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.event.ComponentAdapter;
52 import java.awt.event.ComponentEvent;
53 import java.awt.print.PageFormat;
54 import java.awt.print.Printable;
55 import java.awt.print.PrinterException;
56 import java.beans.PropertyChangeEvent;
57 import java.beans.PropertyChangeListener;
59 import java.io.FileWriter;
60 import java.io.PrintWriter;
61 import java.util.List;
63 import javax.swing.SwingUtilities;
69 * @version $Revision: 1.161 $
71 public class AlignmentPanel extends GAlignmentPanel implements
72 AdjustmentListener, Printable, AlignmentViewPanel,
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 * true, suppresses invoking the same method recursively.
109 private boolean dontScrollComplement = false;
111 private PropertyChangeListener propertyChangeListener;
114 * Creates a new AlignmentPanel object.
119 public AlignmentPanel(AlignFrame af, final AlignViewport av)
123 vpRanges = av.getRanges();
124 setSeqPanel(new SeqPanel(av, this));
125 setIdPanel(new IdPanel(av, this));
127 setScalePanel(new ScalePanel(av, this));
129 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
130 idwidthAdjuster = new IdwidthAdjuster(this);
131 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
133 setAnnotationPanel(new AnnotationPanel(this));
134 setAlabels(new AnnotationLabels(this));
136 annotationScroller.setViewportView(getAnnotationPanel());
137 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
139 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
140 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
142 setScrollValues(0, 0);
144 hscroll.addAdjustmentListener(this);
145 vscroll.addAdjustmentListener(this);
147 addComponentListener(new ComponentAdapter()
150 public void componentResized(ComponentEvent evt)
152 // reset the viewport ranges when the alignment panel is resized
153 // in particular, this initialises the end residue value when Jalview
155 if (av.getWrapAlignment())
157 int widthInRes = getSeqPanel().seqCanvas
158 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
159 vpRanges.setViewportWidth(widthInRes);
163 int widthInRes = getSeqPanel().seqCanvas.getWidth()
165 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
166 / av.getCharHeight();
168 vpRanges.setViewportWidth(widthInRes);
169 vpRanges.setViewportHeight(heightInSeq);
175 final AlignmentPanel ap = this;
176 propertyChangeListener = new PropertyChangeListener()
179 public void propertyChange(PropertyChangeEvent evt)
181 if (evt.getPropertyName().equals("alignment"))
183 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
188 av.addPropertyChangeListener(propertyChangeListener);
190 av.getRanges().addPropertyChangeListener(this);
192 adjustAnnotationHeight();
197 public AlignViewportI getAlignViewport()
202 public void alignmentChanged()
204 av.alignmentChanged(this);
206 alignFrame.updateEditMenuBar();
208 paintAlignment(true);
215 public void fontChanged()
217 // set idCanvas bufferedImage to null
218 // to prevent drawing old image
219 FontMetrics fm = getFontMetrics(av.getFont());
221 scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
223 idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
224 .getCharHeight() + fm.getDescent()));
226 getIdPanel().getIdCanvas().gg = null;
227 getSeqPanel().seqCanvas.img = null;
228 getAnnotationPanel().adjustPanelHeight();
230 Dimension d = calculateIdWidth();
232 d.setSize(d.width + 4, d.height);
233 getIdPanel().getIdCanvas().setPreferredSize(d);
234 hscrollFillerPanel.setPreferredSize(d);
236 if (this.alignFrame.getSplitViewContainer() != null)
238 ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
245 * Calculate the width of the alignment labels based on the displayed names
246 * and any bounds on label width set in preferences.
248 * @return Dimension giving the maximum width of the alignment label panel
249 * that should be used.
251 public Dimension calculateIdWidth()
253 // calculate sensible default width when no preference is available
255 if (av.getIdWidth() < 0)
257 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
258 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
259 r = calculateIdWidth(maxwidth);
260 av.setIdWidth(r.width);
265 r.width = av.getIdWidth();
272 * Calculate the width of the alignment labels based on the displayed names
273 * and any bounds on label width set in preferences.
276 * -1 or maximum width allowed for IdWidth
277 * @return Dimension giving the maximum width of the alignment label panel
278 * that should be used.
