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 av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
426 av.getRanges().scrollToVisible(seqCanvas.cursorX,
431 if (!av.getAlignment().getHiddenSequences().isHidden(seqCanvas.cursorY)
432 && av.getAlignment().getHiddenColumns()
433 .isVisible(seqCanvas.cursorX))
435 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
436 seqCanvas.cursorX, seqCanvas.cursorY);
446 void setSelectionAreaAtCursor(boolean topLeft)
448 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
450 if (av.getSelectionGroup() != null)
452 SequenceGroup sg = av.getSelectionGroup();
453 // Find the top and bottom of this group
454 int min = av.getAlignment().getHeight(), max = 0;
455 for (int i = 0; i < sg.getSize(); i++)
457 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
472 sg.setStartRes(seqCanvas.cursorX);
473 if (sg.getEndRes() < seqCanvas.cursorX)
475 sg.setEndRes(seqCanvas.cursorX);
478 min = seqCanvas.cursorY;
482 sg.setEndRes(seqCanvas.cursorX);
483 if (sg.getStartRes() > seqCanvas.cursorX)
485 sg.setStartRes(seqCanvas.cursorX);
488 max = seqCanvas.cursorY + 1;
493 // Only the user can do this
494 av.setSelectionGroup(null);
498 // Now add any sequences between min and max
499 sg.getSequences(null).clear();
500 for (int i = min; i < max; i++)
502 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
507 if (av.getSelectionGroup() == null)
509 SequenceGroup sg = new SequenceGroup();
510 sg.setStartRes(seqCanvas.cursorX);
511 sg.setEndRes(seqCanvas.cursorX);
512 sg.addSequence(sequence, false);
513 av.setSelectionGroup(sg);
516 ap.paintAlignment(false, false);
520 void insertGapAtCursor(boolean group)
522 groupEditing = group;
523 startseq = seqCanvas.cursorY;
524 lastres = seqCanvas.cursorX;
525 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
529 void deleteGapAtCursor(boolean group)
531 groupEditing = group;
532 startseq = seqCanvas.cursorY;
533 lastres = seqCanvas.cursorX + getKeyboardNo1();
534 editSequence(false, false, seqCanvas.cursorX);
538 void insertNucAtCursor(boolean group, String nuc)
540 // TODO not called - delete?
541 groupEditing = group;
542 startseq = seqCanvas.cursorY;
543 lastres = seqCanvas.cursorX;
544 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
548 void numberPressed(char value)
550 if (keyboardNo1 == null)
552 keyboardNo1 = new StringBuffer();
555 if (keyboardNo2 != null)
557 keyboardNo2.append(value);
561 keyboardNo1.append(value);
569 if (keyboardNo1 != null)
571 int value = Integer.parseInt(keyboardNo1.toString());
575 } catch (Exception x)
586 if (keyboardNo2 != null)
588 int value = Integer.parseInt(keyboardNo2.toString());
592 } catch (Exception x)
606 public void mouseReleased(MouseEvent evt)
608 boolean didDrag = mouseDragging; // did we come here after a drag
609 mouseDragging = false;
610 mouseWheelPressed = false;
612 if (evt.isPopupTrigger()) // Windows: mouseReleased
621 doMouseReleasedDefineMode(evt, didDrag);
635 public void mousePressed(MouseEvent evt)
637 lastMousePress = evt.getPoint();
639 if (SwingUtilities.isMiddleMouseButton(evt))
641 mouseWheelPressed = true;
645 boolean isControlDown = Platform.isControlDown(evt);
646 if (evt.isShiftDown() || isControlDown)
656 doMousePressedDefineMode(evt);
660 int seq = findSeq(evt);
661 int res = findColumn(evt);
663 if (seq < 0 || res < 0)
668 if ((seq < av.getAlignment().getHeight())
669 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
686 public void mouseOverSequence(SequenceI sequence, int index, int pos)
688 String tmp = sequence.hashCode() + " " + index + " " + pos;
690 if (lastMessage == null || !lastMessage.equals(tmp))
692 // System.err.println("mouseOver Sequence: "+tmp);
693 ssm.mouseOverSequence(sequence, index, pos, av);
699 * Highlight the mapped region described by the search results object (unless
700 * unchanged). This supports highlight of protein while mousing over linked
701 * cDNA and vice versa. The status bar is also updated to show the location of
702 * the start of the highlighted region.
