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 // so any annotation colour changes are propagated - though they
501 // probably won't be unless the annotation row colours are removed
503 ap.alignmentChanged();
510 item = new JMenuItem(MessageManager.getString("action.show_tree_for_matrix"));
511 item.setToolTipText(MessageManager.getString("action.show_tree_for_matrix_tooltip"));
512 item.addActionListener(new ActionListener()
516 public void actionPerformed(ActionEvent e)
519 ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
527 item = new JMenuItem(MessageManager.getString("action.cluster_matrix"));
528 item.setToolTipText(MessageManager.getString("action.cluster_matrix_tooltip"));
529 item.addActionListener(new ActionListener()
532 public void actionPerformed(ActionEvent e)
534 new Thread(new Runnable()
540 ap.alignFrame.setProgressBar(MessageManager.formatMessage("action.clustering_matrix_for",cm.getAnnotDescr(),5f), progBar = System.currentTimeMillis());
541 cm.setGroupSet(GroupSet.makeGroups(cm, true));
542 cm.randomlyReColourGroups();
543 cm.transferGroupColorsTo(alignmentAnnotation);
544 ap.alignmentChanged();
545 ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
546 ap.alignFrame.setProgressBar(null, progBar);
557 * A helper method that adds menu options for calculation and visualisation of
558 * group and/or alignment consensus annotation to a popup menu. This is
559 * designed to be reusable for either unwrapped mode (popup menu is shown on
560 * component AnnotationLabels), or wrapped mode (popup menu is shown on
561 * IdPanel when the mouse is over an annotation label).
567 static void addConsensusMenuOptions(AlignmentPanel ap,
568 AlignmentAnnotation ann, JPopupMenu pop)
572 final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
573 MessageManager.getString("label.ignore_gaps_consensus"),
574 (ann.groupRef != null) ? ann.groupRef.getIgnoreGapsConsensus()
575 : ap.av.isIgnoreGapsConsensus());
576 final AlignmentAnnotation aaa = ann;
577 cbmi.addActionListener(new ActionListener()
580 public void actionPerformed(ActionEvent e)
582 if (aaa.groupRef != null)
584 aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
585 ap.getAnnotationPanel()
586 .paint(ap.getAnnotationPanel().getGraphics());
590 ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
592 ap.alignmentChanged();
597 if (aaa.groupRef != null)
600 * group consensus options
602 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
603 MessageManager.getString("label.show_group_histogram"),
604 ann.groupRef.isShowConsensusHistogram());
605 chist.addActionListener(new ActionListener()
608 public void actionPerformed(ActionEvent e)
610 aaa.groupRef.setShowConsensusHistogram(chist.getState());
615 final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
616 MessageManager.getString("label.show_group_logo"),
617 ann.groupRef.isShowSequenceLogo());
618 cprofl.addActionListener(new ActionListener()
621 public void actionPerformed(ActionEvent e)
623 aaa.groupRef.setshowSequenceLogo(cprofl.getState());
628 final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
629 MessageManager.getString("label.normalise_group_logo"),
630 ann.groupRef.isNormaliseSequenceLogo());
631 cproflnorm.addActionListener(new ActionListener()
634 public void actionPerformed(ActionEvent e)
636 aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
637 // automatically enable logo display if we're clicked
638 aaa.groupRef.setshowSequenceLogo(true);
647 * alignment consensus options
649 final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
650 MessageManager.getString("label.show_histogram"),
651 ap.av.isShowConsensusHistogram());
652 chist.addActionListener(new ActionListener()
655 public void actionPerformed(ActionEvent e)
657 ap.av.setShowConsensusHistogram(chist.getState());
658 ap.alignFrame.setMenusForViewport();
663 final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
664 MessageManager.getString("label.show_logo"),
665 ap.av.isShowSequenceLogo());
666 cprof.addActionListener(new ActionListener()
669 public void actionPerformed(ActionEvent e)
671 ap.av.setShowSequenceLogo(cprof.getState());
672 ap.alignFrame.setMenusForViewport();
677 final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
678 MessageManager.getString("label.normalise_logo"),
679 ap.av.isNormaliseSequenceLogo());
680 cprofnorm.addActionListener(new ActionListener()
683 public void actionPerformed(ActionEvent e)
685 ap.av.setShowSequenceLogo(true);
686 ap.av.setNormaliseSequenceLogo(cprofnorm.getState());
687 ap.alignFrame.setMenusForViewport();
696 * Reorders annotation rows after a drag of a label
701 public void mouseReleased(MouseEvent evt)
703 if (evt.isPopupTrigger())
709 int start = selectedRow;
710 getSelectedRow(evt.getY() - getScrollOffset());
711 int end = selectedRow;
714 * if dragging to resize instead, start == end
718 // Swap these annotations
719 AlignmentAnnotation startAA = ap.av.getAlignment()
720 .getAlignmentAnnotation()[start];
723 end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
725 AlignmentAnnotation endAA = ap.av.getAlignment()
726 .getAlignmentAnnotation()[end];
728 ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
729 ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
735 ap.getAnnotationPanel().repaint();
739 * Removes the height adjuster image on leaving the panel, unless currently
743 public void mouseExited(MouseEvent evt)
745 if (resizePanel && dragEvent == null)
753 * A mouse drag may be either an adjustment of the panel height (if flag
754 * resizePanel is set on), or a reordering of the annotation rows. The former
755 * is dealt with by this method, the latter in mouseReleased.
