2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentUtils;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.Annotation;
26 import jalview.datamodel.SequenceGroup;
27 import jalview.datamodel.SequenceI;
28 import jalview.util.MessageManager;
29 import jalview.util.ParseHtmlBodyAndLinks;
31 import java.awt.Checkbox;
32 import java.awt.CheckboxMenuItem;
33 import java.awt.Color;
34 import java.awt.Dimension;
35 import java.awt.FlowLayout;
36 import java.awt.FontMetrics;
37 import java.awt.Frame;
38 import java.awt.Graphics;
39 import java.awt.Image;
40 import java.awt.MenuItem;
41 import java.awt.Panel;
42 import java.awt.PopupMenu;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.InputEvent;
46 import java.awt.event.ItemEvent;
47 import java.awt.event.ItemListener;
48 import java.awt.event.MouseEvent;
49 import java.awt.event.MouseListener;
50 import java.awt.event.MouseMotionListener;
51 import java.util.Arrays;
52 import java.util.Collections;
53 import java.util.Vector;
55 public class AnnotationLabels extends Panel
56 implements ActionListener, MouseListener, MouseMotionListener
60 boolean active = false;
66 boolean resizing = false;
70 static String ADDNEW = "Add New Row";
72 static String EDITNAME = "Edit Label/Description";
74 static String HIDE = "Hide This Row";
76 static String SHOWALL = "Show All Hidden Rows";
78 static String OUTPUT_TEXT = "Show Values In Textbox";
80 static String COPYCONS_SEQ = "Copy Consensus Sequence";
88 private boolean hasHiddenRows;
90 public AnnotationLabels(AlignmentPanel ap)
97 * this retrieves the adjustable height glyph from resources. we don't use
98 * it at the moment. java.net.URL url =
99 * getClass().getResource("/images/idwidth.gif"); Image temp = null;
101 * if (url != null) { temp =
102 * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
104 * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
105 * mt.waitForID(0); } catch (Exception ex) { }
107 * BufferedImage bi = new BufferedImage(temp.getHeight(this),
108 * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
109 * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
110 * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
112 addMouseListener(this);
113 addMouseMotionListener(this);
116 public AnnotationLabels(AlignViewport av)
121 public void setScrollOffset(int y, boolean repaint)
133 * @return -2 if no rows are visible at all, -1 if no visible rows were
136 int getSelectedRow(int y)
139 AlignmentAnnotation[] aa = ap.av.getAlignment()
140 .getAlignmentAnnotation();
147 for (int i = 0; i < aa.length; i++)
154 height += aa[i].height;
166 public void actionPerformed(ActionEvent evt)
168 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
170 if (evt.getActionCommand().equals(ADDNEW))
172 AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
173 new Annotation[ap.av.getAlignment().getWidth()]);
175 if (!editLabelDescription(newAnnotation))
180 ap.av.getAlignment().addAnnotation(newAnnotation);
181 ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
183 else if (evt.getActionCommand().equals(EDITNAME))
185 editLabelDescription(aa[selectedRow]);
187 else if (evt.getActionCommand().equals(HIDE))
189 aa[selectedRow].visible = false;
191 else if (evt.getActionCommand().equals(SHOWALL))
193 for (int i = 0; i < aa.length; i++)
195 aa[i].visible = (aa[i].annotations == null) ? false : true;
198 else if (evt.getActionCommand().equals(OUTPUT_TEXT))
200 CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
202 Frame frame = new Frame();
204 jalview.bin.JalviewLite.addFrame(frame,
205 ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
207 cap.setText(aa[selectedRow].toString());
209 else if (evt.getActionCommand().equals(COPYCONS_SEQ))
211 SequenceI cons = av.getConsensusSeq();
214 copy_annotseqtoclipboard(cons);
222 * Adjust size and repaint
224 protected void refresh()
226 ap.annotationPanel.adjustPanelHeight();
227 setSize(getSize().width, ap.annotationPanel.getSize().height);
229 ap.paintAlignment(true);
232 boolean editLabelDescription(AlignmentAnnotation annotation)
234 Checkbox padGaps = new Checkbox(
235 "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
238 EditNameDialog dialog = new EditNameDialog(annotation.label,
239 annotation.description, " Annotation Label",
240 "Annotation Description", ap.alignFrame,
241 "Edit Annotation Name / Description", 500, 180, false);
243 Panel empty = new Panel(new FlowLayout());
248 dialog.setVisible(true);
252 annotation.label = dialog.getName();
253 annotation.description = dialog.getDescription();
254 annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
265 boolean resizePanel = false;
268 public void mouseMoved(MouseEvent evt)
270 resizePanel = evt.getY() < 10 && evt.getX() < 14;