280 public Dimension calculateIdWidth(int maxwidth)
282 Container c = new Container();
284 FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
285 Font.ITALIC, av.font.getSize()));
287 AlignmentI al = av.getAlignment();
292 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
294 SequenceI s = al.getSequenceAt(i);
296 id = s.getDisplayId(av.getShowJVSuffix());
298 if (fm.stringWidth(id) > idWidth)
300 idWidth = fm.stringWidth(id);
306 // Also check annotation label widths
309 if (al.getAlignmentAnnotation() != null)
311 fm = c.getFontMetrics(getAlabels().getFont());
313 while (i < al.getAlignmentAnnotation().length)
315 String label = al.getAlignmentAnnotation()[i].label;
317 if (fm.stringWidth(label) > idWidth)
319 idWidth = fm.stringWidth(label);
326 return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
331 * Highlight the given results on the alignment.
334 public void highlightSearchResults(SearchResultsI results)
336 scrollToPosition(results);
337 getSeqPanel().seqCanvas.highlightSearchResults(results);
341 * Scroll the view to show the position of the highlighted region in results
342 * (if any) and redraw the overview
346 public boolean scrollToPosition(SearchResultsI results)
348 return scrollToPosition(results, 0, true, false);
352 * Scroll the view to show the position of the highlighted region in results
355 * @param searchResults
356 * @param redrawOverview
359 public boolean scrollToPosition(SearchResultsI searchResults,
360 boolean redrawOverview)
362 return scrollToPosition(searchResults, 0, redrawOverview, false);
366 * Scroll the view to show the position of the highlighted region in results
370 * @param verticalOffset
371 * if greater than zero, allows scrolling to a position below the
372 * first displayed sequence
373 * @param redrawOverview
374 * - when set, the overview will be recalculated (takes longer)
376 * if true, try to centre the search results horizontally in the view
377 * @return false if results were not found
379 public boolean scrollToPosition(SearchResultsI results,
380 int verticalOffset, boolean redrawOverview, boolean centre)
382 int startv, endv, starts, ends;
383 // TODO: properly locate search results in view when large numbers of hidden
384 // columns exist before highlighted region
385 // do we need to scroll the panel?
386 // TODO: tons of nullpointerexceptions raised here.
387 if (results != null && results.getSize() > 0 && av != null
388 && av.getAlignment() != null)
390 int seqIndex = av.getAlignment().findIndex(results);
395 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
397 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
405 // System.err.println(this.av.viewName + " Seq : " + seqIndex
406 // + " Scroll to " + start + "," + end);
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())
426 if (av.hasHiddenColumns())
428 start = av.getColumnSelection().findColumnPosition(start);
429 end = av.getColumnSelection().findColumnPosition(end);
432 if (!av.getColumnSelection().isVisible(r[0]))
434 // don't scroll - position isn't visible
441 * allow for offset of target sequence (actually scroll to one above it)
443 seqIndex = Math.max(0, seqIndex - verticalOffset);
445 // System.out.println("start=" + start + ", end=" + end + ", startv="
446 // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
447 // + av.getStartSeq() + ", ends=" + av.getEndSeq());
448 if (!av.getWrapAlignment())
450 if ((startv = vpRanges.getStartRes()) >= start)
453 * Scroll left to make start of search results visible
455 // setScrollValues(start - 1, seqIndex); // plus one residue
456 setScrollValues(start, seqIndex);
458 else if ((endv = vpRanges.getEndRes()) <= end)
461 * Scroll right to make end of search results visible
463 // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
464 setScrollValues(startv + end - endv, seqIndex);
466 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
469 * Scroll up to make start of search results visible
471 setScrollValues(vpRanges.getStartRes(), seqIndex);
473 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
476 * Scroll down to make end of search results visible
478 setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
482 * Else results are already visible - no need to scroll
487 vpRanges.scrollToWrappedVisible(start);
491 paintAlignment(redrawOverview);
498 * @return DOCUMENT ME!
500 public OverviewPanel getOverviewPanel()
502 return overviewPanel;
511 public void setOverviewPanel(OverviewPanel op)
519 * Hide or show annotation panel
522 public void setAnnotationVisible(boolean b)
524 if (!av.getWrapAlignment())
526 annotationSpaceFillerHolder.setVisible(b);
527 annotationScroller.setVisible(b);
533 * automatically adjust annotation panel height for new annotation whilst
534 * ensuring the alignment is still visible.
