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++)
196 if (!aa[i].visible && aa[i].annotations!=null)
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);
388 * @param evt DOCUMENT ME!
390 public void mouseClicked(MouseEvent evt)
392 if (!SwingUtilities.isRightMouseButton(evt))
397 AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
399 if ( (aa == null) || (aa.length == 0))
401 JPopupMenu pop = new JPopupMenu("Annotations");
402 JMenuItem item = new JMenuItem(ADDNEW);
403 item.addActionListener(this);
405 pop.show(this, evt.getX(), evt.getY());
410 JPopupMenu pop = new JPopupMenu("Annotations");
411 JMenuItem item = new JMenuItem(ADDNEW);
412 item.addActionListener(this);
414 item = new JMenuItem(EDITNAME);
415 item.addActionListener(this);
417 item = new JMenuItem(HIDE);
418 item.addActionListener(this);
420 item = new JMenuItem(DELETE);
421 item.addActionListener(this);
423 item = new JMenuItem(SHOWALL);
424 item.addActionListener(this);
426 item = new JMenuItem(OUTPUT_TEXT);
427 item.addActionListener(this);
429 // annotation object should be typed
430 if (aa[selectedRow] == ap.av.consensus)
433 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
434 "Ignore Gaps In Consensus",
435 ap.av.getIgnoreGapsConsensus());
436 cbmi.addActionListener(new ActionListener()
438 public void actionPerformed(ActionEvent e)
440 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
444 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
445 consclipbrd.addActionListener(this);
446 pop.add(consclipbrd);
449 pop.show(this, evt.getX(), evt.getY());
453 * do a single sequence copy to jalview and the system clipboard
455 * @param sq sequence to be copied to clipboard
457 protected void copy_annotseqtoclipboard(SequenceI sq)
459 SequenceI[] seqs = new SequenceI[]
462 String[] omitHidden = null;
463 SequenceI[] dseqs = new SequenceI[]
465 sq.getDatasetSequence()};
466 if (dseqs[0] == null)
468 dseqs[0] = new Sequence(sq);
469 dseqs[0].setSequence(
470 jalview.analysis.AlignSeq.extractGaps(
471 jalview.util.Comparison.GapChars,
472 sq.getSequenceAsString()));
474 sq.setDatasetSequence(dseqs[0]);
476 Alignment ds = new Alignment(dseqs);
477 if (av.hasHiddenColumns)
479 omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
480 sq.getLength(), seqs);
483 String output = new FormatAdapter().formatSequences(
488 Toolkit.getDefaultToolkit().getSystemClipboard()
489 .setContents(new StringSelection(output), Desktop.instance);
491 Vector hiddenColumns = null;
492 if (av.hasHiddenColumns)
494 hiddenColumns = new Vector();
495 for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
497 int[] region = (int[])
498 av.getColumnSelection().getHiddenColumns().elementAt(i);
500 hiddenColumns.addElement(new int[]
506 Desktop.jalviewClipboard = new Object[]
509 ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
516 * @param g1 DOCUMENT ME!
518 public void paintComponent(Graphics g)
521 int width = getWidth();
524 width = ap.calculateIdWidth().width + 4;
527 Graphics2D g2 = (Graphics2D) g;
530 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
531 RenderingHints.VALUE_ANTIALIAS_ON);
534 drawComponent(g2, width);
541 * @param g DOCUMENT ME!
543 public void drawComponent(Graphics g, int width)
545 if (av.getFont().getSize() < 10)
551 g.setFont(av.getFont());
554 FontMetrics fm = g.getFontMetrics(g.getFont());
555 g.setColor(Color.white);
556 g.fillRect(0, 0, getWidth(), getHeight());
558 g.translate(0, scrollOffset);
559 g.setColor(Color.black);
561 AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
562 int fontHeight = g.getFont().getSize();
570 for (int i = 0; i < aa.length; i++)
572 g.setColor(Color.black);
582 offset = -aa[i].height/2;
586 offset += fm.getHeight()/2;
587 offset -= fm.getDescent();
590 offset += fm.getDescent();
592 x = width - fm.stringWidth(aa[i].label) - 3;
594 if (aa[i].graphGroup > -1)
597 for (int gg = 0; gg < aa.length; gg++)
599 if (aa[gg].graphGroup == aa[i].graphGroup)
605 if (groupSize * (fontHeight + 8) < aa[i].height)
607 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
610 for (int gg = 0; gg < aa.length; gg++)
612 if (aa[gg].graphGroup == aa[i].graphGroup)
614 x = width - fm.stringWidth(aa[gg].label) - 3;
615 g.drawString(aa[gg].label, x,y - graphExtras);
616 if (aa[gg].annotations[0] != null)
618 g.setColor(aa[gg].annotations[0].colour);
621 g.drawLine(x, y - graphExtras - 3,
622 x + fm.stringWidth(aa[gg].label),
623 y - graphExtras - 3);
625 g.setColor(Color.black);
626 graphExtras += fontHeight + 8;
632 g.drawString(aa[i].label, x, y +offset);
639 g.drawImage(image, 2, 0 - scrollOffset, this);
641 else if (dragEvent != null && aa != null)
643 g.setColor(Color.lightGray);
644 g.drawString(aa[selectedRow].label, dragEvent.getX(),
645 dragEvent.getY() - scrollOffset);
648 if ( (aa == null) || (aa.length < 1))
650 g.drawString("Right click", 2, 8);
651 g.drawString("to add annotation", 2, 18);