2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
22 import java.util.Hashtable;
23 import java.util.Vector;
26 import java.awt.event.*;
27 import java.awt.print.*;
30 import jalview.api.AlignmentViewPanel;
31 import jalview.bin.Cache;
32 import jalview.datamodel.*;
33 import jalview.jbgui.*;
34 import jalview.schemes.*;
35 import jalview.structure.SelectionSource;
36 import jalview.structure.StructureSelectionManager;
42 * @version $Revision: 1.161 $
44 public class AlignmentPanel extends GAlignmentPanel implements
45 AdjustmentListener, Printable, AlignmentViewPanel
47 public AlignViewport av;
49 OverviewPanel overviewPanel;
55 IdwidthAdjuster idwidthAdjuster;
58 public AlignFrame alignFrame;
60 ScalePanel scalePanel;
62 AnnotationPanel annotationPanel;
64 AnnotationLabels alabels;
66 // this value is set false when selection area being dragged
67 boolean fastPaint = true;
74 * Creates a new AlignmentPanel object.
81 public AlignmentPanel(AlignFrame af, final AlignViewport av)
85 seqPanel = new SeqPanel(av, this);
86 idPanel = new IdPanel(av, this);
88 scalePanel = new ScalePanel(av, this);
90 idPanelHolder.add(idPanel, BorderLayout.CENTER);
91 idwidthAdjuster = new IdwidthAdjuster(this);
92 idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
94 annotationPanel = new AnnotationPanel(this);
95 alabels = new AnnotationLabels(this);
97 annotationScroller.setViewportView(annotationPanel);
98 annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
100 scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
101 seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
103 setScrollValues(0, 0);
105 setAnnotationVisible(av.getShowAnnotation());
107 hscroll.addAdjustmentListener(this);
108 vscroll.addAdjustmentListener(this);
110 final AlignmentPanel ap = this;
111 av.addPropertyChangeListener(new PropertyChangeListener()
113 public void propertyChange(PropertyChangeEvent evt)
115 if (evt.getPropertyName().equals("alignment"))
117 PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
123 adjustAnnotationHeight();
127 public void alignmentChanged()
129 av.alignmentChanged(this);
131 alignFrame.updateEditMenuBar();
133 paintAlignment(true);
140 public void fontChanged()
142 // set idCanvas bufferedImage to null
143 // to prevent drawing old image
144 FontMetrics fm = getFontMetrics(av.getFont());
146 scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
148 idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
151 idPanel.idCanvas.gg = null;
152 seqPanel.seqCanvas.img = null;
153 annotationPanel.adjustPanelHeight();
155 Dimension d = calculateIdWidth();
156 d.setSize(d.width + 4, d.height);
157 idPanel.idCanvas.setPreferredSize(d);
158 hscrollFillerPanel.setPreferredSize(d);
160 if (overviewPanel != null)
162 overviewPanel.setBoxPosition();
169 * Calculate the width of the alignment labels based on the displayed names
170 * and any bounds on label width set in preferences.
172 * @return Dimension giving the maximum width of the alignment label panel
173 * that should be used.
175 public Dimension calculateIdWidth()
177 Container c = new Container();
179 FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
180 Font.ITALIC, av.font.getSize()));
182 AlignmentI al = av.getAlignment();
183 int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
184 int maxwidth = Math.max(20,
185 Math.min(afwidth - 200, (int) 2 * afwidth / 3));
190 while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
192 SequenceI s = al.getSequenceAt(i);
194 id = s.getDisplayId(av.getShowJVSuffix());
196 if (fm.stringWidth(id) > idWidth)
198 idWidth = fm.stringWidth(id);
204 // Also check annotation label widths
207 if (al.getAlignmentAnnotation() != null)
209 fm = c.getFontMetrics(alabels.getFont());
211 while (i < al.getAlignmentAnnotation().length)
213 String label = al.getAlignmentAnnotation()[i].label;
215 if (fm.stringWidth(label) > idWidth)
217 idWidth = fm.stringWidth(label);
224 return new Dimension(Math.min(maxwidth, idWidth), 12);
228 * Highlight the given results on the alignment.
