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 // TODO: once JAL-2759 is ready, change this loop to something more
368 while (!hidden.isVisible(seqCanvas.cursorX)
369 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0
372 seqCanvas.cursorX += dx;
375 if (seqCanvas.cursorX >= maxWidth
376 || !hidden.isVisible(seqCanvas.cursorX))
378 seqCanvas.cursorX = original;
382 scrollToVisible(false);
386 * Scroll to make the cursor visible in the viewport.
389 * just jump to the location rather than scrolling
391 void scrollToVisible(boolean jump)
393 if (seqCanvas.cursorX < 0)
395 seqCanvas.cursorX = 0;
397 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
399 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
402 if (seqCanvas.cursorY < 0)
404 seqCanvas.cursorY = 0;
406 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
408 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
413 boolean repaintNeeded = true;
416 // only need to repaint if the viewport did not move, as otherwise it will
418 repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
423 if (av.getWrapAlignment())
425 // scrollToWrappedVisible expects x-value to have hidden cols subtracted
426 int x = av.getAlignment().getHiddenColumns()
427 .findColumnPosition(seqCanvas.cursorX);
428 av.getRanges().scrollToWrappedVisible(x);
432 av.getRanges().scrollToVisible(seqCanvas.cursorX,
437 if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
439 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
440 seqCanvas.cursorX, seqCanvas.cursorY);
450 void setSelectionAreaAtCursor(boolean topLeft)
452 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
454 if (av.getSelectionGroup() != null)
456 SequenceGroup sg = av.getSelectionGroup();
457 // Find the top and bottom of this group
458 int min = av.getAlignment().getHeight(), max = 0;
459 for (int i = 0; i < sg.getSize(); i++)
461 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
476 sg.setStartRes(seqCanvas.cursorX);
477 if (sg.getEndRes() < seqCanvas.cursorX)
479 sg.setEndRes(seqCanvas.cursorX);
482 min = seqCanvas.cursorY;
486 sg.setEndRes(seqCanvas.cursorX);
487 if (sg.getStartRes() > seqCanvas.cursorX)
489 sg.setStartRes(seqCanvas.cursorX);
492 max = seqCanvas.cursorY + 1;
497 // Only the user can do this
498 av.setSelectionGroup(null);
502 // Now add any sequences between min and max
503 sg.getSequences(null).clear();
504 for (int i = min; i < max; i++)
506 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
511 if (av.getSelectionGroup() == null)
513 SequenceGroup sg = new SequenceGroup();
514 sg.setStartRes(seqCanvas.cursorX);
515 sg.setEndRes(seqCanvas.cursorX);
516 sg.addSequence(sequence, false);
517 av.setSelectionGroup(sg);
520 ap.paintAlignment(false, false);
524 void insertGapAtCursor(boolean group)
526 groupEditing = group;
527 startseq = seqCanvas.cursorY;
528 lastres = seqCanvas.cursorX;
529 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
533 void deleteGapAtCursor(boolean group)
535 groupEditing = group;
536 startseq = seqCanvas.cursorY;
537 lastres = seqCanvas.cursorX + getKeyboardNo1();
538 editSequence(false, false, seqCanvas.cursorX);
542 void insertNucAtCursor(boolean group, String nuc)
544 // TODO not called - delete?
