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;
39 import java.awt.BorderLayout;
40 import java.awt.Color;
41 import java.awt.Container;
42 import java.awt.Dimension;
44 import java.awt.FontMetrics;
45 import java.awt.Graphics;
46 import java.awt.Insets;
47 import java.awt.event.AdjustmentEvent;
48 import java.awt.event.AdjustmentListener;
49 import java.awt.print.PageFormat;
50 import java.awt.print.Printable;
51 import java.awt.print.PrinterException;
52 import java.beans.PropertyChangeEvent;
53 import java.beans.PropertyChangeListener;
55 import java.io.FileWriter;
56 import java.io.PrintWriter;
57 import java.util.List;
59 import javax.swing.SwingUtilities;
65 * @version $Revision: 1.161 $
67 public class AlignmentPanel extends GAlignmentPanel implements
68 AdjustmentListener, Printable, AlignmentViewPanel
70 public AlignViewport av;
72 OverviewPanel overviewPanel;
74 private SeqPanel seqPanel;
76 private IdPanel idPanel;
78 private boolean headless;
80 IdwidthAdjuster idwidthAdjuster;
83 public AlignFrame alignFrame;
85 private ScalePanel scalePanel;
87 private AnnotationPanel annotationPanel;
89 private AnnotationLabels alabels;
91 // this value is set false when selection area being dragged
92 boolean fastPaint = true;
94 private int hextent = 0;
96 private int vextent = 0;
99 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
100 * true, suppresses invoking the same method recursively.
102 private boolean dontScrollComplement;
104 private PropertyChangeListener propertyChangeListener;
107 * Creates a new AlignmentPanel object.
112 public AlignmentPanel(AlignFrame af, final AlignViewport av)
116 setSeqPanel(new SeqPanel(av, this));
117 setIdPanel(new IdPanel(av, this));
119 setScalePanel(new ScalePanel(av, this));
121 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
122 idwidthAdjuster = new IdwidthAdjuster(this);
123 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
125 setAnnotationPanel(new AnnotationPanel(this));
126 setAlabels(new AnnotationLabels(this));
128 annotationScroller.setViewportView(getAnnotationPanel());
129 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
131 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
132 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
134 setScrollValues(0, 0);
136 hscroll.addAdjustmentListener(this);
137 vscroll.addAdjustmentListener(this);
139 final AlignmentPanel ap = this;
140 propertyChangeListener = new PropertyChangeListener()
143 public void propertyChange(PropertyChangeEvent evt)
145 if (evt.getPropertyName().equals("alignment"))
147 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
152 av.addPropertyChangeListener(propertyChangeListener);
154 adjustAnnotationHeight();
159 public AlignViewportI getAlignViewport()
164 public void alignmentChanged()
166 av.alignmentChanged(this);
168 alignFrame.updateEditMenuBar();
170 paintAlignment(true);
177 public void fontChanged()
179 // set idCanvas bufferedImage to null
180 // to prevent drawing old image
181 FontMetrics fm = getFontMetrics(av.getFont());
183 scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
185 idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
186 .getCharHeight() + fm.getDescent()));
188 getIdPanel().getIdCanvas().gg = null;
189 getSeqPanel().seqCanvas.img = null;
190 getAnnotationPanel().adjustPanelHeight();
192 Dimension d = calculateIdWidth();
194 d.setSize(d.width + 4, d.height);
195 getIdPanel().getIdCanvas().setPreferredSize(d);
196 hscrollFillerPanel.setPreferredSize(d);
198 if (overviewPanel != null)
200 overviewPanel.setBoxPosition();
202 if (this.alignFrame.getSplitViewContainer() != null)
204 ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
211 * Calculate the width of the alignment labels based on the displayed names
212 * and any bounds on label width set in preferences.
214 * @return Dimension giving the maximum width of the alignment label panel
215 * that should be used.
217 public Dimension calculateIdWidth()
219 // calculate sensible default width when no preference is available
221 if (av.getIdWidth() < 0)
223 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
224 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
225 r = calculateIdWidth(maxwidth);
226 av.setIdWidth(r.width);
231 r.width = av.getIdWidth();
238 * Calculate the width of the alignment labels based on the displayed names
239 * and any bounds on label width set in preferences.
242 * -1 or maximum width allowed for IdWidth
243 * @return Dimension giving the maximum width of the alignment label panel
244 * that should be used.
