doing that.
884 /* if (isDontScrollComplement())
886 setDontScrollComplement(false);
890 av.scrollComplementaryAlignment();
895 * Repaint the alignment including the annotations and overview panels (if
899 public void paintAlignment(boolean updateOverview)
901 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
902 av.isShowAutocalculatedAbove());
903 sorter.sort(getAlignment().getAlignmentAnnotation(),
904 av.getSortAnnotationsBy());
909 // TODO: determine if this paintAlignment changed structure colours
910 av.getStructureSelectionManager().sequenceColoursChanged(this);
912 if (overviewPanel != null)
914 overviewPanel.updateOverviewImage();
926 public void paintComponent(Graphics g)
930 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
931 idPanelHolder.setPreferredSize(d);
932 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
936 * set scroll bar positions; first suppress this being 'followed' in any
937 * complementary split pane
939 setDontScrollComplement(true);
941 if (av.getWrapAlignment())
943 int maxwidth = av.getAlignment().getWidth();
945 if (av.hasHiddenColumns())
947 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
950 int canvasWidth = getSeqPanel().seqCanvas
951 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
955 / getSeqPanel().seqCanvas
956 .getWrappedCanvasWidth(getSeqPanel().seqCanvas
958 vscroll.setMaximum(max);
959 vscroll.setUnitIncrement(1);
960 vscroll.setVisibleAmount(1);
965 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
979 * @return DOCUMENT ME!
981 * @throws PrinterException
985 public int print(Graphics pg, PageFormat pf, int pi)
986 throws PrinterException
988 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
990 int pwidth = (int) pf.getImageableWidth();
991 int pheight = (int) pf.getImageableHeight();
993 if (av.getWrapAlignment())
995 return printWrappedAlignment(pwidth, pheight, pi, pg);
999 return printUnwrapped(pwidth, pheight, pi, pg, pg);
1015 * @return DOCUMENT ME!
1017 * @throws PrinterException
1021 * Draws the alignment image, including sequence ids, sequences, and
1022 * annotation labels and annotations if shown, on either one or two Graphics
1029 * the graphics context for sequence ids and annotation labels
1030 * @param alignmentGraphics
1031 * the graphics context for sequences and annotations (may or may not
1032 * be the same context as idGraphics)
1034 * @throws PrinterException
1036 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
1037 Graphics idGraphics, Graphics alignmentGraphics)
1038 throws PrinterException
1040 final int idWidth = getVisibleIdWidth(false);
1043 * Get the horizontal offset to where we draw the sequences.
1044 * This is idWidth if using a single Graphics context, else zero.
1046 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
1048 FontMetrics fm = getFontMetrics(av.getFont());
1049 int charHeight = av.getCharHeight();
1050 int scaleHeight = charHeight + fm.getDescent();
1052 idGraphics.setColor(Color.white);
1053 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
1054 idGraphics.setFont(av.getFont());
1057 * How many sequences and residues can we fit on a printable page?
