2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
21 import java.beans.*;
\r
25 import java.awt.event.*;
\r
26 import java.awt.print.*;
\r
27 import javax.swing.*;
\r
29 import jalview.datamodel.*;
\r
30 import jalview.jbgui.*;
\r
31 import jalview.schemes.*;
\r
37 * @version $Revision$
\r
39 public class AlignmentPanel
\r
40 extends GAlignmentPanel implements AdjustmentListener, Printable
\r
42 public AlignViewport av;
\r
43 OverviewPanel overviewPanel;
\r
46 IdwidthAdjuster idwidthAdjuster;
\r
48 /** DOCUMENT ME!! */
\r
49 public AlignFrame alignFrame;
\r
50 ScalePanel scalePanel;
\r
51 AnnotationPanel annotationPanel;
\r
52 AnnotationLabels alabels;
\r
54 // this value is set false when selection area being dragged
\r
55 boolean fastPaint = true;
\r
60 * Creates a new AlignmentPanel object.
\r
62 * @param af DOCUMENT ME!
\r
63 * @param av DOCUMENT ME!
\r
65 public AlignmentPanel(AlignFrame af, final AlignViewport av)
\r
69 seqPanel = new SeqPanel(av, this);
\r
70 idPanel = new IdPanel(av, this);
\r
72 scalePanel = new ScalePanel(av, this);
\r
74 idPanelHolder.add(idPanel, BorderLayout.CENTER);
\r
75 idwidthAdjuster = new IdwidthAdjuster(this);
\r
76 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
\r
78 annotationPanel = new AnnotationPanel(this);
\r
79 alabels = new AnnotationLabels(this);
\r
81 annotationScroller.setViewportView(annotationPanel);
\r
82 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
\r
84 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
\r
85 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
\r
87 setScrollValues(0, 0);
\r
89 setAnnotationVisible(av.getShowAnnotation());
\r
91 hscroll.addAdjustmentListener(this);
\r
92 vscroll.addAdjustmentListener(this);
\r
94 final AlignmentPanel ap = this;
\r
95 av.addPropertyChangeListener(new PropertyChangeListener()
\r
97 public void propertyChange(PropertyChangeEvent evt)
\r
99 if (evt.getPropertyName().equals("alignment"))
\r
101 PaintRefresher.Refresh(ap,
\r
102 av.getSequenceSetId(),
\r
105 alignmentChanged();
\r
111 adjustAnnotationHeight();
\r
115 public void alignmentChanged()
\r
117 av.alignmentChanged(this);
\r
119 alignFrame.updateEditMenuBar();
\r
121 paintAlignment(true);
\r
128 public void fontChanged()
\r
130 // set idCanvas bufferedImage to null
\r
131 // to prevent drawing old image
\r
132 FontMetrics fm = getFontMetrics(av.getFont());
\r
134 scalePanelHolder.setPreferredSize(new Dimension(10,
\r
135 av.charHeight + fm.getDescent()));
\r
136 idSpaceFillerPanel1.setPreferredSize(new Dimension(10,
\r
137 av.charHeight + fm.getDescent()));
\r
139 idPanel.idCanvas.gg = null;
\r
140 seqPanel.seqCanvas.img = null;
\r
141 annotationPanel.adjustPanelHeight();
\r
143 Dimension d = calculateIdWidth();
\r
144 d.setSize(d.width + 4, d.height);
\r
145 idPanel.idCanvas.setPreferredSize(d);
\r
146 hscrollFillerPanel.setPreferredSize(d);
\r
148 if (overviewPanel != null)
\r
150 overviewPanel.setBoxPosition();
\r
159 * @return DOCUMENT ME!
\r
161 public Dimension calculateIdWidth()
\r
163 Container c = new Container();
\r
165 FontMetrics fm = c.getFontMetrics(
\r
166 new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
\r
168 AlignmentI al = av.getAlignment();
\r
174 while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
\r
176 SequenceI s = al.getSequenceAt(i);
\r
178 id = s.getDisplayId(av.getShowJVSuffix());
\r
180 if (fm.stringWidth(id) > idWidth)
\r
182 idWidth = fm.stringWidth(id);
\r
188 // Also check annotation label widths
\r
191 if (al.getAlignmentAnnotation() != null)
\r
193 fm = c.getFontMetrics(alabels.getFont());
\r
195 while (i < al.getAlignmentAnnotation().length)
\r
197 String label = al.getAlignmentAnnotation()[i].label;
\r
199 if (fm.stringWidth(label) > idWidth)
\r
201 idWidth = fm.stringWidth(label);
\r
208 return new Dimension(idWidth, 12);
\r
214 * @param results DOCUMENT ME!