545 groupEditing = group;
546 startseq = seqCanvas.cursorY;
547 lastres = seqCanvas.cursorX;
548 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
552 void numberPressed(char value)
554 if (keyboardNo1 == null)
556 keyboardNo1 = new StringBuffer();
559 if (keyboardNo2 != null)
561 keyboardNo2.append(value);
565 keyboardNo1.append(value);
573 if (keyboardNo1 != null)
575 int value = Integer.parseInt(keyboardNo1.toString());
579 } catch (Exception x)
590 if (keyboardNo2 != null)
592 int value = Integer.parseInt(keyboardNo2.toString());
596 } catch (Exception x)
610 public void mouseReleased(MouseEvent evt)
612 boolean didDrag = mouseDragging; // did we come here after a drag
613 mouseDragging = false;
614 mouseWheelPressed = false;
616 if (evt.isPopupTrigger()) // Windows: mouseReleased
625 doMouseReleasedDefineMode(evt, didDrag);
639 public void mousePressed(MouseEvent evt)
641 lastMousePress = evt.getPoint();
643 if (SwingUtilities.isMiddleMouseButton(evt))
645 mouseWheelPressed = true;
649 boolean isControlDown = Platform.isControlDown(evt);
650 if (evt.isShiftDown() || isControlDown)
660 doMousePressedDefineMode(evt);
664 int seq = findSeq(evt);
665 int res = findColumn(evt);
667 if (seq < 0 || res < 0)
672 if ((seq < av.getAlignment().getHeight())
673 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
690 public void mouseOverSequence(SequenceI sequence, int index, int pos)
692 String tmp = sequence.hashCode() + " " + index + " " + pos;
694 if (lastMessage == null || !lastMessage.equals(tmp))
696 // System.err.println("mouseOver Sequence: "+tmp);
697 ssm.mouseOverSequence(sequence, index, pos, av);
703 * Highlight the mapped region described by the search results object (unless
704 * unchanged). This supports highlight of protein while mousing over linked
705 * cDNA and vice versa. The status bar is also updated to show the location of
706 * the start of the highlighted region.
709 public void highlightSequence(SearchResultsI results)
711 if (results == null || results.equals(lastSearchResults))
715 lastSearchResults = results;
717 boolean wasScrolled = false;
719 if (av.isFollowHighlight())
721 // don't allow highlight of protein/cDNA to also scroll a complementary
722 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
723 // over residue to change abruptly, causing highlighted residue in panel 2
724 // to change, causing a scroll in panel 1 etc)
725 ap.setToScrollComplementPanel(false);
726 wasScrolled = ap.scrollToPosition(results, false);
729 seqCanvas.revalidate();
731 ap.setToScrollComplementPanel(true);
734 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
735 if (seqCanvas.highlightSearchResults(results, noFastPaint))
737 setStatusMessage(results);
742 public VamsasSource getVamsasSource()
744 return this.ap == null ? null : this.ap.av;
748 public void updateColours(SequenceI seq, int index)
750 System.out.println("update the seqPanel colours");
755 * Action on mouse movement is to update the status bar to show the current
756 * sequence position, and (if features are shown) to show any features at the
757 * position in a tooltip. Does nothing if the mouse move does not change
763 public void mouseMoved(MouseEvent evt)
767 // This is because MacOSX creates a mouseMoved
768 // If control is down, other platforms will not.
772 final int column = findColumn(evt);
773 final int seq = findSeq(evt);
775 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
780 if (column == lastMouseColumn && seq == lastMouseSeq)
783 * just a pixel move without change of residue
787 lastMouseColumn = column;
790 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
792 if (column >= sequence.getLength())
798 * set status bar message, returning residue position in sequence
800 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
801 final int pos = setStatusMessage(sequence, column, seq);
802 if (ssm != null && !isGapped)
804 mouseOverSequence(sequence, column, pos);
807 tooltipText.setLength(6); // Cuts the buffer back to <html>
809 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
812 for (int g = 0; g < groups.length; g++)
814 if (groups[g].getStartRes() <= column
815 && groups[g].getEndRes() >= column)
817 if (!groups[g].getName().startsWith("JTreeGroup")
818 && !groups[g].getName().startsWith("JGroup"))
820 tooltipText.append(groups[g].getName());
823 if (groups[g].getDescription() != null)
825 tooltipText.append(": " + groups[g].getDescription());
832 * add any features at the position to the tooltip; if over a gap, only
833 * add features that straddle the gap (pos may be the residue before or
836 if (av.isShowSequenceFeatures())
838 List<SequenceFeature> features = ap.getFeatureRenderer()
839 .findFeaturesAtColumn(sequence, column + 1);
840 seqARep.appendFeatures(tooltipText, pos, features,
841 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
843 if (tooltipText.length() == 6) // <html>
845 setToolTipText(null);
850 String textString = tooltipText.toString();
851 if (lastTooltip == null || !lastTooltip.equals(textString))
853 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
855 setToolTipText(formattedTooltipText);
856 lastTooltip = textString;
861 private Point lastp = null;
866 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
869 public Point getToolTipLocation(MouseEvent event)
871 int x = event.getX(), w = getWidth();
872 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
875 if (!event.isShiftDown() || p == null)
877 p = (tooltipText != null && tooltipText.length() > 6)
878 ? new Point(event.getX() + wdth, event.getY() - 20)
882 * TODO: try to modify position region is not obcured by tooltip
890 * set when the current UI interaction has resulted in a change that requires
891 * shading in overviews and structures to be recalculated. this could be
892 * changed to a something more expressive that indicates what actually has
893 * changed, so selective redraws can be applied (ie. only structures, only
896 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
899 * set if av.getSelectionGroup() refers to a group that is defined on the
900 * alignment view, rather than a transient selection
902 // private boolean editingDefinedGroup = false; // TODO: refactor to
903 // avcontroller or viewModel
906 * Sets the status message in alignment panel, showing the sequence number
907 * (index) and id, and residue and residue position if not at a gap, for the
908 * given sequence and column position. Returns the residue position returned
909 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
910 * if at a gapped position.