271 int row = getSelectedRow(evt.getY() + scrollOffset);
275 ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
276 av.getAlignment().getAlignmentAnnotation()[row]
277 .getDescription(true),
281 tooltip = new Tooltip(phb.getNonHtmlContent(), this);
285 tooltip.setTip(phb.getNonHtmlContent());
288 else if (tooltip != null)
295 * curent drag position
297 MouseEvent dragEvent = null;
300 * flag to indicate drag events should be ignored
302 private boolean dragCancelled = false;
305 * clear any drag events in progress
307 public void cancelDrag()
310 dragCancelled = true;
314 public void mouseDragged(MouseEvent evt)
325 Dimension d = ap.annotationPanelHolder.getSize(),
326 e = ap.annotationSpaceFillerHolder.getSize(),
327 f = ap.seqPanelHolder.getSize();
328 int dif = evt.getY() - oldY;
330 dif /= ap.av.getCharHeight();
331 dif *= ap.av.getCharHeight();
333 if ((d.height - dif) > 20 && (f.height + dif) > 20)
335 ap.annotationPanel.setSize(d.width, d.height - dif);
336 setSize(new Dimension(e.width, d.height - dif));
337 ap.annotationSpaceFillerHolder
338 .setSize(new Dimension(e.width, d.height - dif));
339 ap.annotationPanelHolder
340 .setSize(new Dimension(d.width, d.height - dif));
341 ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
342 av.calcPanelHeight());
344 ap.seqPanelHolder.setPreferredSize(f);
345 ap.setScrollValues(av.getRanges().getStartRes(),
346 av.getRanges().getStartSeq());
348 // ap.paintAlignment(true);
356 if ((diff = 6 - evt.getY()) > 0)
359 ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
360 ap.adjustmentValueChanged(null);
363 else if ((0 < (diff = 6
364 - ap.annotationSpaceFillerHolder.getSize().height
368 ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
369 ap.adjustmentValueChanged(null);
376 public void mouseClicked(MouseEvent evt)
381 public void mouseReleased(MouseEvent evt)
383 if (!resizePanel && !dragCancelled)
385 int start = selectedRow;
387 int end = getSelectedRow(evt.getY() + scrollOffset);
389 if (start > -1 && start != end)
391 // Swap these annotations
392 AlignmentAnnotation startAA = ap.av.getAlignment()
393 .getAlignmentAnnotation()[start];
396 end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
398 AlignmentAnnotation endAA = ap.av.getAlignment()
399 .getAlignmentAnnotation()[end];
401 ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
402 ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
407 dragCancelled = false;
409 ap.annotationPanel.repaint();
413 public void mouseEntered(MouseEvent evt)
415 if (evt.getY() < 10 && evt.getX() < 14)
423 public void mouseExited(MouseEvent evt)
425 dragCancelled = false;
427 if (dragEvent == null)
442 public void mousePressed(MouseEvent evt)
449 dragCancelled = false;
450 // todo: move below to mouseClicked ?
451 selectedRow = getSelectedRow(evt.getY() + scrollOffset);
453 AlignmentAnnotation[] aa = ap.av.getAlignment()
454 .getAlignmentAnnotation();
456 // DETECT RIGHT MOUSE BUTTON IN AWT
457 if ((evt.getModifiers()
458 & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
461 PopupMenu popup = new PopupMenu(
462 MessageManager.getString("label.annotations"));
464 MenuItem item = new MenuItem(ADDNEW);
465 item.addActionListener(this);
469 // this never happens at moment: - see comment on JAL-563
472 item = new MenuItem(SHOWALL);
473 item.addActionListener(this);
477 popup.show(this, evt.getX(), evt.getY());
480 // add the rest if there are actually rows to show
481 item = new MenuItem(EDITNAME);
482 item.addActionListener(this);
484 item = new MenuItem(HIDE);
485 item.addActionListener(this);
491 if (selectedRow < aa.length)
493 if (aa[selectedRow].sequenceRef != null)
495 final String label = aa[selectedRow].label;
496 MenuItem hideType = new MenuItem(
497 MessageManager.getString("label.hide_all") + " " + label);
498 hideType.addActionListener(new ActionListener()
501 public void actionPerformed(ActionEvent e)
503 AlignmentUtils.showOrHideSequenceAnnotations(
504 ap.av.getAlignment(), Collections.singleton(label),
515 item = new MenuItem(SHOWALL);
516 item.addActionListener(this);
520 item = new MenuItem(OUTPUT_TEXT);
521 item.addActionListener(this);
523 if (selectedRow < aa.length)
525 if (aa[selectedRow].autoCalculated)
527 if (aa[selectedRow].label.indexOf("Consensus") > -1)
529 popup.addSeparator();
530 final CheckboxMenuItem cbmi = new CheckboxMenuItem(
531 MessageManager.getString("label.ignore_gaps_consensus"),
532 (aa[selectedRow].groupRef != null)
533 ? aa[selectedRow].groupRef
534 .getIgnoreGapsConsensus()
535 : ap.av.isIgnoreGapsConsensus());
536 final AlignmentAnnotation aaa = aa[selectedRow];
537 cbmi.addItemListener(new ItemListener()
540 public void itemStateChanged(ItemEvent e)
542 if (aaa.groupRef != null)
544 // TODO: pass on reference to ap so the view can be updated.