537 public void adjustAnnotationHeight()
539 // TODO: display vertical annotation scrollbar if necessary
540 // this is called after loading new annotation onto alignment
541 if (alignFrame.getHeight() == 0)
543 System.out.println("NEEDS FIXING");
545 validateAnnotationDimensions(true);
547 paintAlignment(true);
551 * calculate the annotation dimensions and refresh slider values accordingly.
552 * need to do repaints/notifys afterwards.
554 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
556 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
558 if (adjustPanelHeight)
560 int rowHeight = av.getCharHeight();
561 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
564 * Estimate available height in the AlignFrame for alignment +
565 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
566 * hscroll, status bar (as these are not laid out we can't inspect their
567 * actual heights). Insets gives frame borders.
569 int stuff = Platform.isAMac() ? 80 : 100;
570 Insets insets = alignFrame.getInsets();
571 int availableHeight = alignFrame.getHeight() - stuff - insets.top
575 * If not enough vertical space, maximize annotation height while keeping
576 * at least two rows of alignment visible
578 if (annotationHeight + alignmentHeight > availableHeight)
580 annotationHeight = Math.min(annotationHeight, availableHeight - 2
586 // maintain same window layout whilst updating sliders
587 annotationHeight = annotationScroller.getSize().height;
591 annotationScroller.setPreferredSize(new Dimension(annotationScroller
592 .getWidth(), annotationHeight));
594 Dimension e = idPanel.getSize();
595 alabels.setSize(new Dimension(e.width, annotationHeight));
597 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
598 annotationSpaceFillerHolder.getWidth(), annotationHeight));
599 annotationScroller.validate();
600 annotationScroller.addNotify();
604 * update alignment layout for viewport settings
609 public void updateLayout()
612 setAnnotationVisible(av.isShowAnnotation());
613 boolean wrap = av.getWrapAlignment();
614 vpRanges.setStartSeq(0);
615 scalePanelHolder.setVisible(!wrap);
616 hscroll.setVisible(!wrap);
617 idwidthAdjuster.setVisible(!wrap);
621 annotationScroller.setVisible(false);
622 annotationSpaceFillerHolder.setVisible(false);
624 else if (av.isShowAnnotation())
626 annotationScroller.setVisible(true);
627 annotationSpaceFillerHolder.setVisible(true);
632 int widthInRes = getSeqPanel().seqCanvas
633 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
634 vpRanges.setViewportWidth(widthInRes);
638 int widthInRes = (getSeqPanel().seqCanvas.getWidth() / av
639 .getCharWidth()) - 1;
640 int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
641 .getCharHeight()) - 1;
643 vpRanges.setViewportWidth(widthInRes);
644 vpRanges.setViewportHeight(heightInSeq);
647 idSpaceFillerPanel1.setVisible(!wrap);
654 * Adjust row/column scrollers to show a visible position in the alignment.
657 * visible column to scroll to
659 * visible row to scroll to
662 public void setScrollValues(int x, int y)
664 if (av == null || av.getAlignment() == null)
669 if (av.getWrapAlignment())
671 setScrollingForWrappedPanel(x);
676 int width = av.getAlignment().getWidth();
677 int height = av.getAlignment().getHeight();
679 if (av.hasHiddenColumns())
681 // reset the width to exclude hidden columns
682 width = av.getColumnSelection().findColumnPosition(width);
685 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
686 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
693 if (vextent > height)
698 if ((hextent + x) > width)
703 if ((vextent + y) > height)
705 y = height - vextent;
718 // update the scroll values
719 hscroll.setValues(x, hextent, 0, width);
720 vscroll.setValues(y, vextent, 0, height);
731 public void adjustmentValueChanged(AdjustmentEvent evt)
733 int oldX = vpRanges.getStartRes();
734 int oldwidth = vpRanges.getViewportWidth();
735 int oldY = vpRanges.getStartSeq();
736 int oldheight = vpRanges.getViewportHeight();
738 if (av.getWrapAlignment())
740 if (evt.getSource() == hscroll)
742 return; // no horizontal scroll when wrapped
744 else if (evt.getSource() == vscroll)
746 int offy = vscroll.getValue();
747 int rowSize = getSeqPanel().seqCanvas
748 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
750 // if we're scrolling to the position we're already at, stop
751 // this prevents infinite recursion of events when the scroll/viewport