246 public Dimension calculateIdWidth(int maxwidth)
248 Container c = new Container();
250 FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
251 Font.ITALIC, av.font.getSize()));
253 AlignmentI al = av.getAlignment();
258 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
260 SequenceI s = al.getSequenceAt(i);
262 id = s.getDisplayId(av.getShowJVSuffix());
264 if (fm.stringWidth(id) > idWidth)
266 idWidth = fm.stringWidth(id);
272 // Also check annotation label widths
275 if (al.getAlignmentAnnotation() != null)
277 fm = c.getFontMetrics(getAlabels().getFont());
279 while (i < al.getAlignmentAnnotation().length)
281 String label = al.getAlignmentAnnotation()[i].label;
283 if (fm.stringWidth(label) > idWidth)
285 idWidth = fm.stringWidth(label);
292 return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth,
297 * Highlight the given results on the alignment.
300 public void highlightSearchResults(SearchResultsI results)
302 scrollToPosition(results);
303 getSeqPanel().seqCanvas.highlightSearchResults(results);
307 * Scroll the view to show the position of the highlighted region in results
308 * (if any) and redraw the overview
312 public boolean scrollToPosition(SearchResultsI results)
314 return scrollToPosition(results, 0, true, false);
318 * Scroll the view to show the position of the highlighted region in results
321 * @param searchResults
322 * @param redrawOverview
325 public boolean scrollToPosition(SearchResultsI searchResults,
326 boolean redrawOverview)
328 return scrollToPosition(searchResults, 0, redrawOverview, false);
332 * Scroll the view to show the position of the highlighted region in results
336 * @param verticalOffset
337 * if greater than zero, allows scrolling to a position below the
338 * first displayed sequence
339 * @param redrawOverview
340 * - when set, the overview will be recalculated (takes longer)
342 * if true, try to centre the search results horizontally in the view
343 * @return false if results were not found
345 public boolean scrollToPosition(SearchResultsI results,
346 int verticalOffset, boolean redrawOverview, boolean centre)
348 int startv, endv, starts, ends;
349 // TODO: properly locate search results in view when large numbers of hidden
350 // columns exist before highlighted region
351 // do we need to scroll the panel?
352 // TODO: tons of nullpointerexceptions raised here.
353 if (results != null && results.getSize() > 0 && av != null
354 && av.getAlignment() != null)
356 int seqIndex = av.getAlignment().findIndex(results);
361 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
363 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
371 // System.err.println(this.av.viewName + " Seq : " + seqIndex
372 // + " Scroll to " + start + "," + end);
375 * To centre results, scroll to positions half the visible width
376 * left/right of the start/end positions
380 int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
381 start = Math.max(start - offset, 0);
382 end = end + offset - 1;
388 if (end == seq.getEnd())
392 if (av.hasHiddenColumns())
394 start = av.getColumnSelection().findColumnPosition(start);
395 end = av.getColumnSelection().findColumnPosition(end);
398 if (!av.getColumnSelection().isVisible(r[0]))
400 // don't scroll - position isn't visible
407 * allow for offset of target sequence (actually scroll to one above it)
409 seqIndex = Math.max(0, seqIndex - verticalOffset);
411 // System.out.println("start=" + start + ", end=" + end + ", startv="
412 // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
413 // + av.getStartSeq() + ", ends=" + av.getEndSeq());
414 if (!av.getWrapAlignment())
416 if ((startv = av.getStartRes()) >= start)
419 * Scroll left to make start of search results visible
421 // setScrollValues(start - 1, seqIndex); // plus one residue
422 setScrollValues(start, seqIndex);
424 else if ((endv = av.getEndRes()) <= end)
427 * Scroll right to make end of search results visible
429 // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
430 setScrollValues(startv + end - endv, seqIndex);
432 else if ((starts = av.getStartSeq()) > seqIndex)
435 * Scroll up to make start of search results visible
437 setScrollValues(av.getStartRes(), seqIndex);
439 else if ((ends = av.getEndSeq()) <= seqIndex)
442 * Scroll down to make end of search results visible
444 setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
447 * Else results are already visible - no need to scroll
452 scrollToWrappedVisible(start);
455 if (redrawOverview && overviewPanel != null)
457 overviewPanel.setBoxPosition();
459 paintAlignment(redrawOverview);
463 void scrollToWrappedVisible(int res)
465 int cwidth = getSeqPanel().seqCanvas
466 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
467 if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
469 vscroll.setValue((res / cwidth));
470 av.startRes = vscroll.getValue() * cwidth;
478 * @return DOCUMENT ME!
