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.Collections;
63 import java.util.List;
65 import javax.swing.JPanel;
66 import javax.swing.SwingUtilities;
67 import javax.swing.ToolTipManager;
73 * @version $Revision: 1.130 $
75 public class SeqPanel extends JPanel
76 implements MouseListener, MouseMotionListener, MouseWheelListener,
77 SequenceListener, SelectionListener
79 private static final int MAX_TOOLTIP_LENGTH = 300;
81 public SeqCanvas seqCanvas;
83 public AlignmentPanel ap;
86 * last column position for mouseMoved event
88 private int lastMouseColumn;
91 * last sequence offset for mouseMoved event
93 private int lastMouseSeq;
95 protected int lastres;
97 protected int startseq;
99 protected AlignViewport av;
101 ScrollThread scrollThread = null;
103 boolean mouseDragging = false;
105 boolean editingSeqs = false;
107 boolean groupEditing = false;
109 // ////////////////////////////////////////
110 // ///Everything below this is for defining the boundary of the rubberband
111 // ////////////////////////////////////////
114 boolean changeEndSeq = false;
116 boolean changeStartSeq = false;
118 boolean changeEndRes = false;
120 boolean changeStartRes = false;
122 SequenceGroup stretchGroup = null;
124 boolean remove = false;
126 Point lastMousePress;
128 boolean mouseWheelPressed = false;
130 StringBuffer keyboardNo1;
132 StringBuffer keyboardNo2;
134 java.net.URL linkImageURL;
136 private final SequenceAnnotationReport seqARep;
138 StringBuilder tooltipText = new StringBuilder();
142 EditCommand editCommand;
144 StructureSelectionManager ssm;
146 SearchResultsI lastSearchResults;
149 * Creates a new SeqPanel object
154 public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
156 linkImageURL = getClass().getResource("/images/link.gif");
157 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
158 ToolTipManager.sharedInstance().registerComponent(this);
159 ToolTipManager.sharedInstance().setInitialDelay(0);
160 ToolTipManager.sharedInstance().setDismissDelay(10000);
162 setBackground(Color.white);
164 seqCanvas = new SeqCanvas(alignPanel);
165 setLayout(new BorderLayout());
166 add(seqCanvas, BorderLayout.CENTER);
168 this.ap = alignPanel;
170 if (!viewport.isDataset())
172 addMouseMotionListener(this);
173 addMouseListener(this);
174 addMouseWheelListener(this);
175 ssm = viewport.getStructureSelectionManager();
176 ssm.addStructureViewerListener(this);
177 ssm.addSelectionListener(this);
180 lastMouseColumn = -1;
184 int startWrapBlock = -1;
186 int wrappedBlock = -1;
189 * Returns the aligned sequence position (base 0) at the mouse position, or
190 * the closest visible one
195 int findColumn(MouseEvent evt)
200 int startRes = av.getRanges().getStartRes();
201 if (av.getWrapAlignment())
204 int hgap = av.getCharHeight();
205 if (av.getScaleAboveWrapped())
207 hgap += av.getCharHeight();
210 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
211 + hgap + seqCanvas.getAnnotationHeight();
214 y = Math.max(0, y - hgap);
215 x = Math.max(0, x - seqCanvas.getLabelWidthWest());
217 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
223 wrappedBlock = y / cHeight;
224 wrappedBlock += startRes / cwidth;
225 // allow for wrapped view scrolled right (possible from Overview)
226 int startOffset = startRes % cwidth;
227 res = wrappedBlock * cwidth + startOffset
228 + +Math.min(cwidth - 1, x / av.getCharWidth());
232 if (x > seqCanvas.getX() + seqCanvas.getWidth())
234 // make sure we calculate relative to visible alignment, rather than
236 x = seqCanvas.getX() + seqCanvas.getWidth();
238 res = (x / av.getCharWidth()) + startRes;
239 if (res > av.getRanges().getEndRes())
242 res = av.getRanges().getEndRes();
246 if (av.hasHiddenColumns())
248 res = av.getAlignment().getHiddenColumns()
249 .visibleToAbsoluteColumn(res);
256 int findSeq(MouseEvent evt)
261 if (av.getWrapAlignment())
263 int hgap = av.getCharHeight();
264 if (av.getScaleAboveWrapped())
266 hgap += av.getCharHeight();
269 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
270 + hgap + seqCanvas.getAnnotationHeight();
274 seq = Math.min((y % cHeight) / av.getCharHeight(),
275 av.getAlignment().getHeight() - 1);
280 (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
281 av.getAlignment().getHeight() - 1);
288 * When all of a sequence of edits are complete, put the resulting edit list
289 * on the history stack (undo list), and reset flags for editing in progress.