231 public void highlightSearchResults(SearchResults results)
233 scrollToPosition(results);
234 seqPanel.seqCanvas.highlightSearchResults(results);
238 * scroll the view to show the position of the highlighted region in results
239 * (if any) and redraw the overview
243 public boolean scrollToPosition(SearchResults results)
245 return scrollToPosition(results, true);
249 * scroll the view to show the position of the highlighted region in results
253 * @param redrawOverview
254 * - when set, the overview will be recalculated (takes longer)
255 * @return false if results were not found
257 public boolean scrollToPosition(SearchResults results,
258 boolean redrawOverview)
260 int startv, endv, starts, ends, width;
261 // TODO: properly locate search results in view when large numbers of hidden
262 // columns exist before highlighted region
263 // do we need to scroll the panel?
264 // TODO: tons of nullpointereexceptions raised here.
265 if (results != null && results.getSize() > 0 && av != null
266 && av.alignment != null)
268 int seqIndex = av.alignment.findIndex(results);
273 SequenceI seq = av.alignment.getSequenceAt(seqIndex);
275 int[] r=results.getResults(seq, 0, av.alignment.getWidth());
282 // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
288 if (end == seq.getEnd())
292 if (av.hasHiddenColumns)
294 start = av.getColumnSelection().findColumnPosition(start);
295 end = av.getColumnSelection().findColumnPosition(end);
298 if (!av.colSel.isVisible(r[0]))
300 // don't scroll - position isn't visible
305 if (!av.wrapAlignment)
307 if ((startv = av.getStartRes()) >= start)
309 setScrollValues(start - 1, seqIndex);
311 else if ((endv = av.getEndRes()) <= end)
313 setScrollValues(startv + 1 + end - endv, seqIndex);
315 else if ((starts = av.getStartSeq()) > seqIndex)
317 setScrollValues(av.getStartRes(), seqIndex);
319 else if ((ends = av.getEndSeq()) <= seqIndex)
321 setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
326 scrollToWrappedVisible(start);
329 if (redrawOverview && overviewPanel != null)
331 overviewPanel.setBoxPosition();
333 paintAlignment(redrawOverview);
337 void scrollToWrappedVisible(int res)
339 int cwidth = seqPanel.seqCanvas
340 .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
341 if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
343 vscroll.setValue((res / cwidth));
344 av.startRes = vscroll.getValue() * cwidth;
352 * @return DOCUMENT ME!
354 public OverviewPanel getOverviewPanel()
356 return overviewPanel;
365 public void setOverviewPanel(OverviewPanel op)
372 * @param b Hide or show annotation panel
375 public void setAnnotationVisible(boolean b)
377 if (!av.wrapAlignment)
379 annotationSpaceFillerHolder.setVisible(b);
380 annotationScroller.setVisible(b);
386 * automatically adjust annotation panel height for new annotation
387 * whilst ensuring the alignment is still visible.
389 public void adjustAnnotationHeight()
391 // TODO: display vertical annotation scrollbar if necessary
392 // this is called after loading new annotation onto alignment
393 if (alignFrame.getHeight() == 0)
395 System.out.println("NEEDS FIXING");
397 validateAnnotationDimensions(true);
399 paintAlignment(true);
402 * calculate the annotation dimensions and refresh slider values accordingly.
403 * need to do repaints/notifys afterwards.
