2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.
24 import java.util.regex.Pattern;
27 import java.awt.datatransfer.*;
28 import java.awt.event.*;
29 import java.awt.geom.AffineTransform;
30 import java.awt.image.*;
33 import jalview.datamodel.*;
35 import jalview.util.MessageManager;
43 public class AnnotationLabels extends JPanel implements MouseListener,
44 MouseMotionListener, ActionListener
46 static String TOGGLE_LABELSCALE = "Scale Label to Column";
48 static String ADDNEW = "Add New Row";
50 static String EDITNAME = "Edit Label/Description";
52 static String HIDE = "Hide This Row";
54 static String DELETE = "Delete This Row";
56 static String SHOWALL = "Show All Hidden Rows";
58 static String OUTPUT_TEXT = "Export Annotation";
60 static String COPYCONS_SEQ = "Copy Consensus Sequence";
62 boolean resizePanel = false;
70 boolean resizing = false;
80 Font font = new Font("Arial", Font.PLAIN, 11);
82 private boolean hasHiddenRows;
85 * Creates a new AnnotationLabels object.
90 public AnnotationLabels(AlignmentPanel ap)
94 ToolTipManager.sharedInstance().registerComponent(this);
96 java.net.URL url = getClass().getResource("/images/idwidth.gif");
101 temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
106 MediaTracker mt = new MediaTracker(this);
107 mt.addImage(temp, 0);
109 } catch (Exception ex)
113 BufferedImage bi = new BufferedImage(temp.getHeight(this),
114 temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
115 Graphics2D g = (Graphics2D) bi.getGraphics();
116 g.rotate(Math.toRadians(90));
117 g.drawImage(temp, 0, -bi.getWidth(this), this);
120 addMouseListener(this);
121 addMouseMotionListener(this);
122 addMouseWheelListener(ap.annotationPanel);
125 public AnnotationLabels(AlignViewport av)
136 public void setScrollOffset(int y)
143 * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
147 * coordinate position to search for a row
149 void getSelectedRow(int y)
152 AlignmentAnnotation[] aa = ap.av.getAlignment()
153 .getAlignmentAnnotation();
157 for (int i = 0; i < aa.length; i++)
165 height += aa[i].height;
183 public void actionPerformed(ActionEvent evt)
185 AlignmentAnnotation[] aa = ap.av.getAlignment()
186 .getAlignmentAnnotation();
188 if (evt.getActionCommand().equals(ADDNEW))
190 AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
191 null, new Annotation[ap.av.getAlignment().getWidth()]);
193 if (!editLabelDescription(newAnnotation))
198 ap.av.getAlignment().addAnnotation(newAnnotation);
199 ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
201 else if (evt.getActionCommand().equals(EDITNAME))
203 editLabelDescription(aa[selectedRow]);
206 else if (evt.getActionCommand().equals(HIDE))
208 aa[selectedRow].visible = false;
210 else if (evt.getActionCommand().equals(DELETE))
212 ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
214 else if (evt.getActionCommand().equals(SHOWALL))
216 for (int i = 0; i < aa.length; i++)
218 if (!aa[i].visible && aa[i].annotations != null)
220 aa[i].visible = true;
224 else if (evt.getActionCommand().equals(OUTPUT_TEXT))
226 new AnnotationExporter().exportAnnotations(ap,
227 new AlignmentAnnotation[]
228 { aa[selectedRow] }, null, null);
230 else if (evt.getActionCommand().equals(COPYCONS_SEQ))
232 SequenceI cons = null;
233 if (aa[selectedRow].groupRef != null)
235 cons = aa[selectedRow].groupRef.getConsensusSeq();
239 cons = av.getConsensusSeq();
243 copy_annotseqtoclipboard(cons);
247 else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
249 aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
252 ap.validateAnnotationDimensions(false);
256 // ap.paintAlignment(true);
265 boolean editLabelDescription(AlignmentAnnotation annotation)
267 EditNameDialog dialog = new EditNameDialog(annotation.label,
268 annotation.description, " Annotation Name ",
269 "Annotation Description ", "Edit Annotation Name/Description",
277 annotation.label = dialog.getName();
279 String text = dialog.getDescription();
280 if (text != null && text.length() == 0)
284 annotation.description = text;
295 public void mousePressed(MouseEvent evt)
297 getSelectedRow(evt.getY() - scrollOffset);
307 public void mouseReleased(MouseEvent evt)
309 int start = selectedRow;
310 getSelectedRow(evt.getY() - scrollOffset);
311 int end = selectedRow;
315 // Swap these annotations
316 AlignmentAnnotation startAA = ap.av.getAlignment()
317 .getAlignmentAnnotation()[start];
320 end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
322 AlignmentAnnotation endAA = ap.av.getAlignment()