295 if (editCommand != null && editCommand.getSize() > 0)
297 ap.alignFrame.addHistoryItem(editCommand);
298 av.firePropertyChange("alignment", null,
299 av.getAlignment().getSequences());
304 * Tidy up come what may...
309 groupEditing = false;
318 seqCanvas.cursorY = getKeyboardNo1() - 1;
319 scrollToVisible(true);
322 void setCursorColumn()
324 seqCanvas.cursorX = getKeyboardNo1() - 1;
325 scrollToVisible(true);
328 void setCursorRowAndColumn()
330 if (keyboardNo2 == null)
332 keyboardNo2 = new StringBuffer();
336 seqCanvas.cursorX = getKeyboardNo1() - 1;
337 seqCanvas.cursorY = getKeyboardNo2() - 1;
338 scrollToVisible(true);
342 void setCursorPosition()
344 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
346 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
347 scrollToVisible(true);
350 void moveCursor(int dx, int dy)
352 seqCanvas.cursorX += dx;
353 seqCanvas.cursorY += dy;
355 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
357 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
359 int original = seqCanvas.cursorX - dx;
360 int maxWidth = av.getAlignment().getWidth();
362 if (!hidden.isVisible(seqCanvas.cursorX))
364 int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
365 int[] region = hidden.getRegionWithEdgeAtRes(visx);
367 if (region != null) // just in case
372 seqCanvas.cursorX = region[1] + 1;
377 seqCanvas.cursorX = region[0] - 1;
380 seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
383 if (seqCanvas.cursorX >= maxWidth
384 || !hidden.isVisible(seqCanvas.cursorX))
386 seqCanvas.cursorX = original;
390 scrollToVisible(false);
394 * Scroll to make the cursor visible in the viewport.
397 * just jump to the location rather than scrolling
399 void scrollToVisible(boolean jump)
401 if (seqCanvas.cursorX < 0)
403 seqCanvas.cursorX = 0;
405 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
407 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
410 if (seqCanvas.cursorY < 0)
412 seqCanvas.cursorY = 0;
414 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
416 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
421 boolean repaintNeeded = true;
424 // only need to repaint if the viewport did not move, as otherwise it will
426 repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
431 if (av.getWrapAlignment())
433 // scrollToWrappedVisible expects x-value to have hidden cols subtracted
434 int x = av.getAlignment().getHiddenColumns()
435 .absoluteToVisibleColumn(seqCanvas.cursorX);
436 av.getRanges().scrollToWrappedVisible(x);
440 av.getRanges().scrollToVisible(seqCanvas.cursorX,
445 if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
447 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
448 seqCanvas.cursorX, seqCanvas.cursorY);
458 void setSelectionAreaAtCursor(boolean topLeft)
460 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
462 if (av.getSelectionGroup() != null)
464 SequenceGroup sg = av.getSelectionGroup();
465 // Find the top and bottom of this group
466 int min = av.getAlignment().getHeight(), max = 0;
467 for (int i = 0; i < sg.getSize(); i++)
469 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
484 sg.setStartRes(seqCanvas.cursorX);
485 if (sg.getEndRes() < seqCanvas.cursorX)
487 sg.setEndRes(seqCanvas.cursorX);
490 min = seqCanvas.cursorY;
494 sg.setEndRes(seqCanvas.cursorX);
495 if (sg.getStartRes() > seqCanvas.cursorX)
497 sg.setStartRes(seqCanvas.cursorX);
500 max = seqCanvas.cursorY + 1;
505 // Only the user can do this
506 av.setSelectionGroup(null);
510 // Now add any sequences between min and max
511 sg.getSequences(null).clear();
512 for (int i = min; i < max; i++)
514 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
519 if (av.getSelectionGroup() == null)
521 SequenceGroup sg = new SequenceGroup();
522 sg.setStartRes(seqCanvas.cursorX);
523 sg.setEndRes(seqCanvas.cursorX);
524 sg.addSequence(sequence, false);
525 av.setSelectionGroup(sg);
528 ap.paintAlignment(false, false);
532 void insertGapAtCursor(boolean group)
534 groupEditing = group;
535 startseq = seqCanvas.cursorY;
536 lastres = seqCanvas.cursorX;
537 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
541 void deleteGapAtCursor(boolean group)
543 groupEditing = group;
544 startseq = seqCanvas.cursorY;
545 lastres = seqCanvas.cursorX + getKeyboardNo1();
546 editSequence(false, false, seqCanvas.cursorX);
550 void insertNucAtCursor(boolean group, String nuc)
552 // TODO not called - delete?