760 public void mouseDragged(MouseEvent evt)
766 Dimension d = ap.annotationScroller.getPreferredSize();
767 int dif = evt.getY() - oldY;
769 dif /= ap.av.getCharHeight();
770 dif *= ap.av.getCharHeight();
772 if ((d.height - dif) > 20)
774 ap.annotationScroller
775 .setPreferredSize(new Dimension(d.width, d.height - dif));
776 d = ap.annotationSpaceFillerHolder.getPreferredSize();
777 ap.annotationSpaceFillerHolder
778 .setPreferredSize(new Dimension(d.width, d.height - dif));
779 ap.paintAlignment(true, false);
791 * Updates the tooltip as the mouse moves over the labels
796 public void mouseMoved(MouseEvent evt)
798 showOrHideAdjuster(evt);
800 getSelectedRow(evt.getY() - getScrollOffset());
802 if (selectedRow > -1 && ap.av.getAlignment()
803 .getAlignmentAnnotation().length > selectedRow)
805 AlignmentAnnotation[] anns = ap.av.getAlignment()
806 .getAlignmentAnnotation();
807 AlignmentAnnotation aa = anns[selectedRow];
809 String desc = getTooltip(aa);
810 this.setToolTipText(desc);
811 String msg = getStatusMessage(aa, anns);
812 ap.alignFrame.setStatus(msg);
817 * Constructs suitable text to show in the status bar when over an annotation
818 * label, containing the associated sequence name (if any), and the annotation
819 * labels (or all labels for a graph group annotation)
825 static String getStatusMessage(AlignmentAnnotation aa,
826 AlignmentAnnotation[] anns)
833 StringBuilder msg = new StringBuilder(32);
834 if (aa.sequenceRef != null)
836 msg.append(aa.sequenceRef.getName()).append(" : ");
839 if (aa.graphGroup == -1)
841 msg.append(aa.label);
843 else if (anns != null)
845 boolean first = true;
846 for (int i = anns.length - 1; i >= 0; i--)
848 if (anns[i].graphGroup == aa.graphGroup)
854 msg.append(anns[i].label);
860 return msg.toString();
864 * Answers a tooltip, formatted as html, containing the annotation description
865 * (prefixed by associated sequence id if applicable), and the annotation
866 * (non-positional) score if it has one. Answers null if neither description
867 * nor score is found.
872 static String getTooltip(AlignmentAnnotation aa)
878 StringBuilder tooltip = new StringBuilder();
879 if (aa.description != null && !aa.description.equals("New description"))
881 // TODO: we could refactor and merge this code with the code in
882 // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
884 String desc = aa.getDescription(true).trim();
885 if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG))
887 tooltip.append(HTML_START_TAG);
888 desc = desc.replace("<", "<");
890 else if (desc.toLowerCase(Locale.ROOT).endsWith(HTML_END_TAG))
892 desc = desc.substring(0, desc.length() - HTML_END_TAG.length());
894 tooltip.append(desc);
898 // begin the tooltip's html fragment
899 tooltip.append(HTML_START_TAG);
903 if (tooltip.length() > HTML_START_TAG.length())
905 tooltip.append("<br/>");
907 // TODO: limit precision of score to avoid noise from imprecise
909 // (64.7 becomes 64.7+/some tiny value).
