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.
23 import java.awt.Color;
24 import java.awt.Cursor;
25 import java.awt.Dimension;
27 import java.awt.FontMetrics;
28 import java.awt.Graphics;
29 import java.awt.Graphics2D;
30 import java.awt.RenderingHints;
31 import java.awt.Toolkit;
32 import java.awt.datatransfer.StringSelection;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.ActionListener;
35 import java.awt.event.MouseEvent;
36 import java.awt.event.MouseListener;
37 import java.awt.event.MouseMotionListener;
38 import java.awt.geom.AffineTransform;
39 import java.util.Arrays;
40 import java.util.Collections;
41 import java.util.Iterator;
42 import java.util.Locale;
44 import javax.swing.JCheckBoxMenuItem;
45 import javax.swing.JMenuItem;
46 import javax.swing.JPanel;
47 import javax.swing.JPopupMenu;
48 import javax.swing.SwingUtilities;
49 import javax.swing.ToolTipManager;
51 import jalview.analysis.AlignSeq;
52 import jalview.analysis.AlignmentUtils;
53 import jalview.datamodel.Alignment;
54 import jalview.datamodel.AlignmentAnnotation;
55 import jalview.datamodel.Annotation;
56 import jalview.datamodel.ContactMatrixI;
57 import jalview.datamodel.GroupSet;
58 import jalview.datamodel.HiddenColumns;
59 import jalview.datamodel.Sequence;
60 import jalview.datamodel.SequenceGroup;
61 import jalview.datamodel.SequenceI;
62 import jalview.io.FileFormat;
63 import jalview.io.FormatAdapter;
64 import jalview.util.Comparison;
65 import jalview.util.MessageManager;
66 import jalview.util.Platform;
69 * The panel that holds the labels for alignment annotations, providing
70 * tooltips, context menus, drag to reorder rows, and drag to adjust panel
73 public class AnnotationLabels extends JPanel
74 implements MouseListener, MouseMotionListener, ActionListener
76 private static final String HTML_END_TAG = "</html>";
78 private static final String HTML_START_TAG = "<html>";
81 * width in pixels within which height adjuster arrows are shown and active
83 private static final int HEIGHT_ADJUSTER_WIDTH = 50;
86 * height in pixels for allowing height adjuster to be active
88 private static int HEIGHT_ADJUSTER_HEIGHT = 10;
90 private static final Font font = new Font("Arial", Font.PLAIN, 11);
92 private static final String TOGGLE_LABELSCALE = MessageManager
93 .getString("label.scale_label_to_column");
95 private static final String ADDNEW = MessageManager
96 .getString("label.add_new_row");
98 private static final String EDITNAME = MessageManager
99 .getString("label.edit_label_description");
101 private static final String HIDE = MessageManager
102 .getString("label.hide_row");
104 private static final String DELETE = MessageManager
105 .getString("label.delete_row");
107 private static final String SHOWALL = MessageManager
108 .getString("label.show_all_hidden_rows");
110 private static final String OUTPUT_TEXT = MessageManager
111 .getString("label.export_annotation");
113 private static final String COPYCONS_SEQ = MessageManager
114 .getString("label.copy_consensus_sequence");
116 private final boolean debugRedraw = false;
118 private AlignmentPanel ap;
122 private MouseEvent dragEvent;
126 private int selectedRow;
128 private int scrollOffset = 0;
130 private boolean hasHiddenRows;
132 private boolean resizePanel = false;
135 * Creates a new AnnotationLabels object
139 public AnnotationLabels(AlignmentPanel ap)
144 ToolTipManager.sharedInstance().registerComponent(this);
146 addMouseListener(this);
147 addMouseMotionListener(this);
148 addMouseWheelListener(ap.getAnnotationPanel());
151 public AnnotationLabels(AlignViewport av)
162 public void setScrollOffset(int y)
169 * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
173 * coordinate position to search for a row
175 void getSelectedRow(int y)
178 AlignmentAnnotation[] aa = ap.av.getAlignment()
179 .getAlignmentAnnotation();
183 for (int i = 0; i < aa.length; i++)
191 height += aa[i].height;
210 public void actionPerformed(ActionEvent evt)
212 AlignmentAnnotation[] aa = ap.av.getAlignment()
213 .getAlignmentAnnotation();