553 groupEditing = group;
554 startseq = seqCanvas.cursorY;
555 lastres = seqCanvas.cursorX;
556 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
560 void numberPressed(char value)
562 if (keyboardNo1 == null)
564 keyboardNo1 = new StringBuffer();
567 if (keyboardNo2 != null)
569 keyboardNo2.append(value);
573 keyboardNo1.append(value);
581 if (keyboardNo1 != null)
583 int value = Integer.parseInt(keyboardNo1.toString());
587 } catch (Exception x)
598 if (keyboardNo2 != null)
600 int value = Integer.parseInt(keyboardNo2.toString());
604 } catch (Exception x)
618 public void mouseReleased(MouseEvent evt)
620 boolean didDrag = mouseDragging; // did we come here after a drag
621 mouseDragging = false;
622 mouseWheelPressed = false;
624 if (evt.isPopupTrigger()) // Windows: mouseReleased
633 doMouseReleasedDefineMode(evt, didDrag);
647 public void mousePressed(MouseEvent evt)
649 lastMousePress = evt.getPoint();
651 if (SwingUtilities.isMiddleMouseButton(evt))
653 mouseWheelPressed = true;
657 boolean isControlDown = Platform.isControlDown(evt);
658 if (evt.isShiftDown() || isControlDown)
668 doMousePressedDefineMode(evt);
672 int seq = findSeq(evt);
673 int res = findColumn(evt);
675 if (seq < 0 || res < 0)
680 if ((seq < av.getAlignment().getHeight())
681 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
698 public void mouseOverSequence(SequenceI sequence, int index, int pos)
700 String tmp = sequence.hashCode() + " " + index + " " + pos;
702 if (lastMessage == null || !lastMessage.equals(tmp))
704 // System.err.println("mouseOver Sequence: "+tmp);
705 ssm.mouseOverSequence(sequence, index, pos, av);
711 * Highlight the mapped region described by the search results object (unless
712 * unchanged). This supports highlight of protein while mousing over linked
713 * cDNA and vice versa. The status bar is also updated to show the location of
714 * the start of the highlighted region.
717 public void highlightSequence(SearchResultsI results)
719 if (results == null || results.equals(lastSearchResults))
723 lastSearchResults = results;
725 boolean wasScrolled = false;
727 if (av.isFollowHighlight())
729 // don't allow highlight of protein/cDNA to also scroll a complementary
730 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
731 // over residue to change abruptly, causing highlighted residue in panel 2
732 // to change, causing a scroll in panel 1 etc)
733 ap.setToScrollComplementPanel(false);
734 wasScrolled = ap.scrollToPosition(results, false);
737 seqCanvas.revalidate();
739 ap.setToScrollComplementPanel(true);
742 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
743 if (seqCanvas.highlightSearchResults(results, noFastPaint))
745 setStatusMessage(results);
750 public VamsasSource getVamsasSource()
752 return this.ap == null ? null : this.ap.av;
756 public void updateColours(SequenceI seq, int index)
758 System.out.println("update the seqPanel colours");
763 * Action on mouse movement is to update the status bar to show the current
764 * sequence position, and (if features are shown) to show any features at the
765 * position in a tooltip. Does nothing if the mouse move does not change
771 public void mouseMoved(MouseEvent evt)
775 // This is because MacOSX creates a mouseMoved
776 // If control is down, other platforms will not.
