2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 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
39 extends JPanel implements MouseListener,
40 MouseMotionListener, ActionListener
42 static String ADDNEW = "Add New Row";
43 static String EDITNAME = "Edit Label/Description";
44 static String HIDE = "Hide This Row";
45 static String DELETE = "Delete This Row";
46 static String SHOWALL = "Show All Hidden Rows";
47 static String OUTPUT_TEXT = "Export Annotation";
48 static String COPYCONS_SEQ = "Copy Consensus Sequence";
49 boolean resizePanel = false;
53 boolean resizing = false;
58 Font font = new Font("Arial", Font.PLAIN, 11);
61 * Creates a new AnnotationLabels object.
63 * @param ap DOCUMENT ME!
65 public AnnotationLabels(AlignmentPanel ap)
69 ToolTipManager.sharedInstance().registerComponent(this);
71 java.net.URL url = getClass().getResource("/images/idwidth.gif");
76 temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
81 MediaTracker mt = new MediaTracker(this);
89 BufferedImage bi = new BufferedImage(temp.getHeight(this),
91 BufferedImage.TYPE_INT_RGB);
92 Graphics2D g = (Graphics2D) bi.getGraphics();
93 g.rotate(Math.toRadians(90));
94 g.drawImage(temp, 0, -bi.getWidth(this), this);
97 addMouseListener(this);
98 addMouseMotionListener(this);
101 public AnnotationLabels(AlignViewport av)
109 * @param y DOCUMENT ME!
111 public void setScrollOffset(int y)
117 void getSelectedRow(int y)
120 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
124 for (int i = 0; i < aa.length; i++)
131 height += aa[i].height;
146 * @param evt DOCUMENT ME!
148 public void actionPerformed(ActionEvent evt)
151 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
153 if (evt.getActionCommand().equals(ADDNEW))
155 AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
157 new Annotation[ap.av.alignment.getWidth()]);
159 if (!editLabelDescription(newAnnotation))
164 ap.av.alignment.addAnnotation(newAnnotation);
165 ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
168 dif = aa[aa.length - 1].height;
171 else if (evt.getActionCommand().equals(EDITNAME))
173 editLabelDescription(aa[selectedRow]);
176 else if (evt.getActionCommand().equals(HIDE))
178 aa[selectedRow].visible = false;
180 if (aa[selectedRow].label.equals("Quality"))
182 ap.av.quality = null;
185 dif = aa[selectedRow].height * -1;
187 else if (evt.getActionCommand().equals(DELETE))
189 ap.av.alignment.deleteAnnotation(aa[selectedRow]);
190 dif = aa[selectedRow].height * -1;
192 else if (evt.getActionCommand().equals(SHOWALL))
194 for (int i = 0; i < aa.length; i++)
199 aa[i].visible = true;
203 else if (evt.getActionCommand().equals(OUTPUT_TEXT))
205 new AnnotationExporter().exportAnnotations(
207 new AlignmentAnnotation[]
212 else if (evt.getActionCommand().equals(COPYCONS_SEQ))
214 SequenceI cons = av.getConsensusSeq();
217 copy_annotseqtoclipboard(cons);
222 ap.annotationPanel.adjustPanelHeight();
223 ap.annotationScroller.validate();
224 ap.paintAlignment(true);
230 * @param e DOCUMENT ME!
232 boolean editLabelDescription(AlignmentAnnotation annotation)
234 EditNameDialog dialog = new EditNameDialog(annotation.label,
235 annotation.description,
237 "Annotation Description ",
238 "Edit Annotation Name/Description");
245 annotation.label = dialog.getName();
247 String text = dialog.getDescription();
248 if (text!=null && text.length() == 0)
252 annotation.description = text;
260 * @param evt DOCUMENT ME!
262 public void mousePressed(MouseEvent evt)
264 getSelectedRow(evt.getY() - scrollOffset);
271 * @param evt DOCUMENT ME!
273 public void mouseReleased(MouseEvent evt)
275 int start = selectedRow;
276 getSelectedRow(evt.getY() - scrollOffset);
277 int end = selectedRow;
281 //Swap these annotations
282 AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[
284 AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
286 ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
287 ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
293 ap.annotationPanel.repaint();
299 * @param evt DOCUMENT ME!
301 public void mouseEntered(MouseEvent evt)
313 * @param evt DOCUMENT ME!
315 public void mouseExited(MouseEvent evt)
317 if (dragEvent == null)
327 * @param evt DOCUMENT ME!
329 public void mouseDragged(MouseEvent evt)
335 Dimension d = ap.annotationScroller.getPreferredSize();
336 int dif = evt.getY() - oldY;
338 dif /= ap.av.charHeight;
339 dif *= ap.av.charHeight;
341 if ( (d.height - dif) > 20)
343 ap.annotationScroller.setPreferredSize(new Dimension(d.width,
345 d = ap.annotationSpaceFillerHolder.getPreferredSize();
346 ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
347 d.width, d.height - dif));
348 ap.paintAlignment(true);
362 * @param evt DOCUMENT ME!
364 public void mouseMoved(MouseEvent evt)
366 resizePanel = evt.getY() < 10;
368 getSelectedRow(evt.getY() - scrollOffset);
371 && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
373 String desc = ap.av.alignment.
374 getAlignmentAnnotation()[selectedRow].description;
376 if (desc != null && !desc.equals("New description"))
378 setToolTipText(ap.av.alignment.
379 getAlignmentAnnotation()[selectedRow].description);
389 * @param evt DOCUMENT ME!
