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 jalview.api.AlignViewportI;
24 import jalview.bin.Cache;
25 import jalview.commands.EditCommand;
26 import jalview.commands.EditCommand.Action;
27 import jalview.commands.EditCommand.Edit;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.HiddenColumns;
31 import jalview.datamodel.SearchResultMatchI;
32 import jalview.datamodel.SearchResults;
33 import jalview.datamodel.SearchResultsI;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.io.SequenceAnnotationReport;
39 import jalview.renderer.ResidueShaderI;
40 import jalview.schemes.ResidueProperties;
41 import jalview.structure.SelectionListener;
42 import jalview.structure.SelectionSource;
43 import jalview.structure.SequenceListener;
44 import jalview.structure.StructureSelectionManager;
45 import jalview.structure.VamsasSource;
46 import jalview.util.Comparison;
47 import jalview.util.MappingUtils;
48 import jalview.util.MessageManager;
49 import jalview.util.Platform;
50 import jalview.viewmodel.AlignmentViewport;
52 import java.awt.BorderLayout;
53 import java.awt.Color;
55 import java.awt.FontMetrics;
56 import java.awt.Point;
57 import java.awt.event.MouseEvent;
58 import java.awt.event.MouseListener;
59 import java.awt.event.MouseMotionListener;
60 import java.awt.event.MouseWheelEvent;
61 import java.awt.event.MouseWheelListener;
62 import java.util.ArrayList;
63 import java.util.Collections;
64 import java.util.List;
66 import javax.swing.JPanel;
67 import javax.swing.SwingUtilities;
68 import javax.swing.ToolTipManager;
74 * @version $Revision: 1.130 $
76 public class SeqPanel extends JPanel
77 implements MouseListener, MouseMotionListener, MouseWheelListener,
78 SequenceListener, SelectionListener
82 public SeqCanvas seqCanvas;
85 public AlignmentPanel ap;
88 * last column position for mouseMoved event
90 private int lastMouseColumn;
93 * last sequence offset for mouseMoved event
95 private int lastMouseSeq;
97 protected int lastres;
99 protected int startseq;
101 protected AlignViewport av;
103 ScrollThread scrollThread = null;
105 boolean mouseDragging = false;
107 boolean editingSeqs = false;
109 boolean groupEditing = false;
111 // ////////////////////////////////////////
112 // ///Everything below this is for defining the boundary of the rubberband
113 // ////////////////////////////////////////
116 boolean changeEndSeq = false;
118 boolean changeStartSeq = false;
120 boolean changeEndRes = false;
122 boolean changeStartRes = false;
124 SequenceGroup stretchGroup = null;
126 boolean remove = false;
128 Point lastMousePress;
130 boolean mouseWheelPressed = false;
132 StringBuffer keyboardNo1;
134 StringBuffer keyboardNo2;
136 java.net.URL linkImageURL;
138 private final SequenceAnnotationReport seqARep;
140 StringBuilder tooltipText = new StringBuilder();
144 EditCommand editCommand;
146 StructureSelectionManager ssm;
148 SearchResultsI lastSearchResults;
151 * Creates a new SeqPanel object.
158 public SeqPanel(AlignViewport av, AlignmentPanel ap)
160 linkImageURL = getClass().getResource("/images/link.gif");
161 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
162 ToolTipManager.sharedInstance().registerComponent(this);
163 ToolTipManager.sharedInstance().setInitialDelay(0);
164 ToolTipManager.sharedInstance().setDismissDelay(10000);
166 setBackground(Color.white);
168 seqCanvas = new SeqCanvas(ap);
169 setLayout(new BorderLayout());
170 add(seqCanvas, BorderLayout.CENTER);
176 addMouseMotionListener(this);
177 addMouseListener(this);
178 addMouseWheelListener(this);
179 ssm = av.getStructureSelectionManager();
180 ssm.addStructureViewerListener(this);
181 ssm.addSelectionListener(this);
184 lastMouseColumn = -1;
188 int startWrapBlock = -1;
190 int wrappedBlock = -1;
193 * Returns the aligned sequence position (base 0) at the mouse position, or
194 * the closest visible one
199 int findColumn(MouseEvent evt)
204 int startRes = av.getRanges().getStartRes();
205 if (av.getWrapAlignment())
208 int hgap = av.getCharHeight();
209 if (av.getScaleAboveWrapped())
211 hgap += av.getCharHeight();
214 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
215 + hgap + seqCanvas.getAnnotationHeight();
218 y = Math.max(0, y - hgap);
219 x = Math.max(0, x - seqCanvas.getLabelWidthWest());
221 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
227 wrappedBlock = y / cHeight;
228 wrappedBlock += startRes / cwidth;
229 // allow for wrapped view scrolled right (possible from Overview)
230 int startOffset = startRes % cwidth;
231 res = wrappedBlock * cwidth + startOffset
232 + +Math.min(cwidth - 1, x / av.getCharWidth());
236 if (x > seqCanvas.getX() + seqCanvas.getWidth())
238 // make sure we calculate relative to visible alignment, rather than
240 x = seqCanvas.getX() + seqCanvas.getWidth();
242 res = (x / av.getCharWidth()) + startRes;
243 if (res > av.getRanges().getEndRes())
246 res = av.getRanges().getEndRes();
250 if (av.hasHiddenColumns())
252 res = av.getAlignment().getHiddenColumns()
253 .adjustForHiddenColumns(res);
260 int findSeq(MouseEvent evt)
265 if (av.getWrapAlignment())
267 int hgap = av.getCharHeight();
268 if (av.getScaleAboveWrapped())
270 hgap += av.getCharHeight();
273 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
274 + hgap + seqCanvas.getAnnotationHeight();
278 seq = Math.min((y % cHeight) / av.getCharHeight(),
279 av.getAlignment().getHeight() - 1);
284 (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
285 av.getAlignment().getHeight() - 1);
292 * When all of a sequence of edits are complete, put the resulting edit list
293 * on the history stack (undo list), and reset flags for editing in progress.
