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.Cursor;
35 import java.awt.Dimension;
36 import java.awt.FlowLayout;
37 import java.awt.FontMetrics;
38 import java.awt.Frame;
39 import java.awt.Graphics;
40 import java.awt.Image;
41 import java.awt.MenuItem;
42 import java.awt.Panel;
43 import java.awt.PopupMenu;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.event.InputEvent;
47 import java.awt.event.ItemEvent;
48 import java.awt.event.ItemListener;
49 import java.awt.event.MouseEvent;
50 import java.awt.event.MouseListener;
51 import java.awt.event.MouseMotionListener;
52 import java.util.Arrays;
53 import java.util.Collections;
54 import java.util.Vector;
56 public class AnnotationLabels extends Panel
57 implements ActionListener, MouseListener, MouseMotionListener
62 * width in pixels within which height adjuster arrows are shown and active
64 private static final int HEIGHT_ADJUSTER_WIDTH = 50;
67 * height in pixels for allowing height adjuster to be active
69 private static int HEIGHT_ADJUSTER_HEIGHT = 10;
71 boolean active = false;
77 boolean resizing = false;
81 static String ADDNEW = "Add New Row";
83 static String EDITNAME = "Edit Label/Description";
85 static String HIDE = "Hide This Row";
87 static String SHOWALL = "Show All Hidden Rows";
89 static String OUTPUT_TEXT = "Show Values In Textbox";
91 static String COPYCONS_SEQ = "Copy Consensus Sequence";
99 private boolean hasHiddenRows;
101 public AnnotationLabels(AlignmentPanel ap)
106 addMouseListener(this);
107 addMouseMotionListener(this);
110 public AnnotationLabels(AlignViewport av)
115 public void setScrollOffset(int y, boolean repaint)
127 * @return -2 if no rows are visible at all, -1 if no visible rows were
130 int getSelectedRow(int y)
133 AlignmentAnnotation[] aa = ap.av.getAlignment()
134 .getAlignmentAnnotation();
141 for (int i = 0; i < aa.length; i++)
148 height += aa[i].height;
160 public void actionPerformed(ActionEvent evt)
162 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
164 if (evt.getActionCommand().equals(ADDNEW))
166 AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
167 new Annotation[ap.av.getAlignment().getWidth()]);
169 if (!editLabelDescription(newAnnotation))
174 ap.av.getAlignment().addAnnotation(newAnnotation);
175 ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
177 else if (evt.getActionCommand().equals(EDITNAME))
179 editLabelDescription(aa[selectedRow]);
181 else if (evt.getActionCommand().equals(HIDE))
183 aa[selectedRow].visible = false;
185 else if (evt.getActionCommand().equals(SHOWALL))
187 for (int i = 0; i < aa.length; i++)
189 aa[i].visible = (aa[i].annotations == null) ? false : true;
192 else if (evt.getActionCommand().equals(OUTPUT_TEXT))
194 CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
196 Frame frame = new Frame();
198 jalview.bin.JalviewLite.addFrame(frame,
199 ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
201 cap.setText(aa[selectedRow].toString());
203 else if (evt.getActionCommand().equals(COPYCONS_SEQ))
205 SequenceI cons = av.getConsensusSeq();
208 copy_annotseqtoclipboard(cons);
216 * Adjust size and repaint
218 protected void refresh()
220 ap.annotationPanel.adjustPanelHeight();
221 setSize(getSize().width, ap.annotationPanel.getSize().height);
223 // TODO: only paint if we needed to
224 ap.paintAlignment(true, true);
227 boolean editLabelDescription(AlignmentAnnotation annotation)
229 Checkbox padGaps = new Checkbox(
230 "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
233 EditNameDialog dialog = new EditNameDialog(annotation.label,
234 annotation.description, " Annotation Label",
235 "Annotation Description", ap.alignFrame,
236 "Edit Annotation Name / Description", 500, 180, false);
238 Panel empty = new Panel(new FlowLayout());
243 dialog.setVisible(true);
247 annotation.label = dialog.getName();
248 annotation.description = dialog.getDescription();
249 annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
260 boolean resizePanel = false;
263 public void mouseMoved(MouseEvent evt)
265 resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
266 && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
267 setCursor(Cursor.getPredefinedCursor(
268 resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
269 int row = getSelectedRow(evt.getY() + scrollOffset);
273 ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
274 av.getAlignment().getAlignmentAnnotation()[row]
275 .getDescription(true),
279 tooltip = new Tooltip(phb.getNonHtmlContent(), this);
283 tooltip.setTip(phb.getNonHtmlContent());
286 else if (tooltip != null)
293 * curent drag position