\r
216 public void highlightSearchResults(SearchResults results)
\r
218 seqPanel.seqCanvas.highlightSearchResults(results);
\r
220 // do we need to scroll the panel?
\r
221 if (results != null)
\r
223 SequenceI seq = results.getResultSequence(0);
\r
224 int seqIndex = av.alignment.findIndex(seq);
\r
225 int start = seq.findIndex(results.getResultStart(0)) - 1;
\r
226 int end = seq.findIndex(results.getResultEnd(0)) - 1;
\r
228 if (!av.wrapAlignment)
\r
230 if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
\r
231 ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
\r
233 setScrollValues(start, seqIndex);
\r
238 scrollToWrappedVisible(start);
\r
242 paintAlignment(true);
\r
245 void scrollToWrappedVisible(int res)
\r
247 int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
\r
249 if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
\r
251 vscroll.setValue(res / cwidth);
\r
252 av.startRes = vscroll.getValue() * cwidth;
\r
259 * @return DOCUMENT ME!
\r
261 public OverviewPanel getOverviewPanel()
\r
263 return overviewPanel;
\r
269 * @param op DOCUMENT ME!
\r
271 public void setOverviewPanel(OverviewPanel op)
\r
273 overviewPanel = op;
\r
279 * @param b DOCUMENT ME!
\r
281 public void setAnnotationVisible(boolean b)
\r
283 if (!av.wrapAlignment)
\r
285 annotationSpaceFillerHolder.setVisible(b);
\r
286 annotationScroller.setVisible(b);
\r
291 public void adjustAnnotationHeight()
\r
293 if (alignFrame.getHeight() == 0)
\r
295 System.out.println("NEEDS FIXING");
\r
298 int height = annotationPanel.adjustPanelHeight() +
\r
299 hscroll.getPreferredSize().height;
\r
301 if (height > alignFrame.getHeight() / 2)
\r
303 height = alignFrame.getHeight() / 2;
\r
306 hscroll.addNotify();
\r
308 annotationScroller.setPreferredSize(
\r
309 new Dimension(annotationScroller.getWidth(),
\r
310 height + hscroll.getHeight()));
\r
313 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
\r
314 annotationSpaceFillerHolder.getWidth(),
\r
323 * @param wrap DOCUMENT ME!
\r
325 public void setWrapAlignment(boolean wrap)
\r
328 scalePanelHolder.setVisible(!wrap);
\r
329 hscroll.setVisible(!wrap);
\r
330 idwidthAdjuster.setVisible(!wrap);
\r
334 annotationScroller.setVisible(false);
\r
335 annotationSpaceFillerHolder.setVisible(false);
\r
337 else if (av.showAnnotation)
\r
339 annotationScroller.setVisible(true);
\r
340 annotationSpaceFillerHolder.setVisible(true);
\r
343 idSpaceFillerPanel1.setVisible(!wrap);
\r
348 // return value is true if the scroll is valid
\r
349 public boolean scrollUp(boolean up)
\r
353 if (vscroll.getValue() < 1)
\r
359 vscroll.setValue(vscroll.getValue() - 1);
\r
363 if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
\r
369 vscroll.setValue(vscroll.getValue() + 1);
\r
380 * @param right DOCUMENT ME!
\r
382 * @return DOCUMENT ME!
\r
384 public boolean scrollRight(boolean right)
\r
388 if (hscroll.getValue() < 1)
\r
394 hscroll.setValue(hscroll.getValue() - 1);
\r
398 if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
\r
404 hscroll.setValue(hscroll.getValue() + 1);
\r
415 * @param x DOCUMENT ME!
\r
416 * @param y DOCUMENT ME!
\r
418 public void setScrollValues(int x, int y)
\r
421 int width = av.alignment.getWidth();
\r
422 int height = av.alignment.getHeight();
\r
424 if (av.hasHiddenColumns)
\r
426 width = av.getColumnSelection().findColumnPosition(width);
\r
429 av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
\r
431 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
\r
432 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
\r
434 if (hextent > width)
\r
439 if (vextent > height)
\r
444 if ( (hextent + x) > width)
\r
446 x = width - hextent;
\r
449 if ( (vextent + y) > height)
\r
451 y = height - vextent;
\r
464 hscroll.setValues(x, hextent, 0, width);
\r
465 vscroll.setValues(y, vextent, 0, height);
\r
471 * @param evt DOCUMENT ME!
