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/>.
21 import java.util.regex.Pattern;
24 import java.awt.datatransfer.*;
25 import java.awt.event.*;
26 import java.awt.image.*;
29 import jalview.datamodel.*;
38 public class AnnotationLabels extends JPanel implements MouseListener,
39 MouseMotionListener, ActionListener
41 static String TOGGLE_LABELSCALE = "Scale Label to Column";
43 static String ADDNEW = "Add New Row";
45 static String EDITNAME = "Edit Label/Description";
47 static String HIDE = "Hide This Row";
49 static String DELETE = "Delete This Row";
51 static String SHOWALL = "Show All Hidden Rows";
53 static String OUTPUT_TEXT = "Export Annotation";
55 static String COPYCONS_SEQ = "Copy Consensus Sequence";
57 boolean resizePanel = false;
65 boolean resizing = false;
75 Font font = new Font("Arial", Font.PLAIN, 11);
77 private boolean hasHiddenRows;
80 * Creates a new AnnotationLabels object.
85 public AnnotationLabels(AlignmentPanel ap)
89 ToolTipManager.sharedInstance().registerComponent(this);
91 java.net.URL url = getClass().getResource("/images/idwidth.gif");
96 temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
101 MediaTracker mt = new MediaTracker(this);
102 mt.addImage(temp, 0);
104 } catch (Exception ex)
108 BufferedImage bi = new BufferedImage(temp.getHeight(this),
109 temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
110 Graphics2D g = (Graphics2D) bi.getGraphics();
111 g.rotate(Math.toRadians(90));
112 g.drawImage(temp, 0, -bi.getWidth(this), this);
115 addMouseListener(this);
116 addMouseMotionListener(this);
119 public AnnotationLabels(AlignViewport av)
130 public void setScrollOffset(int y)
137 * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
141 * coordinate position to search for a row
143 void getSelectedRow(int y)
146 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
150 for (int i = 0; i < aa.length; i++)
158 height += aa[i].height;
176 public void actionPerformed(ActionEvent evt)
178 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
180 if (evt.getActionCommand().equals(ADDNEW))
182 AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
183 null, new Annotation[ap.av.alignment.getWidth()]);
185 if (!editLabelDescription(newAnnotation))
190 ap.av.alignment.addAnnotation(newAnnotation);
191 ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
193 else if (evt.getActionCommand().equals(EDITNAME))
195 editLabelDescription(aa[selectedRow]);
198 else if (evt.getActionCommand().equals(HIDE))
200 aa[selectedRow].visible = false;
202 else if (evt.getActionCommand().equals(DELETE))
204 ap.av.alignment.deleteAnnotation(aa[selectedRow]);
206 else if (evt.getActionCommand().equals(SHOWALL))
208 for (int i = 0; i < aa.length; i++)
210 if (!aa[i].visible && aa[i].annotations != null)
212 aa[i].visible = true;
216 else if (evt.getActionCommand().equals(OUTPUT_TEXT))
218 new AnnotationExporter().exportAnnotations(ap,
219 new AlignmentAnnotation[]
220 { aa[selectedRow] }, null, null);
222 else if (evt.getActionCommand().equals(COPYCONS_SEQ))
224 SequenceI cons = null;
225 if (aa[selectedRow].groupRef != null)
227 cons = aa[selectedRow].groupRef.getConsensusSeq();
231 cons = av.getConsensusSeq();
235 copy_annotseqtoclipboard(cons);
239 else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
241 aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
244 ap.validateAnnotationDimensions(false);
248 //ap.paintAlignment(true);
257 boolean editLabelDescription(AlignmentAnnotation annotation)
259 EditNameDialog dialog = new EditNameDialog(annotation.label,
260 annotation.description, " Annotation Name ",
261 "Annotation Description ", "Edit Annotation Name/Description",
269 annotation.label = dialog.getName();
271 String text = dialog.getDescription();
272 if (text != null && text.length() == 0)
276 annotation.description = text;
287 public void mousePressed(MouseEvent evt)
289 getSelectedRow(evt.getY() - scrollOffset);
299 public void mouseReleased(MouseEvent evt)
301 int start = selectedRow;
302 getSelectedRow(evt.getY() - scrollOffset);
303 int end = selectedRow;
307 // Swap these annotations
308 AlignmentAnnotation startAA = ap.av.alignment
309 .getAlignmentAnnotation()[start];
312 end = ap.av.alignment.getAlignmentAnnotation().length - 1;
314 AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
316 ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
317 ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
323 ap.annotationPanel.repaint();
332 public void mouseEntered(MouseEvent evt)
347 public void mouseExited(MouseEvent evt)
349 if (dragEvent == null)
362 public void mouseDragged(MouseEvent evt)
368 Dimension d = ap.annotationScroller.getPreferredSize();
369 int dif = evt.getY() - oldY;
371 dif /= ap.av.charHeight;
372 dif *= ap.av.charHeight;
374 if ((d.height - dif) > 20)
376 ap.annotationScroller.setPreferredSize(new Dimension(d.width,
378 d = ap.annotationSpaceFillerHolder.getPreferredSize();
379 ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
380 d.width, d.height - dif));
381 ap.paintAlignment(true);
398 public void mouseMoved(MouseEvent evt)
400 resizePanel = evt.getY() < 10;
402 getSelectedRow(evt.getY() - scrollOffset);
405 && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
407 AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
409 StringBuffer desc = new StringBuffer();
410 if (aa.description != null
411 && !aa.description.equals("New description"))
413 // TODO: we could refactor and merge this code with the code in jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature tooltips
414 desc.append(aa.getDescription(true).trim());
415 // check to see if the description is an html fragment.