215 String action = evt.getActionCommand();
216 if (ADDNEW.equals(action))
219 * non-returning dialog
221 AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
222 null, new Annotation[ap.av.getAlignment().getWidth()]);
223 editLabelDescription(newAnnotation, true);
225 else if (EDITNAME.equals(action))
228 * non-returning dialog
230 editLabelDescription(aa[selectedRow], false);
232 else if (HIDE.equals(action))
234 aa[selectedRow].visible = false;
236 else if (DELETE.equals(action))
238 ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
239 ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]);
241 else if (SHOWALL.equals(action))
243 for (int i = 0; i < aa.length; i++)
245 if (!aa[i].visible && aa[i].annotations != null)
247 aa[i].visible = true;
251 else if (OUTPUT_TEXT.equals(action))
253 new AnnotationExporter(ap).exportAnnotation(aa[selectedRow]);
255 else if (COPYCONS_SEQ.equals(action))
257 SequenceI cons = null;
258 if (aa[selectedRow].groupRef != null)
260 cons = aa[selectedRow].groupRef.getConsensusSeq();
264 cons = av.getConsensusSeq();
268 copy_annotseqtoclipboard(cons);
271 else if (TOGGLE_LABELSCALE.equals(action))
273 aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
280 * Shows a dialog where the annotation name and description may be edited. If
281 * parameter addNew is true, then on confirmation, a new AlignmentAnnotation
282 * is added, else an existing annotation is updated.
287 void editLabelDescription(AlignmentAnnotation annotation, boolean addNew)
289 String name = MessageManager.getString("label.annotation_name");
290 String description = MessageManager
291 .getString("label.annotation_description");
292 String title = MessageManager
293 .getString("label.edit_annotation_name_description");
294 EditNameDialog dialog = new EditNameDialog(annotation.label,
295 annotation.description, name, description);
297 dialog.showDialog(ap.alignFrame, title, () -> {
298 annotation.label = dialog.getName();
299 String text = dialog.getDescription();
300 if (text != null && text.length() == 0)
304 annotation.description = text;
307 ap.av.getAlignment().addAnnotation(annotation);
308 ap.av.getAlignment().setAnnotationIndex(annotation, 0);
315 public void mousePressed(MouseEvent evt)
317 getSelectedRow(evt.getY() - getScrollOffset());
319 if (evt.isPopupTrigger())
326 * Build and show the Pop-up menu at the right-click mouse position
330 void showPopupMenu(MouseEvent evt)
333 final AlignmentAnnotation[] aa = ap.av.getAlignment()
334 .getAlignmentAnnotation();
336 JPopupMenu pop = new JPopupMenu(
337 MessageManager.getString("label.annotations"));
338 JMenuItem item = new JMenuItem(ADDNEW);
339 item.addActionListener(this);
344 { // let the user make everything visible again
345 item = new JMenuItem(SHOWALL);
346 item.addActionListener(this);
349 pop.show(this, evt.getX(), evt.getY());
352 item = new JMenuItem(EDITNAME);
353 item.addActionListener(this);
355 item = new JMenuItem(HIDE);
356 item.addActionListener(this);
358 // JAL-1264 hide all sequence-specific annotations of this type
359 if (selectedRow < aa.length)
361 if (aa[selectedRow].sequenceRef != null)
363 final String label = aa[selectedRow].label;
364 JMenuItem hideType = new JMenuItem();
365 String text = MessageManager.getString("label.hide_all") + " "
367 hideType.setText(text);
368 hideType.addActionListener(new ActionListener()
371 public void actionPerformed(ActionEvent e)
373 AlignmentUtils.showOrHideSequenceAnnotations(
374 ap.av.getAlignment(), Collections.singleton(label),
382 item = new JMenuItem(DELETE);
383 item.addActionListener(this);
387 item = new JMenuItem(SHOWALL);
388 item.addActionListener(this);
391 item = new JMenuItem(OUTPUT_TEXT);
392 item.addActionListener(this);
394 // TODO: annotation object should be typed for autocalculated/derived
396 if (selectedRow < aa.length)
398 final String label = aa[selectedRow].label;
399 if (!aa[selectedRow].autoCalculated)
401 if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
403 // display formatting settings for this row.
