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(
538 MessageManager.getString("label.annotations"));
539 JMenuItem item = new JMenuItem(ADDNEW);
540 item.addActionListener(this);
545 { // let the user make everything visible again
546 item = new JMenuItem(SHOWALL);
547 item.addActionListener(this);
550 pop.show(this, evt.getX(), evt.getY());
553 item = new JMenuItem(EDITNAME);
554 item.addActionListener(this);
556 item = new JMenuItem(HIDE);
557 item.addActionListener(this);
559 item = new JMenuItem(DELETE);
560 item.addActionListener(this);
564 item = new JMenuItem(SHOWALL);
565 item.addActionListener(this);
568 item = new JMenuItem(OUTPUT_TEXT);
569 item.addActionListener(this);
571 // TODO: annotation object should be typed for autocalculated/derived
573 if (selectedRow < aa.length)
575 if (!aa[selectedRow].autoCalculated)
577 if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
579 // display formatting settings for this row.
581 // av and sequencegroup need to implement same interface for
582 item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
583 aa[selectedRow].scaleColLabel);
584 item.addActionListener(this);
588 else if (aa[selectedRow].label.indexOf("Consensus") > -1)
591 // av and sequencegroup need to implement same interface for
592 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
593 "Ignore Gaps In Consensus",
594 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
595 .getIgnoreGapsConsensus() : ap.av
596 .getIgnoreGapsConsensus());
597 final AlignmentAnnotation aaa = aa[selectedRow];
598 cbmi.addActionListener(new ActionListener()
600 public void actionPerformed(ActionEvent e)
602 if (aaa.groupRef != null)
604 // TODO: pass on reference to ap so the view can be updated.
605 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
606 ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
610 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
615 // av and sequencegroup need to implement same interface for
616 if (aaa.groupRef != null)
618 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
619 "Show Group Histogram",
620 aa[selectedRow].groupRef.isShowConsensusHistogram());
621 chist.addActionListener(new ActionListener()
623 public void actionPerformed(ActionEvent e)
625 // TODO: pass on reference
631 aaa.groupRef.setShowConsensusHistogram(chist.getState());
633 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
637 final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
639 aa[selectedRow].groupRef.isShowSequenceLogo());
640 cprofl.addActionListener(new ActionListener()
642 public void actionPerformed(ActionEvent e)
644 // TODO: pass on reference
650 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
652 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
656 final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
657 "Normalise Group Logo",
658 aa[selectedRow].groupRef.isNormaliseSequenceLogo());
659 cproflnorm.addActionListener(new ActionListener()
661 public void actionPerformed(ActionEvent e)
664 // TODO: pass on reference
670 aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
671 // automatically enable logo display if we're clicked
672 aaa.groupRef.setshowSequenceLogo(true);
674 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
681 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
682 "Show Histogram", av.isShowConsensusHistogram());
683 chist.addActionListener(new ActionListener()
685 public void actionPerformed(ActionEvent e)
687 // TODO: pass on reference
693 av.setShowConsensusHistogram(chist.getState());
694 ap.alignFrame.setMenusForViewport();
696 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
700 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
701 "Show Logo", av.isShowSequenceLogo());
702 cprof.addActionListener(new ActionListener()
704 public void actionPerformed(ActionEvent e)
706 // TODO: pass on reference
712 av.setShowSequenceLogo(cprof.getState());
713 ap.alignFrame.setMenusForViewport();
715 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
719 final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
720 "Normalise Logo", av.isNormaliseSequenceLogo());
721 cprofnorm.addActionListener(new ActionListener()
723 public void actionPerformed(ActionEvent e)
725 // TODO: pass on reference
731 av.setShowSequenceLogo(true);
732 av.setNormaliseSequenceLogo(cprofnorm.getState());
733 ap.alignFrame.setMenusForViewport();
735 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
740 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
741 consclipbrd.addActionListener(this);
742 pop.add(consclipbrd);
745 pop.show(this, evt.getX(), evt.getY());
749 * do a single sequence copy to jalview and the system clipboard
752 * sequence to be copied to clipboard
754 protected void copy_annotseqtoclipboard(SequenceI sq)
756 SequenceI[] seqs = new SequenceI[]
758 String[] omitHidden = null;
759 SequenceI[] dseqs = new SequenceI[]
760 { sq.getDatasetSequence() };
761 if (dseqs[0] == null)
763 dseqs[0] = new Sequence(sq);
764 dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
765 jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
767 sq.setDatasetSequence(dseqs[0]);
769 Alignment ds = new Alignment(dseqs);
770 if (av.hasHiddenColumns())
772 omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
773 sq.getLength(), seqs);
776 String output = new FormatAdapter().formatSequences("Fasta", seqs,
779 Toolkit.getDefaultToolkit().getSystemClipboard()
780 .setContents(new StringSelection(output), Desktop.instance);
782 Vector hiddenColumns = null;
783 if (av.hasHiddenColumns())
785 hiddenColumns = new Vector();
786 for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
788 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
791 hiddenColumns.addElement(new int[]
792 { region[0], region[1] });
796 Desktop.jalviewClipboard = new Object[]
797 { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
798 // sequence as special.