545 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
549 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
551 ap.paintAlignment(true);
555 if (aaa.groupRef != null)
557 final CheckboxMenuItem chist = new CheckboxMenuItem(
559 .getString("label.show_group_histogram"),
560 aa[selectedRow].groupRef.isShowConsensusHistogram());
561 chist.addItemListener(new ItemListener()
564 public void itemStateChanged(ItemEvent e)
566 // TODO: pass on reference
572 aaa.groupRef.setShowConsensusHistogram(chist.getState());
574 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
578 final CheckboxMenuItem cprofl = new CheckboxMenuItem(
579 MessageManager.getString("label.show_group_logo"),
580 aa[selectedRow].groupRef.isShowSequenceLogo());
581 cprofl.addItemListener(new ItemListener()
584 public void itemStateChanged(ItemEvent e)
586 // TODO: pass on reference
592 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
594 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
599 final CheckboxMenuItem cprofn = new CheckboxMenuItem(
601 .getString("label.normalise_group_logo"),
602 aa[selectedRow].groupRef.isNormaliseSequenceLogo());
603 cprofn.addItemListener(new ItemListener()
606 public void itemStateChanged(ItemEvent e)
608 // TODO: pass on reference
614 aaa.groupRef.setshowSequenceLogo(true);
615 aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
617 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
624 final CheckboxMenuItem chist = new CheckboxMenuItem(
625 MessageManager.getString("label.show_histogram"),
626 av.isShowConsensusHistogram());
627 chist.addItemListener(new ItemListener()
630 public void itemStateChanged(ItemEvent e)
632 // TODO: pass on reference
638 av.setShowConsensusHistogram(chist.getState());
639 ap.alignFrame.showConsensusHistogram
640 .setState(chist.getState()); // TODO: implement
641 // ap.updateGUI()/alignFrame.updateGUI
644 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
648 final CheckboxMenuItem cprof = new CheckboxMenuItem(
649 MessageManager.getString("label.show_logo"),
650 av.isShowSequenceLogo());
651 cprof.addItemListener(new ItemListener()
654 public void itemStateChanged(ItemEvent e)
656 // TODO: pass on reference
662 av.setShowSequenceLogo(cprof.getState());
663 ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
665 // ap.updateGUI()/alignFrame.updateGUI
669 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
673 final CheckboxMenuItem cprofn = new CheckboxMenuItem(
674 MessageManager.getString("label.normalise_logo"),
675 av.isNormaliseSequenceLogo());
676 cprofn.addItemListener(new ItemListener()
679 public void itemStateChanged(ItemEvent e)
681 // TODO: pass on reference
687 av.setShowSequenceLogo(true);
688 ap.alignFrame.normSequenceLogo
689 .setState(cprofn.getState()); // TODO:
691 // ap.updateGUI()/alignFrame.updateGUI
694 av.setNormaliseSequenceLogo(cprofn.getState());
696 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
702 item = new MenuItem(COPYCONS_SEQ);
703 item.addActionListener(this);
708 popup.show(this, evt.getX(), evt.getY());
713 if (selectedRow > -1 && selectedRow < aa.length)
715 if (aa[selectedRow].groupRef != null)
717 if (evt.getClickCount() >= 2)
719 // todo: make the ap scroll to the selection - not necessary, first
720 // click highlights/scrolls, second selects
721 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
723 SequenceGroup sg = ap.av.getSelectionGroup();
724 if (sg == null || sg == aa[selectedRow].groupRef
725 || !(jalview.util.Platform.isControlDown(evt)
726 || evt.isShiftDown()))
728 if (jalview.util.Platform.isControlDown(evt)
729 || evt.isShiftDown())
731 // clone a new selection group from the associated group
732 ap.av.setSelectionGroup(
733 new SequenceGroup(aa[selectedRow].groupRef));
737 // set selection to the associated group so it can be edited
738 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
743 // modify current selection with associated group
744 int remainToAdd = aa[selectedRow].groupRef.getSize();
745 for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
747 if (jalview.util.Platform.isControlDown(evt))
749 sg.addOrRemove(sgs, --remainToAdd == 0);
753 // notionally, we should also add intermediate sequences from
754 // last added sequence ?