913 * aligned sequence object
917 * index of sequence in alignment
918 * @return sequence position of residue at column, or adjacent residue if at a
921 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
923 char sequenceChar = sequence.getCharAt(column);
924 int pos = sequence.findPosition(column);
925 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
931 * Builds the status message for the current cursor location and writes it to
932 * the status bar, for example
935 * Sequence 3 ID: FER1_SOLLC
936 * Sequence 5 ID: FER1_PEA Residue: THR (4)
937 * Sequence 5 ID: FER1_PEA Residue: B (3)
938 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
943 * sequence position in the alignment (1..)
944 * @param sequenceChar
945 * the character under the cursor
947 * the sequence residue position (if not over a gap)
949 protected void setStatusMessage(SequenceI sequence, int seqIndex,
950 char sequenceChar, int residuePos)
952 StringBuilder text = new StringBuilder(32);
955 * Sequence number (if known), and sequence name.
957 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
958 text.append("Sequence").append(seqno).append(" ID: ")
959 .append(sequence.getName());
961 String residue = null;
964 * Try to translate the display character to residue name (null for gap).
966 boolean isGapped = Comparison.isGap(sequenceChar);
970 boolean nucleotide = av.getAlignment().isNucleotide();
971 String displayChar = String.valueOf(sequenceChar);
974 residue = ResidueProperties.nucleotideName.get(displayChar);
978 residue = "X".equalsIgnoreCase(displayChar) ? "X"
979 : ("*".equals(displayChar) ? "STOP"
980 : ResidueProperties.aa2Triplet.get(displayChar));
982 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
983 .append(": ").append(residue == null ? displayChar : residue);
985 text.append(" (").append(Integer.toString(residuePos)).append(")");
987 ap.alignFrame.statusBar.setText(text.toString());
991 * Set the status bar message to highlight the first matched position in
996 private void setStatusMessage(SearchResultsI results)
998 AlignmentI al = this.av.getAlignment();
999 int sequenceIndex = al.findIndex(results);
1000 if (sequenceIndex == -1)
1004 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
1005 for (SearchResultMatchI m : results.getResults())
1007 SequenceI seq = m.getSequence();
1008 if (seq.getDatasetSequence() != null)
1010 seq = seq.getDatasetSequence();
1015 int start = m.getStart();
1016 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1027 public void mouseDragged(MouseEvent evt)
1029 if (mouseWheelPressed)
1031 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1032 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1034 int oldWidth = av.getCharWidth();
1036 // Which is bigger, left-right or up-down?