705 public void highlightSequence(SearchResultsI results)
707 if (results == null || results.equals(lastSearchResults))
711 lastSearchResults = results;
713 boolean wasScrolled = false;
715 if (av.isFollowHighlight())
717 // don't allow highlight of protein/cDNA to also scroll a complementary
718 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
719 // over residue to change abruptly, causing highlighted residue in panel 2
720 // to change, causing a scroll in panel 1 etc)
721 ap.setToScrollComplementPanel(false);
722 wasScrolled = ap.scrollToPosition(results, false);
725 seqCanvas.revalidate();
727 ap.setToScrollComplementPanel(true);
730 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
731 if (seqCanvas.highlightSearchResults(results, noFastPaint))
733 setStatusMessage(results);
738 public VamsasSource getVamsasSource()
740 return this.ap == null ? null : this.ap.av;
744 public void updateColours(SequenceI seq, int index)
746 System.out.println("update the seqPanel colours");
751 * Action on mouse movement is to update the status bar to show the current
752 * sequence position, and (if features are shown) to show any features at the
753 * position in a tooltip. Does nothing if the mouse move does not change
759 public void mouseMoved(MouseEvent evt)
763 // This is because MacOSX creates a mouseMoved
764 // If control is down, other platforms will not.
768 final int column = findColumn(evt);
769 final int seq = findSeq(evt);
771 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
776 if (column == lastMouseColumn && seq == lastMouseSeq)
779 * just a pixel move without change of residue
783 lastMouseColumn = column;
786 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
788 if (column >= sequence.getLength())
794 * set status bar message, returning residue position in sequence
796 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
797 final int pos = setStatusMessage(sequence, column, seq);
798 if (ssm != null && !isGapped)
800 mouseOverSequence(sequence, column, pos);
803 tooltipText.setLength(6); // Cuts the buffer back to <html>
805 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
808 for (int g = 0; g < groups.length; g++)
810 if (groups[g].getStartRes() <= column
811 && groups[g].getEndRes() >= column)
813 if (!groups[g].getName().startsWith("JTreeGroup")
814 && !groups[g].getName().startsWith("JGroup"))
816 tooltipText.append(groups[g].getName());
819 if (groups[g].getDescription() != null)
821 tooltipText.append(": " + groups[g].getDescription());
828 * add any features at the position to the tooltip; if over a gap, only
829 * add features that straddle the gap (pos may be the residue before or
832 if (av.isShowSequenceFeatures())
834 List<SequenceFeature> features = ap.getFeatureRenderer()
835 .findFeaturesAtColumn(sequence, column + 1);
836 seqARep.appendFeatures(tooltipText, pos, features,
837 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
839 if (tooltipText.length() == 6) // <html>
841 setToolTipText(null);
846 String textString = tooltipText.toString();
847 if (lastTooltip == null || !lastTooltip.equals(textString))
849 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
851 setToolTipText(formattedTooltipText);
852 lastTooltip = textString;
857 private Point lastp = null;
862 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
865 public Point getToolTipLocation(MouseEvent event)
867 int x = event.getX(), w = getWidth();
868 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
871 if (!event.isShiftDown() || p == null)
873 p = (tooltipText != null && tooltipText.length() > 6)
874 ? new Point(event.getX() + wdth, event.getY() - 20)
878 * TODO: try to modify position region is not obcured by tooltip
886 * set when the current UI interaction has resulted in a change that requires
887 * shading in overviews and structures to be recalculated. this could be
888 * changed to a something more expressive that indicates what actually has
889 * changed, so selective redraws can be applied (ie. only structures, only
892 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
895 * set if av.getSelectionGroup() refers to a group that is defined on the
896 * alignment view, rather than a transient selection
898 // private boolean editingDefinedGroup = false; // TODO: refactor to
899 // avcontroller or viewModel
902 * Sets the status message in alignment panel, showing the sequence number
903 * (index) and id, and residue and residue position if not at a gap, for the
904 * given sequence and column position. Returns the residue position returned
905 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
906 * if at a gapped position.