299 if (editCommand != null && editCommand.getSize() > 0)
301 ap.alignFrame.addHistoryItem(editCommand);
302 av.firePropertyChange("alignment", null,
303 av.getAlignment().getSequences());
308 * Tidy up come what may...
313 groupEditing = false;
322 seqCanvas.cursorY = getKeyboardNo1() - 1;
323 scrollToVisible(true);
326 void setCursorColumn()
328 seqCanvas.cursorX = getKeyboardNo1() - 1;
329 scrollToVisible(true);
332 void setCursorRowAndColumn()
334 if (keyboardNo2 == null)
336 keyboardNo2 = new StringBuffer();
340 seqCanvas.cursorX = getKeyboardNo1() - 1;
341 seqCanvas.cursorY = getKeyboardNo2() - 1;
342 scrollToVisible(true);
346 void setCursorPosition()
348 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
350 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
351 scrollToVisible(true);
354 void moveCursor(int dx, int dy)
356 seqCanvas.cursorX += dx;
357 seqCanvas.cursorY += dy;
359 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
361 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
363 int original = seqCanvas.cursorX - dx;
364 int maxWidth = av.getAlignment().getWidth();
366 while (!hidden.isVisible(seqCanvas.cursorX)
367 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
369 seqCanvas.cursorX += dx;
372 if (seqCanvas.cursorX >= maxWidth
373 || !hidden.isVisible(seqCanvas.cursorX))
375 seqCanvas.cursorX = original;
379 scrollToVisible(false);
383 * Scroll to make the cursor visible in the viewport.
386 * just jump to the location rather than scrolling
388 void scrollToVisible(boolean jump)
390 if (seqCanvas.cursorX < 0)
392 seqCanvas.cursorX = 0;
394 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
396 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
399 if (seqCanvas.cursorY < 0)
401 seqCanvas.cursorY = 0;
403 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
405 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
410 boolean repaintNeeded = true;
413 // only need to repaint if the viewport did not move, as otherwise it will
415 repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
420 if (av.getWrapAlignment())
422 // scrollToWrappedVisible expects x-value to have hidden cols subtracted
423 int x = av.getAlignment().getHiddenColumns()
424 .findColumnPosition(seqCanvas.cursorX);
425 av.getRanges().scrollToWrappedVisible(x);
429 av.getRanges().scrollToVisible(seqCanvas.cursorX,
434 if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
436 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
437 seqCanvas.cursorX, seqCanvas.cursorY);
447 void setSelectionAreaAtCursor(boolean topLeft)
449 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
451 if (av.getSelectionGroup() != null)
453 SequenceGroup sg = av.getSelectionGroup();
454 // Find the top and bottom of this group
455 int min = av.getAlignment().getHeight(), max = 0;
456 for (int i = 0; i < sg.getSize(); i++)
458 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
473 sg.setStartRes(seqCanvas.cursorX);
474 if (sg.getEndRes() < seqCanvas.cursorX)
476 sg.setEndRes(seqCanvas.cursorX);
479 min = seqCanvas.cursorY;
483 sg.setEndRes(seqCanvas.cursorX);
484 if (sg.getStartRes() > seqCanvas.cursorX)
486 sg.setStartRes(seqCanvas.cursorX);
489 max = seqCanvas.cursorY + 1;
494 // Only the user can do this
495 av.setSelectionGroup(null);
499 // Now add any sequences between min and max
500 sg.getSequences(null).clear();
501 for (int i = min; i < max; i++)
503 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
508 if (av.getSelectionGroup() == null)
510 SequenceGroup sg = new SequenceGroup();
511 sg.setStartRes(seqCanvas.cursorX);
512 sg.setEndRes(seqCanvas.cursorX);
513 sg.addSequence(sequence, false);
514 av.setSelectionGroup(sg);
517 ap.paintAlignment(false, false);
521 void insertGapAtCursor(boolean group)
523 groupEditing = group;
524 startseq = seqCanvas.cursorY;
525 lastres = seqCanvas.cursorX;
526 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
530 void deleteGapAtCursor(boolean group)
532 groupEditing = group;
533 startseq = seqCanvas.cursorY;
534 lastres = seqCanvas.cursorX + getKeyboardNo1();
535 editSequence(false, false, seqCanvas.cursorX);
539 void insertNucAtCursor(boolean group, String nuc)
541 // TODO not called - delete?