480 public OverviewPanel getOverviewPanel()
482 return overviewPanel;
491 public void setOverviewPanel(OverviewPanel op)
499 * Hide or show annotation panel
502 public void setAnnotationVisible(boolean b)
504 if (!av.getWrapAlignment())
506 annotationSpaceFillerHolder.setVisible(b);
507 annotationScroller.setVisible(b);
513 * automatically adjust annotation panel height for new annotation whilst
514 * ensuring the alignment is still visible.
517 public void adjustAnnotationHeight()
519 // TODO: display vertical annotation scrollbar if necessary
520 // this is called after loading new annotation onto alignment
521 if (alignFrame.getHeight() == 0)
523 System.out.println("NEEDS FIXING");
525 validateAnnotationDimensions(true);
527 paintAlignment(true);
531 * calculate the annotation dimensions and refresh slider values accordingly.
532 * need to do repaints/notifys afterwards.
534 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
536 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
538 if (adjustPanelHeight)
540 int rowHeight = av.getCharHeight();
541 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
544 * Estimate available height in the AlignFrame for alignment +
545 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
546 * hscroll, status bar (as these are not laid out we can't inspect their
547 * actual heights). Insets gives frame borders.
549 int stuff = Platform.isAMac() ? 80 : 100;
550 Insets insets = alignFrame.getInsets();
551 int availableHeight = alignFrame.getHeight() - stuff - insets.top
555 * If not enough vertical space, maximize annotation height while keeping
556 * at least two rows of alignment visible
558 if (annotationHeight + alignmentHeight > availableHeight)
560 annotationHeight = Math.min(annotationHeight, availableHeight - 2
566 // maintain same window layout whilst updating sliders
567 annotationHeight = annotationScroller.getSize().height;
571 annotationScroller.setPreferredSize(new Dimension(annotationScroller
572 .getWidth(), annotationHeight));
574 Dimension e = idPanel.getSize();
575 alabels.setSize(new Dimension(e.width, annotationHeight));
577 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
578 annotationSpaceFillerHolder.getWidth(), annotationHeight));
579 annotationScroller.validate();
580 annotationScroller.addNotify();
584 * update alignment layout for viewport settings
589 public void updateLayout()
592 setAnnotationVisible(av.isShowAnnotation());
593 boolean wrap = av.getWrapAlignment();
595 scalePanelHolder.setVisible(!wrap);
596 hscroll.setVisible(!wrap);
597 idwidthAdjuster.setVisible(!wrap);
601 annotationScroller.setVisible(false);
602 annotationSpaceFillerHolder.setVisible(false);
604 else if (av.isShowAnnotation())
606 annotationScroller.setVisible(true);
607 annotationSpaceFillerHolder.setVisible(true);
610 idSpaceFillerPanel1.setVisible(!wrap);
615 // return value is true if the scroll is valid
616 public boolean scrollUp(boolean up)
620 if (vscroll.getValue() < 1)
626 vscroll.setValue(vscroll.getValue() - 1);
630 if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
636 vscroll.setValue(vscroll.getValue() + 1);
650 * @return DOCUMENT ME!
652 public boolean scrollRight(boolean right)
656 if (hscroll.getValue() < 1)
662 hscroll.setValue(hscroll.getValue() - 1);
666 if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
672 hscroll.setValue(hscroll.getValue() + 1);
681 * Adjust row/column scrollers to show a visible position in the alignment.