416 if (desc.length()<6 || (desc.substring(0,6).toLowerCase().indexOf("<html>")<0))
418 // clean the description ready for embedding in html
419 desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("<"));
420 desc.insert(0, "<html>");
422 // remove terminating html if any
423 int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf("</html>");
425 desc.setLength(desc.length()-7+i);
430 desc.append("<br/>");
435 // begin the tooltip's html fragment
436 desc.append("<html>");
440 // TODO: limit precision of score to avoid noise from imprecise doubles (64.7 becomes 64.7+/some tiny value).
441 desc.append(" Score: " + aa.score);
444 if (desc.length() > 6)
446 desc.append("</html>");
447 System.err.println(desc.toString());
448 this.setToolTipText(desc.toString());
451 this.setToolTipText(null);
462 public void mouseClicked(MouseEvent evt)
464 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
465 if (SwingUtilities.isLeftMouseButton(evt))
467 if (selectedRow > -1 && selectedRow < aa.length)
469 if (aa[selectedRow].groupRef != null)
471 if (evt.getClickCount() >= 2)
473 // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects
474 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
475 ap.av.setSelectionGroup(// new SequenceGroup(
476 aa[selectedRow].groupRef); // );
477 ap.paintAlignment(false);
478 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
479 ap.av.sendSelection();
483 ap.seqPanel.ap.idPanel
484 .highlightSearchResults(aa[selectedRow].groupRef
485 .getSequences(null));
489 else if (aa[selectedRow].sequenceRef != null)
491 Vector sr = new Vector();
492 sr.addElement(aa[selectedRow].sequenceRef);
493 if (evt.getClickCount() == 1)
495 ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
497 else if (evt.getClickCount() >= 2)
499 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
500 SequenceGroup sg = new SequenceGroup();
501 sg.addSequence(aa[selectedRow].sequenceRef, false);
502 ap.av.setSelectionGroup(sg);
503 ap.av.sendSelection();
504 ap.paintAlignment(false);
505 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
511 if (!SwingUtilities.isRightMouseButton(evt))
516 JPopupMenu pop = new JPopupMenu("Annotations");
517 JMenuItem item = new JMenuItem(ADDNEW);
518 item.addActionListener(this);
523 { // let the user make everything visible again
524 item = new JMenuItem(SHOWALL);
525 item.addActionListener(this);
528 pop.show(this, evt.getX(), evt.getY());
531 item = new JMenuItem(EDITNAME);
532 item.addActionListener(this);
534 item = new JMenuItem(HIDE);
535 item.addActionListener(this);
537 item = new JMenuItem(DELETE);
538 item.addActionListener(this);
542 item = new JMenuItem(SHOWALL);
543 item.addActionListener(this);
546 item = new JMenuItem(OUTPUT_TEXT);
547 item.addActionListener(this);
549 // TODO: annotation object should be typed for autocalculated/derived
551 if (selectedRow < aa.length)
553 if (!aa[selectedRow].autoCalculated)
555 if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
557 // display formatting settings for this row.
559 // av and sequencegroup need to implement same interface for
560 item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
561 aa[selectedRow].scaleColLabel);
562 item.addActionListener(this);
566 else if (aa[selectedRow].label.indexOf("Consensus") > -1)
569 // av and sequencegroup need to implement same interface for
570 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
571 "Ignore Gaps In Consensus",
572 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
573 .getIgnoreGapsConsensus() : ap.av
574 .getIgnoreGapsConsensus());
575 final AlignmentAnnotation aaa = aa[selectedRow];
576 cbmi.addActionListener(new ActionListener()
578 public void actionPerformed(ActionEvent e)
580 if (aaa.groupRef != null)
582 // TODO: pass on reference to ap so the view can be updated.