323 .getAlignmentAnnotation()[end];
325 ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
326 ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
332 ap.annotationPanel.repaint();
341 public void mouseEntered(MouseEvent evt)
356 public void mouseExited(MouseEvent evt)
358 if (dragEvent == null)
371 public void mouseDragged(MouseEvent evt)
377 Dimension d = ap.annotationScroller.getPreferredSize();
378 int dif = evt.getY() - oldY;
380 dif /= ap.av.charHeight;
381 dif *= ap.av.charHeight;
383 if ((d.height - dif) > 20)
385 ap.annotationScroller.setPreferredSize(new Dimension(d.width,
387 d = ap.annotationSpaceFillerHolder.getPreferredSize();
388 ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
389 d.width, d.height - dif));
390 ap.paintAlignment(true);
407 public void mouseMoved(MouseEvent evt)
409 resizePanel = evt.getY() < 10;
411 getSelectedRow(evt.getY() - scrollOffset);
414 && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
416 AlignmentAnnotation aa = ap.av.getAlignment()
417 .getAlignmentAnnotation()[selectedRow];
419 StringBuffer desc = new StringBuffer();
420 if (aa.description != null
421 && !aa.description.equals("New description"))
423 // TODO: we could refactor and merge this code with the code in
424 // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
426 desc.append(aa.getDescription(true).trim());
427 // check to see if the description is an html fragment.
428 if (desc.length() < 6
429 || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
431 // clean the description ready for embedding in html
432 desc = new StringBuffer(Pattern.compile("<").matcher(desc)
433 .replaceAll("<"));
434 desc.insert(0, "<html>");
438 // remove terminating html if any
439 int i = desc.substring(desc.length() - 7).toLowerCase()
440 .lastIndexOf("</html>");
443 desc.setLength(desc.length() - 7 + i);
448 desc.append("<br/>");
454 // begin the tooltip's html fragment
455 desc.append("<html>");
459 // TODO: limit precision of score to avoid noise from imprecise doubles
460 // (64.7 becomes 64.7+/some tiny value).
461 desc.append(" Score: " + aa.score);
464 if (desc.length() > 6)
466 desc.append("</html>");
467 this.setToolTipText(desc.toString());
470 this.setToolTipText(null);
481 public void mouseClicked(MouseEvent evt)
483 AlignmentAnnotation[] aa = ap.av.getAlignment()
484 .getAlignmentAnnotation();
485 if (SwingUtilities.isLeftMouseButton(evt))
487 if (selectedRow > -1 && selectedRow < aa.length)
489 if (aa[selectedRow].groupRef != null)
491 if (evt.getClickCount() >= 2)
493 // todo: make the ap scroll to the selection - not necessary, first
494 // click highlights/scrolls, second selects
495 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
496 ap.av.setSelectionGroup(// new SequenceGroup(
497 aa[selectedRow].groupRef); // );
498 ap.paintAlignment(false);
499 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
500 ap.av.sendSelection();
504 ap.seqPanel.ap.idPanel
505 .highlightSearchResults(aa[selectedRow].groupRef
506 .getSequences(null));
510 else if (aa[selectedRow].sequenceRef != null)
512 Vector sr = new Vector();
513 sr.addElement(aa[selectedRow].sequenceRef);
514 if (evt.getClickCount() == 1)
516 ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
518 else if (evt.getClickCount() >= 2)
520 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
521 SequenceGroup sg = new SequenceGroup();
522 sg.addSequence(aa[selectedRow].sequenceRef, false);
523 ap.av.setSelectionGroup(sg);
524 ap.av.sendSelection();
525 ap.paintAlignment(false);
526 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
532 if (!SwingUtilities.isRightMouseButton(evt))
537 JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations"));
538 JMenuItem item = new JMenuItem(ADDNEW);
539 item.addActionListener(this);
544 { // let the user make everything visible again
545 item = new JMenuItem(SHOWALL);
546 item.addActionListener(this);
549 pop.show(this, evt.getX(), evt.getY());
552 item = new JMenuItem(EDITNAME);
553 item.addActionListener(this);
555 item = new JMenuItem(HIDE);
556 item.addActionListener(this);
558 item = new JMenuItem(DELETE);
559 item.addActionListener(this);
563 item = new JMenuItem(SHOWALL);
564 item.addActionListener(this);
567 item = new JMenuItem(OUTPUT_TEXT);
568 item.addActionListener(this);
570 // TODO: annotation object should be typed for autocalculated/derived
572 if (selectedRow < aa.length)
574 if (!aa[selectedRow].autoCalculated)
576 if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
578 // display formatting settings for this row.