752 // ranges values are the same
753 if ((offy * rowSize == oldX) && (oldwidth == rowSize))
759 vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize);
764 // This is only called if file loaded is a jar file that
765 // was wrapped when saved and user has wrap alignment true
766 // as preference setting
767 SwingUtilities.invokeLater(new Runnable()
772 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
781 if (evt.getSource() == hscroll)
783 int x = hscroll.getValue();
784 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
786 // if we're scrolling to the position we're already at, stop
787 // this prevents infinite recursion of events when the scroll/viewport
788 // ranges values are the same
789 if ((x == oldX) && (width == oldwidth))
793 vpRanges.setViewportStartAndWidth(x, width);
795 else if (evt.getSource() == vscroll)
797 int y = vscroll.getValue();
798 int height = getSeqPanel().seqCanvas.getHeight()
799 / av.getCharHeight();
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
804 if ((y == oldY) && (height == oldheight))
808 vpRanges.setViewportStartAndHeight(y, height);
818 * Repaint the alignment including the annotations and overview panels (if
822 public void paintAlignment(boolean updateOverview)
824 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
825 av.isShowAutocalculatedAbove());
826 sorter.sort(getAlignment().getAlignmentAnnotation(),
827 av.getSortAnnotationsBy());
832 // TODO: determine if this paintAlignment changed structure colours
833 av.getStructureSelectionManager().sequenceColoursChanged(this);
835 if (overviewPanel != null)
837 overviewPanel.updateOverviewImage();
849 public void paintComponent(Graphics g)
853 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
854 idPanelHolder.setPreferredSize(d);
855 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
859 * set scroll bar positions
861 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
865 * Set vertical scroll bar parameters for wrapped panel
867 * the residue to scroll to
869 private void setScrollingForWrappedPanel(int res)
871 // get the width of the alignment in residues
872 int maxwidth = av.getAlignment().getWidth();
873 if (av.hasHiddenColumns())
875 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
878 // get the width of the canvas in residues
879 int canvasWidth = getSeqPanel().seqCanvas
880 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
883 // position we want to scroll to is number of canvasWidth's to get there
884 int current = res / canvasWidth;
886 // max scroll position: add one because extent is 1 and scrollbar value
887 // can only be set to at most max - extent
888 int max = maxwidth / canvasWidth + 1;
889 vscroll.setUnitIncrement(1);
890 vscroll.setValues(current, 1, 0, max);
904 * @return DOCUMENT ME!
906 * @throws PrinterException
910 public int print(Graphics pg, PageFormat pf, int pi)
911 throws PrinterException
913 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
915 int pwidth = (int) pf.getImageableWidth();
916 int pheight = (int) pf.getImageableHeight();
918 if (av.getWrapAlignment())
920 return printWrappedAlignment(pwidth, pheight, pi, pg);
924 return printUnwrapped(pwidth, pheight, pi, pg, pg);
940 * @return DOCUMENT ME!
942 * @throws PrinterException
946 * Draws the alignment image, including sequence ids, sequences, and
947 * annotation labels and annotations if shown, on either one or two Graphics
954 * the graphics context for sequence ids and annotation labels
955 * @param alignmentGraphics
956 * the graphics context for sequences and annotations (may or may not
957 * be the same context as idGraphics)
959 * @throws PrinterException
961 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
962 Graphics idGraphics, Graphics alignmentGraphics)
963 throws PrinterException
965 final int idWidth = getVisibleIdWidth(false);
968 * Get the horizontal offset to where we draw the sequences.
969 * This is idWidth if using a single Graphics context, else zero.
971 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
973 FontMetrics fm = getFontMetrics(av.getFont());
974 int charHeight = av.getCharHeight();
975 int scaleHeight = charHeight + fm.getDescent();
977 idGraphics.setColor(Color.white);
978 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
979 idGraphics.setFont(av.getFont());
982 * How many sequences and residues can we fit on a printable page?
