2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AnnotationSorter;
24 import jalview.api.AlignViewportI;
25 import jalview.api.AlignmentViewPanel;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SearchResultsI;
30 import jalview.datamodel.SequenceFeature;
31 import jalview.datamodel.SequenceGroup;
32 import jalview.datamodel.SequenceI;
33 import jalview.jbgui.GAlignmentPanel;
34 import jalview.math.AlignmentDimension;
35 import jalview.schemes.ResidueProperties;
36 import jalview.structure.StructureSelectionManager;
37 import jalview.util.MessageManager;
38 import jalview.util.Platform;
39 import jalview.viewmodel.ViewportListenerI;
40 import jalview.viewmodel.ViewportRanges;
42 import java.awt.BorderLayout;
43 import java.awt.Color;
44 import java.awt.Container;
45 import java.awt.Dimension;
47 import java.awt.FontMetrics;
48 import java.awt.Graphics;
49 import java.awt.Insets;
50 import java.awt.event.AdjustmentEvent;
51 import java.awt.event.AdjustmentListener;
52 import java.awt.event.ComponentAdapter;
53 import java.awt.event.ComponentEvent;
54 import java.awt.print.PageFormat;
55 import java.awt.print.Printable;
56 import java.awt.print.PrinterException;
57 import java.beans.PropertyChangeEvent;
58 import java.beans.PropertyChangeListener;
60 import java.io.FileWriter;
61 import java.io.PrintWriter;
62 import java.util.List;
64 import javax.swing.SwingUtilities;
70 * @version $Revision: 1.161 $
72 public class AlignmentPanel extends GAlignmentPanel implements
73 AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
75 public AlignViewport av;
77 ViewportRanges vpRanges;
79 OverviewPanel overviewPanel;
81 private SeqPanel seqPanel;
83 private IdPanel idPanel;
85 private boolean headless;
87 IdwidthAdjuster idwidthAdjuster;
90 public AlignFrame alignFrame;
92 private ScalePanel scalePanel;
94 private AnnotationPanel annotationPanel;
96 private AnnotationLabels alabels;
98 // this value is set false when selection area being dragged
99 boolean fastPaint = true;
101 private int hextent = 0;
103 private int vextent = 0;
106 * Flag set while scrolling to follow complementary cDNA/protein scroll. When
107 * false, suppresses invoking the same method recursively.
109 private boolean scrollComplementaryPanel = true;
111 private PropertyChangeListener propertyChangeListener;
113 private CalculationChooser calculationDialog;
116 * Creates a new AlignmentPanel object.
121 public AlignmentPanel(AlignFrame af, final AlignViewport av)
125 vpRanges = av.getRanges();
126 setSeqPanel(new SeqPanel(av, this));
127 setIdPanel(new IdPanel(av, this));
129 setScalePanel(new ScalePanel(av, this));
131 idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
132 idwidthAdjuster = new IdwidthAdjuster(this);
133 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
135 setAnnotationPanel(new AnnotationPanel(this));
136 setAlabels(new AnnotationLabels(this));
138 annotationScroller.setViewportView(getAnnotationPanel());
139 annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
141 scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
142 seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
144 setScrollValues(0, 0);
146 hscroll.addAdjustmentListener(this);
147 vscroll.addAdjustmentListener(this);
149 addComponentListener(new ComponentAdapter()
152 public void componentResized(ComponentEvent evt)
154 // reset the viewport ranges when the alignment panel is resized
155 // in particular, this initialises the end residue value when Jalview
157 if (av.getWrapAlignment())
159 int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
160 getSeqPanel().seqCanvas.getWidth());
161 vpRanges.setViewportWidth(widthInRes);
165 int widthInRes = getSeqPanel().seqCanvas.getWidth()
167 int heightInSeq = getSeqPanel().seqCanvas.getHeight()
168 / av.getCharHeight();
170 vpRanges.setViewportWidth(widthInRes);
171 vpRanges.setViewportHeight(heightInSeq);
177 final AlignmentPanel ap = this;
178 propertyChangeListener = new PropertyChangeListener()
181 public void propertyChange(PropertyChangeEvent evt)
183 if (evt.getPropertyName().equals("alignment"))
185 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
190 av.addPropertyChangeListener(propertyChangeListener);
192 av.getRanges().addPropertyChangeListener(this);
194 adjustAnnotationHeight();
199 public AlignViewportI getAlignViewport()
204 public void alignmentChanged()
206 av.alignmentChanged(this);
208 if (getCalculationDialog() != null)
210 getCalculationDialog().validateCalcTypes();
213 alignFrame.updateEditMenuBar();
215 paintAlignment(true);
222 public void fontChanged()
224 // set idCanvas bufferedImage to null
225 // to prevent drawing old image
226 FontMetrics fm = getFontMetrics(av.getFont());
228 scalePanelHolder.setPreferredSize(
229 new Dimension(10, av.getCharHeight() + fm.getDescent()));
230 idSpaceFillerPanel1.setPreferredSize(
231 new Dimension(10, av.getCharHeight() + fm.getDescent()));
232 idwidthAdjuster.invalidate();
233 scalePanelHolder.invalidate();
234 getIdPanel().getIdCanvas().gg = null;
235 getSeqPanel().seqCanvas.img = null;
236 getAnnotationPanel().adjustPanelHeight();
238 Dimension d = calculateIdWidth();
240 d.setSize(d.width + 4, d.height);
241 getIdPanel().getIdCanvas().setPreferredSize(d);
242 hscrollFillerPanel.setPreferredSize(d);
244 if (this.alignFrame.getSplitViewContainer() != null)
246 ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
253 * Calculate the width of the alignment labels based on the displayed names
254 * and any bounds on label width set in preferences.