\r
473 public void adjustmentValueChanged(AdjustmentEvent evt)
\r
476 int oldX = av.getStartRes();
\r
477 int oldY = av.getStartSeq();
\r
479 if (evt.getSource() == hscroll)
\r
481 int x = hscroll.getValue();
\r
484 (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
\r
487 if (evt.getSource() == vscroll)
\r
489 int offy = vscroll.getValue();
\r
491 if (av.getWrapAlignment())
\r
495 int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
\r
496 seqCanvas.getWidth());
\r
497 av.setStartRes(offy * rowSize);
\r
498 av.setEndRes( (offy + 1) * rowSize);
\r
502 //This is only called if file loaded is a jar file that
\r
503 //was wrapped when saved and user has wrap alignment true
\r
504 //as preference setting
\r
505 SwingUtilities.invokeLater(new Runnable()
\r
509 setScrollValues(av.getStartRes(), av.getStartSeq());
\r
516 av.setStartSeq(offy);
\r
517 av.setEndSeq(offy +
\r
518 (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
\r
522 if (overviewPanel != null)
\r
524 overviewPanel.setBoxPosition();
\r
527 int scrollX = av.startRes - oldX;
\r
528 int scrollY = av.startSeq - oldY;
\r
530 if (av.getWrapAlignment() || !fastPaint)
\r
536 // Make sure we're not trying to draw a panel
\r
537 // larger than the visible window
\r
538 if (scrollX > av.endRes - av.startRes)
\r
540 scrollX = av.endRes - av.startRes;
\r
542 else if (scrollX < av.startRes - av.endRes)
\r
544 scrollX = av.startRes - av.endRes;
\r
547 if (scrollX != 0 || scrollY != 0)
\r
549 idPanel.idCanvas.fastPaint(scrollY);
\r
550 seqPanel.seqCanvas.fastPaint(scrollX,
\r
552 scalePanel.repaint();
\r
554 if (av.getShowAnnotation())
\r
556 annotationPanel.fastPaint(scrollX);
\r
562 public void paintAlignment(boolean updateOverview)
\r
568 jalview.structure.StructureSelectionManager.getStructureSelectionManager()
\r
569 .sequenceColoursChanged(this);
\r
571 if (overviewPanel != null)
\r
573 overviewPanel.updateOverviewImage();
\r
581 * @param g DOCUMENT ME!
\r
583 public void paintComponent(Graphics g)
\r
587 Dimension d = idPanel.idCanvas.getPreferredSize();
\r
588 idPanelHolder.setPreferredSize(d);
\r
589 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
\r
592 if (av.getWrapAlignment())
\r
594 int maxwidth = av.alignment.getWidth();
\r
596 if (av.hasHiddenColumns)
\r
598 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
601 int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
\r
602 seqCanvas.getWidth());
\r
603 if (canvasWidth > 0)
\r
605 int max = maxwidth /
\r
606 seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
\r
609 vscroll.setMaximum(max);
\r
610 vscroll.setUnitIncrement(1);
\r
611 vscroll.setVisibleAmount(1);
\r
616 setScrollValues(av.getStartRes(), av.getStartSeq());
\r
623 * @param pg DOCUMENT ME!
\r
624 * @param pf DOCUMENT ME!
\r
625 * @param pi DOCUMENT ME!
\r
627 * @return DOCUMENT ME!
\r
629 * @throws PrinterException DOCUMENT ME!
\r
631 public int print(Graphics pg, PageFormat pf, int pi)
\r
632 throws PrinterException
\r
634 pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
\r
636 int pwidth = (int) pf.getImageableWidth();
\r
637 int pheight = (int) pf.getImageableHeight();
\r
639 if (av.getWrapAlignment())
\r
641 return printWrappedAlignment(pg, pwidth, pheight, pi);
\r
645 return printUnwrapped(pg, pwidth, pheight, pi);
\r
652 * @param pg DOCUMENT ME!
\r
653 * @param pwidth DOCUMENT ME!
\r
654 * @param pheight DOCUMENT ME!
\r
655 * @param pi DOCUMENT ME!
\r
657 * @return DOCUMENT ME!
\r
659 * @throws PrinterException DOCUMENT ME!