1059 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1061 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1063 int alignmentWidth = av.getAlignment().getWidth();
1064 int pagesWide = (alignmentWidth / totalRes) + 1;
1066 final int startRes = (pi % pagesWide) * totalRes;
1067 int endRes = (startRes + totalRes) - 1;
1069 if (endRes > (alignmentWidth - 1))
1071 endRes = alignmentWidth - 1;
1074 final int startSeq = (pi / pagesWide) * totalSeq;
1075 int endSeq = startSeq + totalSeq;
1077 int alignmentHeight = av.getAlignment().getHeight();
1078 if (endSeq > alignmentHeight)
1080 endSeq = alignmentHeight;
1083 int pagesHigh = ((alignmentHeight / totalSeq) + 1)
1086 if (av.isShowAnnotation())
1088 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1091 pagesHigh /= pageHeight;
1093 if (pi >= (pagesWide * pagesHigh))
1095 return Printable.NO_SUCH_PAGE;
1097 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
1101 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1103 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1104 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1105 pageWidth - idWidth, scaleHeight);
1106 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1109 * Draw the sequence ids, offset for scale height,
1110 * then reset to top left (0, 0)
1112 idGraphics.translate(0, scaleHeight);
1113 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1114 Color currentColor = null;
1115 Color currentTextColor = null;
1118 for (int i = startSeq; i < endSeq; i++)
1120 seq = av.getAlignment().getSequenceAt(i);
1121 if ((av.getSelectionGroup() != null)
1122 && av.getSelectionGroup().getSequences(null).contains(seq))
1125 * gray out ids of sequences in selection group (if any)
1127 currentColor = Color.gray;
1128 currentTextColor = Color.black;
1132 currentColor = av.getSequenceColour(seq);
1133 currentTextColor = Color.black;
1136 idGraphics.setColor(currentColor);
1137 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1140 idGraphics.setColor(currentTextColor);
1143 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1144 if (av.isRightAlignIds())
1146 fm = idGraphics.getFontMetrics();
1148 - fm.stringWidth(displayId)
1152 idGraphics.drawString(displayId, xPos,
1153 (((i - startSeq) * charHeight) + charHeight)
1154 - (charHeight / 5));
1156 idGraphics.setFont(av.getFont());
1157 idGraphics.translate(0, -scaleHeight);
1160 * draw the sequences, offset for scale height, and id width (if using a
1161 * single graphics context), then reset to (0, scale height)
1163 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1164 getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
1165 startSeq, endSeq, 0);
1166 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1168 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1171 * draw annotation labels; drawComponent() translates by
1172 * getScrollOffset(), so compensate for that first;
1173 * then reset to (0, scale height)
1175 int offset = getAlabels().getScrollOffset();
1176 idGraphics.translate(0, -offset);
1177 idGraphics.translate(0, alignmentDrawnHeight);
1178 getAlabels().drawComponent(idGraphics, idWidth);
1179 idGraphics.translate(0, -alignmentDrawnHeight);
1182 * draw the annotations starting at
1183 * (idOffset, alignmentHeight) from (0, scaleHeight)
1185 alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
1186 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1187 alignmentGraphics, -1, startRes, endRes + 1);
1190 return Printable.PAGE_EXISTS;
1205 * @return DOCUMENT ME!
1207 * @throws PrinterException
1210 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1211 Graphics pg) throws PrinterException
1213 int annotationHeight = 0;
1214 AnnotationLabels labels = null;
1215 if (av.isShowAnnotation())
1217 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1218 labels = new AnnotationLabels(av);
1221 int hgap = av.getCharHeight();
1222 if (av.getScaleAboveWrapped())
1224 hgap += av.getCharHeight();
1227 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1230 int idWidth = getVisibleIdWidth(false);
1232 int maxwidth = av.getAlignment().getWidth();
1233 if (av.hasHiddenColumns())
1235 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1238 int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
1241 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1243 pg.setColor(Color.white);
1244 pg.fillRect(0, 0, pwidth, pheight);
1245 pg.setFont(av.getFont());
1249 pg.setColor(Color.black);
1251 pg.translate(0, -pi * pheight);
1253 pg.setClip(0, pi * pheight, pwidth, pheight);
1259 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1261 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1262 SequenceI s = av.getAlignment().getSequenceAt(i);