295 MouseEvent dragEvent = null;
298 * flag to indicate drag events should be ignored
300 private boolean dragCancelled = false;
303 * clear any drag events in progress
305 public void cancelDrag()
308 dragCancelled = true;
312 public void mouseDragged(MouseEvent evt)
323 Dimension d = ap.annotationPanelHolder.getSize(),
324 e = ap.annotationSpaceFillerHolder.getSize(),
325 f = ap.seqPanelHolder.getSize();
326 int dif = evt.getY() - oldY;
328 dif /= ap.av.getCharHeight();
329 dif *= ap.av.getCharHeight();
331 if ((d.height - dif) > 20 && (f.height + dif) > 20)
333 ap.annotationPanel.setSize(d.width, d.height - dif);
334 setSize(new Dimension(e.width, d.height - dif));
335 ap.annotationSpaceFillerHolder
336 .setSize(new Dimension(e.width, d.height - dif));
337 ap.annotationPanelHolder
338 .setSize(new Dimension(d.width, d.height - dif));
339 ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
340 av.calcPanelHeight());
342 ap.seqPanelHolder.setPreferredSize(f);
343 ap.setScrollValues(av.getRanges().getStartRes(),
344 av.getRanges().getStartSeq());
346 // ap.paintAlignment(true);
354 if ((diff = 6 - evt.getY()) > 0)
357 ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
358 ap.adjustmentValueChanged(null);
361 else if ((0 < (diff = 6
362 - ap.annotationSpaceFillerHolder.getSize().height
366 ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
367 ap.adjustmentValueChanged(null);
374 public void mouseClicked(MouseEvent evt)
379 public void mouseReleased(MouseEvent evt)
381 if (!resizePanel && !dragCancelled)
383 int start = selectedRow;
385 int end = getSelectedRow(evt.getY() + scrollOffset);
387 if (start > -1 && start != end)
389 // Swap these annotations
390 AlignmentAnnotation startAA = ap.av.getAlignment()
391 .getAlignmentAnnotation()[start];
394 end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
396 AlignmentAnnotation endAA = ap.av.getAlignment()
397 .getAlignmentAnnotation()[end];
399 ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
400 ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
405 dragCancelled = false;
406 setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
408 ap.annotationPanel.repaint();
412 public void mouseEntered(MouseEvent evt)
414 if (evt.getY() < 10 && evt.getX() < 14)
419 setCursor(Cursor.getPredefinedCursor(
420 resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
424 public void mouseExited(MouseEvent evt)
426 dragCancelled = false;
428 if (dragEvent == null)
443 public void mousePressed(MouseEvent evt)
450 dragCancelled = false;
451 // todo: move below to mouseClicked ?
452 selectedRow = getSelectedRow(evt.getY() + scrollOffset);
454 AlignmentAnnotation[] aa = ap.av.getAlignment()
455 .getAlignmentAnnotation();
457 // DETECT RIGHT MOUSE BUTTON IN AWT
458 if ((evt.getModifiers()
459 & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
462 PopupMenu popup = new PopupMenu(
463 MessageManager.getString("label.annotations"));
465 MenuItem item = new MenuItem(ADDNEW);
466 item.addActionListener(this);
470 // this never happens at moment: - see comment on JAL-563
473 item = new MenuItem(SHOWALL);
474 item.addActionListener(this);
478 popup.show(this, evt.getX(), evt.getY());
481 // add the rest if there are actually rows to show
482 item = new MenuItem(EDITNAME);
483 item.addActionListener(this);
485 item = new MenuItem(HIDE);
486 item.addActionListener(this);
492 if (selectedRow < aa.length)
494 if (aa[selectedRow].sequenceRef != null)
496 final String label = aa[selectedRow].label;
497 MenuItem hideType = new MenuItem(
498 MessageManager.getString("label.hide_all") + " " + label);
499 hideType.addActionListener(new ActionListener()
502 public void actionPerformed(ActionEvent e)
504 AlignmentUtils.showOrHideSequenceAnnotations(
505 ap.av.getAlignment(), Collections.singleton(label),
516 item = new MenuItem(SHOWALL);
517 item.addActionListener(this);
521 item = new MenuItem(OUTPUT_TEXT);
522 item.addActionListener(this);
524 if (selectedRow < aa.length)
526 if (aa[selectedRow].autoCalculated)
528 if (aa[selectedRow].label.indexOf("Consensus") > -1)
530 popup.addSeparator();
531 final CheckboxMenuItem cbmi = new CheckboxMenuItem(
532 MessageManager.getString("label.ignore_gaps_consensus"),
533 (aa[selectedRow].groupRef != null)
534 ? aa[selectedRow].groupRef
535 .getIgnoreGapsConsensus()
536 : ap.av.isIgnoreGapsConsensus());
537 final AlignmentAnnotation aaa = aa[selectedRow];
538 cbmi.addItemListener(new ItemListener()
541 public void itemStateChanged(ItemEvent e)
543 if (aaa.groupRef != null)
545 // TODO: pass on reference to ap so the view can be updated.