405 // av and sequencegroup need to implement same interface for
406 item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
407 aa[selectedRow].scaleColLabel);
408 item.addActionListener(this);
412 else if (label.indexOf("Consensus") > -1)
414 addConsensusMenuOptions(ap, aa[selectedRow], pop);
416 final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
417 consclipbrd.addActionListener(this);
418 pop.add(consclipbrd);
421 addColourOrFilterByOptions(ap,aa[selectedRow],pop);
423 if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
425 addContactMatrixOptions(ap,aa[selectedRow],pop);
426 // Set/adjust threshold for grouping ?
427 // colour alignment by this [type]
428 // select/hide columns by this row
433 pop.show(this, evt.getX(), evt.getY());
436 static void addColourOrFilterByOptions(final AlignmentPanel ap,
437 final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
440 item = new JMenuItem(MessageManager.getString("label.colour_by_annotation"));
441 item.addActionListener(new ActionListener()
445 public void actionPerformed(ActionEvent e)
447 AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false);
451 if (alignmentAnnotation.sequenceRef!=null)
453 item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")");
454 item.addActionListener(new ActionListener()
457 public void actionPerformed(ActionEvent e)
459 AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,true);
464 item = new JMenuItem(MessageManager.getString("action.select_by_annotation"));
465 item.addActionListener(new ActionListener()
469 public void actionPerformed(ActionEvent e)
471 AnnotationColumnChooser.displayFor(ap.av,ap,alignmentAnnotation);
476 static void addContactMatrixOptions(final AlignmentPanel ap,
477 final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
480 final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation);
488 JCheckBoxMenuItem chitem = new JCheckBoxMenuItem(MessageManager.getString("action.show_groups_on_matrix"));
489 chitem.setToolTipText(MessageManager.getString("action.show_groups_on_matrix_tooltip"));
490 boolean showGroups = alignmentAnnotation.isShowGroupsForContactMatrix();
491 final AlignmentAnnotation sel_row=alignmentAnnotation;
492 chitem.setState(showGroups);
493 chitem.addActionListener(new ActionListener()
497 public void actionPerformed(ActionEvent e)
499 sel_row.setShowGroupsForContactMatrix(chitem.getState());
500 ap.getAnnotationPanel()
501 .paint(ap.getAnnotationPanel().getGraphics());
508 item = new JMenuItem(MessageManager.getString("action.show_tree_for_matrix"));
509 item.setToolTipText(MessageManager.getString("action.show_tree_for_matrix_tooltip"));
510 item.addActionListener(new ActionListener()
514 public void actionPerformed(ActionEvent e)
517 ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
525 item = new JMenuItem(MessageManager.getString("action.cluster_matrix"));
526 item.setToolTipText(MessageManager.getString("action.cluster_matrix_tooltip"));
527 item.addActionListener(new ActionListener()
530 public void actionPerformed(ActionEvent e)
532 new Thread(new Runnable()
538 ap.alignFrame.setProgressBar(MessageManager.formatMessage("action.clustering_matrix_for",cm.getAnnotDescr(),5f), progBar = System.currentTimeMillis());
539 cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
540 ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
541 ap.alignFrame.setProgressBar(null, progBar);
552 * A helper method that adds menu options for calculation and visualisation of
553 * group and/or alignment consensus annotation to a popup menu. This is
554 * designed to be reusable for either unwrapped mode (popup menu is shown on
555 * component AnnotationLabels), or wrapped mode (popup menu is shown on
556 * IdPanel when the mouse is over an annotation label).