405 protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
406 int height = annotationPanel.adjustPanelHeight();
408 if (hscroll.isVisible())
410 height += hscroll.getPreferredSize().height;
412 if (height > alignFrame.getHeight() / 2)
414 height = alignFrame.getHeight() / 2;
416 if (!adjustPanelHeight)
418 // maintain same window layout whilst updating sliders
419 height=annotationScroller.getSize().height;
423 annotationScroller.setPreferredSize(new Dimension(annotationScroller
424 .getWidth(), height));
426 annotationSpaceFillerHolder.setPreferredSize(new Dimension(
427 annotationSpaceFillerHolder.getWidth(), height));
428 annotationScroller.validate();// repaint();
429 annotationScroller.addNotify();
438 public void setWrapAlignment(boolean wrap)
441 scalePanelHolder.setVisible(!wrap);
442 hscroll.setVisible(!wrap);
443 idwidthAdjuster.setVisible(!wrap);
447 annotationScroller.setVisible(false);
448 annotationSpaceFillerHolder.setVisible(false);
450 else if (av.showAnnotation)
452 annotationScroller.setVisible(true);
453 annotationSpaceFillerHolder.setVisible(true);
456 idSpaceFillerPanel1.setVisible(!wrap);
461 // return value is true if the scroll is valid
462 public boolean scrollUp(boolean up)
466 if (vscroll.getValue() < 1)
472 vscroll.setValue(vscroll.getValue() - 1);
476 if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
482 vscroll.setValue(vscroll.getValue() + 1);
496 * @return DOCUMENT ME!
498 public boolean scrollRight(boolean right)
502 if (hscroll.getValue() < 1)
508 hscroll.setValue(hscroll.getValue() - 1);
512 if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
518 hscroll.setValue(hscroll.getValue() + 1);
527 * Adjust row/column scrollers to show a visible position in the alignment.
529 * @param x visible column to scroll to
531 * @param y visible row to scroll to
534 public void setScrollValues(int x, int y)
536 // System.err.println("Scroll to "+x+","+y);
537 if (av == null || av.alignment == null)
541 int width = av.alignment.getWidth();
542 int height = av.alignment.getHeight();
544 if (av.hasHiddenColumns)
546 width = av.getColumnSelection().findColumnPosition(width);
549 av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
551 hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
552 vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
559 if (vextent > height)
564 if ((hextent + x) > width)
569 if ((vextent + y) > height)
571 y = height - vextent;
584 hscroll.setValues(x, hextent, 0, width);
585 vscroll.setValues(y, vextent, 0, height);
594 public void adjustmentValueChanged(AdjustmentEvent evt)
597 int oldX = av.getStartRes();
598 int oldY = av.getStartSeq();
600 if (evt.getSource() == hscroll)
602 int x = hscroll.getValue();
604 av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
607 if (evt.getSource() == vscroll)
609 int offy = vscroll.getValue();
611 if (av.getWrapAlignment())
615 int rowSize = seqPanel.seqCanvas
616 .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
617 av.setStartRes(offy * rowSize);
618 av.setEndRes((offy + 1) * rowSize);
622 // This is only called if file loaded is a jar file that
623 // was wrapped when saved and user has wrap alignment true
624 // as preference setting
625 SwingUtilities.invokeLater(new Runnable()
629 setScrollValues(av.getStartRes(), av.getStartSeq());
636 av.setStartSeq(offy);
638 + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
642 if (overviewPanel != null)
644 overviewPanel.setBoxPosition();
647 int scrollX = av.startRes - oldX;
648 int scrollY = av.startSeq - oldY;
650 if (av.getWrapAlignment() || !fastPaint)
656 // Make sure we're not trying to draw a panel
657 // larger than the visible window
658 if (scrollX > av.endRes - av.startRes)
660 scrollX = av.endRes - av.startRes;
662 else if (scrollX < av.startRes - av.endRes)
664 scrollX = av.startRes - av.endRes;
667 if (scrollX != 0 || scrollY != 0)
669 idPanel.idCanvas.fastPaint(scrollY);
670 seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
671 scalePanel.repaint();
673 if (av.getShowAnnotation())
675 annotationPanel.fastPaint(scrollX);
681 public void paintAlignment(boolean updateOverview)
687 av.getStructureSelectionManager().sequenceColoursChanged(this);
689 if (overviewPanel != null)
691 overviewPanel.updateOverviewImage();
702 public void paintComponent(Graphics g)
706 Dimension d = idPanel.idCanvas.getPreferredSize();
707 idPanelHolder.setPreferredSize(d);
708 hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
711 if (av.getWrapAlignment())
713 int maxwidth = av.alignment.getWidth();
715 if (av.hasHiddenColumns)
717 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
720 int canvasWidth = seqPanel.seqCanvas
721 .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
726 .getWrappedCanvasWidth(seqPanel.seqCanvas
728 vscroll.setMaximum(max);
729 vscroll.setUnitIncrement(1);
730 vscroll.setVisibleAmount(1);
735 setScrollValues(av.getStartRes(), av.getStartSeq());
749 * @return DOCUMENT ME!