542 groupEditing = group;
543 startseq = seqCanvas.cursorY;
544 lastres = seqCanvas.cursorX;
545 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
549 void numberPressed(char value)
551 if (keyboardNo1 == null)
553 keyboardNo1 = new StringBuffer();
556 if (keyboardNo2 != null)
558 keyboardNo2.append(value);
562 keyboardNo1.append(value);
570 if (keyboardNo1 != null)
572 int value = Integer.parseInt(keyboardNo1.toString());
576 } catch (Exception x)
587 if (keyboardNo2 != null)
589 int value = Integer.parseInt(keyboardNo2.toString());
593 } catch (Exception x)
607 public void mouseReleased(MouseEvent evt)
609 boolean didDrag = mouseDragging; // did we come here after a drag
610 mouseDragging = false;
611 mouseWheelPressed = false;
613 if (evt.isPopupTrigger()) // Windows: mouseReleased
622 doMouseReleasedDefineMode(evt, didDrag);
636 public void mousePressed(MouseEvent evt)
638 lastMousePress = evt.getPoint();
640 if (SwingUtilities.isMiddleMouseButton(evt))
642 mouseWheelPressed = true;
646 boolean isControlDown = Platform.isControlDown(evt);
647 if (evt.isShiftDown() || isControlDown)
657 doMousePressedDefineMode(evt);
661 int seq = findSeq(evt);
662 int res = findColumn(evt);
664 if (seq < 0 || res < 0)
669 if ((seq < av.getAlignment().getHeight())
670 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
687 public void mouseOverSequence(SequenceI sequence, int index, int pos)
689 String tmp = sequence.hashCode() + " " + index + " " + pos;
691 if (lastMessage == null || !lastMessage.equals(tmp))
693 // System.err.println("mouseOver Sequence: "+tmp);
694 ssm.mouseOverSequence(sequence, index, pos, av);
700 * Highlight the mapped region described by the search results object (unless
701 * unchanged). This supports highlight of protein while mousing over linked
702 * cDNA and vice versa. The status bar is also updated to show the location of
703 * the start of the highlighted region.
706 public void highlightSequence(SearchResultsI results)
708 if (results == null || results.equals(lastSearchResults))
712 lastSearchResults = results;
714 boolean wasScrolled = false;
716 if (av.isFollowHighlight())
718 // don't allow highlight of protein/cDNA to also scroll a complementary
719 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
720 // over residue to change abruptly, causing highlighted residue in panel 2
721 // to change, causing a scroll in panel 1 etc)
722 ap.setToScrollComplementPanel(false);
723 wasScrolled = ap.scrollToPosition(results, false);
726 seqCanvas.revalidate();
728 ap.setToScrollComplementPanel(true);
731 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
732 if (seqCanvas.highlightSearchResults(results, noFastPaint))
734 setStatusMessage(results);
739 public VamsasSource getVamsasSource()
741 return this.ap == null ? null : this.ap.av;
745 public void updateColours(SequenceI seq, int index)
747 System.out.println("update the seqPanel colours");
752 * Action on mouse movement is to update the status bar to show the current
753 * sequence position, and (if features are shown) to show any features at the
754 * position in a tooltip. Does nothing if the mouse move does not change
760 public void mouseMoved(MouseEvent evt)
764 // This is because MacOSX creates a mouseMoved
765 // If control is down, other platforms will not.
769 final int column = findColumn(evt);
770 final int seq = findSeq(evt);
772 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
777 if (column == lastMouseColumn && seq == lastMouseSeq)
780 * just a pixel move without change of residue
784 lastMouseColumn = column;
787 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
789 if (column >= sequence.getLength())
795 * set status bar message, returning residue position in sequence
797 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
798 final int pos = setStatusMessage(sequence, column, seq);
799 if (ssm != null && !isGapped)
801 mouseOverSequence(sequence, column, pos);
804 tooltipText.setLength(6); // Cuts the buffer back to <html>
806 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
809 for (int g = 0; g < groups.length; g++)
811 if (groups[g].getStartRes() <= column
812 && groups[g].getEndRes() >= column)
814 if (!groups[g].getName().startsWith("JTreeGroup")
815 && !groups[g].getName().startsWith("JGroup"))
817 tooltipText.append(groups[g].getName());
820 if (groups[g].getDescription() != null)
822 tooltipText.append(": " + groups[g].getDescription());
829 * add any features at the position to the tooltip; if over a gap, only
830 * add features that straddle the gap (pos may be the residue before or
833 if (av.isShowSequenceFeatures())
835 List<SequenceFeature> features = ap.getFeatureRenderer()
836 .findFeaturesAtColumn(sequence, column + 1);
837 seqARep.appendFeatures(tooltipText, pos, features,
838 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
840 if (tooltipText.length() == 6) // <html>
842 setToolTipText(null);
847 String textString = tooltipText.toString();
848 if (lastTooltip == null || !lastTooltip.equals(textString))
850 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
852 setToolTipText(formattedTooltipText);
853 lastTooltip = textString;
858 private Point lastp = null;
863 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
866 public Point getToolTipLocation(MouseEvent event)
868 int x = event.getX(), w = getWidth();
869 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
872 if (!event.isShiftDown() || p == null)
874 p = (tooltipText != null && tooltipText.length() > 6)
875 ? new Point(event.getX() + wdth, event.getY() - 20)
879 * TODO: try to modify position region is not obcured by tooltip
887 * set when the current UI interaction has resulted in a change that requires
888 * shading in overviews and structures to be recalculated. this could be
889 * changed to a something more expressive that indicates what actually has
890 * changed, so selective redraws can be applied (ie. only structures, only
893 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
896 * set if av.getSelectionGroup() refers to a group that is defined on the
897 * alignment view, rather than a transient selection
899 // private boolean editingDefinedGroup = false; // TODO: refactor to
900 // avcontroller or viewModel
903 * Sets the status message in alignment panel, showing the sequence number
904 * (index) and id, and residue and residue position if not at a gap, for the
905 * given sequence and column position. Returns the residue position returned
906 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
907 * if at a gapped position.
