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.setStartRes(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 if (av == null || av.getAlignment() == null)
695 int width = av.getAlignment().getWidth();
696 int height = av.getAlignment().getHeight();
698 if (av.hasHiddenColumns())
700 // reset the width to exclude hidden columns
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())
809 if (overviewPanel != null)
811 overviewPanel.setBoxPosition();
814 int scrollX = av.getStartRes() - oldX;
815 int scrollY = av.getStartSeq() - oldY;
817 if (av.getWrapAlignment() || !fastPaint)
823 // Make sure we're not trying to draw a panel
824 // larger than the visible window
825 if (scrollX > av.getEndRes() - av.getStartRes())
827 scrollX = av.getEndRes() - av.getStartRes();
829 else if (scrollX < av.getStartRes() - av.getEndRes())
831 scrollX = av.getStartRes() - av.getEndRes();
834 if (scrollX != 0 || scrollY != 0)
836 getIdPanel().getIdCanvas().fastPaint(scrollY);
837 getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
838 getScalePanel().repaint();
840 if (av.isShowAnnotation() && scrollX != 0)
842 getAnnotationPanel().fastPaint(scrollX);
847 * If there is one, scroll the (Protein/cDNA) complementary alignment to
848 * match, unless we are ourselves doing that.
850 if (isDontScrollComplement())
852 setDontScrollComplement(false);
856 av.scrollComplementaryAlignment();
861 * Repaint the alignment including the annotations and overview panels (if
865 public void paintAlignment(boolean updateOverview)
867 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
868 av.isShowAutocalculatedAbove());
869 sorter.sort(getAlignment().getAlignmentAnnotation(),
870 av.getSortAnnotationsBy());
875 // TODO: determine if this paintAlignment changed structure colours
876 av.getStructureSelectionManager().sequenceColoursChanged(this);
878 if (overviewPanel != null)
880 overviewPanel.updateOverviewImage();
892 public void paintComponent(Graphics g)
896 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
897 idPanelHolder.setPreferredSize(d);
898 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
902 * set scroll bar positions; first suppress this being 'followed' in any
903 * complementary split pane
905 setDontScrollComplement(true);
907 if (av.getWrapAlignment())
909 int maxwidth = av.getAlignment().getWidth();
911 if (av.hasHiddenColumns())
913 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
916 int canvasWidth = getSeqPanel().seqCanvas
917 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
921 / getSeqPanel().seqCanvas
922 .getWrappedCanvasWidth(getSeqPanel().seqCanvas
924 vscroll.setMaximum(max);
925 vscroll.setUnitIncrement(1);
926 vscroll.setVisibleAmount(1);
931 setScrollValues(av.getStartRes(), av.getStartSeq());
945 * @return DOCUMENT ME!
947 * @throws PrinterException
951 public int print(Graphics pg, PageFormat pf, int pi)
952 throws PrinterException
954 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
956 int pwidth = (int) pf.getImageableWidth();
957 int pheight = (int) pf.getImageableHeight();
959 if (av.getWrapAlignment())
961 return printWrappedAlignment(pwidth, pheight, pi, pg);
965 return printUnwrapped(pwidth, pheight, pi, pg, pg);
981 * @return DOCUMENT ME!
983 * @throws PrinterException
987 * Draws the alignment image, including sequence ids, sequences, and
988 * annotation labels and annotations if shown, on either one or two Graphics
995 * the graphics context for sequence ids and annotation labels
996 * @param alignmentGraphics
997 * the graphics context for sequences and annotations (may or may not
998 * be the same context as idGraphics)
1000 * @throws PrinterException
1002 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
1003 Graphics idGraphics, Graphics alignmentGraphics)
1004 throws PrinterException
1006 final int idWidth = getVisibleIdWidth(false);
1009 * Get the horizontal offset to where we draw the sequences.
1010 * This is idWidth if using a single Graphics context, else zero.
1012 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
1014 FontMetrics fm = getFontMetrics(av.getFont());
1015 int charHeight = av.getCharHeight();
1016 int scaleHeight = charHeight + fm.getDescent();
1018 idGraphics.setColor(Color.white);
1019 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
1020 idGraphics.setFont(av.getFont());
1023 * How many sequences and residues can we fit on a printable page?