984 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
986 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
988 int alignmentWidth = av.getAlignment().getWidth();
989 int pagesWide = (alignmentWidth / totalRes) + 1;
991 final int startRes = (pi % pagesWide) * totalRes;
992 int endRes = (startRes + totalRes) - 1;
994 if (endRes > (alignmentWidth - 1))
996 endRes = alignmentWidth - 1;
999 final int startSeq = (pi / pagesWide) * totalSeq;
1000 int endSeq = startSeq + totalSeq;
1002 int alignmentHeight = av.getAlignment().getHeight();
1003 if (endSeq > alignmentHeight)
1005 endSeq = alignmentHeight;
1008 int pagesHigh = ((alignmentHeight / totalSeq) + 1)
1011 if (av.isShowAnnotation())
1013 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1016 pagesHigh /= pageHeight;
1018 if (pi >= (pagesWide * pagesHigh))
1020 return Printable.NO_SUCH_PAGE;
1022 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
1026 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1028 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1029 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1030 pageWidth - idWidth, scaleHeight);
1031 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1034 * Draw the sequence ids, offset for scale height,
1035 * then reset to top left (0, 0)
1037 idGraphics.translate(0, scaleHeight);
1038 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1039 Color currentColor = null;
1040 Color currentTextColor = null;
1043 for (int i = startSeq; i < endSeq; i++)
1045 seq = av.getAlignment().getSequenceAt(i);
1046 if ((av.getSelectionGroup() != null)
1047 && av.getSelectionGroup().getSequences(null).contains(seq))
1050 * gray out ids of sequences in selection group (if any)
1052 currentColor = Color.gray;
1053 currentTextColor = Color.black;
1057 currentColor = av.getSequenceColour(seq);
1058 currentTextColor = Color.black;
1061 idGraphics.setColor(currentColor);
1062 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1065 idGraphics.setColor(currentTextColor);
1068 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1069 if (av.isRightAlignIds())
1071 fm = idGraphics.getFontMetrics();
1073 - fm.stringWidth(displayId)
1077 idGraphics.drawString(displayId, xPos,
1078 (((i - startSeq) * charHeight) + charHeight)
1079 - (charHeight / 5));
1081 idGraphics.setFont(av.getFont());
1082 idGraphics.translate(0, -scaleHeight);
1085 * draw the sequences, offset for scale height, and id width (if using a
1086 * single graphics context), then reset to (0, scale height)
1088 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1089 getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
1090 startSeq, endSeq, 0);
1091 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1093 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1096 * draw annotation labels; drawComponent() translates by
1097 * getScrollOffset(), so compensate for that first;
1098 * then reset to (0, scale height)
1100 int offset = getAlabels().getScrollOffset();
1101 idGraphics.translate(0, -offset);
1102 idGraphics.translate(0, alignmentDrawnHeight);
1103 getAlabels().drawComponent(idGraphics, idWidth);
1104 idGraphics.translate(0, -alignmentDrawnHeight);
1107 * draw the annotations starting at
1108 * (idOffset, alignmentHeight) from (0, scaleHeight)
1110 alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
1111 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1112 alignmentGraphics, -1, startRes, endRes + 1);
1115 return Printable.PAGE_EXISTS;
1130 * @return DOCUMENT ME!
1132 * @throws PrinterException
1135 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1136 Graphics pg) throws PrinterException
1138 int annotationHeight = 0;
1139 AnnotationLabels labels = null;
1140 if (av.isShowAnnotation())
1142 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1143 labels = new AnnotationLabels(av);
1146 int hgap = av.getCharHeight();
1147 if (av.getScaleAboveWrapped())
1149 hgap += av.getCharHeight();
1152 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1155 int idWidth = getVisibleIdWidth(false);
1157 int maxwidth = av.getAlignment().getWidth();
1158 if (av.hasHiddenColumns())
1160 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1163 int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
1166 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1168 pg.setColor(Color.white);
1169 pg.fillRect(0, 0, pwidth, pheight);
1170 pg.setFont(av.getFont());
1174 pg.setColor(Color.black);
1176 pg.translate(0, -pi * pheight);
1178 pg.setClip(0, pi * pheight, pwidth, pheight);
1184 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1186 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1187 SequenceI s = av.getAlignment().getSequenceAt(i);
1188 String string = s.getDisplayId(av.getShowJVSuffix());
1190 if (av.isRightAlignIds())
1192 FontMetrics fm = pg.getFontMetrics();