909 * aligned sequence object
913 * index of sequence in alignment
914 * @return sequence position of residue at column, or adjacent residue if at a
917 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
919 char sequenceChar = sequence.getCharAt(column);
920 int pos = sequence.findPosition(column);
921 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
927 * Builds the status message for the current cursor location and writes it to
928 * the status bar, for example
931 * Sequence 3 ID: FER1_SOLLC
932 * Sequence 5 ID: FER1_PEA Residue: THR (4)
933 * Sequence 5 ID: FER1_PEA Residue: B (3)
934 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
939 * sequence position in the alignment (1..)
940 * @param sequenceChar
941 * the character under the cursor
943 * the sequence residue position (if not over a gap)
945 protected void setStatusMessage(SequenceI sequence, int seqIndex,
946 char sequenceChar, int residuePos)
948 StringBuilder text = new StringBuilder(32);
951 * Sequence number (if known), and sequence name.
953 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
954 text.append("Sequence").append(seqno).append(" ID: ")
955 .append(sequence.getName());
957 String residue = null;
960 * Try to translate the display character to residue name (null for gap).
962 boolean isGapped = Comparison.isGap(sequenceChar);
966 boolean nucleotide = av.getAlignment().isNucleotide();
967 String displayChar = String.valueOf(sequenceChar);
970 residue = ResidueProperties.nucleotideName.get(displayChar);
974 residue = "X".equalsIgnoreCase(displayChar) ? "X"
975 : ("*".equals(displayChar) ? "STOP"
976 : ResidueProperties.aa2Triplet.get(displayChar));
978 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
979 .append(": ").append(residue == null ? displayChar : residue);
981 text.append(" (").append(Integer.toString(residuePos)).append(")");
983 ap.alignFrame.statusBar.setText(text.toString());
987 * Set the status bar message to highlight the first matched position in
992 private void setStatusMessage(SearchResultsI results)
994 AlignmentI al = this.av.getAlignment();
995 int sequenceIndex = al.findIndex(results);
996 if (sequenceIndex == -1)
1000 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
1001 for (SearchResultMatchI m : results.getResults())
1003 SequenceI seq = m.getSequence();
1004 if (seq.getDatasetSequence() != null)
1006 seq = seq.getDatasetSequence();
1011 int start = m.getStart();
1012 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1023 public void mouseDragged(MouseEvent evt)
1025 if (mouseWheelPressed)
1027 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1028 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1030 int oldWidth = av.getCharWidth();
1032 // Which is bigger, left-right or up-down?
1033 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1034 .abs(evt.getX() - lastMousePress.getX()))
1037 * on drag up or down, decrement or increment font size
1039 int fontSize = av.font.getSize();
1040 boolean fontChanged = false;
1042 if (evt.getY() < lastMousePress.getY())
1047 else if (evt.getY() > lastMousePress.getY())
1060 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1062 av.setFont(newFont, true);
1063 av.setCharWidth(oldWidth);
1067 ap.av.getCodingComplement().setFont(newFont, true);
1068 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1069 .getSplitViewContainer();
1070 splitFrame.adjustLayout();
1071 splitFrame.repaint();
1078 * on drag left or right, decrement or increment character width
1081 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1083 newWidth = av.getCharWidth() - 1;
1084 av.setCharWidth(newWidth);
1086 else if (evt.getX() > lastMousePress.getX())
1088 newWidth = av.getCharWidth() + 1;
1089 av.setCharWidth(newWidth);
1093 ap.paintAlignment(false, false);
1097 * need to ensure newWidth is set on cdna, regardless of which
1098 * panel the mouse drag happened in; protein will compute its