562 static void addConsensusMenuOptions(AlignmentPanel ap,
563 AlignmentAnnotation ann, JPopupMenu pop)
567 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
568 MessageManager.getString("label.ignore_gaps_consensus"),
569 (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus()
570 : ap.av.isIgnoreGapsConsensus());
571 final AlignmentAnnotation aaa = ann;
572 cbmi.addActionListener(new ActionListener()
575 public void actionPerformed(ActionEvent e)
577 if (aaa.groupRef != null)
579 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
580 ap.getAnnotationPanel()
581 .paint(ap.getAnnotationPanel().getGraphics());
585 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
587 ap.alignmentChanged();
592 if (aaa.groupRef != null)
595 * group consensus options
597 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
598 MessageManager.getString("label.show_group_histogram"),
599 ann.groupRef.isShowConsensusHistogram());
600 chist.addActionListener(new ActionListener()
603 public void actionPerformed(ActionEvent e)
605 aaa.groupRef.setShowConsensusHistogram(chist.getState());
610 final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
611 MessageManager.getString("label.show_group_logo"),
612 ann.groupRef.isShowSequenceLogo());
613 cprofl.addActionListener(new ActionListener()
616 public void actionPerformed(ActionEvent e)
618 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
623 final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
624 MessageManager.getString("label.normalise_group_logo"),
625 ann.groupRef.isNormaliseSequenceLogo());
626 cproflnorm.addActionListener(new ActionListener()
629 public void actionPerformed(ActionEvent e)
631 aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
632 // automatically enable logo display if we're clicked
633 aaa.groupRef.setshowSequenceLogo(true);
642 * alignment consensus options
644 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
645 MessageManager.getString("label.show_histogram"),
646 ap.av.isShowConsensusHistogram());
647 chist.addActionListener(new ActionListener()
650 public void actionPerformed(ActionEvent e)
652 ap.av.setShowConsensusHistogram(chist.getState());
653 ap.alignFrame.setMenusForViewport();
658 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
659 MessageManager.getString("label.show_logo"),
660 ap.av.isShowSequenceLogo());
661 cprof.addActionListener(new ActionListener()
664 public void actionPerformed(ActionEvent e)
666 ap.av.setShowSequenceLogo(cprof.getState());
667 ap.alignFrame.setMenusForViewport();
672 final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
673 MessageManager.getString("label.normalise_logo"),
674 ap.av.isNormaliseSequenceLogo());
675 cprofnorm.addActionListener(new ActionListener()
678 public void actionPerformed(ActionEvent e)
680 ap.av.setShowSequenceLogo(true);
681 ap.av.setNormaliseSequenceLogo(cprofnorm.getState());
682 ap.alignFrame.setMenusForViewport();
691 * Reorders annotation rows after a drag of a label
696 public void mouseReleased(MouseEvent evt)
698 if (evt.isPopupTrigger())
704 int start = selectedRow;
705 getSelectedRow(evt.getY() - getScrollOffset());
706 int end = selectedRow;
709 * if dragging to resize instead, start == end
713 // Swap these annotations
714 AlignmentAnnotation startAA = ap.av.getAlignment()
715 .getAlignmentAnnotation()[start];
718 end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
720 AlignmentAnnotation endAA = ap.av.getAlignment()
721 .getAlignmentAnnotation()[end];
723 ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
724 ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
730 ap.getAnnotationPanel().repaint();
734 * Removes the height adjuster image on leaving the panel, unless currently
738 public void mouseExited(MouseEvent evt)
740 if (resizePanel && dragEvent == null)
748 * A mouse drag may be either an adjustment of the panel height (if flag
749 * resizePanel is set on), or a reordering of the annotation rows. The former
750 * is dealt with by this method, the latter in mouseReleased.