583 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
584 ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
588 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
593 // av and sequencegroup need to implement same interface for
594 if (aaa.groupRef != null)
596 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
597 "Show Group Histogram",
598 aa[selectedRow].groupRef.isShowConsensusHistogram());
599 chist.addActionListener(new ActionListener()
601 public void actionPerformed(ActionEvent e)
603 // TODO: pass on reference
609 aaa.groupRef.setShowConsensusHistogram(chist.getState());
611 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
615 final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
617 aa[selectedRow].groupRef.isShowSequenceLogo());
618 cprofl.addActionListener(new ActionListener()
620 public void actionPerformed(ActionEvent e)
622 // TODO: pass on reference
628 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
630 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
637 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
638 "Show Histogram", av.isShowConsensusHistogram());
639 chist.addActionListener(new ActionListener()
641 public void actionPerformed(ActionEvent e)
643 // TODO: pass on reference
649 av.setShowConsensusHistogram(chist.getState());
651 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
655 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
656 "Show Logo", av.isShowSequenceLogo());
657 cprof.addActionListener(new ActionListener()
659 public void actionPerformed(ActionEvent e)
661 // TODO: pass on reference
667 av.setShowSequenceLogo(cprof.getState());
669 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
674 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
675 consclipbrd.addActionListener(this);
676 pop.add(consclipbrd);
679 pop.show(this, evt.getX(), evt.getY());
683 * do a single sequence copy to jalview and the system clipboard
686 * sequence to be copied to clipboard
688 protected void copy_annotseqtoclipboard(SequenceI sq)
690 SequenceI[] seqs = new SequenceI[]
692 String[] omitHidden = null;
693 SequenceI[] dseqs = new SequenceI[]
694 { sq.getDatasetSequence() };
695 if (dseqs[0] == null)
697 dseqs[0] = new Sequence(sq);
698 dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
699 jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
701 sq.setDatasetSequence(dseqs[0]);
703 Alignment ds = new Alignment(dseqs);
704 if (av.hasHiddenColumns)
706 omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
707 sq.getLength(), seqs);
710 String output = new FormatAdapter().formatSequences("Fasta", seqs,
713 Toolkit.getDefaultToolkit().getSystemClipboard()
714 .setContents(new StringSelection(output), Desktop.instance);
716 Vector hiddenColumns = null;
717 if (av.hasHiddenColumns)
719 hiddenColumns = new Vector();
720 for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
722 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
725 hiddenColumns.addElement(new int[]
726 { region[0], region[1] });
730 Desktop.jalviewClipboard = new Object[]
731 { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
732 // sequence as special.
742 public void paintComponent(Graphics g)
745 int width = getWidth();
748 width = ap.calculateIdWidth().width + 4;
751 Graphics2D g2 = (Graphics2D) g;
754 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
755 RenderingHints.VALUE_ANTIALIAS_ON);
758 drawComponent(g2, width);
768 public void drawComponent(Graphics g, int width)
770 if (av.getFont().getSize() < 10)
776 g.setFont(av.getFont());
779 FontMetrics fm = g.getFontMetrics(g.getFont());
780 g.setColor(Color.white);
781 g.fillRect(0, 0, getWidth(), getHeight());
783 g.translate(0, scrollOffset);
784 g.setColor(Color.black);
786 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
787 int fontHeight = g.getFont().getSize();
795 hasHiddenRows = false;
796 for (int i = 0; i < aa.length; i++)
798 g.setColor(Color.black);
802 hasHiddenRows = true;
808 offset = -aa[i].height / 2;
812 offset += fm.getHeight() / 2;
813 offset -= fm.getDescent();
816 offset += fm.getDescent();
818 x = width - fm.stringWidth(aa[i].label) - 3;
820 if (aa[i].graphGroup > -1)
823 for (int gg = 0; gg < aa.length; gg++)
825 if (aa[gg].graphGroup == aa[i].graphGroup)
831 if (groupSize * (fontHeight + 8) < aa[i].height)
833 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
836 for (int gg = 0; gg < aa.length; gg++)
838 if (aa[gg].graphGroup == aa[i].graphGroup)
840 x = width - fm.stringWidth(aa[gg].label) - 3;
841 g.drawString(aa[gg].label, x, y - graphExtras);
842 if (aa[gg].annotations[0] != null)
844 g.setColor(aa[gg].annotations[0].colour);
847 g.drawLine(x, y - graphExtras - 3,
848 x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
850 g.setColor(Color.black);
851 graphExtras += fontHeight + 8;
857 g.drawString(aa[i].label, x, y + offset);
864 g.drawImage(image, 2, 0 - scrollOffset, this);
866 else if (dragEvent != null && aa != null)
868 g.setColor(Color.lightGray);
869 g.drawString(aa[selectedRow].label, dragEvent.getX(),
870 dragEvent.getY() - scrollOffset);
873 if ((aa == null) || (aa.length < 1))
875 g.drawString("Right click", 2, 8);
876 g.drawString("to add annotation", 2, 18);