1099 * character width as 1:1 or 3:1
1101 av.getCodingComplement().setCharWidth(newWidth);
1102 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1103 .getSplitViewContainer();
1104 splitFrame.adjustLayout();
1105 splitFrame.repaint();
1110 FontMetrics fm = getFontMetrics(av.getFont());
1111 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1113 lastMousePress = evt.getPoint();
1120 doMouseDraggedDefineMode(evt);
1124 int res = findColumn(evt);
1131 if ((lastres == -1) || (lastres == res))
1136 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1138 // dragLeft, delete gap
1139 editSequence(false, false, res);
1143 editSequence(true, false, res);
1146 mouseDragging = true;
1147 if ((scrollThread != null) && (scrollThread.isRunning()))
1149 scrollThread.setEvent(evt);
1153 // TODO: Make it more clever than many booleans
1154 synchronized void editSequence(boolean insertGap, boolean editSeq,
1158 int fixedRight = -1;
1159 boolean fixedColumns = false;
1160 SequenceGroup sg = av.getSelectionGroup();
1162 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1164 // No group, but the sequence may represent a group
1165 if (!groupEditing && av.hasHiddenRows())
1167 if (av.isHiddenRepSequence(seq))
1169 sg = av.getRepresentedSequences(seq);
1170 groupEditing = true;
1174 StringBuilder message = new StringBuilder(64);
1177 message.append("Edit group:");
1178 if (editCommand == null)
1180 editCommand = new EditCommand(
1181 MessageManager.getString("action.edit_group"));
1186 message.append("Edit sequence: " + seq.getName());
1187 String label = seq.getName();
1188 if (label.length() > 10)
1190 label = label.substring(0, 10);
1192 if (editCommand == null)
1194 editCommand = new EditCommand(MessageManager
1195 .formatMessage("label.edit_params", new String[]
1202 message.append(" insert ");
1206 message.append(" delete ");
1209 message.append(Math.abs(startres - lastres) + " gaps.");
1210 ap.alignFrame.statusBar.setText(message.toString());
1212 // Are we editing within a selection group?
1213 if (groupEditing || (sg != null
1214 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1216 fixedColumns = true;
1218 // sg might be null as the user may only see 1 sequence,
1219 // but the sequence represents a group
1222 if (!av.isHiddenRepSequence(seq))
1227 sg = av.getRepresentedSequences(seq);
1230 fixedLeft = sg.getStartRes();
1231 fixedRight = sg.getEndRes();
1233 if ((startres < fixedLeft && lastres >= fixedLeft)
1234 || (startres >= fixedLeft && lastres < fixedLeft)
1235 || (startres > fixedRight && lastres <= fixedRight)
1236 || (startres <= fixedRight && lastres > fixedRight))
1242 if (fixedLeft > startres)
1244 fixedRight = fixedLeft - 1;
1247 else if (fixedRight < startres)
1249 fixedLeft = fixedRight;
1254 if (av.hasHiddenColumns())
1256 fixedColumns = true;
1257 int y1 = av.getAlignment().getHiddenColumns()
1258 .getHiddenBoundaryLeft(startres);
1259 int y2 = av.getAlignment().getHiddenColumns()
1260 .getHiddenBoundaryRight(startres);
1262 if ((insertGap && startres > y1 && lastres < y1)
1263 || (!insertGap && startres < y2 && lastres > y2))
1269 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1270 // Selection spans a hidden region
1271 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1279 fixedRight = y2 - 1;
1286 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1287 int g, groupSize = vseqs.size();
1288 SequenceI[] groupSeqs = new SequenceI[groupSize];
1289 for (g = 0; g < groupSeqs.length; g++)
1291 groupSeqs[g] = vseqs.get(g);
1297 // If the user has selected the whole sequence, and is dragging to
1298 // the right, we can still extend the alignment and selectionGroup
1299 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1300 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1302 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1303 fixedRight = sg.getEndRes();
1306 // Is it valid with fixed columns??