1263 String string = s.getDisplayId(av.getShowJVSuffix());
1265 if (av.isRightAlignIds())
1267 FontMetrics fm = pg.getFontMetrics();
1268 xPos = idWidth - fm.stringWidth(string) - 4;
1270 pg.drawString(string, xPos,
1271 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1272 - (av.getCharHeight() / 5));
1277 ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
1279 pg.setFont(av.getFont());
1280 labels.drawComponent(pg, idWidth);
1284 - (av.getAlignment().getHeight() * av
1289 } while (ypos < totalHeight);
1291 pg.translate(idWidth, 0);
1293 getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
1296 if ((pi * pheight) < totalHeight)
1298 return Printable.PAGE_EXISTS;
1303 return Printable.NO_SUCH_PAGE;
1308 * get current sequence ID panel width, or nominal value if panel were to be
1309 * displayed using default settings
1313 public int getVisibleIdWidth()
1315 return getVisibleIdWidth(true);
1319 * get current sequence ID panel width, or nominal value if panel were to be
1320 * displayed using default settings
1323 * indicate if the Id width for onscreen or offscreen display should
1327 public int getVisibleIdWidth(boolean onscreen)
1329 // see if rendering offscreen - check preferences and calc width accordingly
1330 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1332 return calculateIdWidth(-1).width + 4;
1334 Integer idwidth = null;
1336 || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1338 int w = getIdPanel().getWidth();
1339 return (w > 0 ? w : calculateIdWidth().width + 4);
1341 return idwidth.intValue() + 4;
1344 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1346 int boarderBottomOffset = 5;
1347 long pSessionId = System.currentTimeMillis();
1348 headless = (System.getProperty("java.awt.headless") != null && System
1349 .getProperty("java.awt.headless").equals("true"));
1350 if (alignFrame != null && !headless)
1354 alignFrame.setProgressBar(MessageManager.formatMessage(
1355 "status.saving_file", new Object[] { type.getLabel() }),
1361 AlignmentDimension aDimension = getAlignmentDimension();
1364 jalview.util.ImageMaker im;
1365 final String imageAction, imageTitle;
1366 if (type == jalview.util.ImageMaker.TYPE.PNG)
1368 imageAction = "Create PNG image from alignment";
1371 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1373 imageAction = "Create EPS file from alignment";
1374 imageTitle = alignFrame.getTitle();
1378 imageAction = "Create SVG file from alignment";
1379 imageTitle = alignFrame.getTitle();
1382 im = new jalview.util.ImageMaker(this, type, imageAction,
1383 aDimension.getWidth(), aDimension.getHeight()
1384 + boarderBottomOffset, file, imageTitle,
1385 alignFrame, pSessionId, headless);
1386 Graphics graphics = im.getGraphics();
1387 if (av.getWrapAlignment())
1389 if (graphics != null)
1391 printWrappedAlignment(aDimension.getWidth(),
1392 aDimension.getHeight() + boarderBottomOffset, 0,
1399 if (graphics != null)
1401 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
1402 0, graphics, graphics);
1407 } catch (OutOfMemoryError err)
1410 System.out.println("########################\n" + "OUT OF MEMORY "
1411 + file + "\n" + "########################");
1412 new OOMWarning("Creating Image for " + file, err);
1413 // System.out.println("Create IMAGE: " + err);
1414 } catch (Exception ex)
1416 ex.printStackTrace();
1424 public AlignmentDimension getAlignmentDimension()
1426 int maxwidth = av.getAlignment().getWidth();
1427 if (av.hasHiddenColumns())
1429 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
1432 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1433 + getScalePanel().getHeight();
1434 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1436 if (av.getWrapAlignment())
1438 height = getWrappedHeight();
1441 // need to obtain default alignment width and then add in any
1442 // additional allowance for id margin
1443 // this duplicates the calculation in getWrappedHeight but adjusts for
1445 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1446 - alignFrame.getInsets().left
1447 - alignFrame.getInsets().right - getVisibleIdWidth()
1448 + getVisibleIdWidth(false);
1452 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1456 else if (av.isShowAnnotation())
1458 height += getAnnotationPanel().adjustPanelHeight() + 3;
1460 return new AlignmentDimension(width, height);
1467 public void makeEPS(File epsFile)
1469 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1475 public void makePNG(File pngFile)
1477 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1480 public void makeSVG(File svgFile)
1482 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1485 public void makePNGImageMap(File imgMapFile, String imageName)