256 * @return Dimension giving the maximum width of the alignment label panel
257 * that should be used.
259 public Dimension calculateIdWidth()
261 // calculate sensible default width when no preference is available
263 if (av.getIdWidth() < 0)
265 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
266 int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
267 r = calculateIdWidth(maxwidth);
268 av.setIdWidth(r.width);
273 r.width = av.getIdWidth();
280 * Calculate the width of the alignment labels based on the displayed names
281 * and any bounds on label width set in preferences.
284 * -1 or maximum width allowed for IdWidth
285 * @return Dimension giving the maximum width of the alignment label panel
286 * that should be used.
288 public Dimension calculateIdWidth(int maxwidth)
290 Container c = new Container();
292 FontMetrics fm = c.getFontMetrics(
293 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
295 AlignmentI al = av.getAlignment();
300 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
302 SequenceI s = al.getSequenceAt(i);
304 id = s.getDisplayId(av.getShowJVSuffix());
306 if (fm.stringWidth(id) > idWidth)
308 idWidth = fm.stringWidth(id);
314 // Also check annotation label widths
317 if (al.getAlignmentAnnotation() != null)
319 fm = c.getFontMetrics(getAlabels().getFont());
321 while (i < al.getAlignmentAnnotation().length)
323 String label = al.getAlignmentAnnotation()[i].label;
325 if (fm.stringWidth(label) > idWidth)
327 idWidth = fm.stringWidth(label);
334 return new Dimension(
335 maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12);
339 * Highlight the given results on the alignment.
342 public void highlightSearchResults(SearchResultsI results)
344 scrollToPosition(results);
345 getSeqPanel().seqCanvas.highlightSearchResults(results);
349 * Scroll the view to show the position of the highlighted region in results
350 * (if any) and redraw the overview
354 public boolean scrollToPosition(SearchResultsI results)
356 return scrollToPosition(results, 0, true, false);
360 * Scroll the view to show the position of the highlighted region in results
363 * @param searchResults
364 * @param redrawOverview
367 public boolean scrollToPosition(SearchResultsI searchResults,
368 boolean redrawOverview)
370 return scrollToPosition(searchResults, 0, redrawOverview, false);
374 * Scroll the view to show the position of the highlighted region in results
378 * @param verticalOffset
379 * if greater than zero, allows scrolling to a position below the
380 * first displayed sequence
381 * @param redrawOverview
382 * - when set, the overview will be recalculated (takes longer)
384 * if true, try to centre the search results horizontally in the view
385 * @return false if results were not found
387 public boolean scrollToPosition(SearchResultsI results,
388 int verticalOffset, boolean redrawOverview, boolean centre)
390 int startv, endv, starts, ends;
391 // TODO: properly locate search results in view when large numbers of hidden
392 // columns exist before highlighted region
393 // do we need to scroll the panel?
394 // TODO: tons of nullpointerexceptions raised here.
395 if (results != null && results.getSize() > 0 && av != null
396 && av.getAlignment() != null)
398 int seqIndex = av.getAlignment().findIndex(results);
403 SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
405 int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
414 * To centre results, scroll to positions half the visible width
415 * left/right of the start/end positions
419 int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
421 start = Math.max(start - offset, 0);
422 end = end + offset - 1;
428 if (end == seq.getEnd())
432 if (av.hasHiddenColumns())
434 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
435 start = hidden.findColumnPosition(start);
436 end = hidden.findColumnPosition(end);
439 if (!hidden.isVisible(r[0]))
441 // don't scroll - position isn't visible
448 * allow for offset of target sequence (actually scroll to one above it)
450 seqIndex = Math.max(0, seqIndex - verticalOffset);
452 if (!av.getWrapAlignment())
454 if ((startv = vpRanges.getStartRes()) >= start)
457 * Scroll left to make start of search results visible
459 setScrollValues(start, seqIndex);
461 else if ((endv = vpRanges.getEndRes()) <= end)
464 * Scroll right to make end of search results visible
466 setScrollValues(startv + end - endv, seqIndex);
468 else if ((starts = vpRanges.getStartSeq()) > seqIndex)
471 * Scroll up to make start of search results visible
473 setScrollValues(vpRanges.getStartRes(), seqIndex);
475 else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
478 * Scroll down to make end of search results visible
480 setScrollValues(vpRanges.getStartRes(),
481 starts + seqIndex - ends + 1);
484 * Else results are already visible - no need to scroll
489 vpRanges.scrollToWrappedVisible(start);
493 paintAlignment(redrawOverview);
500 * @return DOCUMENT ME!