1037 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1038 .abs(evt.getX() - lastMousePress.getX()))
1041 * on drag up or down, decrement or increment font size
1043 int fontSize = av.font.getSize();
1044 boolean fontChanged = false;
1046 if (evt.getY() < lastMousePress.getY())
1051 else if (evt.getY() > lastMousePress.getY())
1064 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1066 av.setFont(newFont, true);
1067 av.setCharWidth(oldWidth);
1071 ap.av.getCodingComplement().setFont(newFont, true);
1072 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1073 .getSplitViewContainer();
1074 splitFrame.adjustLayout();
1075 splitFrame.repaint();
1082 * on drag left or right, decrement or increment character width
1085 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1087 newWidth = av.getCharWidth() - 1;
1088 av.setCharWidth(newWidth);
1090 else if (evt.getX() > lastMousePress.getX())
1092 newWidth = av.getCharWidth() + 1;
1093 av.setCharWidth(newWidth);
1097 ap.paintAlignment(false, false);
1101 * need to ensure newWidth is set on cdna, regardless of which
1102 * panel the mouse drag happened in; protein will compute its
1103 * character width as 1:1 or 3:1
1105 av.getCodingComplement().setCharWidth(newWidth);
1106 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1107 .getSplitViewContainer();
1108 splitFrame.adjustLayout();
1109 splitFrame.repaint();
1114 FontMetrics fm = getFontMetrics(av.getFont());
1115 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1117 lastMousePress = evt.getPoint();
1124 doMouseDraggedDefineMode(evt);
1128 int res = findColumn(evt);
1135 if ((lastres == -1) || (lastres == res))
1140 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1142 // dragLeft, delete gap
1143 editSequence(false, false, res);
1147 editSequence(true, false, res);
1150 mouseDragging = true;
1151 if ((scrollThread != null) && (scrollThread.isRunning()))
1153 scrollThread.setEvent(evt);
1157 // TODO: Make it more clever than many booleans
1158 synchronized void editSequence(boolean insertGap, boolean editSeq,
1162 int fixedRight = -1;
1163 boolean fixedColumns = false;
1164 SequenceGroup sg = av.getSelectionGroup();
1166 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1168 // No group, but the sequence may represent a group
1169 if (!groupEditing && av.hasHiddenRows())
1171 if (av.isHiddenRepSequence(seq))
1173 sg = av.getRepresentedSequences(seq);
1174 groupEditing = true;
1178 StringBuilder message = new StringBuilder(64);
1181 message.append("Edit group:");
1182 if (editCommand == null)
1184 editCommand = new EditCommand(
1185 MessageManager.getString("action.edit_group"));
1190 message.append("Edit sequence: " + seq.getName());
1191 String label = seq.getName();
1192 if (label.length() > 10)
1194 label = label.substring(0, 10);
1196 if (editCommand == null)
1198 editCommand = new EditCommand(MessageManager
1199 .formatMessage("label.edit_params", new String[]
1206 message.append(" insert ");
1210 message.append(" delete ");
1213 message.append(Math.abs(startres - lastres) + " gaps.");
1214 ap.alignFrame.statusBar.setText(message.toString());
1216 // Are we editing within a selection group?
1217 if (groupEditing || (sg != null
1218 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1220 fixedColumns = true;
1222 // sg might be null as the user may only see 1 sequence,
1223 // but the sequence represents a group
1226 if (!av.isHiddenRepSequence(seq))
1231 sg = av.getRepresentedSequences(seq);
1234 fixedLeft = sg.getStartRes();
1235 fixedRight = sg.getEndRes();
1237 if ((startres < fixedLeft && lastres >= fixedLeft)
1238 || (startres >= fixedLeft && lastres < fixedLeft)
1239 || (startres > fixedRight && lastres <= fixedRight)
1240 || (startres <= fixedRight && lastres > fixedRight))
1246 if (fixedLeft > startres)
1248 fixedRight = fixedLeft - 1;
1251 else if (fixedRight < startres)
1253 fixedLeft = fixedRight;
1258 if (av.hasHiddenColumns())
1260 fixedColumns = true;
1261 int y1 = av.getAlignment().getHiddenColumns()
1262 .getHiddenBoundaryLeft(startres);
1263 int y2 = av.getAlignment().getHiddenColumns()
1264 .getHiddenBoundaryRight(startres);
1266 if ((insertGap && startres > y1 && lastres < y1)
1267 || (!insertGap && startres < y2 && lastres > y2))
1273 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1274 // Selection spans a hidden region
1275 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1283 fixedRight = y2 - 1;
1290 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1291 int g, groupSize = vseqs.size();
1292 SequenceI[] groupSeqs = new SequenceI[groupSize];
1293 for (g = 0; g < groupSeqs.length; g++)
1295 groupSeqs[g] = vseqs.get(g);
1301 // If the user has selected the whole sequence, and is dragging to
1302 // the right, we can still extend the alignment and selectionGroup
1303 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1304 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1306 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1307 fixedRight = sg.getEndRes();
1310 // Is it valid with fixed columns??