1025 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1027 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1029 int alignmentWidth = av.getAlignment().getWidth();
1030 int pagesWide = (alignmentWidth / totalRes) + 1;
1032 final int startRes = (pi % pagesWide) * totalRes;
1033 int endRes = (startRes + totalRes) - 1;
1035 if (endRes > (alignmentWidth - 1))
1037 endRes = alignmentWidth - 1;
1040 final int startSeq = (pi / pagesWide) * totalSeq;
1041 int endSeq = startSeq + totalSeq;
1043 int alignmentHeight = av.getAlignment().getHeight();
1044 if (endSeq > alignmentHeight)
1046 endSeq = alignmentHeight;
1049 int pagesHigh = ((alignmentHeight / totalSeq) + 1)
1052 if (av.isShowAnnotation())
1054 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1057 pagesHigh /= pageHeight;
1059 if (pi >= (pagesWide * pagesHigh))
1061 return Printable.NO_SUCH_PAGE;
1063 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
1067 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1069 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1070 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1071 pageWidth - idWidth, scaleHeight);
1072 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1075 * Draw the sequence ids, offset for scale height,
1076 * then reset to top left (0, 0)
1078 idGraphics.translate(0, scaleHeight);
1079 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1080 Color currentColor = null;
1081 Color currentTextColor = null;
1084 for (int i = startSeq; i < endSeq; i++)
1086 seq = av.getAlignment().getSequenceAt(i);
1087 if ((av.getSelectionGroup() != null)
1088 && av.getSelectionGroup().getSequences(null).contains(seq))
1091 * gray out ids of sequences in selection group (if any)
1093 currentColor = Color.gray;
1094 currentTextColor = Color.black;
1098 currentColor = av.getSequenceColour(seq);
1099 currentTextColor = Color.black;
1102 idGraphics.setColor(currentColor);
1103 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1106 idGraphics.setColor(currentTextColor);
1109 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1110 if (av.isRightAlignIds())
1112 fm = idGraphics.getFontMetrics();
1114 - fm.stringWidth(displayId)
1118 idGraphics.drawString(displayId, xPos,
1119 (((i - startSeq) * charHeight) + charHeight)
1120 - (charHeight / 5));
1122 idGraphics.setFont(av.getFont());
1123 idGraphics.translate(0, -scaleHeight);
1126 * draw the sequences, offset for scale height, and id width (if using a
1127 * single graphics context), then reset to (0, scale height)
1129 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1130 getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
1131 startSeq, endSeq, 0);
1132 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1134 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1137 * draw annotation labels; drawComponent() translates by
1138 * getScrollOffset(), so compensate for that first;
1139 * then reset to (0, scale height)
1141 int offset = getAlabels().getScrollOffset();
1142 idGraphics.translate(0, -offset);
1143 idGraphics.translate(0, alignmentDrawnHeight);
1144 getAlabels().drawComponent(idGraphics, idWidth);
1145 idGraphics.translate(0, -alignmentDrawnHeight);
1148 * draw the annotations starting at
1149 * (idOffset, alignmentHeight) from (0, scaleHeight)
1151 alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
1152 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1153 alignmentGraphics, -1, startRes, endRes + 1);
1156 return Printable.PAGE_EXISTS;
1171 * @return DOCUMENT ME!
