2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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);
78 * Creates a new AnnotationLabels object.
83 public AnnotationLabels(AlignmentPanel ap)
87 ToolTipManager.sharedInstance().registerComponent(this);
89 java.net.URL url = getClass().getResource("/images/idwidth.gif");
94 temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
99 MediaTracker mt = new MediaTracker(this);
100 mt.addImage(temp, 0);
102 } catch (Exception ex)
106 BufferedImage bi = new BufferedImage(temp.getHeight(this), temp
107 .getWidth(this), BufferedImage.TYPE_INT_RGB);
108 Graphics2D g = (Graphics2D) bi.getGraphics();
109 g.rotate(Math.toRadians(90));
110 g.drawImage(temp, 0, -bi.getWidth(this), this);
113 addMouseListener(this);
114 addMouseMotionListener(this);
117 public AnnotationLabels(AlignViewport av)
128 public void setScrollOffset(int y)
134 void getSelectedRow(int y)
137 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
141 for (int i = 0; i < aa.length; i++)
148 height += aa[i].height;
166 public void actionPerformed(ActionEvent evt)
168 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
170 if (evt.getActionCommand().equals(ADDNEW))
172 AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
173 null, new Annotation[ap.av.alignment.getWidth()]);
175 if (!editLabelDescription(newAnnotation))
180 ap.av.alignment.addAnnotation(newAnnotation);
181 ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
183 else if (evt.getActionCommand().equals(EDITNAME))
185 editLabelDescription(aa[selectedRow]);
188 else if (evt.getActionCommand().equals(HIDE))
190 aa[selectedRow].visible = false;
192 if (aa[selectedRow].label.equals("Quality"))
194 ap.av.quality = null;
197 else if (evt.getActionCommand().equals(DELETE))
199 ap.av.alignment.deleteAnnotation(aa[selectedRow]);
201 else if (evt.getActionCommand().equals(SHOWALL))
203 for (int i = 0; i < aa.length; i++)
205 if (!aa[i].visible && aa[i].annotations != null)
207 aa[i].visible = true;
211 else if (evt.getActionCommand().equals(OUTPUT_TEXT))
213 new AnnotationExporter().exportAnnotations(ap,
214 new AlignmentAnnotation[]
215 { aa[selectedRow] }, null, null);
217 else if (evt.getActionCommand().equals(COPYCONS_SEQ))
219 SequenceI cons = null;
220 if (aa[selectedRow].groupRef!=null)
222 cons = aa[selectedRow].groupRef.getConsensusSeq();
224 cons = av.getConsensusSeq();
228 copy_annotseqtoclipboard(cons);
232 else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
234 aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
237 ap.annotationPanel.adjustPanelHeight();
238 ap.annotationScroller.validate();
239 ap.paintAlignment(true);
248 boolean editLabelDescription(AlignmentAnnotation annotation)
250 EditNameDialog dialog = new EditNameDialog(annotation.label,
251 annotation.description, " Annotation Name ",
252 "Annotation Description ", "Edit Annotation Name/Description");
259 annotation.label = dialog.getName();
261 String text = dialog.getDescription();
262 if (text != null && text.length() == 0)
266 annotation.description = text;
277 public void mousePressed(MouseEvent evt)
279 getSelectedRow(evt.getY() - scrollOffset);
289 public void mouseReleased(MouseEvent evt)
291 int start = selectedRow;
292 getSelectedRow(evt.getY() - scrollOffset);
293 int end = selectedRow;
297 // Swap these annotations
298 AlignmentAnnotation startAA = ap.av.alignment
299 .getAlignmentAnnotation()[start];
300 AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
302 ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
303 ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
309 ap.annotationPanel.repaint();
318 public void mouseEntered(MouseEvent evt)
333 public void mouseExited(MouseEvent evt)
335 if (dragEvent == null)
348 public void mouseDragged(MouseEvent evt)
