2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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/>.
21 import java.util.regex.Pattern;
24 import java.awt.datatransfer.*;
25 import java.awt.event.*;
26 import java.awt.geom.AffineTransform;
27 import java.awt.image.*;
30 import jalview.datamodel.*;
39 public class AnnotationLabels extends JPanel implements MouseListener,
40 MouseMotionListener, ActionListener
42 static String TOGGLE_LABELSCALE = "Scale Label to Column";
44 static String ADDNEW = "Add New Row";
46 static String EDITNAME = "Edit Label/Description";
48 static String HIDE = "Hide This Row";
50 static String DELETE = "Delete This Row";
52 static String SHOWALL = "Show All Hidden Rows";
54 static String OUTPUT_TEXT = "Export Annotation";
56 static String COPYCONS_SEQ = "Copy Consensus Sequence";
58 boolean resizePanel = false;
66 boolean resizing = false;
76 Font font = new Font("Arial", Font.PLAIN, 11);
78 private boolean hasHiddenRows;
81 * Creates a new AnnotationLabels object.
86 public AnnotationLabels(AlignmentPanel ap)
90 ToolTipManager.sharedInstance().registerComponent(this);
92 java.net.URL url = getClass().getResource("/images/idwidth.gif");
97 temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
102 MediaTracker mt = new MediaTracker(this);
103 mt.addImage(temp, 0);
105 } catch (Exception ex)
109 BufferedImage bi = new BufferedImage(temp.getHeight(this),
110 temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
111 Graphics2D g = (Graphics2D) bi.getGraphics();
112 g.rotate(Math.toRadians(90));
113 g.drawImage(temp, 0, -bi.getWidth(this), this);
116 addMouseListener(this);
117 addMouseMotionListener(this);
120 public AnnotationLabels(AlignViewport av)
131 public void setScrollOffset(int y)
138 * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
142 * coordinate position to search for a row
144 void getSelectedRow(int y)
147 AlignmentAnnotation[] aa = ap.av.getAlignment()
148 .getAlignmentAnnotation();
152 for (int i = 0; i < aa.length; i++)
160 height += aa[i].height;
178 public void actionPerformed(ActionEvent evt)
180 AlignmentAnnotation[] aa = ap.av.getAlignment()
181 .getAlignmentAnnotation();
183 if (evt.getActionCommand().equals(ADDNEW))
185 AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
186 null, new Annotation[ap.av.getAlignment().getWidth()]);
188 if (!editLabelDescription(newAnnotation))
193 ap.av.getAlignment().addAnnotation(newAnnotation);
194 ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
196 else if (evt.getActionCommand().equals(EDITNAME))
198 editLabelDescription(aa[selectedRow]);
201 else if (evt.getActionCommand().equals(HIDE))
203 aa[selectedRow].visible = false;
205 else if (evt.getActionCommand().equals(DELETE))
207 ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
209 else if (evt.getActionCommand().equals(SHOWALL))
211 for (int i = 0; i < aa.length; i++)
213 if (!aa[i].visible && aa[i].annotations != null)
215 aa[i].visible = true;
219 else if (evt.getActionCommand().equals(OUTPUT_TEXT))
221 new AnnotationExporter().exportAnnotations(ap,
222 new AlignmentAnnotation[]
223 { aa[selectedRow] }, null, null);
225 else if (evt.getActionCommand().equals(COPYCONS_SEQ))
227 SequenceI cons = null;
228 if (aa[selectedRow].groupRef != null)
230 cons = aa[selectedRow].groupRef.getConsensusSeq();
234 cons = av.getConsensusSeq();
238 copy_annotseqtoclipboard(cons);
242 else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
244 aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
247 ap.validateAnnotationDimensions(false);
251 // ap.paintAlignment(true);
260 boolean editLabelDescription(AlignmentAnnotation annotation)
262 EditNameDialog dialog = new EditNameDialog(annotation.label,
263 annotation.description, " Annotation Name ",
264 "Annotation Description ", "Edit Annotation Name/Description",
272 annotation.label = dialog.getName();
274 String text = dialog.getDescription();
275 if (text != null && text.length() == 0)
279 annotation.description = text;
290 public void mousePressed(MouseEvent evt)
292 getSelectedRow(evt.getY() - scrollOffset);
302 public void mouseReleased(MouseEvent evt)
304 int start = selectedRow;
305 getSelectedRow(evt.getY() - scrollOffset);
306 int end = selectedRow;
310 // Swap these annotations
311 AlignmentAnnotation startAA = ap.av.getAlignment()
312 .getAlignmentAnnotation()[start];
315 end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
317 AlignmentAnnotation endAA = ap.av.getAlignment()
318 .getAlignmentAnnotation()[end];