1173 * @throws PrinterException
1176 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1177 Graphics pg) throws PrinterException
1179 int annotationHeight = 0;
1180 AnnotationLabels labels = null;
1181 if (av.isShowAnnotation())
1183 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1184 labels = new AnnotationLabels(av);
1187 int hgap = av.getCharHeight();
1188 if (av.getScaleAboveWrapped())
1190 hgap += av.getCharHeight();
1193 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1196 int idWidth = getVisibleIdWidth(false);
1198 int maxwidth = av.getAlignment().getWidth();
1199 if (av.hasHiddenColumns())
1201 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1204 int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
1207 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1209 pg.setColor(Color.white);
1210 pg.fillRect(0, 0, pwidth, pheight);
1211 pg.setFont(av.getFont());
1215 pg.setColor(Color.black);
1217 pg.translate(0, -pi * pheight);
1219 pg.setClip(0, pi * pheight, pwidth, pheight);
1225 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1227 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1228 SequenceI s = av.getAlignment().getSequenceAt(i);
1229 String string = s.getDisplayId(av.getShowJVSuffix());
1231 if (av.isRightAlignIds())
1233 FontMetrics fm = pg.getFontMetrics();
1234 xPos = idWidth - fm.stringWidth(string) - 4;
1236 pg.drawString(string, xPos,
1237 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1238 - (av.getCharHeight() / 5));
1243 ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
1245 pg.setFont(av.getFont());
1246 labels.drawComponent(pg, idWidth);
1250 - (av.getAlignment().getHeight() * av
1255 } while (ypos < totalHeight);
1257 pg.translate(idWidth, 0);
1259 getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
1262 if ((pi * pheight) < totalHeight)
1264 return Printable.PAGE_EXISTS;
1269 return Printable.NO_SUCH_PAGE;
1274 * get current sequence ID panel width, or nominal value if panel were to be
1275 * displayed using default settings
1279 public int getVisibleIdWidth()
1281 return getVisibleIdWidth(true);
1285 * get current sequence ID panel width, or nominal value if panel were to be
1286 * displayed using default settings
1289 * indicate if the Id width for onscreen or offscreen display should
1293 public int getVisibleIdWidth(boolean onscreen)
1295 // see if rendering offscreen - check preferences and calc width accordingly
1296 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1298 return calculateIdWidth(-1).width + 4;
1300 Integer idwidth = null;
1302 || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1304 int w = getIdPanel().getWidth();
1305 return (w > 0 ? w : calculateIdWidth().width + 4);
1307 return idwidth.intValue() + 4;
1310 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1312 int boarderBottomOffset = 5;
1313 long pSessionId = System.currentTimeMillis();
1314 headless = (System.getProperty("java.awt.headless") != null && System
1315 .getProperty("java.awt.headless").equals("true"));
1316 if (alignFrame != null && !headless)
1320 alignFrame.setProgressBar(MessageManager.formatMessage(
1321 "status.saving_file", new Object[] { type.getLabel() }),
1327 AlignmentDimension aDimension = getAlignmentDimension();
1330 jalview.util.ImageMaker im;
1331 final String imageAction, imageTitle;
1332 if (type == jalview.util.ImageMaker.TYPE.PNG)
1334 imageAction = "Create PNG image from alignment";
1337 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1339 imageAction = "Create EPS file from alignment";
1340 imageTitle = alignFrame.getTitle();
1344 imageAction = "Create SVG file from alignment";
1345 imageTitle = alignFrame.getTitle();
1348 im = new jalview.util.ImageMaker(this, type, imageAction,
1349 aDimension.getWidth(), aDimension.getHeight()
1350 + boarderBottomOffset, file, imageTitle,
1351 alignFrame, pSessionId, headless);
1352 Graphics graphics = im.getGraphics();
1353 if (av.getWrapAlignment())
1355 if (graphics != null)
1357 printWrappedAlignment(aDimension.getWidth(),
1358 aDimension.getHeight() + boarderBottomOffset, 0,
1365 if (graphics != null)
1367 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
1368 0, graphics, graphics);
1373 } catch (OutOfMemoryError err)
1376 System.out.println("########################\n" + "OUT OF MEMORY "
1377 + file + "\n" + "########################");
1378 new OOMWarning("Creating Image for " + file, err);
1379 // System.out.println("Create IMAGE: " + err);
1380 } catch (Exception ex)
1382 ex.printStackTrace();
1390 public AlignmentDimension getAlignmentDimension()
1392 int maxwidth = av.getAlignment().getWidth();
1393 if (av.hasHiddenColumns())
1395 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
1398 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1399 + getScalePanel().getHeight();
1400 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1402 if (av.getWrapAlignment())
1404 height = getWrappedHeight();