354 Dimension d = ap.annotationScroller.getPreferredSize();
355 int dif = evt.getY() - oldY;
357 dif /= ap.av.charHeight;
358 dif *= ap.av.charHeight;
360 if ((d.height - dif) > 20)
362 ap.annotationScroller.setPreferredSize(new Dimension(d.width,
364 d = ap.annotationSpaceFillerHolder.getPreferredSize();
365 ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
366 d.width, d.height - dif));
367 ap.paintAlignment(true);
384 public void mouseMoved(MouseEvent evt)
386 resizePanel = evt.getY() < 10;
388 getSelectedRow(evt.getY() - scrollOffset);
391 && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
393 AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
395 StringBuffer desc = new StringBuffer("<html>");
397 if (aa.description != null
398 && !aa.description.equals("New description"))
400 desc.append(aa.getDescription(true));
406 desc.append("Score: " + aa.score);
409 if (desc.length() != 6)
411 desc.append("</html>");
412 this.setToolTipText(desc.toString());
415 this.setToolTipText(null);
426 public void mouseClicked(MouseEvent evt)
428 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
429 if (SwingUtilities.isLeftMouseButton(evt))
431 if (selectedRow < aa.length)
433 if (aa[selectedRow].groupRef!=null)
435 ap.seqPanel.ap.idPanel.highlightSearchResults(aa[selectedRow].groupRef.getSequences(null));
436 if (evt.getClickCount()>=2)
438 // todo: make the ap scroll to the selection
439 ap.av.setSelectionGroup(new SequenceGroup(aa[selectedRow].groupRef));
440 ap.paintAlignment(false);
444 if (aa[selectedRow].sequenceRef!=null){
445 Vector sr = new Vector();
446 sr.addElement(aa[selectedRow].sequenceRef);
447 if (evt.getClickCount()==1)
449 ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
451 if (evt.getClickCount()>=2)
453 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
454 SequenceGroup sg = new SequenceGroup();
455 sg.addSequence(aa[selectedRow].sequenceRef,false);
456 ap.av.setSelectionGroup(sg);
457 ap.paintAlignment(false);
458 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
464 if (!SwingUtilities.isRightMouseButton(evt))
470 JPopupMenu pop = new JPopupMenu("Annotations");
471 JMenuItem item = new JMenuItem(ADDNEW);
472 item.addActionListener(this);
474 if ((aa == null) || (aa.length == 0))
476 item = new JMenuItem(SHOWALL);
477 item.addActionListener(this);
479 pop.show(this, evt.getX(), evt.getY());
484 item = new JMenuItem(EDITNAME);
485 item.addActionListener(this);
487 item = new JMenuItem(HIDE);
488 item.addActionListener(this);
490 item = new JMenuItem(DELETE);
491 item.addActionListener(this);
493 item = new JMenuItem(SHOWALL);
494 item.addActionListener(this);
496 item = new JMenuItem(OUTPUT_TEXT);
497 item.addActionListener(this);
499 // TODO: annotation object should be typed for autocalculated/derived property methods
500 if (selectedRow < aa.length)
502 if (!aa[selectedRow].autoCalculated) {
503 if (aa[selectedRow].graph==AlignmentAnnotation.NO_GRAPH)
505 // display formatting settings for this row.
507 // av and sequencegroup need to implement same interface for
508 item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
509 aa[selectedRow].scaleColLabel);
510 item.addActionListener(this);
514 else if (aa[selectedRow].label.indexOf("Consensus") > -1)
517 // av and sequencegroup need to implement same interface for
518 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
519 "Ignore Gaps In Consensus",
520 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
521 .getIgnoreGapsConsensus()
522 : ap.av.getIgnoreGapsConsensus());
523 final AlignmentAnnotation aaa = aa[selectedRow];
524 cbmi.addActionListener(new ActionListener()
526 public void actionPerformed(ActionEvent e)
528 if (aaa.groupRef != null)
530 // TODO: pass on reference to ap so the view can be updated.