546 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
550 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
552 ap.paintAlignment(true, true);
556 if (aaa.groupRef != null)
558 final CheckboxMenuItem chist = new CheckboxMenuItem(
560 .getString("label.show_group_histogram"),
561 aa[selectedRow].groupRef.isShowConsensusHistogram());
562 chist.addItemListener(new ItemListener()
565 public void itemStateChanged(ItemEvent e)
567 // TODO: pass on reference
573 aaa.groupRef.setShowConsensusHistogram(chist.getState());
575 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
579 final CheckboxMenuItem cprofl = new CheckboxMenuItem(
580 MessageManager.getString("label.show_group_logo"),
581 aa[selectedRow].groupRef.isShowSequenceLogo());
582 cprofl.addItemListener(new ItemListener()
585 public void itemStateChanged(ItemEvent e)
587 // TODO: pass on reference
593 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
595 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
600 final CheckboxMenuItem cprofn = new CheckboxMenuItem(
602 .getString("label.normalise_group_logo"),
603 aa[selectedRow].groupRef.isNormaliseSequenceLogo());
604 cprofn.addItemListener(new ItemListener()
607 public void itemStateChanged(ItemEvent e)
609 // TODO: pass on reference
615 aaa.groupRef.setshowSequenceLogo(true);
616 aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
618 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
625 final CheckboxMenuItem chist = new CheckboxMenuItem(
626 MessageManager.getString("label.show_histogram"),
627 av.isShowConsensusHistogram());
628 chist.addItemListener(new ItemListener()
631 public void itemStateChanged(ItemEvent e)
633 // TODO: pass on reference
639 av.setShowConsensusHistogram(chist.getState());
640 ap.alignFrame.showConsensusHistogram
641 .setState(chist.getState()); // TODO: implement
642 // ap.updateGUI()/alignFrame.updateGUI
645 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
649 final CheckboxMenuItem cprof = new CheckboxMenuItem(
650 MessageManager.getString("label.show_logo"),
651 av.isShowSequenceLogo());
652 cprof.addItemListener(new ItemListener()
655 public void itemStateChanged(ItemEvent e)
657 // TODO: pass on reference
663 av.setShowSequenceLogo(cprof.getState());
664 ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
666 // ap.updateGUI()/alignFrame.updateGUI
670 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
674 final CheckboxMenuItem cprofn = new CheckboxMenuItem(
675 MessageManager.getString("label.normalise_logo"),
676 av.isNormaliseSequenceLogo());
677 cprofn.addItemListener(new ItemListener()
680 public void itemStateChanged(ItemEvent e)
682 // TODO: pass on reference
688 av.setShowSequenceLogo(true);
689 ap.alignFrame.normSequenceLogo
690 .setState(cprofn.getState()); // TODO:
692 // ap.updateGUI()/alignFrame.updateGUI
695 av.setNormaliseSequenceLogo(cprofn.getState());
697 // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
703 item = new MenuItem(COPYCONS_SEQ);
704 item.addActionListener(this);
709 popup.show(this, evt.getX(), evt.getY());
714 if (selectedRow > -1 && selectedRow < aa.length)
716 if (aa[selectedRow].groupRef != null)
718 if (evt.getClickCount() >= 2)
720 // todo: make the ap scroll to the selection - not necessary, first
721 // click highlights/scrolls, second selects
722 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
724 SequenceGroup sg = ap.av.getSelectionGroup();
725 if (sg == null || sg == aa[selectedRow].groupRef
726 || !(jalview.util.Platform.isControlDown(evt)
727 || evt.isShiftDown()))
729 if (jalview.util.Platform.isControlDown(evt)
730 || evt.isShiftDown())
732 // clone a new selection group from the associated group
733 ap.av.setSelectionGroup(
734 new SequenceGroup(aa[selectedRow].groupRef));
738 // set selection to the associated group so it can be edited
739 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
744 // modify current selection with associated group
745 int remainToAdd = aa[selectedRow].groupRef.getSize();
746 for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
748 if (jalview.util.Platform.isControlDown(evt))
750 sg.addOrRemove(sgs, --remainToAdd == 0);
754 // notionally, we should also add intermediate sequences from
755 // last added sequence ?