1311 // Find the next gap before the end
1312 // of the visible region boundary
1313 boolean blank = false;
1314 for (; fixedRight > lastres; fixedRight--)
1318 for (g = 0; g < groupSize; g++)
1320 for (int j = 0; j < startres - lastres; j++)
1322 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1337 if (sg.getSize() == av.getAlignment().getHeight())
1339 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1340 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1346 int alWidth = av.getAlignment().getWidth();
1347 if (av.hasHiddenRows())
1349 int hwidth = av.getAlignment().getHiddenSequences()
1351 if (hwidth > alWidth)
1356 // We can still insert gaps if the selectionGroup
1357 // contains all the sequences
1358 sg.setEndRes(sg.getEndRes() + startres - lastres);
1359 fixedRight = alWidth + startres - lastres;
1370 else if (!insertGap)
1372 // / Are we able to delete?
1373 // ie are all columns blank?
1375 for (g = 0; g < groupSize; g++)
1377 for (int j = startres; j < lastres; j++)
1379 if (groupSeqs[g].getLength() <= j)
1384 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1386 // Not a gap, block edit not valid
1396 // dragging to the right
1397 if (fixedColumns && fixedRight != -1)
1399 for (int j = lastres; j < startres; j++)
1401 insertChar(j, groupSeqs, fixedRight);
1406 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1407 startres - lastres);
1412 // dragging to the left
1413 if (fixedColumns && fixedRight != -1)
1415 for (int j = lastres; j > startres; j--)
1417 deleteChar(startres, groupSeqs, fixedRight);
1422 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1423 lastres - startres);
1429 // ///Editing a single sequence///////////
1433 // dragging to the right
1434 if (fixedColumns && fixedRight != -1)
1436 for (int j = lastres; j < startres; j++)
1438 insertChar(j, new SequenceI[] { seq }, fixedRight);
1443 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1444 startres - lastres);
1451 // dragging to the left
1452 if (fixedColumns && fixedRight != -1)
1454 for (int j = lastres; j > startres; j--)
1456 if (!Comparison.isGap(seq.getCharAt(startres)))
1461 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1466 // could be a keyboard edit trying to delete none gaps
1468 for (int m = startres; m < lastres; m++)
1470 if (!Comparison.isGap(seq.getCharAt(m)))
1479 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1485 {// insertGap==false AND editSeq==TRUE;
1486 if (fixedColumns && fixedRight != -1)
1488 for (int j = lastres; j < startres; j++)
1490 insertChar(j, new SequenceI[] { seq }, fixedRight);
1495 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1496 startres - lastres);
1503 seqCanvas.repaint();
1506 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1508 int blankColumn = fixedColumn;
1509 for (int s = 0; s < seq.length; s++)
1511 // Find the next gap before the end of the visible region boundary
1512 // If lastCol > j, theres a boundary after the gap insertion
1514 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1516 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1518 // Theres a space, so break and insert the gap
1523 if (blankColumn <= j)
1525 blankColumn = fixedColumn;
1531 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1533 appendEdit(Action.INSERT_GAP, seq, j, 1);
1538 * Helper method to add and perform one edit action.
1545 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1549 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1550 av.getAlignment().getGapCharacter());
1552 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1555 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1558 appendEdit(Action.DELETE_GAP, seq, j, 1);
1560 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1570 public void mouseEntered(MouseEvent e)
1577 if ((scrollThread != null) && (scrollThread.isRunning()))
1579 scrollThread.stopScrolling();
1580 scrollThread = null;
1591 public void mouseExited(MouseEvent e)
1593 if (av.getWrapAlignment())
1598 if (mouseDragging && scrollThread == null)
1600 scrollThread = new ScrollThread();
1605 * Handler for double-click on a position with one or more sequence features.
1606 * Opens the Amend Features dialog to allow feature details to be amended, or
1607 * the feature deleted.