780 final int column = findColumn(evt);
781 final int seq = findSeq(evt);
783 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
788 if (column == lastMouseColumn && seq == lastMouseSeq)
791 * just a pixel move without change of residue
795 lastMouseColumn = column;
798 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
800 if (column >= sequence.getLength())
806 * set status bar message, returning residue position in sequence
808 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
809 final int pos = setStatusMessage(sequence, column, seq);
810 if (ssm != null && !isGapped)
812 mouseOverSequence(sequence, column, pos);
815 tooltipText.setLength(6); // Cuts the buffer back to <html>
817 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
820 for (int g = 0; g < groups.length; g++)
822 if (groups[g].getStartRes() <= column
823 && groups[g].getEndRes() >= column)
825 if (!groups[g].getName().startsWith("JTreeGroup")
826 && !groups[g].getName().startsWith("JGroup"))
828 tooltipText.append(groups[g].getName());
831 if (groups[g].getDescription() != null)
833 tooltipText.append(": " + groups[g].getDescription());
840 * add any features at the position to the tooltip; if over a gap, only
841 * add features that straddle the gap (pos may be the residue before or
844 if (av.isShowSequenceFeatures())
846 List<SequenceFeature> features = ap.getFeatureRenderer()
847 .findFeaturesAtColumn(sequence, column + 1);
848 seqARep.appendFeatures(tooltipText, pos, features,
849 this.ap.getSeqPanel().seqCanvas.fr);
851 if (tooltipText.length() == 6) // <html>
853 setToolTipText(null);
858 if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
860 tooltipText.setLength(MAX_TOOLTIP_LENGTH);
861 tooltipText.append("...");
863 String textString = tooltipText.toString();
864 if (lastTooltip == null || !lastTooltip.equals(textString))
866 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
868 setToolTipText(formattedTooltipText);
869 lastTooltip = textString;
874 private Point lastp = null;
879 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
882 public Point getToolTipLocation(MouseEvent event)
884 int x = event.getX(), w = getWidth();
885 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
888 if (!event.isShiftDown() || p == null)
890 p = (tooltipText != null && tooltipText.length() > 6)
891 ? new Point(event.getX() + wdth, event.getY() - 20)
895 * TODO: try to modify position region is not obcured by tooltip
903 * set when the current UI interaction has resulted in a change that requires
904 * shading in overviews and structures to be recalculated. this could be
905 * changed to a something more expressive that indicates what actually has
906 * changed, so selective redraws can be applied (ie. only structures, only
909 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
912 * set if av.getSelectionGroup() refers to a group that is defined on the
913 * alignment view, rather than a transient selection
915 // private boolean editingDefinedGroup = false; // TODO: refactor to
916 // avcontroller or viewModel
919 * Sets the status message in alignment panel, showing the sequence number
920 * (index) and id, and residue and residue position if not at a gap, for the
921 * given sequence and column position. Returns the residue position returned
922 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
923 * if at a gapped position.
926 * aligned sequence object
930 * index of sequence in alignment
931 * @return sequence position of residue at column, or adjacent residue if at a
934 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
936 char sequenceChar = sequence.getCharAt(column);
937 int pos = sequence.findPosition(column);
938 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
944 * Builds the status message for the current cursor location and writes it to
945 * the status bar, for example
948 * Sequence 3 ID: FER1_SOLLC
949 * Sequence 5 ID: FER1_PEA Residue: THR (4)
950 * Sequence 5 ID: FER1_PEA Residue: B (3)
951 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
956 * sequence position in the alignment (1..)
957 * @param sequenceChar
958 * the character under the cursor
960 * the sequence residue position (if not over a gap)
962 protected void setStatusMessage(SequenceI sequence, int seqIndex,
963 char sequenceChar, int residuePos)
965 StringBuilder text = new StringBuilder(32);
968 * Sequence number (if known), and sequence name.
970 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
971 text.append("Sequence").append(seqno).append(" ID: ")
972 .append(sequence.getName());
974 String residue = null;
977 * Try to translate the display character to residue name (null for gap).
979 boolean isGapped = Comparison.isGap(sequenceChar);
983 boolean nucleotide = av.getAlignment().isNucleotide();
984 String displayChar = String.valueOf(sequenceChar);
987 residue = ResidueProperties.nucleotideName.get(displayChar);
991 residue = "X".equalsIgnoreCase(displayChar) ? "X"
992 : ("*".equals(displayChar) ? "STOP"
993 : ResidueProperties.aa2Triplet.get(displayChar));
995 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
996 .append(": ").append(residue == null ? displayChar : residue);
998 text.append(" (").append(Integer.toString(residuePos)).append(")");
1000 ap.alignFrame.statusBar.setText(text.toString());
1004 * Set the status bar message to highlight the first matched position in
1009 private void setStatusMessage(SearchResultsI results)
1011 AlignmentI al = this.av.getAlignment();
1012 int sequenceIndex = al.findIndex(results);
1013 if (sequenceIndex == -1)
1017 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
1018 for (SearchResultMatchI m : results.getResults())
1020 SequenceI seq = m.getSequence();
1021 if (seq.getDatasetSequence() != null)
1023 seq = seq.getDatasetSequence();
1028 int start = m.getStart();
1029 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1040 public void mouseDragged(MouseEvent evt)
1042 if (mouseWheelPressed)
1044 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1045 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1047 int oldWidth = av.getCharWidth();
1049 // Which is bigger, left-right or up-down?