684 * visible column to scroll to
686 * visible row to scroll to
689 public void setScrollValues(int x, int y)
691 // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
692 if (av == null || av.getAlignment() == null)
696 int width = av.getAlignment().getWidth();
697 int height = av.getAlignment().getHeight();
699 if (av.hasHiddenColumns())
701 width = av.getColumnSelection().findColumnPosition(width);
704 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
705 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
712 if (vextent > height)
717 if ((hextent + x) > width)
722 if ((vextent + y) > height)
724 y = height - vextent;
737 // update endRes after x has (possibly) been adjusted
738 av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
739 .getCharWidth())) - 1);
742 * each scroll adjustment triggers adjustmentValueChanged, which resets the
743 * 'do not scroll complement' flag; ensure it is the same for both
746 boolean flag = isDontScrollComplement();
747 hscroll.setValues(x, hextent, 0, width);
748 setDontScrollComplement(flag);
749 vscroll.setValues(y, vextent, 0, height);
759 public void adjustmentValueChanged(AdjustmentEvent evt)
761 int oldX = av.getStartRes();
762 int oldY = av.getStartSeq();
764 if (evt.getSource() == hscroll)
766 int x = hscroll.getValue();
768 av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
769 .getCharWidth())) - 1);
772 if (evt.getSource() == vscroll)
774 int offy = vscroll.getValue();
776 if (av.getWrapAlignment())
780 int rowSize = getSeqPanel().seqCanvas
781 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
782 av.setStartRes(offy * rowSize);
783 av.setEndRes((offy + 1) * rowSize);
787 // This is only called if file loaded is a jar file that
788 // was wrapped when saved and user has wrap alignment true
789 // as preference setting
790 SwingUtilities.invokeLater(new Runnable()
795 setScrollValues(av.getStartRes(), av.getStartSeq());
802 av.setStartSeq(offy);
804 + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
808 if (overviewPanel != null)
810 overviewPanel.setBoxPosition();
813 int scrollX = av.startRes - oldX;
814 int scrollY = av.startSeq - oldY;
816 if (av.getWrapAlignment() || !fastPaint)
822 // Make sure we're not trying to draw a panel
823 // larger than the visible window
824 if (scrollX > av.endRes - av.startRes)
826 scrollX = av.endRes - av.startRes;
828 else if (scrollX < av.startRes - av.endRes)
830 scrollX = av.startRes - av.endRes;
833 if (scrollX != 0 || scrollY != 0)
835 getIdPanel().getIdCanvas().fastPaint(scrollY);
836 getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
837 getScalePanel().repaint();
839 if (av.isShowAnnotation() && scrollX != 0)
841 getAnnotationPanel().fastPaint(scrollX);
846 * If there is one, scroll the (Protein/cDNA) complementary alignment to
847 * match, unless we are ourselves doing that.
849 if (isDontScrollComplement())
851 setDontScrollComplement(false);
855 av.scrollComplementaryAlignment();
860 * Repaint the alignment including the annotations and overview panels (if
864 public void paintAlignment(boolean updateOverview)
866 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
867 av.isShowAutocalculatedAbove());
868 sorter.sort(getAlignment().getAlignmentAnnotation(),
869 av.getSortAnnotationsBy());
874 // TODO: determine if this paintAlignment changed structure colours
875 av.getStructureSelectionManager().sequenceColoursChanged(this);
877 if (overviewPanel != null)
879 overviewPanel.updateOverviewImage();
891 public void paintComponent(Graphics g)
895 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
896 idPanelHolder.setPreferredSize(d);
897 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
901 * set scroll bar positions; first suppress this being 'followed' in any
902 * complementary split pane
904 setDontScrollComplement(true);
906 if (av.getWrapAlignment())
908 int maxwidth = av.getAlignment().getWidth();
910 if (av.hasHiddenColumns())
912 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
915 int canvasWidth = getSeqPanel().seqCanvas
916 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
920 / getSeqPanel().seqCanvas
921 .getWrappedCanvasWidth(getSeqPanel().seqCanvas
923 vscroll.setMaximum(max);
924 vscroll.setUnitIncrement(1);
925 vscroll.setVisibleAmount(1);
930 setScrollValues(av.getStartRes(), av.getStartSeq());
944 * @return DOCUMENT ME!
946 * @throws PrinterException
950 public int print(Graphics pg, PageFormat pf, int pi)
951 throws PrinterException
953 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
955 int pwidth = (int) pf.getImageableWidth();
956 int pheight = (int) pf.getImageableHeight();
958 if (av.getWrapAlignment())
960 return printWrappedAlignment(pwidth, pheight, pi, pg);
964 return printUnwrapped(pwidth, pheight, pi, pg, pg);
980 * @return DOCUMENT ME!
982 * @throws PrinterException
986 * Draws the alignment image, including sequence ids, sequences, and
987 * annotation labels and annotations if shown, on either one or two Graphics
994 * the graphics context for sequence ids and annotation labels
995 * @param alignmentGraphics
996 * the graphics context for sequences and annotations (may or may not
997 * be the same context as idGraphics)
999 * @throws PrinterException
1001 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
1002 Graphics idGraphics, Graphics alignmentGraphics)
1003 throws PrinterException
1005 final int idWidth = getVisibleIdWidth(false);
1008 * Get the horizontal offset to where we draw the sequences.
1009 * This is idWidth if using a single Graphics context, else zero.