320 ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
321 ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
327 ap.annotationPanel.repaint();
336 public void mouseEntered(MouseEvent evt)
351 public void mouseExited(MouseEvent evt)
353 if (dragEvent == null)
366 public void mouseDragged(MouseEvent evt)
372 Dimension d = ap.annotationScroller.getPreferredSize();
373 int dif = evt.getY() - oldY;
375 dif /= ap.av.charHeight;
376 dif *= ap.av.charHeight;
378 if ((d.height - dif) > 20)
380 ap.annotationScroller.setPreferredSize(new Dimension(d.width,
382 d = ap.annotationSpaceFillerHolder.getPreferredSize();
383 ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
384 d.width, d.height - dif));
385 ap.paintAlignment(true);
402 public void mouseMoved(MouseEvent evt)
404 resizePanel = evt.getY() < 10;
406 getSelectedRow(evt.getY() - scrollOffset);
409 && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
411 AlignmentAnnotation aa = ap.av.getAlignment()
412 .getAlignmentAnnotation()[selectedRow];
414 StringBuffer desc = new StringBuffer();
415 if (aa.description != null
416 && !aa.description.equals("New description"))
418 // TODO: we could refactor and merge this code with the code in
419 // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
421 desc.append(aa.getDescription(true).trim());
422 // check to see if the description is an html fragment.
423 if (desc.length() < 6
424 || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
426 // clean the description ready for embedding in html
427 desc = new StringBuffer(Pattern.compile("<").matcher(desc)
428 .replaceAll("<"));
429 desc.insert(0, "<html>");
433 // remove terminating html if any
434 int i = desc.substring(desc.length() - 7).toLowerCase()
435 .lastIndexOf("</html>");
438 desc.setLength(desc.length() - 7 + i);
443 desc.append("<br/>");
449 // begin the tooltip's html fragment
450 desc.append("<html>");
454 // TODO: limit precision of score to avoid noise from imprecise doubles
455 // (64.7 becomes 64.7+/some tiny value).
456 desc.append(" Score: " + aa.score);
459 if (desc.length() > 6)
461 desc.append("</html>");
462 this.setToolTipText(desc.toString());
465 this.setToolTipText(null);
476 public void mouseClicked(MouseEvent evt)
478 AlignmentAnnotation[] aa = ap.av.getAlignment()
479 .getAlignmentAnnotation();
480 if (SwingUtilities.isLeftMouseButton(evt))
482 if (selectedRow > -1 && selectedRow < aa.length)
484 if (aa[selectedRow].groupRef != null)
486 if (evt.getClickCount() >= 2)
488 // todo: make the ap scroll to the selection - not necessary, first
489 // click highlights/scrolls, second selects
490 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
491 ap.av.setSelectionGroup(// new SequenceGroup(
492 aa[selectedRow].groupRef); // );
493 ap.paintAlignment(false);
494 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
495 ap.av.sendSelection();
499 ap.seqPanel.ap.idPanel
500 .highlightSearchResults(aa[selectedRow].groupRef
501 .getSequences(null));
505 else if (aa[selectedRow].sequenceRef != null)
507 Vector sr = new Vector();
508 sr.addElement(aa[selectedRow].sequenceRef);
509 if (evt.getClickCount() == 1)
511 ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
513 else if (evt.getClickCount() >= 2)
515 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
516 SequenceGroup sg = new SequenceGroup();
517 sg.addSequence(aa[selectedRow].sequenceRef, false);
518 ap.av.setSelectionGroup(sg);
519 ap.av.sendSelection();
520 ap.paintAlignment(false);
521 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
527 if (!SwingUtilities.isRightMouseButton(evt))
532 JPopupMenu pop = new JPopupMenu("Annotations");
533 JMenuItem item = new JMenuItem(ADDNEW);
534 item.addActionListener(this);
539 { // let the user make everything visible again
540 item = new JMenuItem(SHOWALL);
541 item.addActionListener(this);
544 pop.show(this, evt.getX(), evt.getY());
547 item = new JMenuItem(EDITNAME);
548 item.addActionListener(this);
550 item = new JMenuItem(HIDE);
551 item.addActionListener(this);
553 item = new JMenuItem(DELETE);
554 item.addActionListener(this);
558 item = new JMenuItem(SHOWALL);
559 item.addActionListener(this);
562 item = new JMenuItem(OUTPUT_TEXT);
563 item.addActionListener(this);
565 // TODO: annotation object should be typed for autocalculated/derived
567 if (selectedRow < aa.length)
569 if (!aa[selectedRow].autoCalculated)
571 if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
573 // display formatting settings for this row.