808 public void paintComponent(Graphics g)
811 int width = getWidth();
814 width = ap.calculateIdWidth().width + 4;
817 Graphics2D g2 = (Graphics2D) g;
820 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
821 RenderingHints.VALUE_ANTIALIAS_ON);
824 drawComponent(g2, true, width);
829 * Draw the full set of annotation Labels for the alignment at the given
833 * Graphics2D instance (needed for font scaling)
835 * Width for scaling labels
838 public void drawComponent(Graphics g, int width)
840 drawComponent(g, false, width);
843 private final boolean debugRedraw = false;
846 * Draw the full set of annotation Labels for the alignment at the given
850 * Graphics2D instance (needed for font scaling)
852 * - true indicates that only current visible area needs to be
855 * Width for scaling labels
857 public void drawComponent(Graphics g, boolean clip, int width)
859 if (av.getFont().getSize() < 10)
865 g.setFont(av.getFont());
868 FontMetrics fm = g.getFontMetrics(g.getFont());
869 g.setColor(Color.white);
870 g.fillRect(0, 0, getWidth(), getHeight());
872 g.translate(0, scrollOffset);
873 g.setColor(Color.black);
875 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
876 int fontHeight = g.getFont().getSize();
881 Font baseFont = g.getFont();
882 FontMetrics baseMetrics = fm;
883 int ofontH = fontHeight;
886 int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel
887 .getVisibleVRange() : null;
888 if (clip && visr != null)
893 boolean visible = true, before = false, after = false;
896 hasHiddenRows = false;
898 for (int i = 0; i < aa.length; i++)
903 hasHiddenRows = true;
916 System.out.println("before vis: " + i);
920 // don't draw what isn't visible
930 System.out.println("Scroll offset: " + sOffset
931 + " after vis: " + i);
935 // don't draw what isn't visible
939 g.setColor(Color.black);
941 offset = -aa[i].height / 2;
945 offset += fm.getHeight() / 2;
946 offset -= fm.getDescent();
949 offset += fm.getDescent();
951 x = width - fm.stringWidth(aa[i].label) - 3;
953 if (aa[i].graphGroup > -1)
956 // TODO: JAL-1291 revise rendering model so the graphGroup map is
957 // computed efficiently for all visible labels
958 for (int gg = 0; gg < aa.length; gg++)
960 if (aa[gg].graphGroup == aa[i].graphGroup)
965 if (groupSize * (fontHeight + 8) < aa[i].height)
967 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
972 float h = aa[i].height / (float) groupSize, s;
979 fontHeight = -8 + (int) h;
980 s = ((float) fontHeight) / (float) ofontH;
981 Font f = baseFont.deriveFont(AffineTransform
982 .getScaleInstance(s, s));
984 fm = g.getFontMetrics();
985 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
990 for (int gg = 0; gg < aa.length; gg++)
992 if (aa[gg].graphGroup == aa[i].graphGroup)
994 x = width - fm.stringWidth(aa[gg].label) - 3;
995 g.drawString(aa[gg].label, x, y - graphExtras);
997 if (aa[gg]._linecolour != null)
1000 g.setColor(aa[gg]._linecolour);
1001 g.drawLine(x, y - graphExtras + 3,
1002 x + fm.stringWidth(aa[gg].label), y - graphExtras
1006 g.setColor(Color.black);
1007 graphExtras += fontHeight + 8;
1011 g.setFont(baseFont);
1013 fontHeight = ofontH;
1017 g.drawString(aa[i].label, x, y + offset);
1024 g.drawImage(image, 2, 0 - scrollOffset, this);
1026 else if (dragEvent != null && aa != null)
1028 g.setColor(Color.lightGray);
1029 g.drawString(aa[selectedRow].label, dragEvent.getX(),
1030 dragEvent.getY() - scrollOffset);
1033 if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
1035 g.drawString(MessageManager.getString("label.right_click"), 2, 8);
1036 g.drawString(MessageManager.getString("label.to_add_annotation"), 2,