580 // av and sequencegroup need to implement same interface for
581 item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
582 aa[selectedRow].scaleColLabel);
583 item.addActionListener(this);
587 else if (aa[selectedRow].label.indexOf("Consensus") > -1)
590 // av and sequencegroup need to implement same interface for
591 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
592 "Ignore Gaps In Consensus",
593 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
594 .getIgnoreGapsConsensus() : ap.av
595 .getIgnoreGapsConsensus());
596 final AlignmentAnnotation aaa = aa[selectedRow];
597 cbmi.addActionListener(new ActionListener()
599 public void actionPerformed(ActionEvent e)
601 if (aaa.groupRef != null)
603 // TODO: pass on reference to ap so the view can be updated.
604 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
605 ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
609 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
614 // av and sequencegroup need to implement same interface for
615 if (aaa.groupRef != null)
617 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
618 "Show Group Histogram",
619 aa[selectedRow].groupRef.isShowConsensusHistogram());
620 chist.addActionListener(new ActionListener()
622 public void actionPerformed(ActionEvent e)
624 // TODO: pass on reference
630 aaa.groupRef.setShowConsensusHistogram(chist.getState());
632 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
636 final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
638 aa[selectedRow].groupRef.isShowSequenceLogo());
639 cprofl.addActionListener(new ActionListener()
641 public void actionPerformed(ActionEvent e)
643 // TODO: pass on reference
649 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
651 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
655 final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
656 "Normalise Group Logo",
657 aa[selectedRow].groupRef.isNormaliseSequenceLogo());
658 cproflnorm.addActionListener(new ActionListener()
660 public void actionPerformed(ActionEvent e)
663 // TODO: pass on reference
669 aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
670 // automatically enable logo display if we're clicked
671 aaa.groupRef.setshowSequenceLogo(true);
673 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
680 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
681 "Show Histogram", av.isShowConsensusHistogram());
682 chist.addActionListener(new ActionListener()
684 public void actionPerformed(ActionEvent e)
686 // TODO: pass on reference
692 av.setShowConsensusHistogram(chist.getState());
693 ap.alignFrame.setMenusForViewport();
695 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
699 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
700 "Show Logo", av.isShowSequenceLogo());
701 cprof.addActionListener(new ActionListener()
703 public void actionPerformed(ActionEvent e)
705 // TODO: pass on reference
711 av.setShowSequenceLogo(cprof.getState());
712 ap.alignFrame.setMenusForViewport();
714 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
718 final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
719 "Normalise Logo", av.isNormaliseSequenceLogo());
720 cprofnorm.addActionListener(new ActionListener()
722 public void actionPerformed(ActionEvent e)
724 // TODO: pass on reference
730 av.setShowSequenceLogo(true);
731 av.setNormaliseSequenceLogo(cprofnorm.getState());
732 ap.alignFrame.setMenusForViewport();
734 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
739 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
740 consclipbrd.addActionListener(this);
741 pop.add(consclipbrd);
744 pop.show(this, evt.getX(), evt.getY());
748 * do a single sequence copy to jalview and the system clipboard
751 * sequence to be copied to clipboard
753 protected void copy_annotseqtoclipboard(SequenceI sq)
755 SequenceI[] seqs = new SequenceI[]
757 String[] omitHidden = null;
758 SequenceI[] dseqs = new SequenceI[]
759 { sq.getDatasetSequence() };
760 if (dseqs[0] == null)
762 dseqs[0] = new Sequence(sq);
763 dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
764 jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
766 sq.setDatasetSequence(dseqs[0]);
768 Alignment ds = new Alignment(dseqs);
769 if (av.hasHiddenColumns())
771 omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
772 sq.getLength(), seqs);
775 String output = new FormatAdapter().formatSequences("Fasta", seqs,
778 Toolkit.getDefaultToolkit().getSystemClipboard()
779 .setContents(new StringSelection(output), Desktop.instance);
781 Vector hiddenColumns = null;
782 if (av.hasHiddenColumns())
784 hiddenColumns = new Vector();
785 for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
787 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
790 hiddenColumns.addElement(new int[]
791 { region[0], region[1] });
795 Desktop.jalviewClipboard = new Object[]
796 { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
797 // sequence as special.