\r
661 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
\r
662 throws PrinterException
\r
664 int idWidth = getVisibleIdWidth();
\r
665 FontMetrics fm = getFontMetrics(av.getFont());
\r
666 int scaleHeight = av.charHeight + fm.getDescent();
\r
668 pg.setColor(Color.white);
\r
669 pg.fillRect(0, 0, pwidth, pheight);
\r
670 pg.setFont(av.getFont());
\r
672 ////////////////////////////////////
\r
673 /// How many sequences and residues can we fit on a printable page?
\r
674 int totalRes = (pwidth - idWidth) / av.getCharWidth();
\r
676 int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -
\r
679 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
\r
681 /////////////////////////////
\r
682 /// Only print these sequences and residues on this page
\r
685 /////////////////////////////
\r
686 /// Only print these sequences and residues on this page
\r
689 /////////////////////////////
\r
690 /// Only print these sequences and residues on this page
\r
693 /////////////////////////////
\r
694 /// Only print these sequences and residues on this page
\r
696 startRes = (pi % pagesWide) * totalRes;
\r
697 endRes = (startRes + totalRes) - 1;
\r
699 if (endRes > (av.getAlignment().getWidth() - 1))
\r
701 endRes = av.getAlignment().getWidth() - 1;
\r
704 startSeq = (pi / pagesWide) * totalSeq;
\r
705 endSeq = startSeq + totalSeq;
\r
707 if (endSeq > av.getAlignment().getHeight())
\r
709 endSeq = av.getAlignment().getHeight();
\r
712 int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
\r
714 if (av.showAnnotation)
\r
716 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
\r
719 pagesHigh /= pheight;
\r
721 if (pi >= (pagesWide * pagesHigh))
\r
723 return Printable.NO_SUCH_PAGE;
\r
727 pg.translate(idWidth, 0);
\r
728 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
\r
729 pg.translate( -idWidth, scaleHeight);
\r
733 Color currentColor = null;
\r
734 Color currentTextColor = null;
\r
736 pg.setFont(idPanel.idCanvas.idfont);
\r
739 for (int i = startSeq; i < endSeq; i++)
\r
741 seq = av.getAlignment().getSequenceAt(i);
\r
742 if ( (av.getSelectionGroup() != null) &&
\r
743 av.getSelectionGroup().getSequences(null).contains(seq))
\r
745 currentColor = Color.gray;
\r
746 currentTextColor = Color.black;
\r
750 currentColor = av.getSequenceColour(seq);
\r
751 currentTextColor = Color.black;
\r
754 pg.setColor(currentColor);
\r
755 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
\r
756 av.getCharHeight());
\r
758 pg.setColor(currentTextColor);
\r
761 if (av.rightAlignIds)
\r
763 fm = pg.getFontMetrics();
\r
764 xPos = idWidth - fm.stringWidth(
\r
765 seq.getDisplayId(av.getShowJVSuffix())
\r
769 pg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
\r
771 ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
\r
772 (av.getCharHeight() / 5));
\r
775 pg.setFont(av.getFont());
\r
777 // draw main sequence panel
\r
778 pg.translate(idWidth, 0);
\r
779 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
\r
781 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
\r
783 pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
\r
784 alabels.drawComponent( (Graphics2D) pg, idWidth);
\r
785 pg.translate(idWidth + 3, 0);
\r
786 annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
\r
790 return Printable.PAGE_EXISTS;
\r
796 * @param pg DOCUMENT ME!
\r
797 * @param pwidth DOCUMENT ME!
\r
798 * @param pheight DOCUMENT ME!
\r
799 * @param pi DOCUMENT ME!
\r
801 * @return DOCUMENT ME!
\r
803 * @throws PrinterException DOCUMENT ME!