755 public void mouseDragged(MouseEvent evt)
761 Dimension d = ap.annotationScroller.getPreferredSize();
762 int dif = evt.getY() - oldY;
764 dif /= ap.av.getCharHeight();
765 dif *= ap.av.getCharHeight();
767 if ((d.height - dif) > 20)
769 ap.annotationScroller
770 .setPreferredSize(new Dimension(d.width, d.height - dif));
771 d = ap.annotationSpaceFillerHolder.getPreferredSize();
772 ap.annotationSpaceFillerHolder
773 .setPreferredSize(new Dimension(d.width, d.height - dif));
774 ap.paintAlignment(true, false);
786 * Updates the tooltip as the mouse moves over the labels
791 public void mouseMoved(MouseEvent evt)
793 showOrHideAdjuster(evt);
795 getSelectedRow(evt.getY() - getScrollOffset());
797 if (selectedRow > -1 && ap.av.getAlignment()
798 .getAlignmentAnnotation().length > selectedRow)
800 AlignmentAnnotation[] anns = ap.av.getAlignment()
801 .getAlignmentAnnotation();
802 AlignmentAnnotation aa = anns[selectedRow];
804 String desc = getTooltip(aa);
805 this.setToolTipText(desc);
806 String msg = getStatusMessage(aa, anns);
807 ap.alignFrame.setStatus(msg);
812 * Constructs suitable text to show in the status bar when over an annotation
813 * label, containing the associated sequence name (if any), and the annotation
814 * labels (or all labels for a graph group annotation)
820 static String getStatusMessage(AlignmentAnnotation aa,
821 AlignmentAnnotation[] anns)
828 StringBuilder msg = new StringBuilder(32);
829 if (aa.sequenceRef != null)
831 msg.append(aa.sequenceRef.getName()).append(" : ");
834 if (aa.graphGroup == -1)
836 msg.append(aa.label);
838 else if (anns != null)
840 boolean first = true;
841 for (int i = anns.length - 1; i >= 0; i--)
843 if (anns[i].graphGroup == aa.graphGroup)
849 msg.append(anns[i].label);
855 return msg.toString();
859 * Answers a tooltip, formatted as html, containing the annotation description
860 * (prefixed by associated sequence id if applicable), and the annotation
861 * (non-positional) score if it has one. Answers null if neither description
862 * nor score is found.
867 static String getTooltip(AlignmentAnnotation aa)
873 StringBuilder tooltip = new StringBuilder();
874 if (aa.description != null && !aa.description.equals("New description"))
876 // TODO: we could refactor and merge this code with the code in
877 // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
879 String desc = aa.getDescription(true).trim();
880 if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG))
882 tooltip.append(HTML_START_TAG);
883 desc = desc.replace("<", "<");
885 else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG))
887 desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
889 tooltip.append(desc);
893 // begin the tooltip's html fragment
894 tooltip.append(HTML_START_TAG);
898 if (tooltip.length() > HTML_START_TAG.length())
900 tooltip.append("<br/>");
902 // TODO: limit precision of score to avoid noise from imprecise
904 // (64.7 becomes 64.7+/some tiny value).
905 tooltip.append(" Score: ").append(String.valueOf(aa.score));
908 if (tooltip.length() > HTML_START_TAG.length())
910 return tooltip.append(HTML_END_TAG).toString();
914 * nothing in the tooltip (except "<html>")
920 * Shows the height adjuster image if the mouse moves into the top left
921 * region, or hides it if the mouse leaves the regio
925 protected void showOrHideAdjuster(MouseEvent evt)
927 boolean was = resizePanel;
928 resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
929 && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
931 if (resizePanel != was)
934 .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR
935 : Cursor.DEFAULT_CURSOR));
941 public void mouseClicked(MouseEvent evt)
943 final AlignmentAnnotation[] aa = ap.av.getAlignment()
944 .getAlignmentAnnotation();
945 if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt))
947 if (selectedRow > -1 && selectedRow < aa.length)
949 if (aa[selectedRow].groupRef != null)
951 if (evt.getClickCount() >= 2)
953 // todo: make the ap scroll to the selection - not necessary, first
954 // click highlights/scrolls, second selects
955 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
957 SequenceGroup sg = ap.av.getSelectionGroup();
958 if (sg == null || sg == aa[selectedRow].groupRef
959 || !(Platform.isControlDown(evt) || evt.isShiftDown()))
961 if (Platform.isControlDown(evt) || evt.isShiftDown())
963 // clone a new selection group from the associated group
964 ap.av.setSelectionGroup(
965 new SequenceGroup(aa[selectedRow].groupRef));
969 // set selection to the associated group so it can be edited
970 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
975 // modify current selection with associated group
976 int remainToAdd = aa[selectedRow].groupRef.getSize();
977 for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
979 if (jalview.util.Platform.isControlDown(evt))
981 sg.addOrRemove(sgs, --remainToAdd == 0);
985 // notionally, we should also add intermediate sequences from
986 // last added sequence ?