910 * aligned sequence object
914 * index of sequence in alignment
915 * @return sequence position of residue at column, or adjacent residue if at a
918 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
920 char sequenceChar = sequence.getCharAt(column);
921 int pos = sequence.findPosition(column);
922 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
928 * Builds the status message for the current cursor location and writes it to
929 * the status bar, for example
932 * Sequence 3 ID: FER1_SOLLC
933 * Sequence 5 ID: FER1_PEA Residue: THR (4)
934 * Sequence 5 ID: FER1_PEA Residue: B (3)
935 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
940 * sequence position in the alignment (1..)
941 * @param sequenceChar
942 * the character under the cursor
944 * the sequence residue position (if not over a gap)
946 protected void setStatusMessage(SequenceI sequence, int seqIndex,
947 char sequenceChar, int residuePos)
949 StringBuilder text = new StringBuilder(32);
952 * Sequence number (if known), and sequence name.
954 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
955 text.append("Sequence").append(seqno).append(" ID: ")
956 .append(sequence.getName());
958 String residue = null;
961 * Try to translate the display character to residue name (null for gap).
963 boolean isGapped = Comparison.isGap(sequenceChar);
967 boolean nucleotide = av.getAlignment().isNucleotide();
968 String displayChar = String.valueOf(sequenceChar);
971 residue = ResidueProperties.nucleotideName.get(displayChar);
975 residue = "X".equalsIgnoreCase(displayChar) ? "X"
976 : ("*".equals(displayChar) ? "STOP"
977 : ResidueProperties.aa2Triplet.get(displayChar));
979 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
980 .append(": ").append(residue == null ? displayChar : residue);
982 text.append(" (").append(Integer.toString(residuePos)).append(")");
984 ap.alignFrame.statusBar.setText(text.toString());
988 * Set the status bar message to highlight the first matched position in
993 private void setStatusMessage(SearchResultsI results)
995 AlignmentI al = this.av.getAlignment();
996 int sequenceIndex = al.findIndex(results);
997 if (sequenceIndex == -1)
1001 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
1002 for (SearchResultMatchI m : results.getResults())
1004 SequenceI seq = m.getSequence();
1005 if (seq.getDatasetSequence() != null)
1007 seq = seq.getDatasetSequence();
1012 int start = m.getStart();
1013 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1024 public void mouseDragged(MouseEvent evt)
1026 if (mouseWheelPressed)
1028 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1029 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1031 int oldWidth = av.getCharWidth();
1033 // Which is bigger, left-right or up-down?