751 * @throws PrinterException
754 public int print(Graphics pg, PageFormat pf, int pi)
755 throws PrinterException
757 pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
759 int pwidth = (int) pf.getImageableWidth();
760 int pheight = (int) pf.getImageableHeight();
762 if (av.getWrapAlignment())
764 return printWrappedAlignment(pg, pwidth, pheight, pi);
768 return printUnwrapped(pg, pwidth, pheight, pi);
784 * @return DOCUMENT ME!
786 * @throws PrinterException
789 public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
790 throws PrinterException
792 int idWidth = getVisibleIdWidth();
793 FontMetrics fm = getFontMetrics(av.getFont());
794 int scaleHeight = av.charHeight + fm.getDescent();
796 pg.setColor(Color.white);
797 pg.fillRect(0, 0, pwidth, pheight);
798 pg.setFont(av.getFont());
800 // //////////////////////////////////
801 // / How many sequences and residues can we fit on a printable page?
802 int totalRes = (pwidth - idWidth) / av.getCharWidth();
804 int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1;
806 int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
808 // ///////////////////////////
809 // / Only print these sequences and residues on this page
812 // ///////////////////////////
813 // / Only print these sequences and residues on this page
816 // ///////////////////////////
817 // / Only print these sequences and residues on this page
820 // ///////////////////////////
821 // / Only print these sequences and residues on this page
823 startRes = (pi % pagesWide) * totalRes;
824 endRes = (startRes + totalRes) - 1;
826 if (endRes > (av.getAlignment().getWidth() - 1))
828 endRes = av.getAlignment().getWidth() - 1;
831 startSeq = (pi / pagesWide) * totalSeq;
832 endSeq = startSeq + totalSeq;
834 if (endSeq > av.getAlignment().getHeight())
836 endSeq = av.getAlignment().getHeight();
839 int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
841 if (av.showAnnotation)
843 pagesHigh += annotationPanel.adjustPanelHeight() + 3;
846 pagesHigh /= pheight;
848 if (pi >= (pagesWide * pagesHigh))
850 return Printable.NO_SUCH_PAGE;
854 pg.translate(idWidth, 0);
855 scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
857 pg.translate(-idWidth, scaleHeight);
861 Color currentColor = null;
862 Color currentTextColor = null;
864 pg.setFont(idPanel.idCanvas.idfont);
867 for (int i = startSeq; i < endSeq; i++)
869 seq = av.getAlignment().getSequenceAt(i);
870 if ((av.getSelectionGroup() != null)
871 && av.getSelectionGroup().getSequences(null).contains(seq))
873 currentColor = Color.gray;
874 currentTextColor = Color.black;
878 currentColor = av.getSequenceColour(seq);
879 currentTextColor = Color.black;
882 pg.setColor(currentColor);
883 pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
886 pg.setColor(currentTextColor);
889 if (av.rightAlignIds)
891 fm = pg.getFontMetrics();
893 - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
898 seq.getDisplayId(av.getShowJVSuffix()),
900 (((i - startSeq) * av.charHeight) + av.getCharHeight())
901 - (av.getCharHeight() / 5));
904 pg.setFont(av.getFont());
906 // draw main sequence panel
907 pg.translate(idWidth, 0);
908 seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
910 if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
912 pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
913 alabels.drawComponent((Graphics2D) pg, idWidth);
914 pg.translate(idWidth + 3, 0);
915 annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
918 return Printable.PAGE_EXISTS;
933 * @return DOCUMENT ME!