1011 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
1013 FontMetrics fm = getFontMetrics(av.getFont());
1014 int charHeight = av.getCharHeight();
1015 int scaleHeight = charHeight + fm.getDescent();
1017 idGraphics.setColor(Color.white);
1018 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
1019 idGraphics.setFont(av.getFont());
1022 * How many sequences and residues can we fit on a printable page?
1024 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1026 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1028 int alignmentWidth = av.getAlignment().getWidth();
1029 int pagesWide = (alignmentWidth / totalRes) + 1;
1031 final int startRes = (pi % pagesWide) * totalRes;
1032 int endRes = (startRes + totalRes) - 1;
1034 if (endRes > (alignmentWidth - 1))
1036 endRes = alignmentWidth - 1;
1039 final int startSeq = (pi / pagesWide) * totalSeq;
1040 int endSeq = startSeq + totalSeq;
1042 int alignmentHeight = av.getAlignment().getHeight();
1043 if (endSeq > alignmentHeight)
1045 endSeq = alignmentHeight;
1048 int pagesHigh = ((alignmentHeight / totalSeq) + 1)
1051 if (av.isShowAnnotation())
1053 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1056 pagesHigh /= pageHeight;
1058 if (pi >= (pagesWide * pagesHigh))
1060 return Printable.NO_SUCH_PAGE;
1062 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
1066 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1068 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1069 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1070 pageWidth - idWidth, scaleHeight);
1071 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1074 * Draw the sequence ids, offset for scale height,
1075 * then reset to top left (0, 0)
1077 idGraphics.translate(0, scaleHeight);
1078 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1079 Color currentColor = null;
1080 Color currentTextColor = null;
1083 for (int i = startSeq; i < endSeq; i++)
1085 seq = av.getAlignment().getSequenceAt(i);
1086 if ((av.getSelectionGroup() != null)
1087 && av.getSelectionGroup().getSequences(null).contains(seq))
1090 * gray out ids of sequences in selection group (if any)
1092 currentColor = Color.gray;
1093 currentTextColor = Color.black;
1097 currentColor = av.getSequenceColour(seq);
1098 currentTextColor = Color.black;
1101 idGraphics.setColor(currentColor);
1102 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1105 idGraphics.setColor(currentTextColor);
1108 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1109 if (av.isRightAlignIds())
1111 fm = idGraphics.getFontMetrics();
1113 - fm.stringWidth(displayId)
1117 idGraphics.drawString(displayId, xPos,
1118 (((i - startSeq) * charHeight) + charHeight)
1119 - (charHeight / 5));
1121 idGraphics.setFont(av.getFont());
1122 idGraphics.translate(0, -scaleHeight);
1125 * draw the sequences, offset for scale height, and id width (if using a
1126 * single graphics context), then reset to (0, scale height)
1128 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1129 getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
1130 startSeq, endSeq, 0);
1131 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1133 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1136 * draw annotation labels; drawComponent() translates by
1137 * getScrollOffset(), so compensate for that first;
1138 * then reset to (0, scale height)
1140 int offset = getAlabels().getScrollOffset();
1141 idGraphics.translate(0, -offset);
1142 idGraphics.translate(0, alignmentDrawnHeight);
1143 getAlabels().drawComponent(idGraphics, idWidth);
1144 idGraphics.translate(0, -alignmentDrawnHeight);
1147 * draw the annotations starting at
1148 * (idOffset, alignmentHeight) from (0, scaleHeight)
1150 alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
1151 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1152 alignmentGraphics, -1, startRes, endRes + 1);
1155 return Printable.PAGE_EXISTS;
1170 * @return DOCUMENT ME!