1193 xPos = idWidth - fm.stringWidth(string) - 4;
1195 pg.drawString(string, xPos,
1196 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1197 - (av.getCharHeight() / 5));
1202 ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
1204 pg.setFont(av.getFont());
1205 labels.drawComponent(pg, idWidth);
1209 - (av.getAlignment().getHeight() * av
1214 } while (ypos < totalHeight);
1216 pg.translate(idWidth, 0);
1218 getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
1221 if ((pi * pheight) < totalHeight)
1223 return Printable.PAGE_EXISTS;
1228 return Printable.NO_SUCH_PAGE;
1233 * get current sequence ID panel width, or nominal value if panel were to be
1234 * displayed using default settings
1238 public int getVisibleIdWidth()
1240 return getVisibleIdWidth(true);
1244 * get current sequence ID panel width, or nominal value if panel were to be
1245 * displayed using default settings
1248 * indicate if the Id width for onscreen or offscreen display should
1252 public int getVisibleIdWidth(boolean onscreen)
1254 // see if rendering offscreen - check preferences and calc width accordingly
1255 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1257 return calculateIdWidth(-1).width + 4;
1259 Integer idwidth = null;
1261 || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1263 int w = getIdPanel().getWidth();
1264 return (w > 0 ? w : calculateIdWidth().width + 4);
1266 return idwidth.intValue() + 4;
1269 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1271 int boarderBottomOffset = 5;
1272 long pSessionId = System.currentTimeMillis();
1273 headless = (System.getProperty("java.awt.headless") != null && System
1274 .getProperty("java.awt.headless").equals("true"));
1275 if (alignFrame != null && !headless)
1279 alignFrame.setProgressBar(MessageManager.formatMessage(
1280 "status.saving_file", new Object[] { type.getLabel() }),
1286 AlignmentDimension aDimension = getAlignmentDimension();
1289 jalview.util.ImageMaker im;
1290 final String imageAction, imageTitle;
1291 if (type == jalview.util.ImageMaker.TYPE.PNG)
1293 imageAction = "Create PNG image from alignment";
1296 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1298 imageAction = "Create EPS file from alignment";
1299 imageTitle = alignFrame.getTitle();
1303 imageAction = "Create SVG file from alignment";
1304 imageTitle = alignFrame.getTitle();
1307 im = new jalview.util.ImageMaker(this, type, imageAction,
1308 aDimension.getWidth(), aDimension.getHeight()
1309 + boarderBottomOffset, file, imageTitle,
1310 alignFrame, pSessionId, headless);
1311 Graphics graphics = im.getGraphics();
1312 if (av.getWrapAlignment())
1314 if (graphics != null)
1316 printWrappedAlignment(aDimension.getWidth(),
1317 aDimension.getHeight() + boarderBottomOffset, 0,
1324 if (graphics != null)
1326 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
1327 0, graphics, graphics);
1332 } catch (OutOfMemoryError err)
1335 System.out.println("########################\n" + "OUT OF MEMORY "
1336 + file + "\n" + "########################");
1337 new OOMWarning("Creating Image for " + file, err);
1338 // System.out.println("Create IMAGE: " + err);
1339 } catch (Exception ex)
1341 ex.printStackTrace();
1349 public AlignmentDimension getAlignmentDimension()
1351 int maxwidth = av.getAlignment().getWidth();
1352 if (av.hasHiddenColumns())
1354 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
1357 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1358 + getScalePanel().getHeight();
1359 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1361 if (av.getWrapAlignment())
1363 height = getWrappedHeight();
1366 // need to obtain default alignment width and then add in any
1367 // additional allowance for id margin
1368 // this duplicates the calculation in getWrappedHeight but adjusts for
1370 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1371 - alignFrame.getInsets().left
1372 - alignFrame.getInsets().right - getVisibleIdWidth()
1373 + getVisibleIdWidth(false);
1377 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1381 else if (av.isShowAnnotation())
1383 height += getAnnotationPanel().adjustPanelHeight() + 3;
1385 return new AlignmentDimension(width, height);
1392 public void makeEPS(File epsFile)
1394 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1400 public void makePNG(File pngFile)
1402 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1405 public void makeSVG(File svgFile)
1407 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1410 public void makePNGImageMap(File imgMapFile, String imageName)
1412 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1413 // ////////////////////////////////////////////
1414 int idWidth = getVisibleIdWidth(false);
1415 FontMetrics fm = getFontMetrics(av.getFont());
1416 int scaleHeight = av.getCharHeight() + fm.getDescent();