935 * @throws PrinterException
938 public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
939 int pi) throws PrinterException
942 int annotationHeight = 0;
943 AnnotationLabels labels = null;
944 if (av.showAnnotation)
946 annotationHeight = annotationPanel.adjustPanelHeight();
947 labels = new AnnotationLabels(av);
950 int hgap = av.charHeight;
951 if (av.scaleAboveWrapped)
953 hgap += av.charHeight;
956 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
959 int idWidth = getVisibleIdWidth();
961 int maxwidth = av.alignment.getWidth();
962 if (av.hasHiddenColumns)
964 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
967 int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
970 int totalHeight = cHeight * (maxwidth / resWidth + 1);
972 pg.setColor(Color.white);
973 pg.fillRect(0, 0, pwidth, pheight);
974 pg.setFont(av.getFont());
978 pg.setColor(Color.black);
980 pg.translate(0, -pi * pheight);
982 pg.setClip(0, pi * pheight, pwidth, pheight);
988 for (int i = 0; i < av.alignment.getHeight(); i++)
990 pg.setFont(idPanel.idCanvas.idfont);
991 SequenceI s = av.alignment.getSequenceAt(i);
992 String string = s.getDisplayId(av.getShowJVSuffix());
994 if (av.rightAlignIds)
996 FontMetrics fm = pg.getFontMetrics();
997 xPos = idWidth - fm.stringWidth(string) - 4;
999 pg.drawString(string, xPos,
1000 ((i * av.charHeight) + ypos + av.charHeight)
1001 - (av.charHeight / 5));
1005 pg.translate(-3, ypos
1006 + (av.getAlignment().getHeight() * av.charHeight));
1008 pg.setFont(av.getFont());
1009 labels.drawComponent(pg, idWidth);
1010 pg.translate(+3, -ypos
1011 - (av.getAlignment().getHeight() * av.charHeight));
1015 } while (ypos < totalHeight);
1017 pg.translate(idWidth, 0);
1019 seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
1022 if ((pi * pheight) < totalHeight)
1024 return Printable.PAGE_EXISTS;
1029 return Printable.NO_SUCH_PAGE;
1033 int getVisibleIdWidth()
1035 return idPanel.getWidth() > 0 ? idPanel.getWidth()
1036 : calculateIdWidth().width + 4;
1039 void makeAlignmentImage(int type, File file)
1041 int maxwidth = av.alignment.getWidth();
1042 if (av.hasHiddenColumns)
1044 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
1047 int height = ((av.alignment.getHeight() + 1) * av.charHeight)
1048 + scalePanel.getHeight();
1049 int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
1051 if (av.getWrapAlignment())
1053 height = getWrappedHeight();
1054 if (System.getProperty("java.awt.headless") != null
1055 && System.getProperty("java.awt.headless").equals("true"))
1058 width = alignFrame.getWidth() - vscroll.getPreferredSize().width
1059 - alignFrame.getInsets().left
1060 - alignFrame.getInsets().right;
1064 width = seqPanel.getWidth() + getVisibleIdWidth();
1068 else if (av.getShowAnnotation())
1070 height += annotationPanel.adjustPanelHeight() + 3;
1076 jalview.util.ImageMaker im;
1077 if (type == jalview.util.ImageMaker.PNG)
1079 im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
1080 "Create PNG image from alignment", width, height, file,
1085 im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
1086 "Create EPS file from alignment", width, height, file,
1087 alignFrame.getTitle());
1090 if (av.getWrapAlignment())
1092 if (im.getGraphics() != null)
1094 printWrappedAlignment(im.getGraphics(), width, height, 0);
1100 if (im.getGraphics() != null)
1102 printUnwrapped(im.getGraphics(), width, height, 0);
1106 } catch (OutOfMemoryError err)
1109 System.out.println("########################\n" + "OUT OF MEMORY "
1110 + file + "\n" + "########################");