575 // av and sequencegroup need to implement same interface for
576 item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
577 aa[selectedRow].scaleColLabel);
578 item.addActionListener(this);
582 else if (aa[selectedRow].label.indexOf("Consensus") > -1)
585 // av and sequencegroup need to implement same interface for
586 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
587 "Ignore Gaps In Consensus",
588 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
589 .getIgnoreGapsConsensus() : ap.av
590 .getIgnoreGapsConsensus());
591 final AlignmentAnnotation aaa = aa[selectedRow];
592 cbmi.addActionListener(new ActionListener()
594 public void actionPerformed(ActionEvent e)
596 if (aaa.groupRef != null)
598 // TODO: pass on reference to ap so the view can be updated.
599 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
600 ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
604 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
609 // av and sequencegroup need to implement same interface for
610 if (aaa.groupRef != null)
612 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
613 "Show Group Histogram",
614 aa[selectedRow].groupRef.isShowConsensusHistogram());
615 chist.addActionListener(new ActionListener()
617 public void actionPerformed(ActionEvent e)
619 // TODO: pass on reference
625 aaa.groupRef.setShowConsensusHistogram(chist.getState());
627 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
631 final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
633 aa[selectedRow].groupRef.isShowSequenceLogo());
634 cprofl.addActionListener(new ActionListener()
636 public void actionPerformed(ActionEvent e)
638 // TODO: pass on reference
644 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
646 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
650 final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
651 "Normalise Group Logo",
652 aa[selectedRow].groupRef.isNormaliseSequenceLogo());
653 cproflnorm.addActionListener(new ActionListener()
655 public void actionPerformed(ActionEvent e)
658 // TODO: pass on reference
664 aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
665 // automatically enable logo display if we're clicked
666 aaa.groupRef.setshowSequenceLogo(true);
668 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
675 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
676 "Show Histogram", av.isShowConsensusHistogram());
677 chist.addActionListener(new ActionListener()
679 public void actionPerformed(ActionEvent e)
681 // TODO: pass on reference
687 av.setShowConsensusHistogram(chist.getState());
688 ap.alignFrame.setMenusForViewport();
690 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
694 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
695 "Show Logo", av.isShowSequenceLogo());
696 cprof.addActionListener(new ActionListener()
698 public void actionPerformed(ActionEvent e)
700 // TODO: pass on reference
706 av.setShowSequenceLogo(cprof.getState());
707 ap.alignFrame.setMenusForViewport();
709 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
713 final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
714 "Normalise Logo", av.isNormaliseSequenceLogo());
715 cprofnorm.addActionListener(new ActionListener()
717 public void actionPerformed(ActionEvent e)
719 // TODO: pass on reference
725 av.setShowSequenceLogo(true);
726 av.setNormaliseSequenceLogo(cprofnorm.getState());
727 ap.alignFrame.setMenusForViewport();
729 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
734 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
735 consclipbrd.addActionListener(this);
736 pop.add(consclipbrd);
739 pop.show(this, evt.getX(), evt.getY());
743 * do a single sequence copy to jalview and the system clipboard
746 * sequence to be copied to clipboard
748 protected void copy_annotseqtoclipboard(SequenceI sq)
750 SequenceI[] seqs = new SequenceI[]
752 String[] omitHidden = null;
753 SequenceI[] dseqs = new SequenceI[]
754 { sq.getDatasetSequence() };
755 if (dseqs[0] == null)
757 dseqs[0] = new Sequence(sq);
758 dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
759 jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
761 sq.setDatasetSequence(dseqs[0]);
763 Alignment ds = new Alignment(dseqs);
764 if (av.hasHiddenColumns())
766 omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
767 sq.getLength(), seqs);
770 String output = new FormatAdapter().formatSequences("Fasta", seqs,
773 Toolkit.getDefaultToolkit().getSystemClipboard()
774 .setContents(new StringSelection(output), Desktop.instance);
776 Vector hiddenColumns = null;
777 if (av.hasHiddenColumns())
779 hiddenColumns = new Vector();
780 for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
782 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
785 hiddenColumns.addElement(new int[]
786 { region[0], region[1] });
790 Desktop.jalviewClipboard = new Object[]
791 { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
792 // sequence as special.