1172 * @throws PrinterException
1175 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1176 Graphics pg) throws PrinterException
1178 int annotationHeight = 0;
1179 AnnotationLabels labels = null;
1180 if (av.isShowAnnotation())
1182 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1183 labels = new AnnotationLabels(av);
1186 int hgap = av.getCharHeight();
1187 if (av.getScaleAboveWrapped())
1189 hgap += av.getCharHeight();
1192 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1195 int idWidth = getVisibleIdWidth(false);
1197 int maxwidth = av.getAlignment().getWidth();
1198 if (av.hasHiddenColumns())
1200 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1203 int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
1206 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1208 pg.setColor(Color.white);
1209 pg.fillRect(0, 0, pwidth, pheight);
1210 pg.setFont(av.getFont());
1214 pg.setColor(Color.black);
1216 pg.translate(0, -pi * pheight);
1218 pg.setClip(0, pi * pheight, pwidth, pheight);
1224 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1226 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1227 SequenceI s = av.getAlignment().getSequenceAt(i);
1228 String string = s.getDisplayId(av.getShowJVSuffix());
1230 if (av.isRightAlignIds())
1232 FontMetrics fm = pg.getFontMetrics();
1233 xPos = idWidth - fm.stringWidth(string) - 4;
1235 pg.drawString(string, xPos,
1236 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1237 - (av.getCharHeight() / 5));
1242 ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
1244 pg.setFont(av.getFont());
1245 labels.drawComponent(pg, idWidth);
1249 - (av.getAlignment().getHeight() * av
1254 } while (ypos < totalHeight);
1256 pg.translate(idWidth, 0);
1258 getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
1261 if ((pi * pheight) < totalHeight)
1263 return Printable.PAGE_EXISTS;
1268 return Printable.NO_SUCH_PAGE;
1273 * get current sequence ID panel width, or nominal value if panel were to be
1274 * displayed using default settings
1278 public int getVisibleIdWidth()
1280 return getVisibleIdWidth(true);
1284 * get current sequence ID panel width, or nominal value if panel were to be
1285 * displayed using default settings
1288 * indicate if the Id width for onscreen or offscreen display should
1292 public int getVisibleIdWidth(boolean onscreen)
1294 // see if rendering offscreen - check preferences and calc width accordingly
1295 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1297 return calculateIdWidth(-1).width + 4;
1299 Integer idwidth = null;
1301 || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1303 int w = getIdPanel().getWidth();
1304 return (w > 0 ? w : calculateIdWidth().width + 4);
1306 return idwidth.intValue() + 4;
1309 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1311 int boarderBottomOffset = 5;
1312 long pSessionId = System.currentTimeMillis();
1313 headless = (System.getProperty("java.awt.headless") != null && System
1314 .getProperty("java.awt.headless").equals("true"));
1315 if (alignFrame != null && !headless)
1319 alignFrame.setProgressBar(MessageManager.formatMessage(
1320 "status.saving_file", new Object[] { type.getLabel() }),
1326 AlignmentDimension aDimension = getAlignmentDimension();
1329 jalview.util.ImageMaker im;
1330 final String imageAction, imageTitle;
1331 if (type == jalview.util.ImageMaker.TYPE.PNG)
1333 imageAction = "Create PNG image from alignment";
1336 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1338 imageAction = "Create EPS file from alignment";
1339 imageTitle = alignFrame.getTitle();
1343 imageAction = "Create SVG file from alignment";
1344 imageTitle = alignFrame.getTitle();
1347 im = new jalview.util.ImageMaker(this, type, imageAction,
1348 aDimension.getWidth(), aDimension.getHeight()
1349 + boarderBottomOffset, file, imageTitle,
1350 alignFrame, pSessionId, headless);
1351 Graphics graphics = im.getGraphics();
1352 if (av.getWrapAlignment())
1354 if (graphics != null)
1356 printWrappedAlignment(aDimension.getWidth(),
1357 aDimension.getHeight() + boarderBottomOffset, 0,
1364 if (graphics != null)
1366 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
1367 0, graphics, graphics);
1372 } catch (OutOfMemoryError err)
1375 System.out.println("########################\n" + "OUT OF MEMORY "
1376 + file + "\n" + "########################");
1377 new OOMWarning("Creating Image for " + file, err);
1378 // System.out.println("Create IMAGE: " + err);
1379 } catch (Exception ex)
1381 ex.printStackTrace();
1389 public AlignmentDimension getAlignmentDimension()
1391 int maxwidth = av.getAlignment().getWidth();
1392 if (av.hasHiddenColumns())
1394 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
1397 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1398 + getScalePanel().getHeight();
1399 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1401 if (av.getWrapAlignment())
1403 height = getWrappedHeight();