1050 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1051 .abs(evt.getX() - lastMousePress.getX()))
1054 * on drag up or down, decrement or increment font size
1056 int fontSize = av.font.getSize();
1057 boolean fontChanged = false;
1059 if (evt.getY() < lastMousePress.getY())
1064 else if (evt.getY() > lastMousePress.getY())
1077 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1079 av.setFont(newFont, true);
1080 av.setCharWidth(oldWidth);
1084 ap.av.getCodingComplement().setFont(newFont, true);
1085 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1086 .getSplitViewContainer();
1087 splitFrame.adjustLayout();
1088 splitFrame.repaint();
1095 * on drag left or right, decrement or increment character width
1098 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1100 newWidth = av.getCharWidth() - 1;
1101 av.setCharWidth(newWidth);
1103 else if (evt.getX() > lastMousePress.getX())
1105 newWidth = av.getCharWidth() + 1;
1106 av.setCharWidth(newWidth);
1110 ap.paintAlignment(false, false);
1114 * need to ensure newWidth is set on cdna, regardless of which
1115 * panel the mouse drag happened in; protein will compute its
1116 * character width as 1:1 or 3:1
1118 av.getCodingComplement().setCharWidth(newWidth);
1119 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1120 .getSplitViewContainer();
1121 splitFrame.adjustLayout();
1122 splitFrame.repaint();
1127 FontMetrics fm = getFontMetrics(av.getFont());
1128 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1130 lastMousePress = evt.getPoint();
1137 doMouseDraggedDefineMode(evt);
1141 int res = findColumn(evt);
1148 if ((lastres == -1) || (lastres == res))
1153 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1155 // dragLeft, delete gap
1156 editSequence(false, false, res);
1160 editSequence(true, false, res);
1163 mouseDragging = true;
1164 if ((scrollThread != null) && (scrollThread.isRunning()))
1166 scrollThread.setEvent(evt);
1170 // TODO: Make it more clever than many booleans
1171 synchronized void editSequence(boolean insertGap, boolean editSeq,
1175 int fixedRight = -1;
1176 boolean fixedColumns = false;
1177 SequenceGroup sg = av.getSelectionGroup();
1179 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1181 // No group, but the sequence may represent a group
1182 if (!groupEditing && av.hasHiddenRows())
1184 if (av.isHiddenRepSequence(seq))
1186 sg = av.getRepresentedSequences(seq);
1187 groupEditing = true;
1191 StringBuilder message = new StringBuilder(64);
1194 message.append("Edit group:");
1195 if (editCommand == null)
1197 editCommand = new EditCommand(
1198 MessageManager.getString("action.edit_group"));
1203 message.append("Edit sequence: " + seq.getName());
1204 String label = seq.getName();
1205 if (label.length() > 10)
1207 label = label.substring(0, 10);
1209 if (editCommand == null)
1211 editCommand = new EditCommand(MessageManager
1212 .formatMessage("label.edit_params", new String[]
1219 message.append(" insert ");
1223 message.append(" delete ");
1226 message.append(Math.abs(startres - lastres) + " gaps.");
1227 ap.alignFrame.statusBar.setText(message.toString());
1229 // Are we editing within a selection group?
1230 if (groupEditing || (sg != null
1231 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1233 fixedColumns = true;
1235 // sg might be null as the user may only see 1 sequence,
1236 // but the sequence represents a group
1239 if (!av.isHiddenRepSequence(seq))
1244 sg = av.getRepresentedSequences(seq);
1247 fixedLeft = sg.getStartRes();
1248 fixedRight = sg.getEndRes();
1250 if ((startres < fixedLeft && lastres >= fixedLeft)
1251 || (startres >= fixedLeft && lastres < fixedLeft)
1252 || (startres > fixedRight && lastres <= fixedRight)
1253 || (startres <= fixedRight && lastres > fixedRight))
1259 if (fixedLeft > startres)
1261 fixedRight = fixedLeft - 1;
1264 else if (fixedRight < startres)
1266 fixedLeft = fixedRight;
1271 if (av.hasHiddenColumns())
1273 fixedColumns = true;
1274 int y1 = av.getAlignment().getHiddenColumns()
1275 .getNextHiddenBoundary(true, startres);
1276 int y2 = av.getAlignment().getHiddenColumns()
1277 .getNextHiddenBoundary(false, startres);
1279 if ((insertGap && startres > y1 && lastres < y1)
1280 || (!insertGap && startres < y2 && lastres > y2))
1286 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1287 // Selection spans a hidden region
1288 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1296 fixedRight = y2 - 1;
1303 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1304 int g, groupSize = vseqs.size();
1305 SequenceI[] groupSeqs = new SequenceI[groupSize];
1306 for (g = 0; g < groupSeqs.length; g++)
1308 groupSeqs[g] = vseqs.get(g);
1314 // If the user has selected the whole sequence, and is dragging to
1315 // the right, we can still extend the alignment and selectionGroup
1316 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1317 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1319 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1320 fixedRight = sg.getEndRes();
1323 // Is it valid with fixed columns??