502 public OverviewPanel getOverviewPanel()
504 return overviewPanel;
513 public void setOverviewPanel(OverviewPanel op)
521 * Hide or show annotation panel
524 public void setAnnotationVisible(boolean b)
526 if (!av.getWrapAlignment())
528 annotationSpaceFillerHolder.setVisible(b);
529 annotationScroller.setVisible(b);
535 * automatically adjust annotation panel height for new annotation whilst
536 * ensuring the alignment is still visible.
539 public void adjustAnnotationHeight()
541 // TODO: display vertical annotation scrollbar if necessary
542 // this is called after loading new annotation onto alignment
543 if (alignFrame.getHeight() == 0)
545 System.out.println("NEEDS FIXING");
547 validateAnnotationDimensions(true);
549 paintAlignment(true);
553 * calculate the annotation dimensions and refresh slider values accordingly.
554 * need to do repaints/notifys afterwards.
556 protected void validateAnnotationDimensions(boolean adjustPanelHeight)
558 int annotationHeight = getAnnotationPanel().adjustPanelHeight();
560 if (adjustPanelHeight)
562 int rowHeight = av.getCharHeight();
563 int alignmentHeight = rowHeight * av.getAlignment().getHeight();
566 * Estimate available height in the AlignFrame for alignment +
567 * annotations. Deduct an estimate for title bar, menu bar, scale panel,
568 * hscroll, status bar (as these are not laid out we can't inspect their
569 * actual heights). Insets gives frame borders.
571 int stuff = Platform.isAMac() ? 80 : 100;
572 Insets insets = alignFrame.getInsets();
573 int availableHeight = alignFrame.getHeight() - stuff - insets.top
577 * If not enough vertical space, maximize annotation height while keeping
578 * at least two rows of alignment visible
580 if (annotationHeight + alignmentHeight > availableHeight)
582 annotationHeight = Math.min(annotationHeight,
583 availableHeight - 2 * rowHeight);
588 // maintain same window layout whilst updating sliders
589 annotationHeight = annotationScroller.getSize().height;
593 annotationScroller.setPreferredSize(
594 new Dimension(annotationScroller.getWidth(), annotationHeight));
596 Dimension e = idPanel.getSize();
597 alabels.setSize(new Dimension(e.width, annotationHeight));
599 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
600 annotationSpaceFillerHolder.getWidth(), annotationHeight));
601 annotationScroller.validate();
602 annotationScroller.addNotify();
606 * update alignment layout for viewport settings
611 public void updateLayout()
614 setAnnotationVisible(av.isShowAnnotation());
615 boolean wrap = av.getWrapAlignment();
616 vpRanges.setStartSeq(0);
617 scalePanelHolder.setVisible(!wrap);
618 hscroll.setVisible(!wrap);
619 idwidthAdjuster.setVisible(!wrap);
623 annotationScroller.setVisible(false);
624 annotationSpaceFillerHolder.setVisible(false);
626 else if (av.isShowAnnotation())
628 annotationScroller.setVisible(true);
629 annotationSpaceFillerHolder.setVisible(true);
632 int canvasWidth = getSeqPanel().seqCanvas.getWidth();
634 { // may not yet be laid out
637 int widthInRes = getSeqPanel().seqCanvas
638 .getWrappedCanvasWidth(canvasWidth);
639 vpRanges.setViewportWidth(widthInRes);
643 int widthInRes = (canvasWidth / av.getCharWidth());
644 int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
645 / av.getCharHeight());
647 vpRanges.setViewportWidth(widthInRes);
648 vpRanges.setViewportHeight(heightInSeq);
652 idSpaceFillerPanel1.setVisible(!wrap);
658 * Adjust row/column scrollers to show a visible position in the alignment.
661 * visible column to scroll to
663 * visible row to scroll to
666 public void setScrollValues(int xpos, int ypos)
671 if (av == null || av.getAlignment() == null)
676 if (av.getWrapAlignment())
678 setScrollingForWrappedPanel(x);
682 int width = av.getAlignment().getWidth();
683 int height = av.getAlignment().getHeight();
685 if (av.hasHiddenColumns())
687 // reset the width to exclude hidden columns
688 width = av.getAlignment().getHiddenColumns()
689 .findColumnPosition(width);
692 hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
693 vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
700 if (vextent > height)
705 if ((hextent + x) > width)
710 if ((vextent + y) > height)
712 y = height - vextent;
725 // update the scroll values
726 hscroll.setValues(x, hextent, 0, width);
727 vscroll.setValues(y, vextent, 0, height);
732 * Respond to adjustment event when horizontal or vertical scrollbar is
736 * adjustment event encoding whether hscroll or vscroll changed
739 public void adjustmentValueChanged(AdjustmentEvent evt)
741 if (av.getWrapAlignment())
743 adjustScrollingWrapped(evt);
747 if (evt.getSource() == hscroll)
749 int oldX = vpRanges.getStartRes();
750 int oldwidth = vpRanges.getViewportWidth();
751 int x = hscroll.getValue();
752 int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
754 // if we're scrolling to the position we're already at, stop
755 // this prevents infinite recursion of events when the scroll/viewport
756 // ranges values are the same
757 if ((x == oldX) && (width == oldwidth))
761 vpRanges.setViewportStartAndWidth(x, width);
763 else if (evt.getSource() == vscroll)
765 int oldY = vpRanges.getStartSeq();
766 int oldheight = vpRanges.getViewportHeight();
767 int y = vscroll.getValue();
768 int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
770 // if we're scrolling to the position we're already at, stop
771 // this prevents infinite recursion of events when the scroll/viewport
772 // ranges values are the same
773 if ((y == oldY) && (height == oldheight))
777 vpRanges.setViewportStartAndHeight(y, height);
786 * Responds to a scroll change by setting the start position of the viewport.