1406 // need to obtain default alignment width and then add in any
1407 // additional allowance for id margin
1408 // this duplicates the calculation in getWrappedHeight but adjusts for
1410 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1411 - alignFrame.getInsets().left
1412 - alignFrame.getInsets().right - getVisibleIdWidth()
1413 + getVisibleIdWidth(false);
1417 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1421 else if (av.isShowAnnotation())
1423 height += getAnnotationPanel().adjustPanelHeight() + 3;
1425 return new AlignmentDimension(width, height);
1432 public void makeEPS(File epsFile)
1434 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1440 public void makePNG(File pngFile)
1442 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1445 public void makeSVG(File svgFile)
1447 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1450 public void makePNGImageMap(File imgMapFile, String imageName)
1452 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1453 // ////////////////////////////////////////////
1454 int idWidth = getVisibleIdWidth(false);
1455 FontMetrics fm = getFontMetrics(av.getFont());
1456 int scaleHeight = av.getCharHeight() + fm.getDescent();
1459 // ////////////////////////////////
1460 if (imgMapFile != null)
1464 int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
1465 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
1466 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1467 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1468 out.println("<img src=\"" + imageName
1469 + "\" border=\"0\" usemap=\"#Map\" >"
1470 + "<map name=\"Map\">");
1472 for (s = 0; s < sSize; s++)
1474 sy = s * av.getCharHeight() + scaleHeight;
1476 SequenceI seq = av.getAlignment().getSequenceAt(s);
1477 SequenceFeature[] features = seq.getSequenceFeatures();
1478 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1479 for (res = 0; res < alwidth; res++)
1481 StringBuilder text = new StringBuilder();
1482 String triplet = null;
1483 if (av.getAlignment().isNucleotide())
1485 triplet = ResidueProperties.nucleotideName.get(seq
1486 .getCharAt(res) + "");
1490 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
1494 if (triplet == null)
1499 int alIndex = seq.findPosition(res);
1500 gSize = groups.length;
1501 for (g = 0; g < gSize; g++)
1503 if (text.length() < 1)
1505 text.append("<area shape=\"rect\" coords=\"")
1506 .append((idWidth + res * av.getCharWidth()))
1507 .append(",").append(sy).append(",")
1508 .append((idWidth + (res + 1) * av.getCharWidth()))
1509 .append(",").append((av.getCharHeight() + sy))
1510 .append("\"").append(" onMouseOver=\"toolTip('")
1511 .append(alIndex).append(" ").append(triplet);
1514 if (groups[g].getStartRes() < res
1515 && groups[g].getEndRes() > res)
1517 text.append("<br><em>").append(groups[g].getName())
1522 if (features != null)
1524 if (text.length() < 1)
1526 text.append("<area shape=\"rect\" coords=\"")
1527 .append((idWidth + res * av.getCharWidth()))
1528 .append(",").append(sy).append(",")
1529 .append((idWidth + (res + 1) * av.getCharWidth()))
1530 .append(",").append((av.getCharHeight() + sy))
1531 .append("\"").append(" onMouseOver=\"toolTip('")
1532 .append(alIndex).append(" ").append(triplet);
1534 fSize = features.length;
1535 for (f = 0; f < fSize; f++)
1538 if ((features[f].getBegin() <= seq.findPosition(res))
1539 && (features[f].getEnd() >= seq.findPosition(res)))
1541 if (features[f].isContactFeature())
1543 if (features[f].getBegin() == seq.findPosition(res)
1544 || features[f].getEnd() == seq
1547 text.append("<br>").append(features[f].getType())
1548 .append(" ").append(features[f].getBegin())
1549 .append(":").append(features[f].getEnd());
1554 text.append("<br>");
1555 text.append(features[f].getType());
1556 if (features[f].getDescription() != null
1557 && !features[f].getType().equals(
1558 features[f].getDescription()))
1560 text.append(" ").append(features[f].getDescription());
1563 if (features[f].getValue("status") != null)
1565 text.append(" (").append(features[f].getValue("status"))
1573 if (text.length() > 1)
1575 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1576 out.println(text.toString());
1580 out.println("</map></body></html>");
1583 } catch (Exception ex)
1585 ex.printStackTrace();
1587 } // /////////END OF IMAGE MAP
1591 int getWrappedHeight()
1593 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1595 if (System.getProperty("java.awt.headless") != null
1596 && System.getProperty("java.awt.headless").equals("true"))
1598 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1599 - vscroll.getPreferredSize().width
1600 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1603 int chunkWidth = getSeqPanel().seqCanvas
1604 .getWrappedCanvasWidth(seqPanelWidth);
1606 int hgap = av.getCharHeight();
1607 if (av.getScaleAboveWrapped())
1609 hgap += av.getCharHeight();
1612 int annotationHeight = 0;
1613 if (av.isShowAnnotation())