1111 new OOMWarning("Creating Image for " + file, err);
1112 // System.out.println("Create IMAGE: " + err);
1113 } catch (Exception ex)
1115 ex.printStackTrace();
1122 public void makeEPS(File epsFile)
1124 makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
1130 public void makePNG(File pngFile)
1132 makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
1135 public void makePNGImageMap(File imgMapFile, String imageName)
1137 // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
1138 // ////////////////////////////////////////////
1139 int idWidth = getVisibleIdWidth();
1140 FontMetrics fm = getFontMetrics(av.getFont());
1141 int scaleHeight = av.charHeight + fm.getDescent();
1144 // ////////////////////////////////
1145 if (imgMapFile != null)
1149 int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
1150 .getWidth(), g, gSize, f, fSize, sy;
1151 StringBuffer text = new StringBuffer();
1152 PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
1153 out.println(jalview.io.HTMLOutput.getImageMapHTML());
1154 out.println("<img src=\"" + imageName
1155 + "\" border=\"0\" usemap=\"#Map\" >"
1156 + "<map name=\"Map\">");
1158 for (s = 0; s < sSize; s++)
1160 sy = s * av.charHeight + scaleHeight;
1162 SequenceI seq = av.alignment.getSequenceAt(s);
1163 SequenceFeature[] features = seq.getDatasetSequence()
1164 .getSequenceFeatures();
1165 SequenceGroup[] groups = av.alignment.findAllGroups(seq);
1166 for (res = 0; res < alwidth; res++)
1168 text = new StringBuffer();
1170 if (av.alignment.isNucleotide())
1172 obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
1177 obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
1186 String triplet = obj.toString();
1187 int alIndex = seq.findPosition(res);
1188 gSize = groups.length;
1189 for (g = 0; g < gSize; g++)
1191 if (text.length() < 1)
1193 text.append("<area shape=\"rect\" coords=\""
1194 + (idWidth + res * av.charWidth) + "," + sy + ","
1195 + (idWidth + (res + 1) * av.charWidth) + ","
1196 + (av.charHeight + sy) + "\""
1197 + " onMouseOver=\"toolTip('" + alIndex + " "
1201 if (groups[g].getStartRes() < res
1202 && groups[g].getEndRes() > res)
1204 text.append("<br><em>" + groups[g].getName() + "</em>");
1208 if (features != null)
1210 if (text.length() < 1)
1212 text.append("<area shape=\"rect\" coords=\""
1213 + (idWidth + res * av.charWidth) + "," + sy + ","
1214 + (idWidth + (res + 1) * av.charWidth) + ","
1215 + (av.charHeight + sy) + "\""
1216 + " onMouseOver=\"toolTip('" + alIndex + " "
1219 fSize = features.length;
1220 for (f = 0; f < fSize; f++)
1223 if ((features[f].getBegin() <= seq.findPosition(res))
1224 && (features[f].getEnd() >= seq.findPosition(res)))
1226 if (features[f].getType().equals("disulfide bond"))
1228 if (features[f].getBegin() == seq.findPosition(res)
1229 || features[f].getEnd() == seq
1232 text.append("<br>disulfide bond "
1233 + features[f].getBegin() + ":"
1234 + features[f].getEnd());
1239 text.append("<br>");
1240 text.append(features[f].getType());
1241 if (features[f].getDescription() != null
1242 && !features[f].getType().equals(
1243 features[f].getDescription()))
1245 text.append(" " + features[f].getDescription());
1248 if (features[f].getValue("status") != null)
1250 text.append(" (" + features[f].getValue("status")
1258 if (text.length() > 1)
1260 text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
1261 out.println(text.toString());
1265 out.println("</map></body></html>");
1268 } catch (Exception ex)
1270 ex.printStackTrace();
1272 } // /////////END OF IMAGE MAP