791 protected void adjustScrollingWrapped(AdjustmentEvent evt)
793 if (evt.getSource() == hscroll)
795 return; // no horizontal scroll when wrapped
797 if (evt.getSource() == vscroll)
799 int newY = vscroll.getValue();
802 * if we're scrolling to the position we're already at, stop
803 * this prevents infinite recursion of events when the scroll/viewport
804 * ranges values are the same
806 int oldX = vpRanges.getStartRes();
807 int oldY = vpRanges.getWrappedScrollPosition(oldX);
815 * limit page up/down to one width's worth of positions
817 int rowSize = vpRanges.getViewportWidth();
818 int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
819 vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
824 // This is only called if file loaded is a jar file that
825 // was wrapped when saved and user has wrap alignment true
826 // as preference setting
827 SwingUtilities.invokeLater(new Runnable()
832 // When updating scrolling to use ViewportChange events, this code
833 // could not be validated and it is not clear if it is now being
834 // called. Log warning here in case it is called and unforeseen
837 "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
839 // scroll to start of panel
840 vpRanges.setStartRes(0);
841 vpRanges.setStartSeq(0);
849 * Repaint the alignment including the annotations and overview panels (if
853 public void paintAlignment(boolean updateOverview)
855 final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
856 av.isShowAutocalculatedAbove());
857 sorter.sort(getAlignment().getAlignmentAnnotation(),
858 av.getSortAnnotationsBy());
863 // TODO: determine if this paintAlignment changed structure colours
864 av.getStructureSelectionManager().sequenceColoursChanged(this);
866 if (overviewPanel != null)
868 overviewPanel.updateOverviewImage();
880 public void paintComponent(Graphics g)
884 Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
885 idPanelHolder.setPreferredSize(d);
886 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
890 * set scroll bar positions
892 setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
896 * Set vertical scroll bar position, and number of increments, for wrapped
899 * @param topLeftColumn
900 * the column position at top left (0..)
902 private void setScrollingForWrappedPanel(int topLeftColumn)
904 int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
905 int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
908 * a scrollbar's value can be set to at most (maximum-extent)
909 * so we add extent (1) to the maxScroll value
911 vscroll.setUnitIncrement(1);
912 vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
925 * @return DOCUMENT ME!
927 * @throws PrinterException
931 public int print(Graphics pg, PageFormat pf, int pi)
932 throws PrinterException
934 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
936 int pwidth = (int) pf.getImageableWidth();
937 int pheight = (int) pf.getImageableHeight();
939 if (av.getWrapAlignment())
941 return printWrappedAlignment(pwidth, pheight, pi, pg);
945 return printUnwrapped(pwidth, pheight, pi, pg, pg);
961 * @return DOCUMENT ME!
963 * @throws PrinterException
967 * Draws the alignment image, including sequence ids, sequences, and
968 * annotation labels and annotations if shown, on either one or two Graphics
975 * the graphics context for sequence ids and annotation labels
976 * @param alignmentGraphics
977 * the graphics context for sequences and annotations (may or may not
978 * be the same context as idGraphics)
980 * @throws PrinterException
982 public int printUnwrapped(int pageWidth, int pageHeight, int pi,
983 Graphics idGraphics, Graphics alignmentGraphics)
984 throws PrinterException
986 final int idWidth = getVisibleIdWidth(false);
989 * Get the horizontal offset to where we draw the sequences.
990 * This is idWidth if using a single Graphics context, else zero.
992 final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
995 FontMetrics fm = getFontMetrics(av.getFont());
996 int charHeight = av.getCharHeight();
997 int scaleHeight = charHeight + fm.getDescent();
999 idGraphics.setColor(Color.white);
1000 idGraphics.fillRect(0, 0, pageWidth, pageHeight);
1001 idGraphics.setFont(av.getFont());
1004 * How many sequences and residues can we fit on a printable page?