1610 public void mouseClicked(MouseEvent evt)
1612 SequenceGroup sg = null;
1613 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1614 if (evt.getClickCount() > 1)
1616 sg = av.getSelectionGroup();
1617 if (sg != null && sg.getSize() == 1
1618 && sg.getEndRes() - sg.getStartRes() < 2)
1620 av.setSelectionGroup(null);
1623 int column = findColumn(evt);
1626 * find features at the position (if not gapped), or straddling
1627 * the position (if at a gap)
1629 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1630 .findFeaturesAtColumn(sequence, column + 1);
1632 if (!features.isEmpty())
1635 * highlight the first feature at the position on the alignment
1637 SearchResultsI highlight = new SearchResults();
1638 highlight.addResult(sequence, features.get(0).getBegin(), features
1640 seqCanvas.highlightSearchResults(highlight, false);
1643 * open the Amend Features dialog; clear highlighting afterwards,
1644 * whether changes were made or not
1646 List<SequenceI> seqs = Collections.singletonList(sequence);
1647 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1649 av.setSearchResults(null); // clear highlighting
1650 seqCanvas.repaint(); // draw new/amended features
1656 public void mouseWheelMoved(MouseWheelEvent e)
1659 if (e.getWheelRotation() > 0)
1661 if (e.isShiftDown())
1663 av.getRanges().scrollRight(true);
1668 av.getRanges().scrollUp(false);
1673 if (e.isShiftDown())
1675 av.getRanges().scrollRight(false);
1679 av.getRanges().scrollUp(true);
1684 * update status bar and tooltip for new position
1685 * (need to synthesize a mouse movement to refresh tooltip)
1688 ToolTipManager.sharedInstance().mouseMoved(e);
1697 public void doMousePressedDefineMode(MouseEvent evt)
1699 final int res = findColumn(evt);
1700 final int seq = findSeq(evt);
1702 updateOverviewAndStructs = false;
1704 startWrapBlock = wrappedBlock;
1706 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1708 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1709 MessageManager.getString(
1710 "label.cannot_edit_annotations_in_wrapped_view"),
1711 MessageManager.getString("label.wrapped_view_no_edit"),
1712 JvOptionPane.WARNING_MESSAGE);
1716 if (seq < 0 || res < 0)
1721 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1723 if ((sequence == null) || (res > sequence.getLength()))
1728 stretchGroup = av.getSelectionGroup();
1730 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1732 stretchGroup = av.getAlignment().findGroup(sequence, res);
1733 if (stretchGroup != null)
1735 // only update the current selection if the popup menu has a group to
1737 av.setSelectionGroup(stretchGroup);
1741 if (evt.isPopupTrigger()) // Mac: mousePressed
1748 * defer right-mouse click handling to mouseReleased on Windows
1749 * (where isPopupTrigger() will answer true)
1750 * NB isRightMouseButton is also true for Cmd-click on Mac
1752 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1759 seqCanvas.cursorX = findColumn(evt);
1760 seqCanvas.cursorY = findSeq(evt);
1761 seqCanvas.repaint();
1765 if (stretchGroup == null)
1767 createStretchGroup(res, sequence);
1770 if (stretchGroup != null)
1772 stretchGroup.addPropertyChangeListener(seqCanvas);
1775 seqCanvas.repaint();
1778 private void createStretchGroup(int res, SequenceI sequence)
1780 // Only if left mouse button do we want to change group sizes
1781 // define a new group here
1782 SequenceGroup sg = new SequenceGroup();
1783 sg.setStartRes(res);
1785 sg.addSequence(sequence, false);
1786 av.setSelectionGroup(sg);
1789 if (av.getConservationSelected())
1791 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1795 if (av.getAbovePIDThreshold())
1797 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1800 // TODO: stretchGroup will always be not null. Is this a merge error ?
1801 // or is there a threading issue here?