1307 // Find the next gap before the end
1308 // of the visible region boundary
1309 boolean blank = false;
1310 for (; fixedRight > lastres; fixedRight--)
1314 for (g = 0; g < groupSize; g++)
1316 for (int j = 0; j < startres - lastres; j++)
1318 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1333 if (sg.getSize() == av.getAlignment().getHeight())
1335 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1336 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1342 int alWidth = av.getAlignment().getWidth();
1343 if (av.hasHiddenRows())
1345 int hwidth = av.getAlignment().getHiddenSequences()
1347 if (hwidth > alWidth)
1352 // We can still insert gaps if the selectionGroup
1353 // contains all the sequences
1354 sg.setEndRes(sg.getEndRes() + startres - lastres);
1355 fixedRight = alWidth + startres - lastres;
1366 else if (!insertGap)
1368 // / Are we able to delete?
1369 // ie are all columns blank?
1371 for (g = 0; g < groupSize; g++)
1373 for (int j = startres; j < lastres; j++)
1375 if (groupSeqs[g].getLength() <= j)
1380 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1382 // Not a gap, block edit not valid
1392 // dragging to the right
1393 if (fixedColumns && fixedRight != -1)
1395 for (int j = lastres; j < startres; j++)
1397 insertChar(j, groupSeqs, fixedRight);
1402 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1403 startres - lastres);
1408 // dragging to the left
1409 if (fixedColumns && fixedRight != -1)
1411 for (int j = lastres; j > startres; j--)
1413 deleteChar(startres, groupSeqs, fixedRight);
1418 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1419 lastres - startres);
1425 // ///Editing a single sequence///////////
1429 // dragging to the right
1430 if (fixedColumns && fixedRight != -1)
1432 for (int j = lastres; j < startres; j++)
1434 insertChar(j, new SequenceI[] { seq }, fixedRight);
1439 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1440 startres - lastres);
1447 // dragging to the left
1448 if (fixedColumns && fixedRight != -1)
1450 for (int j = lastres; j > startres; j--)
1452 if (!Comparison.isGap(seq.getCharAt(startres)))
1457 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1462 // could be a keyboard edit trying to delete none gaps
1464 for (int m = startres; m < lastres; m++)
1466 if (!Comparison.isGap(seq.getCharAt(m)))
1475 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1481 {// insertGap==false AND editSeq==TRUE;
1482 if (fixedColumns && fixedRight != -1)
1484 for (int j = lastres; j < startres; j++)
1486 insertChar(j, new SequenceI[] { seq }, fixedRight);
1491 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1492 startres - lastres);
1499 seqCanvas.repaint();
1502 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1504 int blankColumn = fixedColumn;
1505 for (int s = 0; s < seq.length; s++)
1507 // Find the next gap before the end of the visible region boundary
1508 // If lastCol > j, theres a boundary after the gap insertion
1510 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1512 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1514 // Theres a space, so break and insert the gap
1519 if (blankColumn <= j)
1521 blankColumn = fixedColumn;
1527 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1529 appendEdit(Action.INSERT_GAP, seq, j, 1);
1534 * Helper method to add and perform one edit action.
1541 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1545 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1546 av.getAlignment().getGapCharacter());
1548 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1551 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1554 appendEdit(Action.DELETE_GAP, seq, j, 1);
1556 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1566 public void mouseEntered(MouseEvent e)
1573 if ((scrollThread != null) && (scrollThread.isRunning()))
1575 scrollThread.stopScrolling();
1576 scrollThread = null;
1587 public void mouseExited(MouseEvent e)
1589 if (av.getWrapAlignment())
1594 if (mouseDragging && scrollThread == null)
1596 scrollThread = new ScrollThread();
1601 * Handler for double-click on a position with one or more sequence features.
1602 * Opens the Amend Features dialog to allow feature details to be amended, or
1603 * the feature deleted.