1034 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1035 .abs(evt.getX() - lastMousePress.getX()))
1038 * on drag up or down, decrement or increment font size
1040 int fontSize = av.font.getSize();
1041 boolean fontChanged = false;
1043 if (evt.getY() < lastMousePress.getY())
1048 else if (evt.getY() > lastMousePress.getY())
1061 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1063 av.setFont(newFont, true);
1064 av.setCharWidth(oldWidth);
1068 ap.av.getCodingComplement().setFont(newFont, true);
1069 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1070 .getSplitViewContainer();
1071 splitFrame.adjustLayout();
1072 splitFrame.repaint();
1079 * on drag left or right, decrement or increment character width
1082 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1084 newWidth = av.getCharWidth() - 1;
1085 av.setCharWidth(newWidth);
1087 else if (evt.getX() > lastMousePress.getX())
1089 newWidth = av.getCharWidth() + 1;
1090 av.setCharWidth(newWidth);
1094 ap.paintAlignment(false, false);
1098 * need to ensure newWidth is set on cdna, regardless of which
1099 * panel the mouse drag happened in; protein will compute its
1100 * character width as 1:1 or 3:1
1102 av.getCodingComplement().setCharWidth(newWidth);
1103 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1104 .getSplitViewContainer();
1105 splitFrame.adjustLayout();
1106 splitFrame.repaint();
1111 FontMetrics fm = getFontMetrics(av.getFont());
1112 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1114 lastMousePress = evt.getPoint();
1121 doMouseDraggedDefineMode(evt);
1125 int res = findColumn(evt);
1132 if ((lastres == -1) || (lastres == res))
1137 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1139 // dragLeft, delete gap
1140 editSequence(false, false, res);
1144 editSequence(true, false, res);
1147 mouseDragging = true;
1148 if ((scrollThread != null) && (scrollThread.isRunning()))
1150 scrollThread.setEvent(evt);
1154 // TODO: Make it more clever than many booleans
1155 synchronized void editSequence(boolean insertGap, boolean editSeq,
1159 int fixedRight = -1;
1160 boolean fixedColumns = false;
1161 SequenceGroup sg = av.getSelectionGroup();
1163 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1165 // No group, but the sequence may represent a group
1166 if (!groupEditing && av.hasHiddenRows())
1168 if (av.isHiddenRepSequence(seq))
1170 sg = av.getRepresentedSequences(seq);
1171 groupEditing = true;
1175 StringBuilder message = new StringBuilder(64);
1178 message.append("Edit group:");
1179 if (editCommand == null)
1181 editCommand = new EditCommand(
1182 MessageManager.getString("action.edit_group"));
1187 message.append("Edit sequence: " + seq.getName());
1188 String label = seq.getName();
1189 if (label.length() > 10)
1191 label = label.substring(0, 10);
1193 if (editCommand == null)
1195 editCommand = new EditCommand(MessageManager
1196 .formatMessage("label.edit_params", new String[]
1203 message.append(" insert ");
1207 message.append(" delete ");
1210 message.append(Math.abs(startres - lastres) + " gaps.");
1211 ap.alignFrame.statusBar.setText(message.toString());
1213 // Are we editing within a selection group?
1214 if (groupEditing || (sg != null
1215 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1217 fixedColumns = true;
1219 // sg might be null as the user may only see 1 sequence,
1220 // but the sequence represents a group
1223 if (!av.isHiddenRepSequence(seq))
1228 sg = av.getRepresentedSequences(seq);
1231 fixedLeft = sg.getStartRes();
1232 fixedRight = sg.getEndRes();
1234 if ((startres < fixedLeft && lastres >= fixedLeft)
1235 || (startres >= fixedLeft && lastres < fixedLeft)
1236 || (startres > fixedRight && lastres <= fixedRight)
1237 || (startres <= fixedRight && lastres > fixedRight))
1243 if (fixedLeft > startres)
1245 fixedRight = fixedLeft - 1;
1248 else if (fixedRight < startres)
1250 fixedLeft = fixedRight;
1255 if (av.hasHiddenColumns())
1257 fixedColumns = true;
1258 int y1 = av.getAlignment().getHiddenColumns()
1259 .getHiddenBoundaryLeft(startres);
1260 int y2 = av.getAlignment().getHiddenColumns()
1261 .getHiddenBoundaryRight(startres);
1263 if ((insertGap && startres > y1 && lastres < y1)
1264 || (!insertGap && startres < y2 && lastres > y2))
1270 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1271 // Selection spans a hidden region
1272 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1280 fixedRight = y2 - 1;
1287 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1288 int g, groupSize = vseqs.size();
1289 SequenceI[] groupSeqs = new SequenceI[groupSize];
1290 for (g = 0; g < groupSeqs.length; g++)
1292 groupSeqs[g] = vseqs.get(g);
1298 // If the user has selected the whole sequence, and is dragging to
1299 // the right, we can still extend the alignment and selectionGroup
1300 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1301 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1303 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1304 fixedRight = sg.getEndRes();
1307 // Is it valid with fixed columns??
1308 // Find the next gap before the end
1309 // of the visible region boundary
1310 boolean blank = false;
1311 for (; fixedRight > lastres; fixedRight--)
1315 for (g = 0; g < groupSize; g++)
1317 for (int j = 0; j < startres - lastres; j++)
1319 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1334 if (sg.getSize() == av.getAlignment().getHeight())
1336 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1337 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1343 int alWidth = av.getAlignment().getWidth();
1344 if (av.hasHiddenRows())
1346 int hwidth = av.getAlignment().getHiddenSequences()
1348 if (hwidth > alWidth)
1353 // We can still insert gaps if the selectionGroup
1354 // contains all the sequences
1355 sg.setEndRes(sg.getEndRes() + startres - lastres);
1356 fixedRight = alWidth + startres - lastres;
1367 else if (!insertGap)
1369 // / Are we able to delete?
1370 // ie are all columns blank?