1487 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1488 // ////////////////////////////////////////////
1489 int idWidth = getVisibleIdWidth(false);
1490 FontMetrics fm = getFontMetrics(av.getFont());
1491 int scaleHeight = av.getCharHeight() + fm.getDescent();
1494 // ////////////////////////////////
1495 if (imgMapFile != null)
1499 int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
1500 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
1501 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1502 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1503 out.println("<img src=\"" + imageName
1504 + "\" border=\"0\" usemap=\"#Map\" >"
1505 + "<map name=\"Map\">");
1507 for (s = 0; s < sSize; s++)
1509 sy = s * av.getCharHeight() + scaleHeight;
1511 SequenceI seq = av.getAlignment().getSequenceAt(s);
1512 SequenceFeature[] features = seq.getSequenceFeatures();
1513 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1514 for (res = 0; res < alwidth; res++)
1516 StringBuilder text = new StringBuilder();
1517 String triplet = null;
1518 if (av.getAlignment().isNucleotide())
1520 triplet = ResidueProperties.nucleotideName.get(seq
1521 .getCharAt(res) + "");
1525 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
1529 if (triplet == null)
1534 int alIndex = seq.findPosition(res);
1535 gSize = groups.length;
1536 for (g = 0; g < gSize; g++)
1538 if (text.length() < 1)
1540 text.append("<area shape=\"rect\" coords=\"")
1541 .append((idWidth + res * av.getCharWidth()))
1542 .append(",").append(sy).append(",")
1543 .append((idWidth + (res + 1) * av.getCharWidth()))
1544 .append(",").append((av.getCharHeight() + sy))
1545 .append("\"").append(" onMouseOver=\"toolTip('")
1546 .append(alIndex).append(" ").append(triplet);
1549 if (groups[g].getStartRes() < res
1550 && groups[g].getEndRes() > res)
1552 text.append("<br><em>").append(groups[g].getName())
1557 if (features != null)
1559 if (text.length() < 1)
1561 text.append("<area shape=\"rect\" coords=\"")
1562 .append((idWidth + res * av.getCharWidth()))
1563 .append(",").append(sy).append(",")
1564 .append((idWidth + (res + 1) * av.getCharWidth()))
1565 .append(",").append((av.getCharHeight() + sy))
1566 .append("\"").append(" onMouseOver=\"toolTip('")
1567 .append(alIndex).append(" ").append(triplet);
1569 fSize = features.length;
1570 for (f = 0; f < fSize; f++)
1573 if ((features[f].getBegin() <= seq.findPosition(res))
1574 && (features[f].getEnd() >= seq.findPosition(res)))
1576 if (features[f].isContactFeature())
1578 if (features[f].getBegin() == seq.findPosition(res)
1579 || features[f].getEnd() == seq
1582 text.append("<br>").append(features[f].getType())
1583 .append(" ").append(features[f].getBegin())
1584 .append(":").append(features[f].getEnd());
1589 text.append("<br>");
1590 text.append(features[f].getType());
1591 if (features[f].getDescription() != null
1592 && !features[f].getType().equals(
1593 features[f].getDescription()))
1595 text.append(" ").append(features[f].getDescription());
1598 if (features[f].getValue("status") != null)
1600 text.append(" (").append(features[f].getValue("status"))
1608 if (text.length() > 1)
1610 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1611 out.println(text.toString());
1615 out.println("</map></body></html>");
1618 } catch (Exception ex)
1620 ex.printStackTrace();
1622 } // /////////END OF IMAGE MAP
1626 int getWrappedHeight()
1628 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1630 if (System.getProperty("java.awt.headless") != null
1631 && System.getProperty("java.awt.headless").equals("true"))
1633 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1634 - vscroll.getPreferredSize().width
1635 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1638 int chunkWidth = getSeqPanel().seqCanvas
1639 .getWrappedCanvasWidth(seqPanelWidth);
1641 int hgap = av.getCharHeight();
1642 if (av.getScaleAboveWrapped())
1644 hgap += av.getCharHeight();
1647 int annotationHeight = 0;
1648 if (av.isShowAnnotation())
1650 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1653 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1656 int maxwidth = av.getAlignment().getWidth();
1657 if (av.hasHiddenColumns())
1659 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1662 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1668 * close the panel - deregisters all listeners and nulls any references to
1671 public void closePanel()
1673 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1674 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1675 PaintRefresher.RemoveComponent(this);
1678 * try to ensure references are nulled
1680 if (annotationPanel != null)
1682 annotationPanel.dispose();