1006 int totalRes = (pageWidth - idWidth) / av.getCharWidth();
1008 int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
1010 int alignmentWidth = av.getAlignment().getWidth();
1011 int pagesWide = (alignmentWidth / totalRes) + 1;
1013 final int startRes = (pi % pagesWide) * totalRes;
1014 int endRes = (startRes + totalRes) - 1;
1016 if (endRes > (alignmentWidth - 1))
1018 endRes = alignmentWidth - 1;
1021 final int startSeq = (pi / pagesWide) * totalSeq;
1022 int endSeq = startSeq + totalSeq;
1024 int alignmentHeight = av.getAlignment().getHeight();
1025 if (endSeq > alignmentHeight)
1027 endSeq = alignmentHeight;
1030 int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
1032 if (av.isShowAnnotation())
1034 pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
1037 pagesHigh /= pageHeight;
1039 if (pi >= (pagesWide * pagesHigh))
1041 return Printable.NO_SUCH_PAGE;
1043 final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
1046 * draw the Scale at horizontal offset, then reset to top left (0, 0)
1048 alignmentGraphics.translate(alignmentGraphicsOffset, 0);
1049 getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
1050 pageWidth - idWidth, scaleHeight);
1051 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1054 * Draw the sequence ids, offset for scale height,
1055 * then reset to top left (0, 0)
1057 idGraphics.translate(0, scaleHeight);
1058 idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
1059 Color currentColor = null;
1060 Color currentTextColor = null;
1063 for (int i = startSeq; i < endSeq; i++)
1065 seq = av.getAlignment().getSequenceAt(i);
1066 if ((av.getSelectionGroup() != null)
1067 && av.getSelectionGroup().getSequences(null).contains(seq))
1070 * gray out ids of sequences in selection group (if any)
1072 currentColor = Color.gray;
1073 currentTextColor = Color.black;
1077 currentColor = av.getSequenceColour(seq);
1078 currentTextColor = Color.black;
1081 idGraphics.setColor(currentColor);
1082 idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
1085 idGraphics.setColor(currentTextColor);
1088 String displayId = seq.getDisplayId(av.getShowJVSuffix());
1089 if (av.isRightAlignIds())
1091 fm = idGraphics.getFontMetrics();
1092 xPos = idWidth - fm.stringWidth(displayId) - 4;
1095 idGraphics.drawString(displayId, xPos,
1096 (((i - startSeq) * charHeight) + charHeight)
1097 - (charHeight / 5));
1099 idGraphics.setFont(av.getFont());
1100 idGraphics.translate(0, -scaleHeight);
1103 * draw the sequences, offset for scale height, and id width (if using a
1104 * single graphics context), then reset to (0, scale height)
1106 alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
1107 getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
1108 endRes, startSeq, endSeq);
1109 alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
1111 if (av.isShowAnnotation() && (endSeq == alignmentHeight))
1114 * draw annotation labels; drawComponent() translates by
1115 * getScrollOffset(), so compensate for that first;
1116 * then reset to (0, scale height)
1118 int offset = getAlabels().getScrollOffset();
1119 idGraphics.translate(0, -offset);
1120 idGraphics.translate(0, alignmentDrawnHeight);
1121 getAlabels().drawComponent(idGraphics, idWidth);
1122 idGraphics.translate(0, -alignmentDrawnHeight);
1125 * draw the annotations starting at
1126 * (idOffset, alignmentHeight) from (0, scaleHeight)
1128 alignmentGraphics.translate(alignmentGraphicsOffset,
1129 alignmentDrawnHeight);
1130 getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
1131 alignmentGraphics, -1, startRes, endRes + 1);
1134 return Printable.PAGE_EXISTS;
1149 * @return DOCUMENT ME!
1151 * @throws PrinterException
1154 public int printWrappedAlignment(int pwidth, int pheight, int pi,
1155 Graphics pg) throws PrinterException
1157 int annotationHeight = 0;
1158 AnnotationLabels labels = null;
1159 if (av.isShowAnnotation())
1161 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1162 labels = new AnnotationLabels(av);
1165 int hgap = av.getCharHeight();
1166 if (av.getScaleAboveWrapped())
1168 hgap += av.getCharHeight();
1171 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1174 int idWidth = getVisibleIdWidth(false);
1176 int maxwidth = av.getAlignment().getWidth();
1177 if (av.hasHiddenColumns())
1179 maxwidth = av.getAlignment().getHiddenColumns()
1180 .findColumnPosition(maxwidth) - 1;
1183 int resWidth = getSeqPanel().seqCanvas
1184 .getWrappedCanvasWidth(pwidth - idWidth);
1186 int totalHeight = cHeight * (maxwidth / resWidth + 1);
1188 pg.setColor(Color.white);
1189 pg.fillRect(0, 0, pwidth, pheight);
1190 pg.setFont(av.getFont());
1194 pg.setColor(Color.black);
1196 pg.translate(0, -pi * pheight);
1198 pg.setClip(0, pi * pheight, pwidth, pheight);
1204 for (int i = 0; i < av.getAlignment().getHeight(); i++)
1206 pg.setFont(getIdPanel().getIdCanvas().getIdfont());
1207 SequenceI s = av.getAlignment().getSequenceAt(i);
1208 String string = s.getDisplayId(av.getShowJVSuffix());
1210 if (av.isRightAlignIds())
1212 FontMetrics fm = pg.getFontMetrics();
1213 xPos = idWidth - fm.stringWidth(string) - 4;
1215 pg.drawString(string, xPos,