1407 // need to obtain default alignment width and then add in any
1408 // additional allowance for id margin
1409 // this duplicates the calculation in getWrappedHeight but adjusts for
1411 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1412 - alignFrame.getInsets().left
1413 - alignFrame.getInsets().right - getVisibleIdWidth()
1414 + getVisibleIdWidth(false);
1418 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1422 else if (av.isShowAnnotation())
1424 height += getAnnotationPanel().adjustPanelHeight() + 3;
1426 return new AlignmentDimension(width, height);
1433 public void makeEPS(File epsFile)
1435 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1441 public void makePNG(File pngFile)
1443 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1446 public void makeSVG(File svgFile)
1448 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1451 public void makePNGImageMap(File imgMapFile, String imageName)
1453 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1454 // ////////////////////////////////////////////
1455 int idWidth = getVisibleIdWidth(false);
1456 FontMetrics fm = getFontMetrics(av.getFont());
1457 int scaleHeight = av.getCharHeight() + fm.getDescent();
1460 // ////////////////////////////////
1461 if (imgMapFile != null)
1465 int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
1466 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
1467 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1468 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1469 out.println("<img src=\"" + imageName
1470 + "\" border=\"0\" usemap=\"#Map\" >"
1471 + "<map name=\"Map\">");
1473 for (s = 0; s < sSize; s++)
1475 sy = s * av.getCharHeight() + scaleHeight;
1477 SequenceI seq = av.getAlignment().getSequenceAt(s);
1478 SequenceFeature[] features = seq.getSequenceFeatures();
1479 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1480 for (res = 0; res < alwidth; res++)
1482 StringBuilder text = new StringBuilder();
1483 String triplet = null;
1484 if (av.getAlignment().isNucleotide())
1486 triplet = ResidueProperties.nucleotideName.get(seq
1487 .getCharAt(res) + "");
1491 triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
1495 if (triplet == null)
1500 int alIndex = seq.findPosition(res);
1501 gSize = groups.length;
1502 for (g = 0; g < gSize; g++)
1504 if (text.length() < 1)
1506 text.append("<area shape=\"rect\" coords=\"")
1507 .append((idWidth + res * av.getCharWidth()))
1508 .append(",").append(sy).append(",")
1509 .append((idWidth + (res + 1) * av.getCharWidth()))
1510 .append(",").append((av.getCharHeight() + sy))
1511 .append("\"").append(" onMouseOver=\"toolTip('")
1512 .append(alIndex).append(" ").append(triplet);
1515 if (groups[g].getStartRes() < res
1516 && groups[g].getEndRes() > res)
1518 text.append("<br><em>").append(groups[g].getName())
1523 if (features != null)
1525 if (text.length() < 1)
1527 text.append("<area shape=\"rect\" coords=\"")
1528 .append((idWidth + res * av.getCharWidth()))
1529 .append(",").append(sy).append(",")
1530 .append((idWidth + (res + 1) * av.getCharWidth()))
1531 .append(",").append((av.getCharHeight() + sy))
1532 .append("\"").append(" onMouseOver=\"toolTip('")
1533 .append(alIndex).append(" ").append(triplet);
1535 fSize = features.length;
1536 for (f = 0; f < fSize; f++)
1539 if ((features[f].getBegin() <= seq.findPosition(res))
1540 && (features[f].getEnd() >= seq.findPosition(res)))
1542 if (features[f].isContactFeature())
1544 if (features[f].getBegin() == seq.findPosition(res)
1545 || features[f].getEnd() == seq
1548 text.append("<br>").append(features[f].getType())
1549 .append(" ").append(features[f].getBegin())
1550 .append(":").append(features[f].getEnd());
1555 text.append("<br>");
1556 text.append(features[f].getType());
1557 if (features[f].getDescription() != null
1558 && !features[f].getType().equals(
1559 features[f].getDescription()))
1561 text.append(" ").append(features[f].getDescription());
1564 if (features[f].getValue("status") != null)
1566 text.append(" (").append(features[f].getValue("status"))
1574 if (text.length() > 1)
1576 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1577 out.println(text.toString());
1581 out.println("</map></body></html>");
1584 } catch (Exception ex)
1586 ex.printStackTrace();
1588 } // /////////END OF IMAGE MAP
1592 int getWrappedHeight()
1594 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1596 if (System.getProperty("java.awt.headless") != null
1597 && System.getProperty("java.awt.headless").equals("true"))
1599 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1600 - vscroll.getPreferredSize().width
1601 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1604 int chunkWidth = getSeqPanel().seqCanvas
1605 .getWrappedCanvasWidth(seqPanelWidth);
1607 int hgap = av.getCharHeight();
1608 if (av.getScaleAboveWrapped())
1610 hgap += av.getCharHeight();
1613 int annotationHeight = 0;
1614 if (av.isShowAnnotation())