807 public void paintComponent(Graphics g)
810 int width = getWidth();
813 width = ap.calculateIdWidth().width + 4;
816 Graphics2D g2 = (Graphics2D) g;
819 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
820 RenderingHints.VALUE_ANTIALIAS_ON);
823 drawComponent(g2, true, width);
828 * Draw the full set of annotation Labels for the alignment at the given cursor
830 * @param g Graphics2D instance (needed for font scaling)
831 * @param width Width for scaling labels
834 public void drawComponent(Graphics g, int width)
836 drawComponent(g, false, width);
839 private final boolean debugRedraw = false;
841 * Draw the full set of annotation Labels for the alignment at the given cursor
843 * @param g Graphics2D instance (needed for font scaling)
844 * @param clip - true indicates that only current visible area needs to be rendered
845 * @param width Width for scaling labels
847 public void drawComponent(Graphics g, boolean clip, int width)
849 if (av.getFont().getSize() < 10)
855 g.setFont(av.getFont());
858 FontMetrics fm = g.getFontMetrics(g.getFont());
859 g.setColor(Color.white);
860 g.fillRect(0, 0, getWidth(), getHeight());
862 g.translate(0, scrollOffset);
863 g.setColor(Color.black);
865 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
866 int fontHeight = g.getFont().getSize();
871 Font baseFont = g.getFont();
872 FontMetrics baseMetrics = fm;
873 int ofontH = fontHeight;
876 int[] visr = (ap!=null && ap.annotationPanel!=null) ? ap.annotationPanel.getVisibleVRange() : null;
877 if (clip && visr!=null){
881 boolean visible = true,before=false,after=false;
884 hasHiddenRows = false;
886 for (int i = 0; i < aa.length; i++)
891 hasHiddenRows = true;
896 if (clip) {if (y<sOffset)
901 System.out.println("before vis: "+i);
905 // don't draw what isn't visible
914 System.out.println("Scroll offset: "+sOffset+" after vis: "+i);
918 // don't draw what isn't visible
921 g.setColor(Color.black);
923 offset = -aa[i].height / 2;
927 offset += fm.getHeight() / 2;
928 offset -= fm.getDescent();
931 offset += fm.getDescent();
933 x = width - fm.stringWidth(aa[i].label) - 3;
935 if (aa[i].graphGroup > -1)
938 // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
939 for (int gg = 0; gg < aa.length; gg++)
941 if (aa[gg].graphGroup == aa[i].graphGroup)
946 if (groupSize * (fontHeight + 8) < aa[i].height)
948 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
953 float h = aa[i].height / (float) groupSize, s;
960 fontHeight = -8 + (int) h;
961 s = ((float) fontHeight) / (float) ofontH;
962 Font f = baseFont.deriveFont(AffineTransform
963 .getScaleInstance(s, s));
965 fm = g.getFontMetrics();
966 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
971 for (int gg = 0; gg < aa.length; gg++)
973 if (aa[gg].graphGroup == aa[i].graphGroup)
975 x = width - fm.stringWidth(aa[gg].label) - 3;
976 g.drawString(aa[gg].label, x, y - graphExtras);
978 if (aa[gg]._linecolour != null)
981 g.setColor(aa[gg]._linecolour);
982 g.drawLine(x, y - graphExtras + 3,
983 x + fm.stringWidth(aa[gg].label), y - graphExtras
987 g.setColor(Color.black);
988 graphExtras += fontHeight + 8;
998 g.drawString(aa[i].label, x, y + offset);
1005 g.drawImage(image, 2, 0 - scrollOffset, this);
1007 else if (dragEvent != null && aa != null)
1009 g.setColor(Color.lightGray);
1010 g.drawString(aa[selectedRow].label, dragEvent.getX(),
1011 dragEvent.getY() - scrollOffset);
1014 if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
1016 g.drawString(MessageManager.getString("label.right_click"), 2, 8);
1017 g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);