1615 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1618 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1621 int maxwidth = av.getAlignment().getWidth();
1622 if (av.hasHiddenColumns())
1624 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1627 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1633 * close the panel - deregisters all listeners and nulls any references to
1636 public void closePanel()
1638 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1639 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1640 PaintRefresher.RemoveComponent(this);
1643 * try to ensure references are nulled
1645 if (annotationPanel != null)
1647 annotationPanel.dispose();
1652 av.removePropertyChangeListener(propertyChangeListener);
1653 jalview.structure.StructureSelectionManager ssm = av
1654 .getStructureSelectionManager();
1655 ssm.removeStructureViewerListener(getSeqPanel(), null);
1656 ssm.removeSelectionListener(getSeqPanel());
1657 ssm.removeCommandListener(av);
1658 ssm.removeStructureViewerListener(getSeqPanel(), null);
1659 ssm.removeSelectionListener(getSeqPanel());
1665 if (Cache.log.isDebugEnabled())
1667 Cache.log.warn("Closing alignment panel which is already closed.");
1673 * hides or shows dynamic annotation rows based on groups and av state flags
1675 public void updateAnnotation()
1677 updateAnnotation(false, false);
1680 public void updateAnnotation(boolean applyGlobalSettings)
1682 updateAnnotation(applyGlobalSettings, false);
1685 public void updateAnnotation(boolean applyGlobalSettings,
1686 boolean preserveNewGroupSettings)
1688 av.updateGroupAnnotationSettings(applyGlobalSettings,
1689 preserveNewGroupSettings);
1690 adjustAnnotationHeight();
1694 public AlignmentI getAlignment()
1696 return av == null ? null : av.getAlignment();
1700 public String getViewName()
1706 * Make/Unmake this alignment panel the current input focus
1710 public void setSelected(boolean b)
1714 if (alignFrame.getSplitViewContainer() != null)
1717 * bring enclosing SplitFrame to front first if there is one
1719 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1721 alignFrame.setSelected(b);
1722 } catch (Exception ex)
1728 alignFrame.setDisplayedView(this);
1733 public StructureSelectionManager getStructureSelectionManager()
1735 return av.getStructureSelectionManager();
1739 public void raiseOOMWarning(String string, OutOfMemoryError error)
1741 new OOMWarning(string, error, this);
1745 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1748 return new FeatureRenderer(this);
1752 public jalview.api.FeatureRenderer getFeatureRenderer()
1754 return seqPanel.seqCanvas.getFeatureRenderer();
1757 public void updateFeatureRenderer(
1758 jalview.renderer.seqfeatures.FeatureRenderer fr)
1760 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1763 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1765 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1767 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1771 public ScalePanel getScalePanel()
1776 public void setScalePanel(ScalePanel scalePanel)
1778 this.scalePanel = scalePanel;
1781 public SeqPanel getSeqPanel()
1786 public void setSeqPanel(SeqPanel seqPanel)
1788 this.seqPanel = seqPanel;
1791 public AnnotationPanel getAnnotationPanel()
1793 return annotationPanel;
1796 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1798 this.annotationPanel = annotationPanel;
1801 public AnnotationLabels getAlabels()
1806 public void setAlabels(AnnotationLabels alabels)
1808 this.alabels = alabels;
1811 public IdPanel getIdPanel()
1816 public void setIdPanel(IdPanel idPanel)
1818 this.idPanel = idPanel;
1822 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1823 * The aim is to keep the two alignments 'lined up' on their centre columns.
1826 * holds mapped region(s) of this alignment that we are scrolling
1827 * 'to'; may be modified for sequence offset by this method
1828 * @param verticalOffset
1829 * the number of visible sequences to show above the mapped region
1831 public void scrollToCentre(SearchResultsI sr, int verticalOffset)
1834 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1835 * mapped), we can make the scroll-to location a sequence above the one
1838 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1839 List<SequenceI> seqs = av.getAlignment().getSequences();
1842 * This is like AlignmentI.findIndex(seq) but here we are matching the
1843 * dataset sequence not the aligned sequence
1845 boolean matched = false;
1846 for (SequenceI seq : seqs)
1848 if (mappedTo == seq.getDatasetSequence())
1856 return; // failsafe, shouldn't happen
1860 * Scroll to position but centring the target residue.
1862 scrollToPosition(sr, verticalOffset, true, true);
1866 * Set a flag to say do not scroll any (cDNA/protein) complement.
1870 protected void setDontScrollComplement(boolean b)
1872 this.dontScrollComplement = b;
1875 protected boolean isDontScrollComplement()
1877 return this.dontScrollComplement;