987 sg.addSequence(sgs, --remainToAdd == 0);
992 ap.paintAlignment(false, false);
993 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
994 ap.av.sendSelection();
998 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
999 aa[selectedRow].groupRef.getSequences(null));
1003 else if (aa[selectedRow].sequenceRef != null)
1005 if (evt.getClickCount() == 1)
1007 ap.getSeqPanel().ap.getIdPanel()
1008 .highlightSearchResults(Arrays.asList(new SequenceI[]
1009 { aa[selectedRow].sequenceRef }));
1011 else if (evt.getClickCount() >= 2)
1013 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
1014 SequenceGroup sg = ap.av.getSelectionGroup();
1017 // we make a copy rather than edit the current selection if no
1018 // modifiers pressed
1019 // see Enhancement JAL-1557
1020 if (!(Platform.isControlDown(evt) || evt.isShiftDown()))
1022 sg = new SequenceGroup(sg);
1024 sg.addSequence(aa[selectedRow].sequenceRef, false);
1028 if (Platform.isControlDown(evt))
1030 sg.addOrRemove(aa[selectedRow].sequenceRef, true);
1034 // notionally, we should also add intermediate sequences from
1035 // last added sequence ?
1036 sg.addSequence(aa[selectedRow].sequenceRef, true);
1042 sg = new SequenceGroup();
1044 sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
1045 sg.addSequence(aa[selectedRow].sequenceRef, false);
1047 ap.av.setSelectionGroup(sg);
1048 ap.paintAlignment(false, false);
1049 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
1050 ap.av.sendSelection();
1060 * do a single sequence copy to jalview and the system clipboard
1063 * sequence to be copied to clipboard
1065 protected void copy_annotseqtoclipboard(SequenceI sq)
1067 SequenceI[] seqs = new SequenceI[] { sq };
1068 String[] omitHidden = null;
1069 SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
1070 if (dseqs[0] == null)
1072 dseqs[0] = new Sequence(sq);
1073 dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars,
1074 sq.getSequenceAsString()));
1076 sq.setDatasetSequence(dseqs[0]);
1078 Alignment ds = new Alignment(dseqs);
1079 if (av.hasHiddenColumns())
1081 Iterator<int[]> it = av.getAlignment().getHiddenColumns()
1082 .getVisContigsIterator(0, sq.getLength(), false);
1083 omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
1086 int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
1087 if (av.hasHiddenColumns())
1089 alignmentStartEnd = av.getAlignment().getHiddenColumns()
1090 .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
1093 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1094 seqs, omitHidden, alignmentStartEnd);
1096 Toolkit.getDefaultToolkit().getSystemClipboard()
1097 .setContents(new StringSelection(output), Desktop.instance);
1099 HiddenColumns hiddenColumns = null;
1101 if (av.hasHiddenColumns())
1103 hiddenColumns = new HiddenColumns(
1104 av.getAlignment().getHiddenColumns());
1107 Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
1109 // sequence ? need to
1111 // sequence as special.
1122 public void paintComponent(Graphics g)
1125 int width = getWidth();
1128 width = ap.calculateIdWidth().width;
1131 Graphics2D g2 = (Graphics2D) g;
1134 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
1135 RenderingHints.VALUE_ANTIALIAS_ON);
1138 drawComponent(g2, true, width);
1143 * Draw the full set of annotation Labels for the alignment at the given
1147 * Graphics2D instance (needed for font scaling)
1149 * Width for scaling labels
1152 public void drawComponent(Graphics g, int width)
1154 drawComponent(g, false, width);
1158 * Draw the full set of annotation Labels for the alignment at the given
1162 * Graphics2D instance (needed for font scaling)
1164 * - true indicates that only current visible area needs to be
1167 * Width for scaling labels
1169 public void drawComponent(Graphics g, boolean clip, int width)
1171 if (av.getFont().getSize() < 10)
1177 g.setFont(av.getFont());