802 public void paintComponent(Graphics g)
805 int width = getWidth();
808 width = ap.calculateIdWidth().width + 4;
811 Graphics2D g2 = (Graphics2D) g;
814 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
815 RenderingHints.VALUE_ANTIALIAS_ON);
818 drawComponent(g2, width);
828 public void drawComponent(Graphics g, int width)
830 if (av.getFont().getSize() < 10)
836 g.setFont(av.getFont());
839 FontMetrics fm = g.getFontMetrics(g.getFont());
840 g.setColor(Color.white);
841 g.fillRect(0, 0, getWidth(), getHeight());
843 g.translate(0, scrollOffset);
844 g.setColor(Color.black);
846 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
847 int fontHeight = g.getFont().getSize();
852 Font baseFont = g.getFont();
853 FontMetrics baseMetrics = fm;
854 int ofontH = fontHeight;
855 boolean visible = true;
858 hasHiddenRows = false;
859 for (int i = 0; i < aa.length; i++)
862 g.setColor(Color.black);
866 hasHiddenRows = true;
872 offset = -aa[i].height / 2;
876 offset += fm.getHeight() / 2;
877 offset -= fm.getDescent();
880 offset += fm.getDescent();
882 x = width - fm.stringWidth(aa[i].label) - 3;
884 if (aa[i].graphGroup > -1)
887 for (int gg = 0; gg < aa.length; gg++)
889 if (aa[gg].graphGroup == aa[i].graphGroup)
894 if (groupSize * (fontHeight + 8) < aa[i].height)
896 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
901 float h = aa[i].height / (float) groupSize, s;
908 fontHeight = -8 + (int) h;
909 s = ((float) fontHeight) / (float) ofontH;
910 Font f = baseFont.deriveFont(AffineTransform
911 .getScaleInstance(s, s));
913 fm = g.getFontMetrics();
914 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
919 for (int gg = 0; gg < aa.length; gg++)
921 if (aa[gg].graphGroup == aa[i].graphGroup)
923 x = width - fm.stringWidth(aa[gg].label) - 3;
924 g.drawString(aa[gg].label, x, y - graphExtras);
926 if (aa[gg]._linecolour != null)
929 g.setColor(aa[gg]._linecolour);
930 g.drawLine(x, y - graphExtras + 3,
931 x + fm.stringWidth(aa[gg].label), y - graphExtras
935 g.setColor(Color.black);
936 graphExtras += fontHeight + 8;
946 g.drawString(aa[i].label, x, y + offset);
953 g.drawImage(image, 2, 0 - scrollOffset, this);
955 else if (dragEvent != null && aa != null)
957 g.setColor(Color.lightGray);
958 g.drawString(aa[selectedRow].label, dragEvent.getX(),
959 dragEvent.getY() - scrollOffset);
962 if ((aa == null) || (aa.length < 1))
964 g.drawString("Right click", 2, 8);
965 g.drawString("to add annotation", 2, 18);