1372 for (g = 0; g < groupSize; g++)
1374 for (int j = startres; j < lastres; j++)
1376 if (groupSeqs[g].getLength() <= j)
1381 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1383 // Not a gap, block edit not valid
1393 // dragging to the right
1394 if (fixedColumns && fixedRight != -1)
1396 for (int j = lastres; j < startres; j++)
1398 insertChar(j, groupSeqs, fixedRight);
1403 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1404 startres - lastres);
1409 // dragging to the left
1410 if (fixedColumns && fixedRight != -1)
1412 for (int j = lastres; j > startres; j--)
1414 deleteChar(startres, groupSeqs, fixedRight);
1419 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1420 lastres - startres);
1426 // ///Editing a single sequence///////////
1430 // dragging to the right
1431 if (fixedColumns && fixedRight != -1)
1433 for (int j = lastres; j < startres; j++)
1435 insertChar(j, new SequenceI[] { seq }, fixedRight);
1440 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1441 startres - lastres);
1448 // dragging to the left
1449 if (fixedColumns && fixedRight != -1)
1451 for (int j = lastres; j > startres; j--)
1453 if (!Comparison.isGap(seq.getCharAt(startres)))
1458 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1463 // could be a keyboard edit trying to delete none gaps
1465 for (int m = startres; m < lastres; m++)
1467 if (!Comparison.isGap(seq.getCharAt(m)))
1476 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1482 {// insertGap==false AND editSeq==TRUE;
1483 if (fixedColumns && fixedRight != -1)
1485 for (int j = lastres; j < startres; j++)
1487 insertChar(j, new SequenceI[] { seq }, fixedRight);
1492 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1493 startres - lastres);
1500 seqCanvas.repaint();
1503 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1505 int blankColumn = fixedColumn;
1506 for (int s = 0; s < seq.length; s++)
1508 // Find the next gap before the end of the visible region boundary
1509 // If lastCol > j, theres a boundary after the gap insertion
1511 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1513 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1515 // Theres a space, so break and insert the gap
1520 if (blankColumn <= j)
1522 blankColumn = fixedColumn;
1528 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1530 appendEdit(Action.INSERT_GAP, seq, j, 1);
1535 * Helper method to add and perform one edit action.
1542 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1546 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1547 av.getAlignment().getGapCharacter());
1549 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1552 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1555 appendEdit(Action.DELETE_GAP, seq, j, 1);
1557 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1567 public void mouseEntered(MouseEvent e)
1574 if ((scrollThread != null) && (scrollThread.isRunning()))
1576 scrollThread.stopScrolling();
1577 scrollThread = null;
1588 public void mouseExited(MouseEvent e)
1590 if (av.getWrapAlignment())
1595 if (mouseDragging && scrollThread == null)
1597 scrollThread = new ScrollThread();
1602 * Handler for double-click on a position with one or more sequence features.
1603 * Opens the Amend Features dialog to allow feature details to be amended, or
1604 * the feature deleted.
1607 public void mouseClicked(MouseEvent evt)
1609 SequenceGroup sg = null;
1610 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1611 if (evt.getClickCount() > 1)
1613 sg = av.getSelectionGroup();
1614 if (sg != null && sg.getSize() == 1
1615 && sg.getEndRes() - sg.getStartRes() < 2)
1617 av.setSelectionGroup(null);
1620 int column = findColumn(evt);
1623 * find features at the position (if not gapped), or straddling
1624 * the position (if at a gap)
1626 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1627 .findFeaturesAtColumn(sequence, column + 1);
1629 if (!features.isEmpty())
1632 * highlight the first feature at the position on the alignment
1634 SearchResultsI highlight = new SearchResults();
1635 highlight.addResult(sequence, features.get(0).getBegin(), features
1637 seqCanvas.highlightSearchResults(highlight, false);
1640 * open the Amend Features dialog; clear highlighting afterwards,
1641 * whether changes were made or not
1643 List<SequenceI> seqs = Collections.singletonList(sequence);
1644 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1646 av.setSearchResults(null); // clear highlighting
1647 seqCanvas.repaint(); // draw new/amended features
1653 public void mouseWheelMoved(MouseWheelEvent e)
1656 if (e.getWheelRotation() > 0)
1658 if (e.isShiftDown())
1660 av.getRanges().scrollRight(true);
1665 av.getRanges().scrollUp(false);
1670 if (e.isShiftDown())
1672 av.getRanges().scrollRight(false);
1676 av.getRanges().scrollUp(true);
1681 * update status bar and tooltip for new position
1682 * (need to synthesize a mouse movement to refresh tooltip)
1685 ToolTipManager.sharedInstance().mouseMoved(e);
1694 public void doMousePressedDefineMode(MouseEvent evt)
1696 final int res = findColumn(evt);
1697 final int seq = findSeq(evt);
1699 updateOverviewAndStructs = false;
1701 startWrapBlock = wrappedBlock;
1703 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1705 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1706 MessageManager.getString(
1707 "label.cannot_edit_annotations_in_wrapped_view"),
1708 MessageManager.getString("label.wrapped_view_no_edit"),
1709 JvOptionPane.WARNING_MESSAGE);
1713 if (seq < 0 || res < 0)
1718 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1720 if ((sequence == null) || (res > sequence.getLength()))
1725 stretchGroup = av.getSelectionGroup();
1727 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1729 stretchGroup = av.getAlignment().findGroup(sequence, res);
1730 if (stretchGroup != null)
1732 // only update the current selection if the popup menu has a group to
1734 av.setSelectionGroup(stretchGroup);
1738 if (evt.isPopupTrigger()) // Mac: mousePressed
1745 * defer right-mouse click handling to mouseReleased on Windows
1746 * (where isPopupTrigger() will answer true)
1747 * NB isRightMouseButton is also true for Cmd-click on Mac
1749 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1756 seqCanvas.cursorX = findColumn(evt);
1757 seqCanvas.cursorY = findSeq(evt);
1758 seqCanvas.repaint();
1762 if (stretchGroup == null)
1764 createStretchGroup(res, sequence);
1767 if (stretchGroup != null)
1769 stretchGroup.addPropertyChangeListener(seqCanvas);
1772 seqCanvas.repaint();
1775 private void createStretchGroup(int res, SequenceI sequence)
1777 // Only if left mouse button do we want to change group sizes
1778 // define a new group here
1779 SequenceGroup sg = new SequenceGroup();
1780 sg.setStartRes(res);
1782 sg.addSequence(sequence, false);
1783 av.setSelectionGroup(sg);
1786 if (av.getConservationSelected())
1788 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1792 if (av.getAbovePIDThreshold())
1794 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1797 // TODO: stretchGroup will always be not null. Is this a merge error ?