1802 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1804 // Edit end res position of selected group
1805 changeEndRes = true;
1807 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1809 // Edit end res position of selected group
1810 changeStartRes = true;
1812 stretchGroup.getWidth();
1817 * Build and show a pop-up menu at the right-click mouse position
1823 void showPopupMenu(MouseEvent evt)
1825 final int column = findColumn(evt);
1826 final int seq = findSeq(evt);
1827 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1828 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1829 .findFeaturesAtColumn(sequence, column + 1);
1830 List<String> links = new ArrayList<>();
1831 for (SequenceFeature sf : allFeatures)
1833 if (sf.links != null)
1835 for (String link : sf.links)
1842 PopupMenu pop = new PopupMenu(ap, null, links);
1843 pop.show(this, evt.getX(), evt.getY());
1847 * Update the display after mouse up on a selection or group
1850 * mouse released event details
1852 * true if this event is happening after a mouse drag (rather than a
1855 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1857 if (stretchGroup == null)
1862 stretchGroup.removePropertyChangeListener(seqCanvas);
1864 // always do this - annotation has own state
1865 // but defer colourscheme update until hidden sequences are passed in
1866 boolean vischange = stretchGroup.recalcConservation(true);
1867 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1869 if (stretchGroup.cs != null)
1871 stretchGroup.cs.alignmentChanged(stretchGroup,
1872 av.getHiddenRepSequences());
1874 ResidueShaderI groupColourScheme = stretchGroup
1875 .getGroupColourScheme();
1876 String name = stretchGroup.getName();
1877 if (stretchGroup.cs.conservationApplied())
1879 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1881 if (stretchGroup.cs.getThreshold() > 0)
1883 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1886 PaintRefresher.Refresh(this, av.getSequenceSetId());
1887 // TODO: structure colours only need updating if stretchGroup used to or now
1888 // does contain sequences with structure views
1889 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1890 updateOverviewAndStructs = false;
1891 changeEndRes = false;
1892 changeStartRes = false;
1893 stretchGroup = null;
1903 public void doMouseDraggedDefineMode(MouseEvent evt)
1905 int res = findColumn(evt);
1906 int y = findSeq(evt);
1908 if (wrappedBlock != startWrapBlock)
1913 if (stretchGroup == null)
1918 if (res >= av.getAlignment().getWidth())
1920 res = av.getAlignment().getWidth() - 1;
1923 if (stretchGroup.getEndRes() == res)
1925 // Edit end res position of selected group
1926 changeEndRes = true;
1928 else if (stretchGroup.getStartRes() == res)
1930 // Edit start res position of selected group
1931 changeStartRes = true;
1934 if (res < av.getRanges().getStartRes())
1936 res = av.getRanges().getStartRes();
1941 if (res > (stretchGroup.getStartRes() - 1))
1943 stretchGroup.setEndRes(res);
1944 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1947 else if (changeStartRes)
1949 if (res < (stretchGroup.getEndRes() + 1))
1951 stretchGroup.setStartRes(res);
1952 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1956 int dragDirection = 0;
1962 else if (y < oldSeq)
1967 while ((y != oldSeq) && (oldSeq > -1)
1968 && (y < av.getAlignment().getHeight()))
1970 // This routine ensures we don't skip any sequences, as the
1971 // selection is quite slow.
1972 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1974 oldSeq += dragDirection;
1981 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1983 if (stretchGroup.getSequences(null).contains(nextSeq))
1985 stretchGroup.deleteSequence(seq, false);
1986 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1992 stretchGroup.addSequence(seq, false);
1995 stretchGroup.addSequence(nextSeq, false);
1996 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2005 mouseDragging = true;
2007 if ((scrollThread != null) && (scrollThread.isRunning()))
2009 scrollThread.setEvent(evt);
2013 void scrollCanvas(MouseEvent evt)
2017 if ((scrollThread != null) && (scrollThread.isRunning()))
2019 scrollThread.stopScrolling();
2020 scrollThread = null;
2022 mouseDragging = false;
2026 if (scrollThread == null)
2028 scrollThread = new ScrollThread();
2031 mouseDragging = true;
2032 scrollThread.setEvent(evt);
2037 // this class allows scrolling off the bottom of the visible alignment
2038 class ScrollThread extends Thread
2042 private volatile boolean threadRunning = true;
2044 public ScrollThread()
2049 public void setEvent(MouseEvent e)
2054 public void stopScrolling()
2056 threadRunning = false;
2059 public boolean isRunning()
2061 return threadRunning;
2067 while (threadRunning)
2071 if (mouseDragging && (evt.getY() < 0)
2072 && (av.getRanges().getStartSeq() > 0))
2074 av.getRanges().scrollUp(true);
2077 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2078 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2080 av.getRanges().scrollUp(false);
2083 if (mouseDragging && (evt.getX() < 0))
2085 av.getRanges().scrollRight(false);
2087 else if (mouseDragging && (evt.getX() >= getWidth()))
2089 av.getRanges().scrollRight(true);
2096 } catch (Exception ex)
2104 * modify current selection according to a received message.