531 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
532 ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
536 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
541 // av and sequencegroup need to implement same interface for
542 if (aaa.groupRef != null)
544 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
545 "Show Full Profile", aa[selectedRow].groupRef
546 .isIncludeAllConsSymbols());
547 cprof.addActionListener(new ActionListener()
549 public void actionPerformed(ActionEvent e)
551 // TODO: pass on reference
557 aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
559 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
564 /* final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
565 "Show Full Profile", aa[selectedRow].groupRef
566 .isIncludeAllConsSymbols());
567 cprof.addActionListener(new ActionListener()
569 public void actionPerformed(ActionEvent e)
571 // TODO: pass on reference
577 aaa.groupRef.setIncludeAllConsSymbols(cprof.getState());
579 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
584 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
585 consclipbrd.addActionListener(this);
586 pop.add(consclipbrd);
589 pop.show(this, evt.getX(), evt.getY());
593 * do a single sequence copy to jalview and the system clipboard
596 * sequence to be copied to clipboard
598 protected void copy_annotseqtoclipboard(SequenceI sq)
600 SequenceI[] seqs = new SequenceI[]
602 String[] omitHidden = null;
603 SequenceI[] dseqs = new SequenceI[]
604 { sq.getDatasetSequence() };
605 if (dseqs[0] == null)
607 dseqs[0] = new Sequence(sq);
608 dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
609 jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
611 sq.setDatasetSequence(dseqs[0]);
613 Alignment ds = new Alignment(dseqs);
614 if (av.hasHiddenColumns)
616 omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
617 sq.getLength(), seqs);
620 String output = new FormatAdapter().formatSequences("Fasta", seqs,
623 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
624 new StringSelection(output), Desktop.instance);
626 Vector hiddenColumns = null;
627 if (av.hasHiddenColumns)
629 hiddenColumns = new Vector();
630 for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
632 int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
635 hiddenColumns.addElement(new int[]
636 { region[0], region[1] });
640 Desktop.jalviewClipboard = new Object[]
641 { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
642 // sequence as special.
652 public void paintComponent(Graphics g)
655 int width = getWidth();
658 width = ap.calculateIdWidth().width + 4;
661 Graphics2D g2 = (Graphics2D) g;
664 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
665 RenderingHints.VALUE_ANTIALIAS_ON);
668 drawComponent(g2, width);
678 public void drawComponent(Graphics g, int width)
680 if (av.getFont().getSize() < 10)
686 g.setFont(av.getFont());
689 FontMetrics fm = g.getFontMetrics(g.getFont());
690 g.setColor(Color.white);
691 g.fillRect(0, 0, getWidth(), getHeight());
693 g.translate(0, scrollOffset);
694 g.setColor(Color.black);
696 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
697 int fontHeight = g.getFont().getSize();
705 for (int i = 0; i < aa.length; i++)
707 g.setColor(Color.black);
716 offset = -aa[i].height / 2;
720 offset += fm.getHeight() / 2;
721 offset -= fm.getDescent();
724 offset += fm.getDescent();
726 x = width - fm.stringWidth(aa[i].label) - 3;
728 if (aa[i].graphGroup > -1)
731 for (int gg = 0; gg < aa.length; gg++)
733 if (aa[gg].graphGroup == aa[i].graphGroup)
739 if (groupSize * (fontHeight + 8) < aa[i].height)
741 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
744 for (int gg = 0; gg < aa.length; gg++)
746 if (aa[gg].graphGroup == aa[i].graphGroup)
748 x = width - fm.stringWidth(aa[gg].label) - 3;
749 g.drawString(aa[gg].label, x, y - graphExtras);
750 if (aa[gg].annotations[0] != null)
752 g.setColor(aa[gg].annotations[0].colour);
755 g.drawLine(x, y - graphExtras - 3, x
756 + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
758 g.setColor(Color.black);
759 graphExtras += fontHeight + 8;
765 g.drawString(aa[i].label, x, y + offset);
772 g.drawImage(image, 2, 0 - scrollOffset, this);
774 else if (dragEvent != null && aa != null)
776 g.setColor(Color.lightGray);
777 g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent
782 if ((aa == null) || (aa.length < 1))
784 g.drawString("Right click", 2, 8);
785 g.drawString("to add annotation", 2, 18);