756 sg.addSequence(sgs, --remainToAdd == 0);
760 ap.paintAlignment(false, false);
761 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
762 ap.av.sendSelection();
766 ap.seqPanel.ap.idPanel.highlightSearchResults(
767 aa[selectedRow].groupRef.getSequences(null));
771 else if (aa[selectedRow].sequenceRef != null)
773 if (evt.getClickCount() == 1)
775 ap.seqPanel.ap.idPanel
776 .highlightSearchResults(Arrays.asList(new SequenceI[]
777 { aa[selectedRow].sequenceRef }));
779 else if (evt.getClickCount() >= 2)
781 ap.seqPanel.ap.idPanel.highlightSearchResults(null);
782 SequenceGroup sg = ap.av.getSelectionGroup();
785 // we make a copy rather than edit the current selection if no
787 // see Enhancement JAL-1557
788 if (!(jalview.util.Platform.isControlDown(evt)
789 || evt.isShiftDown()))
791 sg = new SequenceGroup(sg);
793 sg.addSequence(aa[selectedRow].sequenceRef, false);
797 if (jalview.util.Platform.isControlDown(evt))
799 sg.addOrRemove(aa[selectedRow].sequenceRef, true);
803 // notionally, we should also add intermediate sequences from
804 // last added sequence ?
805 sg.addSequence(aa[selectedRow].sequenceRef, true);
811 sg = new SequenceGroup();
813 sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
814 sg.addSequence(aa[selectedRow].sequenceRef, false);
816 ap.av.setSelectionGroup(sg);
817 ap.paintAlignment(false, false);
818 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
819 ap.av.sendSelection();
834 protected void copy_annotseqtoclipboard(SequenceI sq)
836 if (sq == null || sq.getLength() < 1)
840 jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
841 jalview.appletgui.AlignFrame.copiedSequences
842 .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
843 + "\t" + sq.getSequenceAsString() + "\n");
844 if (av.hasHiddenColumns())
846 jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
847 av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
852 public void update(Graphics g)
858 public void paint(Graphics g)
860 int w = getSize().width;
861 int h = getSize().height;
862 if (image == null || w != image.getWidth(this)
863 || h != image.getHeight(this))
865 image = createImage(w, ap.annotationPanel.getSize().height);
868 drawComponent(image.getGraphics(), w);
869 g.drawImage(image, 0, 0, this);
872 public void drawComponent(Graphics g, int width)
874 g.setFont(av.getFont());
875 FontMetrics fm = g.getFontMetrics(av.getFont());
876 g.setColor(Color.white);
877 g.fillRect(0, 0, getSize().width, getSize().height);
879 g.translate(0, -scrollOffset);
880 g.setColor(Color.black);
882 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
883 int y = 0, fy = g.getFont().getSize();
888 hasHiddenRows = false;
889 for (int i = 0; i < aa.length; i++)
893 hasHiddenRows = true;
897 x = width - fm.stringWidth(aa[i].label) - 3;
900 offset = -(aa[i].height - fy) / 2;
902 g.drawString(aa[i].label, x, y + offset);
905 g.translate(0, +scrollOffset);
907 if (!resizePanel && !dragCancelled && dragEvent != null && aa != null)
909 g.setColor(Color.lightGray);
910 g.drawString(aa[selectedRow].label, dragEvent.getX(),
914 if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
916 g.setColor(Color.black);
917 g.drawString(MessageManager.getString("label.right_click"), 2, 8);
918 g.drawString(MessageManager.getString("label.to_add_annotation"), 2,