1324 // Find the next gap before the end
1325 // of the visible region boundary
1326 boolean blank = false;
1327 for (; fixedRight > lastres; fixedRight--)
1331 for (g = 0; g < groupSize; g++)
1333 for (int j = 0; j < startres - lastres; j++)
1335 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1350 if (sg.getSize() == av.getAlignment().getHeight())
1352 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1354 .getNextHiddenBoundary(false, startres)))
1360 int alWidth = av.getAlignment().getWidth();
1361 if (av.hasHiddenRows())
1363 int hwidth = av.getAlignment().getHiddenSequences()
1365 if (hwidth > alWidth)
1370 // We can still insert gaps if the selectionGroup
1371 // contains all the sequences
1372 sg.setEndRes(sg.getEndRes() + startres - lastres);
1373 fixedRight = alWidth + startres - lastres;
1384 else if (!insertGap)
1386 // / Are we able to delete?
1387 // ie are all columns blank?
1389 for (g = 0; g < groupSize; g++)
1391 for (int j = startres; j < lastres; j++)
1393 if (groupSeqs[g].getLength() <= j)
1398 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1400 // Not a gap, block edit not valid
1410 // dragging to the right
1411 if (fixedColumns && fixedRight != -1)
1413 for (int j = lastres; j < startres; j++)
1415 insertChar(j, groupSeqs, fixedRight);
1420 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1421 startres - lastres);
1426 // dragging to the left
1427 if (fixedColumns && fixedRight != -1)
1429 for (int j = lastres; j > startres; j--)
1431 deleteChar(startres, groupSeqs, fixedRight);
1436 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1437 lastres - startres);
1443 // ///Editing a single sequence///////////
1447 // dragging to the right
1448 if (fixedColumns && fixedRight != -1)
1450 for (int j = lastres; j < startres; j++)
1452 insertChar(j, new SequenceI[] { seq }, fixedRight);
1457 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1458 startres - lastres);
1465 // dragging to the left
1466 if (fixedColumns && fixedRight != -1)
1468 for (int j = lastres; j > startres; j--)
1470 if (!Comparison.isGap(seq.getCharAt(startres)))
1475 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1480 // could be a keyboard edit trying to delete none gaps
1482 for (int m = startres; m < lastres; m++)
1484 if (!Comparison.isGap(seq.getCharAt(m)))
1493 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1499 {// insertGap==false AND editSeq==TRUE;
1500 if (fixedColumns && fixedRight != -1)
1502 for (int j = lastres; j < startres; j++)
1504 insertChar(j, new SequenceI[] { seq }, fixedRight);
1509 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1510 startres - lastres);
1517 seqCanvas.repaint();
1520 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1522 int blankColumn = fixedColumn;
1523 for (int s = 0; s < seq.length; s++)
1525 // Find the next gap before the end of the visible region boundary
1526 // If lastCol > j, theres a boundary after the gap insertion
1528 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1530 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1532 // Theres a space, so break and insert the gap
1537 if (blankColumn <= j)
1539 blankColumn = fixedColumn;
1545 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1547 appendEdit(Action.INSERT_GAP, seq, j, 1);
1552 * Helper method to add and perform one edit action.
1559 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1563 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1564 av.getAlignment().getGapCharacter());
1566 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1569 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1572 appendEdit(Action.DELETE_GAP, seq, j, 1);
1574 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1584 public void mouseEntered(MouseEvent e)
1591 if ((scrollThread != null) && (scrollThread.isRunning()))
1593 scrollThread.stopScrolling();
1594 scrollThread = null;
1605 public void mouseExited(MouseEvent e)
1607 if (av.getWrapAlignment())
1612 if (mouseDragging && scrollThread == null)
1614 scrollThread = new ScrollThread();
1619 * Handler for double-click on a position with one or more sequence features.