1616 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1619 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1622 int maxwidth = av.getAlignment().getWidth();
1623 if (av.hasHiddenColumns())
1625 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1628 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1634 * close the panel - deregisters all listeners and nulls any references to
1637 public void closePanel()
1639 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1640 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1641 PaintRefresher.RemoveComponent(this);
1644 * try to ensure references are nulled
1646 if (annotationPanel != null)
1648 annotationPanel.dispose();
1653 av.removePropertyChangeListener(propertyChangeListener);
1654 jalview.structure.StructureSelectionManager ssm = av
1655 .getStructureSelectionManager();
1656 ssm.removeStructureViewerListener(getSeqPanel(), null);
1657 ssm.removeSelectionListener(getSeqPanel());
1658 ssm.removeCommandListener(av);
1659 ssm.removeStructureViewerListener(getSeqPanel(), null);
1660 ssm.removeSelectionListener(getSeqPanel());
1666 if (Cache.log.isDebugEnabled())
1668 Cache.log.warn("Closing alignment panel which is already closed.");
1674 * hides or shows dynamic annotation rows based on groups and av state flags
1676 public void updateAnnotation()
1678 updateAnnotation(false, false);
1681 public void updateAnnotation(boolean applyGlobalSettings)
1683 updateAnnotation(applyGlobalSettings, false);
1686 public void updateAnnotation(boolean applyGlobalSettings,
1687 boolean preserveNewGroupSettings)
1689 av.updateGroupAnnotationSettings(applyGlobalSettings,
1690 preserveNewGroupSettings);
1691 adjustAnnotationHeight();
1695 public AlignmentI getAlignment()
1697 return av == null ? null : av.getAlignment();
1701 public String getViewName()
1707 * Make/Unmake this alignment panel the current input focus
1711 public void setSelected(boolean b)
1715 if (alignFrame.getSplitViewContainer() != null)
1718 * bring enclosing SplitFrame to front first if there is one
1720 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1722 alignFrame.setSelected(b);
1723 } catch (Exception ex)
1729 alignFrame.setDisplayedView(this);
1734 public StructureSelectionManager getStructureSelectionManager()
1736 return av.getStructureSelectionManager();
1740 public void raiseOOMWarning(String string, OutOfMemoryError error)
1742 new OOMWarning(string, error, this);
1746 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1749 return new FeatureRenderer(this);
1753 public jalview.api.FeatureRenderer getFeatureRenderer()
1755 return seqPanel.seqCanvas.getFeatureRenderer();
1758 public void updateFeatureRenderer(
1759 jalview.renderer.seqfeatures.FeatureRenderer fr)
1761 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1764 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1766 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1768 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1772 public ScalePanel getScalePanel()
1777 public void setScalePanel(ScalePanel scalePanel)
1779 this.scalePanel = scalePanel;
1782 public SeqPanel getSeqPanel()
1787 public void setSeqPanel(SeqPanel seqPanel)
1789 this.seqPanel = seqPanel;
1792 public AnnotationPanel getAnnotationPanel()
1794 return annotationPanel;
1797 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1799 this.annotationPanel = annotationPanel;
1802 public AnnotationLabels getAlabels()
1807 public void setAlabels(AnnotationLabels alabels)
1809 this.alabels = alabels;
1812 public IdPanel getIdPanel()
1817 public void setIdPanel(IdPanel idPanel)
1819 this.idPanel = idPanel;
1823 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1824 * The aim is to keep the two alignments 'lined up' on their centre columns.
1827 * holds mapped region(s) of this alignment that we are scrolling
1828 * 'to'; may be modified for sequence offset by this method
1829 * @param verticalOffset
1830 * the number of visible sequences to show above the mapped region
1832 public void scrollToCentre(SearchResultsI sr, int verticalOffset)
1835 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1836 * mapped), we can make the scroll-to location a sequence above the one
1839 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1840 List<SequenceI> seqs = av.getAlignment().getSequences();
1843 * This is like AlignmentI.findIndex(seq) but here we are matching the
1844 * dataset sequence not the aligned sequence
1846 boolean matched = false;
1847 for (SequenceI seq : seqs)
1849 if (mappedTo == seq.getDatasetSequence())
1857 return; // failsafe, shouldn't happen
1861 * Scroll to position but centring the target residue.
1863 scrollToPosition(sr, verticalOffset, true, true);
1867 * Set a flag to say do not scroll any (cDNA/protein) complement.
1871 protected void setDontScrollComplement(boolean b)
1873 this.dontScrollComplement = b;
1876 protected boolean isDontScrollComplement()
1878 return this.dontScrollComplement;