755 sg.addSequence(sgs, --remainToAdd == 0);
759 ap.paintAlignment(false);
760 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
761 ap.av.sendSelection();
765 ap.seqPanel.ap.idPanel.highlightSearchResults(
766 aa[selectedRow].groupRef.getSequences(null));
770 else if (aa[selectedRow].sequenceRef != null)
772 if (evt.getClickCount() == 1)
774 ap.seqPanel.ap.idPanel
775 .highlightSearchResults(Arrays.asList(new SequenceI[]
776 { aa[selectedRow].sequenceRef }));
778 else if (evt.getClickCount() >= 2)
780 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
781 SequenceGroup sg = ap.av.getSelectionGroup();
784 // we make a copy rather than edit the current selection if no
786 // see Enhancement JAL-1557
787 if (!(jalview.util.Platform.isControlDown(evt)
788 || evt.isShiftDown()))
790 sg = new SequenceGroup(sg);
792 sg.addSequence(aa[selectedRow].sequenceRef, false);
796 if (jalview.util.Platform.isControlDown(evt))
798 sg.addOrRemove(aa[selectedRow].sequenceRef, true);
802 // notionally, we should also add intermediate sequences from
803 // last added sequence ?
804 sg.addSequence(aa[selectedRow].sequenceRef, true);
810 sg = new SequenceGroup();
812 sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
813 sg.addSequence(aa[selectedRow].sequenceRef, false);
815 ap.av.setSelectionGroup(sg);
816 ap.paintAlignment(false);
817 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
818 ap.av.sendSelection();
833 protected void copy_annotseqtoclipboard(SequenceI sq)
835 if (sq == null || sq.getLength() < 1)
839 jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
840 jalview.appletgui.AlignFrame.copiedSequences
841 .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
842 + "\t" + sq.getSequenceAsString() + "\n");
843 if (av.hasHiddenColumns())
845 jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
846 av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
851 public void update(Graphics g)
857 public void paint(Graphics g)
859 int w = getSize().width;
860 int h = getSize().height;
861 if (image == null || w != image.getWidth(this)
862 || h != image.getHeight(this))
864 image = createImage(w, ap.annotationPanel.getSize().height);
867 drawComponent(image.getGraphics(), w);
868 g.drawImage(image, 0, 0, this);
871 public void drawComponent(Graphics g, int width)
873 g.setFont(av.getFont());
874 FontMetrics fm = g.getFontMetrics(av.getFont());
875 g.setColor(Color.white);
876 g.fillRect(0, 0, getSize().width, getSize().height);
878 g.translate(0, -scrollOffset);
879 g.setColor(Color.black);
881 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
882 int y = 0, fy = g.getFont().getSize();
887 hasHiddenRows = false;
888 for (int i = 0; i < aa.length; i++)
892 hasHiddenRows = true;
896 x = width - fm.stringWidth(aa[i].label) - 3;
899 offset = -(aa[i].height - fy) / 2;
901 g.drawString(aa[i].label, x, y + offset);
904 g.translate(0, +scrollOffset);
907 g.setColor(Color.red);
909 g.drawLine(2, 8, 5, 2);
910 g.drawLine(5, 2, 8, 8);
912 else if (!dragCancelled && dragEvent != null && aa != null)
914 g.setColor(Color.lightGray);
915 g.drawString(aa[selectedRow].label, dragEvent.getX(),
919 if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
921 g.setColor(Color.black);
922 g.drawString(MessageManager.getString("label.right_click"), 2, 8);
923 g.drawString(MessageManager.getString("label.to_add_annotation"), 2,