1419 // ////////////////////////////////
1420 if (imgMapFile != null)
1424 int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
1425 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
1426 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1427 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1428 out.println("<img src=\"" + imageName
1429 + "\" border=\"0\" usemap=\"#Map\" >"
1430 + "<map name=\"Map\">");
1432 for (s = 0; s < sSize; s++)
1434 sy = s * av.getCharHeight() + scaleHeight;
1436 SequenceI seq = av.getAlignment().getSequenceAt(s);
1437 SequenceFeature[] features = seq.getSequenceFeatures();
1438 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1439 for (res = 0; res < alwidth; res++)
1441 StringBuilder text = new StringBuilder();
1442 String triplet = null;
1443 if (av.getAlignment().isNucleotide())
1445 triplet = ResidueProperties.nucleotideName.get(seq
1446 .getCharAt(res) + "");
1450 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
1454 if (triplet == null)
1459 int alIndex = seq.findPosition(res);
1460 gSize = groups.length;
1461 for (g = 0; g < gSize; g++)
1463 if (text.length() < 1)
1465 text.append("<area shape=\"rect\" coords=\"")
1466 .append((idWidth + res * av.getCharWidth()))
1467 .append(",").append(sy).append(",")
1468 .append((idWidth + (res + 1) * av.getCharWidth()))
1469 .append(",").append((av.getCharHeight() + sy))
1470 .append("\"").append(" onMouseOver=\"toolTip('")
1471 .append(alIndex).append(" ").append(triplet);
1474 if (groups[g].getStartRes() < res
1475 && groups[g].getEndRes() > res)
1477 text.append("<br><em>").append(groups[g].getName())
1482 if (features != null)
1484 if (text.length() < 1)
1486 text.append("<area shape=\"rect\" coords=\"")
1487 .append((idWidth + res * av.getCharWidth()))
1488 .append(",").append(sy).append(",")
1489 .append((idWidth + (res + 1) * av.getCharWidth()))
1490 .append(",").append((av.getCharHeight() + sy))
1491 .append("\"").append(" onMouseOver=\"toolTip('")
1492 .append(alIndex).append(" ").append(triplet);
1494 fSize = features.length;
1495 for (f = 0; f < fSize; f++)
1498 if ((features[f].getBegin() <= seq.findPosition(res))
1499 && (features[f].getEnd() >= seq.findPosition(res)))
1501 if (features[f].isContactFeature())
1503 if (features[f].getBegin() == seq.findPosition(res)
1504 || features[f].getEnd() == seq
1507 text.append("<br>").append(features[f].getType())
1508 .append(" ").append(features[f].getBegin())
1509 .append(":").append(features[f].getEnd());
1514 text.append("<br>");
1515 text.append(features[f].getType());
1516 if (features[f].getDescription() != null
1517 && !features[f].getType().equals(
1518 features[f].getDescription()))
1520 text.append(" ").append(features[f].getDescription());
1523 if (features[f].getValue("status") != null)
1525 text.append(" (").append(features[f].getValue("status"))
1533 if (text.length() > 1)
1535 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1536 out.println(text.toString());
1540 out.println("</map></body></html>");
1543 } catch (Exception ex)
1545 ex.printStackTrace();
1547 } // /////////END OF IMAGE MAP
1551 int getWrappedHeight()
1553 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1555 if (System.getProperty("java.awt.headless") != null
1556 && System.getProperty("java.awt.headless").equals("true"))
1558 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1559 - vscroll.getPreferredSize().width
1560 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1563 int chunkWidth = getSeqPanel().seqCanvas
1564 .getWrappedCanvasWidth(seqPanelWidth);
1566 int hgap = av.getCharHeight();
1567 if (av.getScaleAboveWrapped())
1569 hgap += av.getCharHeight();
1572 int annotationHeight = 0;
1573 if (av.isShowAnnotation())
1575 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1578 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1581 int maxwidth = av.getAlignment().getWidth();
1582 if (av.hasHiddenColumns())
1584 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1587 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1593 * close the panel - deregisters all listeners and nulls any references to
1596 public void closePanel()
1598 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1599 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1600 PaintRefresher.RemoveComponent(this);
1603 * try to ensure references are nulled
1605 if (annotationPanel != null)
1607 annotationPanel.dispose();
1612 av.removePropertyChangeListener(propertyChangeListener);
1613 jalview.structure.StructureSelectionManager ssm = av
1614 .getStructureSelectionManager();
1615 ssm.removeStructureViewerListener(getSeqPanel(), null);
1616 ssm.removeSelectionListener(getSeqPanel());
1617 ssm.removeCommandListener(av);
1618 ssm.removeStructureViewerListener(getSeqPanel(), null);