2107 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2108 HiddenColumns hidden, SelectionSource source)
2110 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2111 // handles selection messages...
2112 // TODO: extend config options to allow user to control if selections may be
2113 // shared between viewports.
2114 boolean iSentTheSelection = (av == source
2115 || (source instanceof AlignViewport
2116 && ((AlignmentViewport) source).getSequenceSetId()
2117 .equals(av.getSequenceSetId())));
2119 if (iSentTheSelection)
2121 // respond to our own event by updating dependent dialogs
2122 if (ap.getCalculationDialog() != null)
2124 ap.getCalculationDialog().validateCalcTypes();
2130 // process further ?
2131 if (!av.followSelection)
2137 * Ignore the selection if there is one of our own pending.
2139 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2145 * Check for selection in a view of which this one is a dna/protein
2148 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2153 // do we want to thread this ? (contention with seqsel and colsel locks, I
2156 * only copy colsel if there is a real intersection between
2157 * sequence selection and this panel's alignment
2159 boolean repaint = false;
2160 boolean copycolsel = false;
2162 SequenceGroup sgroup = null;
2163 if (seqsel != null && seqsel.getSize() > 0)
2165 if (av.getAlignment() == null)
2167 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2168 + " ViewId=" + av.getViewId()
2169 + " 's alignment is NULL! returning immediately.");
2172 sgroup = seqsel.intersect(av.getAlignment(),
2173 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2174 if ((sgroup != null && sgroup.getSize() > 0))
2179 if (sgroup != null && sgroup.getSize() > 0)
2181 av.setSelectionGroup(sgroup);
2185 av.setSelectionGroup(null);
2187 av.isSelectionGroupChanged(true);
2192 // the current selection is unset or from a previous message
2193 // so import the new colsel.
2194 if (colsel == null || colsel.isEmpty())
2196 if (av.getColumnSelection() != null)
2198 av.getColumnSelection().clear();
2204 // TODO: shift colSel according to the intersecting sequences
2205 if (av.getColumnSelection() == null)
2207 av.setColumnSelection(new ColumnSelection(colsel));
2211 av.getColumnSelection().setElementsFrom(colsel,
2212 av.getAlignment().getHiddenColumns());
2215 av.isColSelChanged(true);
2219 if (copycolsel && av.hasHiddenColumns()
2220 && (av.getAlignment().getHiddenColumns() == null))
2222 System.err.println("Bad things");
2224 if (repaint) // always true!
2226 // probably finessing with multiple redraws here
2227 PaintRefresher.Refresh(this, av.getSequenceSetId());
2228 // ap.paintAlignment(false);
2231 // lastly, update dependent dialogs
2232 if (ap.getCalculationDialog() != null)
2234 ap.getCalculationDialog().validateCalcTypes();
2240 * If this panel is a cdna/protein translation view of the selection source,
2241 * tries to map the source selection to a local one, and returns true. Else
2248 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2249 ColumnSelection colsel, HiddenColumns hidden,
2250 SelectionSource source)
2252 if (!(source instanceof AlignViewportI))
2256 final AlignViewportI sourceAv = (AlignViewportI) source;
2257 if (sourceAv.getCodingComplement() != av
2258 && av.getCodingComplement() != sourceAv)
2264 * Map sequence selection
2266 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2267 av.setSelectionGroup(sg);
2268 av.isSelectionGroupChanged(true);
2271 * Map column selection
2273 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2275 ColumnSelection cs = new ColumnSelection();
2276 HiddenColumns hs = new HiddenColumns();
2277 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2278 av.setColumnSelection(cs);
2279 av.getAlignment().setHiddenColumns(hs);
2281 // lastly, update any dependent dialogs
2282 if (ap.getCalculationDialog() != null)
2284 ap.getCalculationDialog().validateCalcTypes();
2287 PaintRefresher.Refresh(this, av.getSequenceSetId());