1687 av.removePropertyChangeListener(propertyChangeListener);
1688 jalview.structure.StructureSelectionManager ssm = av
1689 .getStructureSelectionManager();
1690 ssm.removeStructureViewerListener(getSeqPanel(), null);
1691 ssm.removeSelectionListener(getSeqPanel());
1692 ssm.removeCommandListener(av);
1693 ssm.removeStructureViewerListener(getSeqPanel(), null);
1694 ssm.removeSelectionListener(getSeqPanel());
1700 if (Cache.log.isDebugEnabled())
1702 Cache.log.warn("Closing alignment panel which is already closed.");
1708 * hides or shows dynamic annotation rows based on groups and av state flags
1710 public void updateAnnotation()
1712 updateAnnotation(false, false);
1715 public void updateAnnotation(boolean applyGlobalSettings)
1717 updateAnnotation(applyGlobalSettings, false);
1720 public void updateAnnotation(boolean applyGlobalSettings,
1721 boolean preserveNewGroupSettings)
1723 av.updateGroupAnnotationSettings(applyGlobalSettings,
1724 preserveNewGroupSettings);
1725 adjustAnnotationHeight();
1729 public AlignmentI getAlignment()
1731 return av == null ? null : av.getAlignment();
1735 public String getViewName()
1741 * Make/Unmake this alignment panel the current input focus
1745 public void setSelected(boolean b)
1749 if (alignFrame.getSplitViewContainer() != null)
1752 * bring enclosing SplitFrame to front first if there is one
1754 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1756 alignFrame.setSelected(b);
1757 } catch (Exception ex)
1763 alignFrame.setDisplayedView(this);
1768 public StructureSelectionManager getStructureSelectionManager()
1770 return av.getStructureSelectionManager();
1774 public void raiseOOMWarning(String string, OutOfMemoryError error)
1776 new OOMWarning(string, error, this);
1780 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1783 return new FeatureRenderer(this);
1787 public jalview.api.FeatureRenderer getFeatureRenderer()
1789 return seqPanel.seqCanvas.getFeatureRenderer();
1792 public void updateFeatureRenderer(
1793 jalview.renderer.seqfeatures.FeatureRenderer fr)
1795 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1798 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1800 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1802 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1806 public ScalePanel getScalePanel()
1811 public void setScalePanel(ScalePanel scalePanel)
1813 this.scalePanel = scalePanel;
1816 public SeqPanel getSeqPanel()
1821 public void setSeqPanel(SeqPanel seqPanel)
1823 this.seqPanel = seqPanel;
1826 public AnnotationPanel getAnnotationPanel()
1828 return annotationPanel;
1831 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1833 this.annotationPanel = annotationPanel;
1836 public AnnotationLabels getAlabels()
1841 public void setAlabels(AnnotationLabels alabels)
1843 this.alabels = alabels;
1846 public IdPanel getIdPanel()
1851 public void setIdPanel(IdPanel idPanel)
1853 this.idPanel = idPanel;
1857 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1858 * The aim is to keep the two alignments 'lined up' on their centre columns.
1861 * holds mapped region(s) of this alignment that we are scrolling
1862 * 'to'; may be modified for sequence offset by this method
1863 * @param verticalOffset
1864 * the number of visible sequences to show above the mapped region
1866 public void scrollToCentre(SearchResultsI sr, int verticalOffset)
1869 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1870 * mapped), we can make the scroll-to location a sequence above the one
1873 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1874 List<SequenceI> seqs = av.getAlignment().getSequences();
1877 * This is like AlignmentI.findIndex(seq) but here we are matching the
1878 * dataset sequence not the aligned sequence
1880 boolean matched = false;
1881 for (SequenceI seq : seqs)
1883 if (mappedTo == seq.getDatasetSequence())
1891 return; // failsafe, shouldn't happen
1895 * Scroll to position but centring the target residue.
1897 scrollToPosition(sr, verticalOffset, true, true);
1901 * Set a flag to say do not scroll any (cDNA/protein) complement.
1905 protected void setDontScrollComplement(boolean b)
1907 this.dontScrollComplement = b;
1910 protected boolean isDontScrollComplement()
1912 return this.dontScrollComplement;
1918 * @adjustHeight if true, try to recalculate panel height for visible
1921 protected void refresh(boolean adjustHeight)
1923 validateAnnotationDimensions(adjustHeight);
1927 // sort, repaint, update overview
1928 paintAlignment(true);
1932 // lightweight repaint
1938 public void propertyChange(PropertyChangeEvent evt)
1940 int x = vpRanges.getStartRes();
1941 int y = vpRanges.getStartSeq();
1942 setScrollValues(x, y);