\r
805 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
\r
807 throws PrinterException
\r
810 int annotationHeight = 0;
\r
811 AnnotationLabels labels = null;
\r
812 if (av.showAnnotation)
\r
814 annotationHeight = annotationPanel.adjustPanelHeight();
\r
815 labels = new AnnotationLabels(av);
\r
818 int hgap = av.charHeight;
\r
819 if (av.scaleAboveWrapped)
\r
821 hgap += av.charHeight;
\r
824 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
826 + annotationHeight;
\r
828 int idWidth = getVisibleIdWidth();
\r
830 int maxwidth = av.alignment.getWidth();
\r
831 if (av.hasHiddenColumns)
\r
833 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
836 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
\r
839 int totalHeight = cHeight * (maxwidth / resWidth + 1);
\r
841 pg.setColor(Color.white);
\r
842 pg.fillRect(0, 0, pwidth, pheight);
\r
843 pg.setFont(av.getFont());
\r
847 pg.setColor(Color.black);
\r
849 pg.translate(0, -pi * pheight);
\r
851 pg.setClip(0, pi * pheight, pwidth, pheight);
\r
857 for (int i = 0; i < av.alignment.getHeight(); i++)
\r
859 pg.setFont(idPanel.idCanvas.idfont);
\r
860 SequenceI s = av.alignment.getSequenceAt(i);
\r
861 String string = s.getDisplayId(av.getShowJVSuffix());
\r
863 if (av.rightAlignIds)
\r
865 FontMetrics fm = pg.getFontMetrics();
\r
866 xPos = idWidth - fm.stringWidth(string) - 4;
\r
868 pg.drawString(string, xPos,
\r
869 ( (i * av.charHeight) + ypos + av.charHeight) -
\r
870 (av.charHeight / 5));
\r
872 if (labels != null)
\r
876 (av.getAlignment().getHeight() * av.charHeight));
\r
878 pg.setFont(av.getFont());
\r
879 labels.drawComponent(pg, idWidth);
\r
882 (av.getAlignment().getHeight() * av.charHeight));
\r
887 while (ypos < totalHeight);
\r
889 pg.translate(idWidth, 0);
\r
891 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
\r
893 if ( (pi * pheight) < totalHeight)
\r
895 return Printable.PAGE_EXISTS;
\r
900 return Printable.NO_SUCH_PAGE;
\r
904 int getVisibleIdWidth()
\r
907 idPanel.getWidth() > 0 ? idPanel.getWidth() :
\r
908 calculateIdWidth().width + 4;
\r
911 void makeAlignmentImage(int type, File file)
\r
913 int maxwidth = av.alignment.getWidth();
\r
914 if (av.hasHiddenColumns)
\r
916 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
\r
919 int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;
\r
920 int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
\r
922 if (av.getWrapAlignment())
\r
924 height = getWrappedHeight();
\r
925 if (System.getProperty("java.awt.headless") != null
\r
926 && System.getProperty("java.awt.headless").equals("true"))
\r
928 width = alignFrame.getWidth()
\r
929 - vscroll.getPreferredSize().width
\r
930 - alignFrame.getInsets().left
\r
931 - alignFrame.getInsets().right;
\r
935 width = seqPanel.getWidth() + getVisibleIdWidth();
\r
939 else if (av.getShowAnnotation())
\r
941 height += annotationPanel.adjustPanelHeight() + 3;
\r
947 jalview.util.ImageMaker im;
\r
948 if (type == jalview.util.ImageMaker.PNG)
\r
950 im = new jalview.util.ImageMaker(this,
\r
951 jalview.util.ImageMaker.PNG,
\r
952 "Create PNG image from alignment",
\r
953 width, height, file, null);
\r
957 im = new jalview.util.ImageMaker(this,
\r
958 jalview.util.ImageMaker.EPS,
\r
959 "Create EPS file from alignment",
\r
960 width, height, file,
\r
961 alignFrame.getTitle());
\r
964 if (av.getWrapAlignment())
\r
966 if (im.getGraphics() != null)
\r
968 printWrappedAlignment(im.getGraphics(), width, height, 0);
\r
974 if (im.getGraphics() != null)
\r
976 printUnwrapped(im.getGraphics(), width, height, 0);
\r
981 catch (OutOfMemoryError err)
\r
983 System.out.println("########################\n"
\r
984 + "OUT OF MEMORY " + file + "\n"
\r
985 + "########################");
\r
987 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
988 "Out of Memory Creating Image!!"
\r
990 "\nSee help files for increasing Java Virtual Machine memory."
\r
992 JOptionPane.WARNING_MESSAGE);
\r
993 System.out.println("Create IMAGE: " + err);
\r
997 catch (Exception ex)
\r
999 ex.printStackTrace();
\r
1006 public void makeEPS(File epsFile)
\r
1008 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
\r
1014 public void makePNG(File pngFile)
\r
1016 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
\r
1019 public void makePNGImageMap(File imgMapFile, String imageName)
\r
1021 ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
\r
1022 //////////////////////////////////////////////
\r
1023 int idWidth = getVisibleIdWidth();
\r
1024 FontMetrics fm = getFontMetrics(av.getFont());
\r
1025 int scaleHeight = av.charHeight + fm.getDescent();
\r
1028 //////////////////////////////////
\r
1029 if (imgMapFile != null)
\r
1033 int s, sSize = av.alignment.getHeight(),
\r
1034 res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
\r
1035 StringBuffer text = new StringBuffer();
\r
1036 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
\r
1037 out.println(jalview.io.HTMLOutput.getImageMapHTML());
\r
1038 out.println("<img src=\"" + imageName +
\r
1039 "\" border=\"0\" usemap=\"#Map\" >"
\r
1040 + "<map name=\"Map\">");
\r
1042 for (s = 0; s < sSize; s++)
\r
1044 sy = s * av.charHeight + scaleHeight;