1606 public void mouseClicked(MouseEvent evt)
1608 SequenceGroup sg = null;
1609 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1610 if (evt.getClickCount() > 1)
1612 sg = av.getSelectionGroup();
1613 if (sg != null && sg.getSize() == 1
1614 && sg.getEndRes() - sg.getStartRes() < 2)
1616 av.setSelectionGroup(null);
1619 int column = findColumn(evt);
1622 * find features at the position (if not gapped), or straddling
1623 * the position (if at a gap)
1625 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1626 .findFeaturesAtColumn(sequence, column + 1);
1628 if (!features.isEmpty())
1631 * highlight the first feature at the position on the alignment
1633 SearchResultsI highlight = new SearchResults();
1634 highlight.addResult(sequence, features.get(0).getBegin(), features
1636 seqCanvas.highlightSearchResults(highlight, false);
1639 * open the Amend Features dialog; clear highlighting afterwards,
1640 * whether changes were made or not
1642 List<SequenceI> seqs = Collections.singletonList(sequence);
1643 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1645 av.setSearchResults(null); // clear highlighting
1646 seqCanvas.repaint(); // draw new/amended features
1652 public void mouseWheelMoved(MouseWheelEvent e)
1655 if (e.getWheelRotation() > 0)
1657 if (e.isShiftDown())
1659 av.getRanges().scrollRight(true);
1664 av.getRanges().scrollUp(false);
1669 if (e.isShiftDown())
1671 av.getRanges().scrollRight(false);
1675 av.getRanges().scrollUp(true);
1680 * update status bar and tooltip for new position
1681 * (need to synthesize a mouse movement to refresh tooltip)
1684 ToolTipManager.sharedInstance().mouseMoved(e);
1693 public void doMousePressedDefineMode(MouseEvent evt)
1695 final int res = findColumn(evt);
1696 final int seq = findSeq(evt);
1698 updateOverviewAndStructs = false;
1700 startWrapBlock = wrappedBlock;
1702 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1704 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1705 MessageManager.getString(
1706 "label.cannot_edit_annotations_in_wrapped_view"),
1707 MessageManager.getString("label.wrapped_view_no_edit"),
1708 JvOptionPane.WARNING_MESSAGE);
1712 if (seq < 0 || res < 0)
1717 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1719 if ((sequence == null) || (res > sequence.getLength()))
1724 stretchGroup = av.getSelectionGroup();
1726 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1728 stretchGroup = av.getAlignment().findGroup(sequence, res);
1729 if (stretchGroup != null)
1731 // only update the current selection if the popup menu has a group to
1733 av.setSelectionGroup(stretchGroup);
1737 if (evt.isPopupTrigger()) // Mac: mousePressed
1744 * defer right-mouse click handling to mouseReleased on Windows
1745 * (where isPopupTrigger() will answer true)
1746 * NB isRightMouseButton is also true for Cmd-click on Mac
1748 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1755 seqCanvas.cursorX = findColumn(evt);
1756 seqCanvas.cursorY = findSeq(evt);
1757 seqCanvas.repaint();
1761 if (stretchGroup == null)
1763 createStretchGroup(res, sequence);
1766 if (stretchGroup != null)
1768 stretchGroup.addPropertyChangeListener(seqCanvas);
1771 seqCanvas.repaint();
1774 private void createStretchGroup(int res, SequenceI sequence)
1776 // Only if left mouse button do we want to change group sizes
1777 // define a new group here
1778 SequenceGroup sg = new SequenceGroup();
1779 sg.setStartRes(res);
1781 sg.addSequence(sequence, false);
1782 av.setSelectionGroup(sg);
1785 if (av.getConservationSelected())
1787 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1791 if (av.getAbovePIDThreshold())
1793 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1796 // TODO: stretchGroup will always be not null. Is this a merge error ?
1797 // or is there a threading issue here?