1276 int getWrappedHeight()
1278 int seqPanelWidth = seqPanel.seqCanvas.getWidth();
1280 if (System.getProperty("java.awt.headless") != null
1281 && System.getProperty("java.awt.headless").equals("true"))
1283 seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
1284 - vscroll.getPreferredSize().width
1285 - alignFrame.getInsets().left - alignFrame.getInsets().right;
1288 int chunkWidth = seqPanel.seqCanvas
1289 .getWrappedCanvasWidth(seqPanelWidth);
1291 int hgap = av.charHeight;
1292 if (av.scaleAboveWrapped)
1294 hgap += av.charHeight;
1297 int annotationHeight = 0;
1298 if (av.showAnnotation)
1300 annotationHeight = annotationPanel.adjustPanelHeight();
1303 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
1306 int maxwidth = av.alignment.getWidth();
1307 if (av.hasHiddenColumns)
1309 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
1312 int height = ((maxwidth / chunkWidth) + 1) * cHeight;
1318 * close the panel - deregisters all listeners and nulls any references to
1321 public void closePanel()
1323 PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
1324 PaintRefresher.RemoveComponent(idPanel.idCanvas);
1325 PaintRefresher.RemoveComponent(this);
1328 jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
1329 ssm.removeStructureViewerListener(seqPanel, null);
1330 ssm.removeSelectionListener(seqPanel);
1331 av.alignment = null;
1336 if (Cache.log.isDebugEnabled())
1338 Cache.log.warn("Closing alignment panel which is already closed.");
1344 * hides or shows dynamic annotation rows based on groups and av state flags
1346 public void updateAnnotation()
1348 updateAnnotation(false);
1351 public void updateAnnotation(boolean applyGlobalSettings)
1353 // TODO: this should be merged with other annotation update stuff - that
1354 // sits on AlignViewport
1355 boolean updateCalcs = false;
1356 boolean conv = av.isShowGroupConservation();
1357 boolean cons = av.isShowGroupConsensus();
1358 boolean showprf = av.isShowSequenceLogo();
1359 boolean showConsHist = av.isShowConsensusHistogram();
1361 boolean sortg = true;
1363 // remove old automatic annotation
1364 // add any new annotation
1366 Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
1367 // intersect alignment annotation with alignment groups
1369 AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
1370 Hashtable oldrfs = new Hashtable();
1373 for (int an = 0; an < aan.length; an++)
1375 if (aan[an].autoCalculated && aan[an].groupRef != null)
1377 oldrfs.put(aan[an].groupRef, aan[an].groupRef);
1378 av.alignment.deleteAnnotation(aan[an]);
1386 for (int g = 0; g < gr.size(); g++)
1388 updateCalcs = false;
1389 sg = (SequenceGroup) gr.elementAt(g);
1390 if (applyGlobalSettings || !oldrfs.containsKey(sg))
1392 // set defaults for this group's conservation/consensus
1393 sg.setshowSequenceLogo(showprf);
1394 sg.setShowConsensusHistogram(showConsHist);
1399 av.alignment.addAnnotation(sg.getConservationRow(), 0);
1404 av.alignment.addAnnotation(sg.getConsensus(), 0);
1406 // refresh the annotation rows
1409 sg.recalcConservation();
1414 adjustAnnotationHeight();
1418 public AlignmentI getAlignment()
1420 return av.alignment;
1424 * get the name for this view
1427 public String getViewName()
1433 * Make/Unmake this alignment panel the current input focus
1436 public void setSelected(boolean b)
1439 alignFrame.setSelected(b);
1440 } catch (Exception ex) {};
1444 alignFrame.setDisplayedView(this);
1449 public StructureSelectionManager getStructureSelectionManager()
1451 return av.getStructureSelectionManager();