1620 * Opens the Amend Features dialog to allow feature details to be amended, or
1621 * the feature deleted.
1624 public void mouseClicked(MouseEvent evt)
1626 SequenceGroup sg = null;
1627 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1628 if (evt.getClickCount() > 1)
1630 sg = av.getSelectionGroup();
1631 if (sg != null && sg.getSize() == 1
1632 && sg.getEndRes() - sg.getStartRes() < 2)
1634 av.setSelectionGroup(null);
1637 int column = findColumn(evt);
1640 * find features at the position (if not gapped), or straddling
1641 * the position (if at a gap)
1643 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1644 .findFeaturesAtColumn(sequence, column + 1);
1646 if (!features.isEmpty())
1649 * highlight the first feature at the position on the alignment
1651 SearchResultsI highlight = new SearchResults();
1652 highlight.addResult(sequence, features.get(0).getBegin(), features
1654 seqCanvas.highlightSearchResults(highlight, false);
1657 * open the Amend Features dialog; clear highlighting afterwards,
1658 * whether changes were made or not
1660 List<SequenceI> seqs = Collections.singletonList(sequence);
1661 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1663 av.setSearchResults(null); // clear highlighting
1664 seqCanvas.repaint(); // draw new/amended features
1670 public void mouseWheelMoved(MouseWheelEvent e)
1673 double wheelRotation = e.getPreciseWheelRotation();
1674 if (wheelRotation > 0)
1676 if (e.isShiftDown())
1678 av.getRanges().scrollRight(true);
1683 av.getRanges().scrollUp(false);
1686 else if (wheelRotation < 0)
1688 if (e.isShiftDown())
1690 av.getRanges().scrollRight(false);
1694 av.getRanges().scrollUp(true);
1699 * update status bar and tooltip for new position
1700 * (need to synthesize a mouse movement to refresh tooltip)
1703 ToolTipManager.sharedInstance().mouseMoved(e);
1712 public void doMousePressedDefineMode(MouseEvent evt)
1714 final int res = findColumn(evt);
1715 final int seq = findSeq(evt);
1717 updateOverviewAndStructs = false;
1719 startWrapBlock = wrappedBlock;
1721 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1723 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1724 MessageManager.getString(
1725 "label.cannot_edit_annotations_in_wrapped_view"),
1726 MessageManager.getString("label.wrapped_view_no_edit"),
1727 JvOptionPane.WARNING_MESSAGE);
1731 if (seq < 0 || res < 0)
1736 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1738 if ((sequence == null) || (res > sequence.getLength()))
1743 stretchGroup = av.getSelectionGroup();
1745 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1747 stretchGroup = av.getAlignment().findGroup(sequence, res);
1748 if (stretchGroup != null)
1750 // only update the current selection if the popup menu has a group to
1752 av.setSelectionGroup(stretchGroup);
1756 if (evt.isPopupTrigger()) // Mac: mousePressed
1763 * defer right-mouse click handling to mouseReleased on Windows
1764 * (where isPopupTrigger() will answer true)
1765 * NB isRightMouseButton is also true for Cmd-click on Mac
1767 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1774 seqCanvas.cursorX = findColumn(evt);
1775 seqCanvas.cursorY = findSeq(evt);
1776 seqCanvas.repaint();
1780 if (stretchGroup == null)
1782 createStretchGroup(res, sequence);
1785 if (stretchGroup != null)
1787 stretchGroup.addPropertyChangeListener(seqCanvas);
1790 seqCanvas.repaint();
1793 private void createStretchGroup(int res, SequenceI sequence)
1795 // Only if left mouse button do we want to change group sizes
1796 // define a new group here
1797 SequenceGroup sg = new SequenceGroup();
1798 sg.setStartRes(res);
1800 sg.addSequence(sequence, false);
1801 av.setSelectionGroup(sg);
1804 if (av.getConservationSelected())
1806 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1810 if (av.getAbovePIDThreshold())
1812 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1815 // TODO: stretchGroup will always be not null. Is this a merge error ?
1816 // or is there a threading issue here?