910 tooltip.append(" Score: ").append(String.valueOf(aa.score));
913 if (tooltip.length() > HTML_START_TAG.length())
915 return tooltip.append(HTML_END_TAG).toString();
919 * nothing in the tooltip (except "<html>")
925 * Shows the height adjuster image if the mouse moves into the top left
926 * region, or hides it if the mouse leaves the regio
930 protected void showOrHideAdjuster(MouseEvent evt)
932 boolean was = resizePanel;
933 resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
934 && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
936 if (resizePanel != was)
939 .getPredefinedCursor(resizePanel ? Cursor.S_RESIZE_CURSOR
940 : Cursor.DEFAULT_CURSOR));
946 public void mouseClicked(MouseEvent evt)
948 final AlignmentAnnotation[] aa = ap.av.getAlignment()
949 .getAlignmentAnnotation();
950 if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt))
952 if (selectedRow > -1 && selectedRow < aa.length)
954 if (aa[selectedRow].groupRef != null)
956 if (evt.getClickCount() >= 2)
958 // todo: make the ap scroll to the selection - not necessary, first
959 // click highlights/scrolls, second selects
960 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
962 SequenceGroup sg = ap.av.getSelectionGroup();
963 if (sg == null || sg == aa[selectedRow].groupRef
964 || !(Platform.isControlDown(evt) || evt.isShiftDown()))
966 if (Platform.isControlDown(evt) || evt.isShiftDown())
968 // clone a new selection group from the associated group
969 ap.av.setSelectionGroup(
970 new SequenceGroup(aa[selectedRow].groupRef));
974 // set selection to the associated group so it can be edited
975 ap.av.setSelectionGroup(aa[selectedRow].groupRef);
980 // modify current selection with associated group
981 int remainToAdd = aa[selectedRow].groupRef.getSize();
982 for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
984 if (jalview.util.Platform.isControlDown(evt))
986 sg.addOrRemove(sgs, --remainToAdd == 0);
990 // notionally, we should also add intermediate sequences from
991 // last added sequence ?
992 sg.addSequence(sgs, --remainToAdd == 0);
997 ap.paintAlignment(false, false);
998 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
999 ap.av.sendSelection();
1003 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(
1004 aa[selectedRow].groupRef.getSequences(null));
1008 else if (aa[selectedRow].sequenceRef != null)
1010 if (evt.getClickCount() == 1)
1012 ap.getSeqPanel().ap.getIdPanel()
1013 .highlightSearchResults(Arrays.asList(new SequenceI[]
1014 { aa[selectedRow].sequenceRef }));
1016 else if (evt.getClickCount() >= 2)
1018 ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
1019 SequenceGroup sg = ap.av.getSelectionGroup();
1022 // we make a copy rather than edit the current selection if no
1023 // modifiers pressed
1024 // see Enhancement JAL-1557
1025 if (!(Platform.isControlDown(evt) || evt.isShiftDown()))
1027 sg = new SequenceGroup(sg);
1029 sg.addSequence(aa[selectedRow].sequenceRef, false);
1033 if (Platform.isControlDown(evt))
1035 sg.addOrRemove(aa[selectedRow].sequenceRef, true);
1039 // notionally, we should also add intermediate sequences from
1040 // last added sequence ?
1041 sg.addSequence(aa[selectedRow].sequenceRef, true);
1047 sg = new SequenceGroup();
1049 sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
1050 sg.addSequence(aa[selectedRow].sequenceRef, false);
1052 ap.av.setSelectionGroup(sg);
1053 ap.paintAlignment(false, false);
1054 PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
1055 ap.av.sendSelection();
1065 * do a single sequence copy to jalview and the system clipboard
1068 * sequence to be copied to clipboard
1070 protected void copy_annotseqtoclipboard(SequenceI sq)
1072 SequenceI[] seqs = new SequenceI[] { sq };
1073 String[] omitHidden = null;
1074 SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() };
1075 if (dseqs[0] == null)
1077 dseqs[0] = new Sequence(sq);
1078 dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars,
1079 sq.getSequenceAsString()));
1081 sq.setDatasetSequence(dseqs[0]);
1083 Alignment ds = new Alignment(dseqs);
1084 if (av.hasHiddenColumns())
1086 Iterator<int[]> it = av.getAlignment().getHiddenColumns()
1087 .getVisContigsIterator(0, sq.getLength(), false);
1088 omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
1091 int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
1092 if (av.hasHiddenColumns())
1094 alignmentStartEnd = av.getAlignment().getHiddenColumns()
1095 .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
1098 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1099 seqs, omitHidden, alignmentStartEnd);
1101 Toolkit.getDefaultToolkit().getSystemClipboard()
1102 .setContents(new StringSelection(output), Desktop.instance);
1104 HiddenColumns hiddenColumns = null;
1106 if (av.hasHiddenColumns())
1108 hiddenColumns = new HiddenColumns(
1109 av.getAlignment().getHiddenColumns());
1112 Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
1114 // sequence ? need to
1116 // sequence as special.