1798 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1800 // Edit end res position of selected group
1801 changeEndRes = true;
1803 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1805 // Edit end res position of selected group
1806 changeStartRes = true;
1808 stretchGroup.getWidth();
1813 * Build and show a pop-up menu at the right-click mouse position
1819 void showPopupMenu(MouseEvent evt)
1821 final int column = findColumn(evt);
1822 final int seq = findSeq(evt);
1823 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1824 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1825 .findFeaturesAtColumn(sequence, column + 1);
1826 List<String> links = new ArrayList<>();
1827 for (SequenceFeature sf : allFeatures)
1829 if (sf.links != null)
1831 for (String link : sf.links)
1838 PopupMenu pop = new PopupMenu(ap, null, links);
1839 pop.show(this, evt.getX(), evt.getY());
1843 * Update the display after mouse up on a selection or group
1846 * mouse released event details
1848 * true if this event is happening after a mouse drag (rather than a
1851 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1853 if (stretchGroup == null)
1858 stretchGroup.removePropertyChangeListener(seqCanvas);
1860 // always do this - annotation has own state
1861 // but defer colourscheme update until hidden sequences are passed in
1862 boolean vischange = stretchGroup.recalcConservation(true);
1863 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1865 if (stretchGroup.cs != null)
1867 stretchGroup.cs.alignmentChanged(stretchGroup,
1868 av.getHiddenRepSequences());
1870 ResidueShaderI groupColourScheme = stretchGroup
1871 .getGroupColourScheme();
1872 String name = stretchGroup.getName();
1873 if (stretchGroup.cs.conservationApplied())
1875 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1877 if (stretchGroup.cs.getThreshold() > 0)
1879 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1882 PaintRefresher.Refresh(this, av.getSequenceSetId());
1883 // TODO: structure colours only need updating if stretchGroup used to or now
1884 // does contain sequences with structure views
1885 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1886 updateOverviewAndStructs = false;
1887 changeEndRes = false;
1888 changeStartRes = false;
1889 stretchGroup = null;
1899 public void doMouseDraggedDefineMode(MouseEvent evt)
1901 int res = findColumn(evt);
1902 int y = findSeq(evt);
1904 if (wrappedBlock != startWrapBlock)
1909 if (stretchGroup == null)
1914 if (res >= av.getAlignment().getWidth())
1916 res = av.getAlignment().getWidth() - 1;
1919 if (stretchGroup.getEndRes() == res)
1921 // Edit end res position of selected group
1922 changeEndRes = true;
1924 else if (stretchGroup.getStartRes() == res)
1926 // Edit start res position of selected group
1927 changeStartRes = true;
1930 if (res < av.getRanges().getStartRes())
1932 res = av.getRanges().getStartRes();
1937 if (res > (stretchGroup.getStartRes() - 1))
1939 stretchGroup.setEndRes(res);
1940 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1943 else if (changeStartRes)
1945 if (res < (stretchGroup.getEndRes() + 1))
1947 stretchGroup.setStartRes(res);
1948 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1952 int dragDirection = 0;
1958 else if (y < oldSeq)
1963 while ((y != oldSeq) && (oldSeq > -1)
1964 && (y < av.getAlignment().getHeight()))
1966 // This routine ensures we don't skip any sequences, as the
1967 // selection is quite slow.
1968 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1970 oldSeq += dragDirection;
1977 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1979 if (stretchGroup.getSequences(null).contains(nextSeq))
1981 stretchGroup.deleteSequence(seq, false);
1982 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1988 stretchGroup.addSequence(seq, false);
1991 stretchGroup.addSequence(nextSeq, false);
1992 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2001 mouseDragging = true;
2003 if ((scrollThread != null) && (scrollThread.isRunning()))
2005 scrollThread.setEvent(evt);
2009 void scrollCanvas(MouseEvent evt)
2013 if ((scrollThread != null) && (scrollThread.isRunning()))
2015 scrollThread.stopScrolling();
2016 scrollThread = null;
2018 mouseDragging = false;
2022 if (scrollThread == null)
2024 scrollThread = new ScrollThread();
2027 mouseDragging = true;
2028 scrollThread.setEvent(evt);
2033 // this class allows scrolling off the bottom of the visible alignment
2034 class ScrollThread extends Thread
2038 private volatile boolean threadRunning = true;
2040 public ScrollThread()
2045 public void setEvent(MouseEvent e)
2050 public void stopScrolling()
2052 threadRunning = false;
2055 public boolean isRunning()
2057 return threadRunning;
2063 while (threadRunning)
2067 if (mouseDragging && (evt.getY() < 0)
2068 && (av.getRanges().getStartSeq() > 0))
2070 av.getRanges().scrollUp(true);
2073 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2074 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2076 av.getRanges().scrollUp(false);
2079 if (mouseDragging && (evt.getX() < 0))
2081 av.getRanges().scrollRight(false);
2083 else if (mouseDragging && (evt.getX() >= getWidth()))
2085 av.getRanges().scrollRight(true);
2092 } catch (Exception ex)
2100 * modify current selection according to a received message.