1216 ((i * av.getCharHeight()) + ypos + av.getCharHeight())
1217 - (av.getCharHeight() / 5));
1221 pg.translate(-3, ypos
1222 + (av.getAlignment().getHeight() * av.getCharHeight()));
1224 pg.setFont(av.getFont());
1225 labels.drawComponent(pg, idWidth);
1226 pg.translate(+3, -ypos
1227 - (av.getAlignment().getHeight() * av.getCharHeight()));
1231 } while (ypos < totalHeight);
1233 pg.translate(idWidth, 0);
1235 getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth,
1238 if ((pi * pheight) < totalHeight)
1240 return Printable.PAGE_EXISTS;
1245 return Printable.NO_SUCH_PAGE;
1250 * get current sequence ID panel width, or nominal value if panel were to be
1251 * displayed using default settings
1255 public int getVisibleIdWidth()
1257 return getVisibleIdWidth(true);
1261 * get current sequence ID panel width, or nominal value if panel were to be
1262 * displayed using default settings
1265 * indicate if the Id width for onscreen or offscreen display should
1269 public int getVisibleIdWidth(boolean onscreen)
1271 // see if rendering offscreen - check preferences and calc width accordingly
1272 if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
1274 return calculateIdWidth(-1).width + 4;
1276 Integer idwidth = null;
1277 if (onscreen || (idwidth = Cache
1278 .getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
1280 int w = getIdPanel().getWidth();
1281 return (w > 0 ? w : calculateIdWidth().width + 4);
1283 return idwidth.intValue() + 4;
1286 void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
1288 int boarderBottomOffset = 5;
1289 long pSessionId = System.currentTimeMillis();
1290 headless = (System.getProperty("java.awt.headless") != null
1291 && System.getProperty("java.awt.headless").equals("true"));
1292 if (alignFrame != null && !headless)
1296 alignFrame.setProgressBar(MessageManager
1297 .formatMessage("status.saving_file", new Object[]
1298 { type.getLabel() }), pSessionId);
1303 AlignmentDimension aDimension = getAlignmentDimension();
1306 jalview.util.ImageMaker im;
1307 final String imageAction, imageTitle;
1308 if (type == jalview.util.ImageMaker.TYPE.PNG)
1310 imageAction = "Create PNG image from alignment";
1313 else if (type == jalview.util.ImageMaker.TYPE.EPS)
1315 imageAction = "Create EPS file from alignment";
1316 imageTitle = alignFrame.getTitle();
1320 imageAction = "Create SVG file from alignment";
1321 imageTitle = alignFrame.getTitle();
1324 im = new jalview.util.ImageMaker(this, type, imageAction,
1325 aDimension.getWidth(),
1326 aDimension.getHeight() + boarderBottomOffset, file,
1327 imageTitle, alignFrame, pSessionId, headless);
1328 Graphics graphics = im.getGraphics();
1329 if (av.getWrapAlignment())
1331 if (graphics != null)
1333 printWrappedAlignment(aDimension.getWidth(),
1334 aDimension.getHeight() + boarderBottomOffset, 0,
1341 if (graphics != null)
1343 printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
1344 graphics, graphics);
1349 } catch (OutOfMemoryError err)
1352 System.out.println("########################\n" + "OUT OF MEMORY "
1353 + file + "\n" + "########################");
1354 new OOMWarning("Creating Image for " + file, err);
1355 // System.out.println("Create IMAGE: " + err);
1356 } catch (Exception ex)
1358 ex.printStackTrace();
1366 public AlignmentDimension getAlignmentDimension()
1368 int maxwidth = av.getAlignment().getWidth();
1369 if (av.hasHiddenColumns())
1371 maxwidth = av.getAlignment().getHiddenColumns()
1372 .findColumnPosition(maxwidth);
1375 int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
1376 + getScalePanel().getHeight();
1377 int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
1379 if (av.getWrapAlignment())
1381 height = getWrappedHeight();
1384 // need to obtain default alignment width and then add in any
1385 // additional allowance for id margin
1386 // this duplicates the calculation in getWrappedHeight but adjusts for
1388 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1389 - alignFrame.getInsets().left - alignFrame.getInsets().right
1390 - getVisibleIdWidth() + getVisibleIdWidth(false);
1394 width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
1398 else if (av.isShowAnnotation())
1400 height += getAnnotationPanel().adjustPanelHeight() + 3;
1402 return new AlignmentDimension(width, height);
1409 public void makeEPS(File epsFile)
1411 makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
1417 public void makePNG(File pngFile)
1419 makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
1422 public void makeSVG(File svgFile)
1424 makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
1427 public void makePNGImageMap(File imgMapFile, String imageName)
1429 // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
1430 // ////////////////////////////////////////////
1431 int idWidth = getVisibleIdWidth(false);
1432 FontMetrics fm = getFontMetrics(av.getFont());
1433 int scaleHeight = av.getCharHeight() + fm.getDescent();
1436 // ////////////////////////////////
1437 if (imgMapFile != null)
1441 int s, sSize = av.getAlignment().getHeight(), res,
1442 alwidth = av.getAlignment().getWidth(), g, gSize, f, fSize,