1127 public void paintComponent(Graphics g)
1130 int width = getWidth();
1133 width = ap.calculateIdWidth().width;
1136 Graphics2D g2 = (Graphics2D) g;
1139 g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
1140 RenderingHints.VALUE_ANTIALIAS_ON);
1143 drawComponent(g2, true, width);
1148 * Draw the full set of annotation Labels for the alignment at the given
1152 * Graphics2D instance (needed for font scaling)
1154 * Width for scaling labels
1157 public void drawComponent(Graphics g, int width)
1159 drawComponent(g, false, width);
1163 * Draw the full set of annotation Labels for the alignment at the given
1167 * Graphics2D instance (needed for font scaling)
1169 * - true indicates that only current visible area needs to be
1172 * Width for scaling labels
1174 public void drawComponent(Graphics g, boolean clip, int width)
1176 if (av.getFont().getSize() < 10)
1182 g.setFont(av.getFont());
1185 FontMetrics fm = g.getFontMetrics(g.getFont());
1186 g.setColor(Color.white);
1187 g.fillRect(0, 0, getWidth(), getHeight());
1189 g.translate(0, getScrollOffset());
1190 g.setColor(Color.black);
1191 SequenceI lastSeqRef = null;
1192 String lastLabel = null;
1193 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
1194 int fontHeight = g.getFont().getSize();
1197 int graphExtras = 0;
1199 Font baseFont = g.getFont();
1200 FontMetrics baseMetrics = fm;
1201 int ofontH = fontHeight;
1204 int[] visr = (ap != null && ap.getAnnotationPanel() != null)
1205 ? ap.getAnnotationPanel().getVisibleVRange()
1207 if (clip && visr != null)
1210 visHeight = visr[1];
1212 boolean visible = true, before = false, after = false;
1215 hasHiddenRows = false;
1218 for (int i = 0; i < aa.length; i++)
1223 hasHiddenRows = true;
1227 // look ahead to next annotation
1228 for (nexAA = i + 1; nexAA < aa.length
1229 && !aa[nexAA].visible; nexAA++)
1240 System.out.println("before vis: " + i);
1244 // don't draw what isn't visible
1247 if (olY > visHeight)
1255 "Scroll offset: " + sOffset + " after vis: " + i);
1259 // don't draw what isn't visible
1263 g.setColor(Color.black);
1265 offset = -aa[i].height / 2;
1269 offset += fm.getHeight() / 2;
1270 offset -= fm.getDescent();
1274 offset += fm.getDescent();
1276 String label = aa[i].label;
1277 boolean vertBar = false;
1278 if ((lastLabel != null && lastLabel.equals(label)))
1280 label = aa[i].description;
1284 if (nexAA < aa.length && label.equals(aa[nexAA].label)) // &&
1285 // aa[nexY].sequenceRef==aa[i].sequenceRef)
1288 // next label is the same as this label
1289 label = aa[i].description;
1296 if (aa[i].sequenceRef != null)
1298 if (aa[i].sequenceRef != lastSeqRef)
1300 label = aa[i].sequenceRef.getName() + " " + label;
1301 // TODO record relationship between sequence and this annotation and
1309 x = width - fm.stringWidth(label) - 3;
1311 if (aa[i].graphGroup > -1)
1314 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1315 // computed efficiently for all visible labels
1316 for (int gg = 0; gg < aa.length; gg++)
1318 if (aa[gg].graphGroup == aa[i].graphGroup)
1323 if (groupSize * (fontHeight + 8) < aa[i].height)
1325 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
1330 // scale font to fit
1331 float h = aa[i].height / (float) groupSize, s;
1338 fontHeight = -8 + (int) h;
1339 s = ((float) fontHeight) / (float) ofontH;
1341 .deriveFont(AffineTransform.getScaleInstance(s, s));
1343 fm = g.getFontMetrics();
1344 graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
1350 for (int gg = 0; gg < aa.length; gg++)
1352 if (aa[gg].graphGroup == aa[i].graphGroup)
1354 x = width - fm.stringWidth(aa[gg].label) - 3;
1355 g.drawString(aa[gg].label, x, y - graphExtras);
1357 if (aa[gg]._linecolour != null)
1360 g.setColor(aa[gg]._linecolour);
1361 g.drawLine(x, y - graphExtras + 3,
1362 x + fm.stringWidth(aa[gg].label),
1363 y - graphExtras + 3);
1366 g.setColor(Color.black);
1367 graphExtras += fontHeight + 8;
1371 g.setFont(baseFont);
1373 fontHeight = ofontH;
1379 g.drawLine(width - 3, y + offset - fontHeight, width - 3,
1380 (int) (y - 1.5 * aa[i].height - offset - fontHeight));
1381 // g.drawLine(20, y + offset, x - 20, y + offset);
1384 g.drawString(label, x, y + offset);
1386 lastSeqRef = aa[i].sequenceRef;
1390 if (!resizePanel && dragEvent != null && aa != null)
1392 g.setColor(Color.lightGray);
1394 (aa[selectedRow].sequenceRef == null ? ""
1395 : aa[selectedRow].sequenceRef.getName())
1396 + aa[selectedRow].label,
1397 dragEvent.getX(), dragEvent.getY() - getScrollOffset());
1400 if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
1402 g.drawString(MessageManager.getString("label.right_click"), 2, 8);
1403 g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
1408 public int getScrollOffset()
1410 return scrollOffset;
1414 public void mouseEntered(MouseEvent e)