2103 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2104 HiddenColumns hidden, SelectionSource source)
2106 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2107 // handles selection messages...
2108 // TODO: extend config options to allow user to control if selections may be
2109 // shared between viewports.
2110 boolean iSentTheSelection = (av == source
2111 || (source instanceof AlignViewport
2112 && ((AlignmentViewport) source).getSequenceSetId()
2113 .equals(av.getSequenceSetId())));
2115 if (iSentTheSelection)
2117 // respond to our own event by updating dependent dialogs
2118 if (ap.getCalculationDialog() != null)
2120 ap.getCalculationDialog().validateCalcTypes();
2126 // process further ?
2127 if (!av.followSelection)
2133 * Ignore the selection if there is one of our own pending.
2135 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2141 * Check for selection in a view of which this one is a dna/protein
2144 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2149 // do we want to thread this ? (contention with seqsel and colsel locks, I
2152 * only copy colsel if there is a real intersection between
2153 * sequence selection and this panel's alignment
2155 boolean repaint = false;
2156 boolean copycolsel = false;
2158 SequenceGroup sgroup = null;
2159 if (seqsel != null && seqsel.getSize() > 0)
2161 if (av.getAlignment() == null)
2163 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2164 + " ViewId=" + av.getViewId()
2165 + " 's alignment is NULL! returning immediately.");
2168 sgroup = seqsel.intersect(av.getAlignment(),
2169 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2170 if ((sgroup != null && sgroup.getSize() > 0))
2175 if (sgroup != null && sgroup.getSize() > 0)
2177 av.setSelectionGroup(sgroup);
2181 av.setSelectionGroup(null);
2183 av.isSelectionGroupChanged(true);
2188 // the current selection is unset or from a previous message
2189 // so import the new colsel.
2190 if (colsel == null || colsel.isEmpty())
2192 if (av.getColumnSelection() != null)
2194 av.getColumnSelection().clear();
2200 // TODO: shift colSel according to the intersecting sequences
2201 if (av.getColumnSelection() == null)
2203 av.setColumnSelection(new ColumnSelection(colsel));
2207 av.getColumnSelection().setElementsFrom(colsel,
2208 av.getAlignment().getHiddenColumns());
2211 av.isColSelChanged(true);
2215 if (copycolsel && av.hasHiddenColumns()
2216 && (av.getAlignment().getHiddenColumns() == null))
2218 System.err.println("Bad things");
2220 if (repaint) // always true!
2222 // probably finessing with multiple redraws here
2223 PaintRefresher.Refresh(this, av.getSequenceSetId());
2224 // ap.paintAlignment(false);
2227 // lastly, update dependent dialogs
2228 if (ap.getCalculationDialog() != null)
2230 ap.getCalculationDialog().validateCalcTypes();
2236 * If this panel is a cdna/protein translation view of the selection source,
2237 * tries to map the source selection to a local one, and returns true. Else
2244 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2245 ColumnSelection colsel, HiddenColumns hidden,
2246 SelectionSource source)
2248 if (!(source instanceof AlignViewportI))
2252 final AlignViewportI sourceAv = (AlignViewportI) source;
2253 if (sourceAv.getCodingComplement() != av
2254 && av.getCodingComplement() != sourceAv)
2260 * Map sequence selection
2262 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2263 av.setSelectionGroup(sg);
2264 av.isSelectionGroupChanged(true);
2267 * Map column selection
2269 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2271 ColumnSelection cs = new ColumnSelection();
2272 HiddenColumns hs = new HiddenColumns();
2273 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2274 av.setColumnSelection(cs);
2275 av.getAlignment().setHiddenColumns(hs);
2277 // lastly, update any dependent dialogs
2278 if (ap.getCalculationDialog() != null)
2280 ap.getCalculationDialog().validateCalcTypes();
2283 PaintRefresher.Refresh(this, av.getSequenceSetId());