\r
1046 SequenceI seq = av.alignment.getSequenceAt(s);
\r
1047 SequenceFeature[] features = seq.getDatasetSequence().
\r
1048 getSequenceFeatures();
\r
1049 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
\r
1050 for (res = 0; res < alwidth; res++)
\r
1052 text = new StringBuffer();
\r
1053 Object obj = null;
\r
1054 if (av.alignment.isNucleotide())
\r
1056 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +
\r
1061 obj = ResidueProperties.aa2Triplet.get(
\r
1062 seq.getCharAt(res) + "");
\r
1070 String triplet = obj.toString();
\r
1071 int alIndex = seq.findPosition(res);
\r
1072 gSize = groups.length;
\r
1073 for (g = 0; g < gSize; g++)
\r
1075 if (text.length() < 1)
\r
1077 text.append("<area shape=\"rect\" coords=\""
\r
1078 + (idWidth + res * av.charWidth) + ","
\r
1080 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1081 + (av.charHeight + sy) + "\""
\r
1082 + " onMouseOver=\"toolTip('"
\r
1083 + alIndex + " " + triplet);
\r
1086 if (groups[g].getStartRes() < res && groups[g].getEndRes() > res)
\r
1088 text.append("<br><em>" + groups[g].getName() + "</em>");
\r
1092 if (features != null)
\r
1094 if (text.length() < 1)
\r
1096 text.append("<area shape=\"rect\" coords=\""
\r
1097 + (idWidth + res * av.charWidth) + ","
\r
1099 + (idWidth + (res + 1) * av.charWidth) + ","
\r
1100 + (av.charHeight + sy) + "\""
\r
1101 + " onMouseOver=\"toolTip('"
\r
1102 + alIndex + " " + triplet);
\r
1104 fSize = features.length;
\r
1105 for (f = 0; f < fSize; f++)
\r
1108 if ( (features[f].getBegin() <= seq.findPosition(res)) &&
\r
1109 (features[f].getEnd() >= seq.findPosition(res)))
\r
1111 if (features[f].getType().equals("disulfide bond"))
\r
1113 if (features[f].getBegin() == seq.findPosition(res)
\r
1114 || features[f].getEnd() == seq.findPosition(res))
\r
1116 text.append("<br>disulfide bond " + features[f].getBegin() +
\r
1118 features[f].getEnd());
\r
1123 text.append("<br>");
\r
1124 text.append(features[f].getType());
\r
1125 if (features[f].getDescription() != null &&
\r
1127 getType().equals(features[f].getDescription()))
\r
1129 text.append(" " + features[f].getDescription());
\r
1132 if (features[f].getValue("status") != null)
\r
1134 text.append(" (" + features[f].getValue("status") + ")");
\r
1141 if (text.length() > 1)
\r
1143 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
\r
1144 out.println(text.toString());
\r
1148 out.println("</map></body></html>");
\r
1152 catch (Exception ex)
\r
1154 ex.printStackTrace();
\r
1156 } ///////////END OF IMAGE MAP
\r
1160 int getWrappedHeight()
\r
1162 int seqPanelWidth = seqPanel.seqCanvas.getWidth();
\r
1164 if (System.getProperty("java.awt.headless") != null
\r
1165 && System.getProperty("java.awt.headless").equals("true"))
\r
1167 seqPanelWidth = alignFrame.getWidth()
\r
1168 - getVisibleIdWidth()
\r
1169 - vscroll.getPreferredSize().width
\r
1170 - alignFrame.getInsets().left
\r
1171 - alignFrame.getInsets().right;
\r
1174 int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
\r
1178 int hgap = av.charHeight;
\r
1179 if (av.scaleAboveWrapped)
\r
1181 hgap += av.charHeight;
\r
1184 int annotationHeight = 0;
\r
1185 if (av.showAnnotation)
\r
1187 annotationHeight = annotationPanel.adjustPanelHeight();
\r
1190 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
1192 + annotationHeight;
\r
1194 int maxwidth = av.alignment.getWidth();
\r
1195 if (av.hasHiddenColumns)
\r
1197 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
\r
1200 int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
\r