391 public void mouseClicked(MouseEvent evt)
393 if (!SwingUtilities.isRightMouseButton(evt))
398 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
400 if ( (aa == null) || (aa.length == 0))
402 JPopupMenu pop = new JPopupMenu("Annotations");
403 JMenuItem item = new JMenuItem(ADDNEW);
404 item.addActionListener(this);
406 pop.show(this, evt.getX(), evt.getY());
411 JPopupMenu pop = new JPopupMenu("Annotations");
412 JMenuItem item = new JMenuItem(ADDNEW);
413 item.addActionListener(this);
415 item = new JMenuItem(EDITNAME);
416 item.addActionListener(this);
418 item = new JMenuItem(HIDE);
419 item.addActionListener(this);
421 item = new JMenuItem(DELETE);
422 item.addActionListener(this);
424 item = new JMenuItem(SHOWALL);
425 item.addActionListener(this);
427 item = new JMenuItem(OUTPUT_TEXT);
428 item.addActionListener(this);
430 // annotation object should be typed
431 if (aa[selectedRow] == ap.av.consensus)
434 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
435 "Ignore Gaps In Consensus",
436 ap.av.getIgnoreGapsConsensus());
437 cbmi.addActionListener(new ActionListener()
439 public void actionPerformed(ActionEvent e)
441 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
445 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
446 consclipbrd.addActionListener(this);
447 pop.add(consclipbrd);
450 pop.show(this, evt.getX(), evt.getY());
454 * do a single sequence copy to jalview and the system clipboard
456 * @param sq sequence to be copied to clipboard
458 protected void copy_annotseqtoclipboard(SequenceI sq)
460 SequenceI[] seqs = new SequenceI[]
463 String[] omitHidden = null;
464 SequenceI[] dseqs = new SequenceI[]
466 sq.getDatasetSequence()};
467 if (dseqs[0] == null)
469 dseqs[0] = new Sequence(sq);
470 dseqs[0].setSequence(
471 jalview.analysis.AlignSeq.extractGaps(
472 jalview.util.Comparison.GapChars,
473 sq.getSequenceAsString()));
475 sq.setDatasetSequence(dseqs[0]);
477 Alignment ds = new Alignment(dseqs);
478 if (av.hasHiddenColumns)
480 omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
481 sq.getLength(), seqs);
484 String output = new FormatAdapter().formatSequences(
489 Toolkit.getDefaultToolkit().getSystemClipboard()
490 .setContents(new StringSelection(output), Desktop.instance);
492 Vector hiddenColumns = null;
493 if (av.hasHiddenColumns)
495 hiddenColumns = new Vector();
496 for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
498 int[] region = (int[])
499 av.getColumnSelection().getHiddenColumns().elementAt(i);
501 hiddenColumns.addElement(new int[]
507 Desktop.jalviewClipboard = new Object[]
510 ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
517 * @param g1 DOCUMENT ME!
519 public void paintComponent(Graphics g)
522 int width = getWidth();
525 width = ap.calculateIdWidth().width + 4;
528 Graphics2D g2 = (Graphics2D) g;
531 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
532 RenderingHints.VALUE_ANTIALIAS_ON);
535 drawComponent(g2, width);
542 * @param g DOCUMENT ME!
544 public void drawComponent(Graphics g, int width)
546 if (av.getFont().getSize() < 10)
552 g.setFont(av.getFont());
555 FontMetrics fm = g.getFontMetrics(g.getFont());
556 g.setColor(Color.white);
557 g.fillRect(0, 0, getWidth(), getHeight());
559 g.translate(0, scrollOffset);
560 g.setColor(Color.black);
562 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
563 int fontHeight = g.getFont().getSize();
570 for (int i = 0; i < aa.length; i++)
577 x = width - fm.stringWidth(aa[i].label) - 3;
579 if (aa[i].graph > 0 && aa[i].graphHeight > 0)
583 y += (aa[i].height / 3);
585 if (aa[i].graphGroup < 0)
587 graphExtras = y + fontHeight;
591 if (aa[i].graphGroup > -1)
594 for (int gg = 0; gg < aa.length; gg++)
596 if (aa[gg].graphGroup == aa[i].graphGroup)
602 if (groupSize * (fontHeight + 8) < aa[i].height)
604 graphExtras += (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
607 for (int gg = 0; gg < aa.length; gg++)
609 if (aa[gg].graphGroup == aa[i].graphGroup)
611 x = width - fm.stringWidth(aa[gg].label) - 3;
612 g.drawString(aa[gg].label, x, graphExtras);
613 if (aa[gg].annotations[0] != null)
615 g.setColor(aa[gg].annotations[0].colour);
618 g.drawLine(x, graphExtras + 3,
619 x + fm.stringWidth(aa[gg].label),
622 g.setColor(Color.black);
623 graphExtras += fontHeight + 8;
629 g.drawString(aa[i].label, x, y);
634 /* if (aa[i].graphLines != null)
636 for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
638 x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
639 g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
640 g.setColor(aa[i].getGraphLine(gl).colour);
641 Graphics2D g2 = (Graphics2D) g;
642 g2.setStroke(new BasicStroke(1,
643 BasicStroke.CAP_SQUARE,
644 BasicStroke.JOIN_ROUND, 3f,
650 g.drawLine(x, graphExtras,
651 x+fm.stringWidth(aa[i].label),
653 g2.setStroke(new BasicStroke());
656 y += ( (2 * aa[i].height) / 3);
667 g.drawImage(image, 2, 0 - scrollOffset, this);
669 else if (dragEvent != null && aa != null)
671 g.setColor(Color.lightGray);
672 g.drawString(aa[selectedRow].label, dragEvent.getX(),
673 dragEvent.getY() - scrollOffset);
676 if ( (aa == null) || (aa.length < 1))
678 g.drawString("Right click", 2, 8);
679 g.drawString("to add annotation", 2, 18);