1619 ssm.removeSelectionListener(getSeqPanel());
1625 if (Cache.log.isDebugEnabled())
1627 Cache.log.warn("Closing alignment panel which is already closed.");
1633 * hides or shows dynamic annotation rows based on groups and av state flags
1635 public void updateAnnotation()
1637 updateAnnotation(false, false);
1640 public void updateAnnotation(boolean applyGlobalSettings)
1642 updateAnnotation(applyGlobalSettings, false);
1645 public void updateAnnotation(boolean applyGlobalSettings,
1646 boolean preserveNewGroupSettings)
1648 av.updateGroupAnnotationSettings(applyGlobalSettings,
1649 preserveNewGroupSettings);
1650 adjustAnnotationHeight();
1654 public AlignmentI getAlignment()
1656 return av == null ? null : av.getAlignment();
1660 public String getViewName()
1666 * Make/Unmake this alignment panel the current input focus
1670 public void setSelected(boolean b)
1674 if (alignFrame.getSplitViewContainer() != null)
1677 * bring enclosing SplitFrame to front first if there is one
1679 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1681 alignFrame.setSelected(b);
1682 } catch (Exception ex)
1688 alignFrame.setDisplayedView(this);
1693 public StructureSelectionManager getStructureSelectionManager()
1695 return av.getStructureSelectionManager();
1699 public void raiseOOMWarning(String string, OutOfMemoryError error)
1701 new OOMWarning(string, error, this);
1705 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1708 return new FeatureRenderer(this);
1712 public jalview.api.FeatureRenderer getFeatureRenderer()
1714 return seqPanel.seqCanvas.getFeatureRenderer();
1717 public void updateFeatureRenderer(
1718 jalview.renderer.seqfeatures.FeatureRenderer fr)
1720 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1723 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1725 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1727 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1731 public ScalePanel getScalePanel()
1736 public void setScalePanel(ScalePanel scalePanel)
1738 this.scalePanel = scalePanel;
1741 public SeqPanel getSeqPanel()
1746 public void setSeqPanel(SeqPanel seqPanel)
1748 this.seqPanel = seqPanel;
1751 public AnnotationPanel getAnnotationPanel()
1753 return annotationPanel;
1756 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1758 this.annotationPanel = annotationPanel;
1761 public AnnotationLabels getAlabels()
1766 public void setAlabels(AnnotationLabels alabels)
1768 this.alabels = alabels;
1771 public IdPanel getIdPanel()
1776 public void setIdPanel(IdPanel idPanel)
1778 this.idPanel = idPanel;
1782 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1783 * The aim is to keep the two alignments 'lined up' on their centre columns.
1786 * holds mapped region(s) of this alignment that we are scrolling
1787 * 'to'; may be modified for sequence offset by this method
1788 * @param verticalOffset
1789 * the number of visible sequences to show above the mapped region
1791 public void scrollToCentre(SearchResultsI sr, int verticalOffset)
1794 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1795 * mapped), we can make the scroll-to location a sequence above the one
1798 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1799 List<SequenceI> seqs = av.getAlignment().getSequences();
1802 * This is like AlignmentI.findIndex(seq) but here we are matching the
1803 * dataset sequence not the aligned sequence
1805 boolean matched = false;
1806 for (SequenceI seq : seqs)
1808 if (mappedTo == seq.getDatasetSequence())
1816 return; // failsafe, shouldn't happen
1820 * Scroll to position but centring the target residue.
1822 scrollToPosition(sr, verticalOffset, true, true);
1826 * Set a flag to say do not scroll any (cDNA/protein) complement.
1830 protected void setDontScrollComplement(boolean b)
1832 this.dontScrollComplement = b;
1835 protected boolean isDontScrollComplement()
1837 return this.dontScrollComplement;
1843 * @adjustHeight if true, try to recalculate panel height for visible
1846 protected void refresh(boolean adjustHeight)
1848 validateAnnotationDimensions(adjustHeight);
1852 // sort, repaint, update overview
1853 paintAlignment(true);
1857 // lightweight repaint
1864 * Property change event fired when a change is made to the viewport ranges
1865 * object associated with this alignment panel's viewport
1867 public void propertyChange(PropertyChangeEvent evt)
1869 // update this panel's scroll values based on the new viewport ranges values
1870 int x = vpRanges.getStartRes();
1871 int y = vpRanges.getStartSeq();
1872 setScrollValues(x, y);
1874 // now update any complementary alignment (its viewport ranges object
1875 // is different so does not get automatically updated)
1876 if (!isDontScrollComplement())
1878 setDontScrollComplement(true);
1879 av.scrollComplementaryAlignment();
1880 setDontScrollComplement(false);