1180 FontMetrics fm = g.getFontMetrics(g.getFont());
1181 g.setColor(Color.white);
1182 g.fillRect(0, 0, getWidth(), getHeight());
1184 g.translate(0, getScrollOffset());
1185 g.setColor(Color.black);
1186 SequenceI lastSeqRef = null;
1187 String lastLabel = null;
1188 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
1189 int fontHeight = g.getFont().getSize();
1192 int graphExtras = 0;
1194 Font baseFont = g.getFont();
1195 FontMetrics baseMetrics = fm;
1196 int ofontH = fontHeight;
1199 int[] visr = (ap != null && ap.getAnnotationPanel() != null)
1200 ? ap.getAnnotationPanel().getVisibleVRange()
1202 if (clip && visr != null)
1205 visHeight = visr[1];
1207 boolean visible = true, before = false, after = false;
1210 hasHiddenRows = false;
1213 for (int i = 0; i < aa.length; i++)
1218 hasHiddenRows = true;
1222 // look ahead to next annotation
1223 for (nexAA = i + 1; nexAA < aa.length
1224 && !aa[nexAA].visible; nexAA++)
1235 System.out.println("before vis: " + i);
1239 // don't draw what isn't visible
1242 if (olY > visHeight)
1250 "Scroll offset: " + sOffset + " after vis: " + i);
1254 // don't draw what isn't visible
1258 g.setColor(Color.black);
1260 offset = -aa[i].height / 2;
1264 offset += fm.getHeight() / 2;
1265 offset -= fm.getDescent();
1269 offset += fm.getDescent();
1271 String label = aa[i].label;
1272 boolean vertBar = false;
1273 if ((lastLabel != null && lastLabel.equals(label)))
1275 label = aa[i].description;
1279 if (nexAA < aa.length && label.equals(aa[nexAA].label)) // &&
1280 // aa[nexY].sequenceRef==aa[i].sequenceRef)
1283 // next label is the same as this label
1284 label = aa[i].description;
1291 if (aa[i].sequenceRef != null)
1293 if (aa[i].sequenceRef != lastSeqRef)
1295 label = aa[i].sequenceRef.getName() + " " + label;
1296 // TODO record relationship between sequence and this annotation and
1304 x = width - fm.stringWidth(label) - 3;
1306 if (aa[i].graphGroup > -1)
1309 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1310 // computed efficiently for all visible labels
1311 for (int gg = 0; gg < aa.length; gg++)
1313 if (aa[gg].graphGroup == aa[i].graphGroup)
1318 if (groupSize * (fontHeight + 8) < aa[i].height)
1320 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
1325 // scale font to fit
1326 float h = aa[i].height / (float) groupSize, s;
1333 fontHeight = -8 + (int) h;
1334 s = ((float) fontHeight) / (float) ofontH;
1336 .deriveFont(AffineTransform.getScaleInstance(s, s));
1338 fm = g.getFontMetrics();
1339 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
1345 for (int gg = 0; gg < aa.length; gg++)
1347 if (aa[gg].graphGroup == aa[i].graphGroup)
1349 x = width - fm.stringWidth(aa[gg].label) - 3;
1350 g.drawString(aa[gg].label, x, y - graphExtras);
1352 if (aa[gg]._linecolour != null)
1355 g.setColor(aa[gg]._linecolour);
1356 g.drawLine(x, y - graphExtras + 3,
1357 x + fm.stringWidth(aa[gg].label),
1358 y - graphExtras + 3);
1361 g.setColor(Color.black);
1362 graphExtras += fontHeight + 8;
1366 g.setFont(baseFont);
1368 fontHeight = ofontH;
1374 g.drawLine(width - 3, y + offset - fontHeight, width - 3,
1375 (int) (y - 1.5 * aa[i].height - offset - fontHeight));
1376 // g.drawLine(20, y + offset, x - 20, y + offset);
1379 g.drawString(label, x, y + offset);
1381 lastSeqRef = aa[i].sequenceRef;
1385 if (!resizePanel && dragEvent != null && aa != null)
1387 g.setColor(Color.lightGray);
1389 (aa[selectedRow].sequenceRef == null ? ""
1390 : aa[selectedRow].sequenceRef.getName())
1391 + aa[selectedRow].label,
1392 dragEvent.getX(), dragEvent.getY() - getScrollOffset());
1395 if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
1397 g.drawString(MessageManager.getString("label.right_click"), 2, 8);
1398 g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
1403 public int getScrollOffset()
1405 return scrollOffset;
1409 public void mouseEntered(MouseEvent e)