1798 // or is there a threading issue here?
1799 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1801 // Edit end res position of selected group
1802 changeEndRes = true;
1804 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1806 // Edit end res position of selected group
1807 changeStartRes = true;
1809 stretchGroup.getWidth();
1814 * Build and show a pop-up menu at the right-click mouse position
1820 void showPopupMenu(MouseEvent evt)
1822 final int column = findColumn(evt);
1823 final int seq = findSeq(evt);
1824 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1825 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1826 .findFeaturesAtColumn(sequence, column + 1);
1827 List<String> links = new ArrayList<>();
1828 for (SequenceFeature sf : allFeatures)
1830 if (sf.links != null)
1832 for (String link : sf.links)
1839 PopupMenu pop = new PopupMenu(ap, null, links);
1840 pop.show(this, evt.getX(), evt.getY());
1844 * Update the display after mouse up on a selection or group
1847 * mouse released event details
1849 * true if this event is happening after a mouse drag (rather than a
1852 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1854 if (stretchGroup == null)
1859 stretchGroup.removePropertyChangeListener(seqCanvas);
1861 // always do this - annotation has own state
1862 // but defer colourscheme update until hidden sequences are passed in
1863 boolean vischange = stretchGroup.recalcConservation(true);
1864 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1866 if (stretchGroup.cs != null)
1868 stretchGroup.cs.alignmentChanged(stretchGroup,
1869 av.getHiddenRepSequences());
1871 ResidueShaderI groupColourScheme = stretchGroup
1872 .getGroupColourScheme();
1873 String name = stretchGroup.getName();
1874 if (stretchGroup.cs.conservationApplied())
1876 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1878 if (stretchGroup.cs.getThreshold() > 0)
1880 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1883 PaintRefresher.Refresh(this, av.getSequenceSetId());
1884 // TODO: structure colours only need updating if stretchGroup used to or now
1885 // does contain sequences with structure views
1886 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1887 updateOverviewAndStructs = false;
1888 changeEndRes = false;
1889 changeStartRes = false;
1890 stretchGroup = null;
1900 public void doMouseDraggedDefineMode(MouseEvent evt)
1902 int res = findColumn(evt);
1903 int y = findSeq(evt);
1905 if (wrappedBlock != startWrapBlock)
1910 if (stretchGroup == null)
1915 if (res >= av.getAlignment().getWidth())
1917 res = av.getAlignment().getWidth() - 1;
1920 if (stretchGroup.getEndRes() == res)
1922 // Edit end res position of selected group
1923 changeEndRes = true;
1925 else if (stretchGroup.getStartRes() == res)
1927 // Edit start res position of selected group
1928 changeStartRes = true;
1931 if (res < av.getRanges().getStartRes())
1933 res = av.getRanges().getStartRes();
1938 if (res > (stretchGroup.getStartRes() - 1))
1940 stretchGroup.setEndRes(res);
1941 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1944 else if (changeStartRes)
1946 if (res < (stretchGroup.getEndRes() + 1))
1948 stretchGroup.setStartRes(res);
1949 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1953 int dragDirection = 0;
1959 else if (y < oldSeq)
1964 while ((y != oldSeq) && (oldSeq > -1)
1965 && (y < av.getAlignment().getHeight()))
1967 // This routine ensures we don't skip any sequences, as the
1968 // selection is quite slow.