1444 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1445 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1446 out.println("<img src=\"" + imageName
1447 + "\" border=\"0\" usemap=\"#Map\" >"
1448 + "<map name=\"Map\">");
1450 for (s = 0; s < sSize; s++)
1452 sy = s * av.getCharHeight() + scaleHeight;
1454 SequenceI seq = av.getAlignment().getSequenceAt(s);
1455 SequenceFeature[] features = seq.getSequenceFeatures();
1456 SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
1457 for (res = 0; res < alwidth; res++)
1459 StringBuilder text = new StringBuilder();
1460 String triplet = null;
1461 if (av.getAlignment().isNucleotide())
1463 triplet = ResidueProperties.nucleotideName
1464 .get(seq.getCharAt(res) + "");
1468 triplet = ResidueProperties.aa2Triplet
1469 .get(seq.getCharAt(res) + "");
1472 if (triplet == null)
1477 int alIndex = seq.findPosition(res);
1478 gSize = groups.length;
1479 for (g = 0; g < gSize; g++)
1481 if (text.length() < 1)
1483 text.append("<area shape=\"rect\" coords=\"")
1484 .append((idWidth + res * av.getCharWidth()))
1485 .append(",").append(sy).append(",")
1486 .append((idWidth + (res + 1) * av.getCharWidth()))
1487 .append(",").append((av.getCharHeight() + sy))
1488 .append("\"").append(" onMouseOver=\"toolTip('")
1489 .append(alIndex).append(" ").append(triplet);
1492 if (groups[g].getStartRes() < res
1493 && groups[g].getEndRes() > res)
1495 text.append("<br><em>").append(groups[g].getName())
1500 if (features != null)
1502 if (text.length() < 1)
1504 text.append("<area shape=\"rect\" coords=\"")
1505 .append((idWidth + res * av.getCharWidth()))
1506 .append(",").append(sy).append(",")
1507 .append((idWidth + (res + 1) * av.getCharWidth()))
1508 .append(",").append((av.getCharHeight() + sy))
1509 .append("\"").append(" onMouseOver=\"toolTip('")
1510 .append(alIndex).append(" ").append(triplet);
1512 fSize = features.length;
1513 for (f = 0; f < fSize; f++)
1516 if ((features[f].getBegin() <= seq.findPosition(res))
1517 && (features[f].getEnd() >= seq.findPosition(res)))
1519 if (features[f].isContactFeature())
1521 if (features[f].getBegin() == seq.findPosition(res)
1522 || features[f].getEnd() == seq
1525 text.append("<br>").append(features[f].getType())
1526 .append(" ").append(features[f].getBegin())
1527 .append(":").append(features[f].getEnd());
1532 text.append("<br>");
1533 text.append(features[f].getType());
1534 if (features[f].getDescription() != null && !features[f]
1535 .getType().equals(features[f].getDescription()))
1537 text.append(" ").append(features[f].getDescription());
1540 if (features[f].getValue("status") != null)
1543 .append(features[f].getValue("status"))
1551 if (text.length() > 1)
1553 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1554 out.println(text.toString());
1558 out.println("</map></body></html>");
1561 } catch (Exception ex)
1563 ex.printStackTrace();
1565 } // /////////END OF IMAGE MAP
1569 int getWrappedHeight()
1571 int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
1573 if (System.getProperty("java.awt.headless") != null
1574 && System.getProperty("java.awt.headless").equals("true"))
1576 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1577 - vscroll.getPreferredSize().width
1578 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1581 int chunkWidth = getSeqPanel().seqCanvas
1582 .getWrappedCanvasWidth(seqPanelWidth);
1584 int hgap = av.getCharHeight();
1585 if (av.getScaleAboveWrapped())
1587 hgap += av.getCharHeight();
1590 int annotationHeight = 0;
1591 if (av.isShowAnnotation())
1593 annotationHeight = getAnnotationPanel().adjustPanelHeight();
1596 int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
1599 int maxwidth = av.getAlignment().getWidth();
1600 if (av.hasHiddenColumns())
1602 maxwidth = av.getAlignment().getHiddenColumns()
1603 .findColumnPosition(maxwidth) - 1;
1606 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1612 * close the panel - deregisters all listeners and nulls any references to
1615 public void closePanel()
1617 PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
1618 PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
1619 PaintRefresher.RemoveComponent(this);
1624 * try to ensure references are nulled
1626 if (annotationPanel != null)
1628 annotationPanel.dispose();
1633 av.removePropertyChangeListener(propertyChangeListener);
1634 jalview.structure.StructureSelectionManager ssm = av
1635 .getStructureSelectionManager();
1636 ssm.removeStructureViewerListener(getSeqPanel(), null);
1637 ssm.removeSelectionListener(getSeqPanel());
1638 ssm.removeCommandListener(av);
1639 ssm.removeStructureViewerListener(getSeqPanel(), null);
1640 ssm.removeSelectionListener(getSeqPanel());
1646 if (Cache.log.isDebugEnabled())
1648 Cache.log.warn("Closing alignment panel which is already closed.");
1654 * Close any open dialogs that would be orphaned when this one is closed
1656 protected void closeChildFrames()
1658 if (calculationDialog != null)
1660 calculationDialog.closeFrame();
1665 * hides or shows dynamic annotation rows based on groups and av state flags
1667 public void updateAnnotation()
1669 updateAnnotation(false, false);
1672 public void updateAnnotation(boolean applyGlobalSettings)
1674 updateAnnotation(applyGlobalSettings, false);
1677 public void updateAnnotation(boolean applyGlobalSettings,
1678 boolean preserveNewGroupSettings)
1680 av.updateGroupAnnotationSettings(applyGlobalSettings,
1681 preserveNewGroupSettings);
1682 adjustAnnotationHeight();
1686 public AlignmentI getAlignment()
1688 return av == null ? null : av.getAlignment();
1692 public String getViewName()
1698 * Make/Unmake this alignment panel the current input focus
1702 public void setSelected(boolean b)
1706 if (alignFrame.getSplitViewContainer() != null)
1709 * bring enclosing SplitFrame to front first if there is one
1711 ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
1713 alignFrame.setSelected(b);
1714 } catch (Exception ex)
1720 alignFrame.setDisplayedView(this);
1725 public StructureSelectionManager getStructureSelectionManager()
1727 return av.getStructureSelectionManager();
1731 public void raiseOOMWarning(String string, OutOfMemoryError error)
1733 new OOMWarning(string, error, this);
1737 public jalview.api.FeatureRenderer cloneFeatureRenderer()
1740 return new FeatureRenderer(this);
1744 public jalview.api.FeatureRenderer getFeatureRenderer()
1746 return seqPanel.seqCanvas.getFeatureRenderer();
1749 public void updateFeatureRenderer(
1750 jalview.renderer.seqfeatures.FeatureRenderer fr)
1752 fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
1755 public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
1757 if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
1759 getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
1763 public ScalePanel getScalePanel()
1768 public void setScalePanel(ScalePanel scalePanel)
1770 this.scalePanel = scalePanel;
1773 public SeqPanel getSeqPanel()
1778 public void setSeqPanel(SeqPanel seqPanel)
1780 this.seqPanel = seqPanel;
1783 public AnnotationPanel getAnnotationPanel()
1785 return annotationPanel;
1788 public void setAnnotationPanel(AnnotationPanel annotationPanel)
1790 this.annotationPanel = annotationPanel;
1793 public AnnotationLabels getAlabels()
1798 public void setAlabels(AnnotationLabels alabels)
1800 this.alabels = alabels;
1803 public IdPanel getIdPanel()
1808 public void setIdPanel(IdPanel idPanel)
1810 this.idPanel = idPanel;
1814 * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
1815 * The aim is to keep the two alignments 'lined up' on their centre columns.
1818 * holds mapped region(s) of this alignment that we are scrolling
1819 * 'to'; may be modified for sequence offset by this method
1820 * @param verticalOffset
1821 * the number of visible sequences to show above the mapped region
1823 public void scrollToCentre(SearchResultsI sr, int verticalOffset)
1826 * To avoid jumpy vertical scrolling (if some sequences are gapped or not
1827 * mapped), we can make the scroll-to location a sequence above the one
1830 SequenceI mappedTo = sr.getResults().get(0).getSequence();
1831 List<SequenceI> seqs = av.getAlignment().getSequences();
1834 * This is like AlignmentI.findIndex(seq) but here we are matching the
1835 * dataset sequence not the aligned sequence
1837 boolean matched = false;
1838 for (SequenceI seq : seqs)
1840 if (mappedTo == seq.getDatasetSequence())
1848 return; // failsafe, shouldn't happen
1852 * Scroll to position but centring the target residue.
1854 scrollToPosition(sr, verticalOffset, true, true);
1858 * Set a flag to say do not scroll any (cDNA/protein) complement.
1862 protected void setToScrollComplementPanel(boolean b)
1864 this.scrollComplementaryPanel = b;
1868 * Get whether to scroll complement panel
1870 * @return true if cDNA/protein complement panels should be scrolled
1872 protected boolean isSetToScrollComplementPanel()
1874 return this.scrollComplementaryPanel;
1880 * @adjustHeight if true, try to recalculate panel height for visible
1883 protected void refresh(boolean adjustHeight)
1885 validateAnnotationDimensions(adjustHeight);
1889 // sort, repaint, update overview
1890 paintAlignment(true);
1894 // lightweight repaint
1901 * Property change event fired when a change is made to the viewport ranges
1902 * object associated with this alignment panel's viewport
1904 public void propertyChange(PropertyChangeEvent evt)
1906 // update this panel's scroll values based on the new viewport ranges values
1907 int x = vpRanges.getStartRes();
1908 int y = vpRanges.getStartSeq();
1909 setScrollValues(x, y);
1911 // now update any complementary alignment (its viewport ranges object
1912 // is different so does not get automatically updated)
1913 if (isSetToScrollComplementPanel())
1915 setToScrollComplementPanel(false);
1916 av.scrollComplementaryAlignment();
1917 setToScrollComplementPanel(true);
1922 * Set the reference to the PCA/Tree chooser dialog for this panel. This
1923 * reference should be nulled when the dialog is closed.
1925 * @param calculationChooser
1927 public void setCalculationDialog(CalculationChooser calculationChooser)
1929 calculationDialog = calculationChooser;
1933 * Returns the reference to the PCA/Tree chooser dialog for this panel (null
1936 public CalculationChooser getCalculationDialog()
1938 return calculationDialog;