1969 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1971 oldSeq += dragDirection;
1978 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1980 if (stretchGroup.getSequences(null).contains(nextSeq))
1982 stretchGroup.deleteSequence(seq, false);
1983 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1989 stretchGroup.addSequence(seq, false);
1992 stretchGroup.addSequence(nextSeq, false);
1993 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2002 mouseDragging = true;
2004 if ((scrollThread != null) && (scrollThread.isRunning()))
2006 scrollThread.setEvent(evt);
2010 void scrollCanvas(MouseEvent evt)
2014 if ((scrollThread != null) && (scrollThread.isRunning()))
2016 scrollThread.stopScrolling();
2017 scrollThread = null;
2019 mouseDragging = false;
2023 if (scrollThread == null)
2025 scrollThread = new ScrollThread();
2028 mouseDragging = true;
2029 scrollThread.setEvent(evt);
2034 // this class allows scrolling off the bottom of the visible alignment
2035 class ScrollThread extends Thread
2039 private volatile boolean threadRunning = true;
2041 public ScrollThread()
2046 public void setEvent(MouseEvent e)
2051 public void stopScrolling()
2053 threadRunning = false;
2056 public boolean isRunning()
2058 return threadRunning;
2064 while (threadRunning)
2068 if (mouseDragging && (evt.getY() < 0)
2069 && (av.getRanges().getStartSeq() > 0))
2071 av.getRanges().scrollUp(true);
2074 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2075 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2077 av.getRanges().scrollUp(false);
2080 if (mouseDragging && (evt.getX() < 0))
2082 av.getRanges().scrollRight(false);
2084 else if (mouseDragging && (evt.getX() >= getWidth()))
2086 av.getRanges().scrollRight(true);
2093 } catch (Exception ex)
2101 * modify current selection according to a received message.
2104 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2105 HiddenColumns hidden, SelectionSource source)
2107 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2108 // handles selection messages...
2109 // TODO: extend config options to allow user to control if selections may be
2110 // shared between viewports.
2111 boolean iSentTheSelection = (av == source
2112 || (source instanceof AlignViewport
2113 && ((AlignmentViewport) source).getSequenceSetId()
2114 .equals(av.getSequenceSetId())));
2116 if (iSentTheSelection)
2118 // respond to our own event by updating dependent dialogs
2119 if (ap.getCalculationDialog() != null)
2121 ap.getCalculationDialog().validateCalcTypes();
2127 // process further ?
2128 if (!av.followSelection)
2134 * Ignore the selection if there is one of our own pending.
2136 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2142 * Check for selection in a view of which this one is a dna/protein
2145 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2150 // do we want to thread this ? (contention with seqsel and colsel locks, I
2153 * only copy colsel if there is a real intersection between
2154 * sequence selection and this panel's alignment
2156 boolean repaint = false;
2157 boolean copycolsel = false;
2159 SequenceGroup sgroup = null;
2160 if (seqsel != null && seqsel.getSize() > 0)
2162 if (av.getAlignment() == null)
2164 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2165 + " ViewId=" + av.getViewId()
2166 + " 's alignment is NULL! returning immediately.");
2169 sgroup = seqsel.intersect(av.getAlignment(),
2170 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2171 if ((sgroup != null && sgroup.getSize() > 0))
2176 if (sgroup != null && sgroup.getSize() > 0)
2178 av.setSelectionGroup(sgroup);
2182 av.setSelectionGroup(null);
2184 av.isSelectionGroupChanged(true);
2189 // the current selection is unset or from a previous message
2190 // so import the new colsel.
2191 if (colsel == null || colsel.isEmpty())
2193 if (av.getColumnSelection() != null)
2195 av.getColumnSelection().clear();
2201 // TODO: shift colSel according to the intersecting sequences
2202 if (av.getColumnSelection() == null)
2204 av.setColumnSelection(new ColumnSelection(colsel));
2208 av.getColumnSelection().setElementsFrom(colsel,
2209 av.getAlignment().getHiddenColumns());
2212 av.isColSelChanged(true);
2216 if (copycolsel && av.hasHiddenColumns()
2217 && (av.getAlignment().getHiddenColumns() == null))
2219 System.err.println("Bad things");
2221 if (repaint) // always true!
2223 // probably finessing with multiple redraws here
2224 PaintRefresher.Refresh(this, av.getSequenceSetId());
2225 // ap.paintAlignment(false);
2228 // lastly, update dependent dialogs
2229 if (ap.getCalculationDialog() != null)
2231 ap.getCalculationDialog().validateCalcTypes();
2237 * If this panel is a cdna/protein translation view of the selection source,
2238 * tries to map the source selection to a local one, and returns true. Else
2245 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2246 ColumnSelection colsel, HiddenColumns hidden,
2247 SelectionSource source)
2249 if (!(source instanceof AlignViewportI))
2253 final AlignViewportI sourceAv = (AlignViewportI) source;
2254 if (sourceAv.getCodingComplement() != av
2255 && av.getCodingComplement() != sourceAv)
2261 * Map sequence selection
2263 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2264 av.setSelectionGroup(sg);
2265 av.isSelectionGroupChanged(true);
2268 * Map column selection
2270 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2272 ColumnSelection cs = new ColumnSelection();
2273 HiddenColumns hs = new HiddenColumns();
2274 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2275 av.setColumnSelection(cs);
2276 av.getAlignment().setHiddenColumns(hs);
2278 // lastly, update any dependent dialogs
2279 if (ap.getCalculationDialog() != null)
2281 ap.getCalculationDialog().validateCalcTypes();
2284 PaintRefresher.Refresh(this, av.getSequenceSetId());