1817 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1819 // Edit end res position of selected group
1820 changeEndRes = true;
1822 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1824 // Edit end res position of selected group
1825 changeStartRes = true;
1827 stretchGroup.getWidth();
1832 * Build and show a pop-up menu at the right-click mouse position
1838 void showPopupMenu(MouseEvent evt)
1840 final int column = findColumn(evt);
1841 final int seq = findSeq(evt);
1842 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1843 List<SequenceFeature> features = ap.getFeatureRenderer()
1844 .findFeaturesAtColumn(sequence, column + 1);
1846 PopupMenu pop = new PopupMenu(ap, null, features);
1847 pop.show(this, evt.getX(), evt.getY());
1851 * Update the display after mouse up on a selection or group
1854 * mouse released event details
1856 * true if this event is happening after a mouse drag (rather than a
1859 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1861 if (stretchGroup == null)
1866 stretchGroup.removePropertyChangeListener(seqCanvas);
1868 // always do this - annotation has own state
1869 // but defer colourscheme update until hidden sequences are passed in
1870 boolean vischange = stretchGroup.recalcConservation(true);
1871 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1873 if (stretchGroup.cs != null)
1875 stretchGroup.cs.alignmentChanged(stretchGroup,
1876 av.getHiddenRepSequences());
1878 ResidueShaderI groupColourScheme = stretchGroup
1879 .getGroupColourScheme();
1880 String name = stretchGroup.getName();
1881 if (stretchGroup.cs.conservationApplied())
1883 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1885 if (stretchGroup.cs.getThreshold() > 0)
1887 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1890 PaintRefresher.Refresh(this, av.getSequenceSetId());
1891 // TODO: structure colours only need updating if stretchGroup used to or now
1892 // does contain sequences with structure views
1893 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1894 updateOverviewAndStructs = false;
1895 changeEndRes = false;
1896 changeStartRes = false;
1897 stretchGroup = null;
1907 public void doMouseDraggedDefineMode(MouseEvent evt)
1909 int res = findColumn(evt);
1910 int y = findSeq(evt);
1912 if (wrappedBlock != startWrapBlock)
1917 if (stretchGroup == null)
1922 if (res >= av.getAlignment().getWidth())
1924 res = av.getAlignment().getWidth() - 1;
1927 if (stretchGroup.getEndRes() == res)
1929 // Edit end res position of selected group
1930 changeEndRes = true;
1932 else if (stretchGroup.getStartRes() == res)
1934 // Edit start res position of selected group
1935 changeStartRes = true;
1938 if (res < av.getRanges().getStartRes())
1940 res = av.getRanges().getStartRes();
1945 if (res > (stretchGroup.getStartRes() - 1))
1947 stretchGroup.setEndRes(res);
1948 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1951 else if (changeStartRes)
1953 if (res < (stretchGroup.getEndRes() + 1))
1955 stretchGroup.setStartRes(res);
1956 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1960 int dragDirection = 0;
1966 else if (y < oldSeq)
1971 while ((y != oldSeq) && (oldSeq > -1)
1972 && (y < av.getAlignment().getHeight()))
1974 // This routine ensures we don't skip any sequences, as the
1975 // selection is quite slow.
1976 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1978 oldSeq += dragDirection;
1985 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1987 if (stretchGroup.getSequences(null).contains(nextSeq))
1989 stretchGroup.deleteSequence(seq, false);
1990 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1996 stretchGroup.addSequence(seq, false);
1999 stretchGroup.addSequence(nextSeq, false);
2000 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2009 mouseDragging = true;
2011 if ((scrollThread != null) && (scrollThread.isRunning()))
2013 scrollThread.setEvent(evt);
2017 void scrollCanvas(MouseEvent evt)
2021 if ((scrollThread != null) && (scrollThread.isRunning()))
2023 scrollThread.stopScrolling();
2024 scrollThread = null;
2026 mouseDragging = false;
2030 if (scrollThread == null)
2032 scrollThread = new ScrollThread();
2035 mouseDragging = true;
2036 scrollThread.setEvent(evt);
2041 // this class allows scrolling off the bottom of the visible alignment
2042 class ScrollThread extends Thread
2046 private volatile boolean threadRunning = true;
2048 public ScrollThread()
2053 public void setEvent(MouseEvent e)
2058 public void stopScrolling()
2060 threadRunning = false;
2063 public boolean isRunning()
2065 return threadRunning;
2071 while (threadRunning)
2075 if (mouseDragging && (evt.getY() < 0)
2076 && (av.getRanges().getStartSeq() > 0))
2078 av.getRanges().scrollUp(true);
2081 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2082 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2084 av.getRanges().scrollUp(false);
2087 if (mouseDragging && (evt.getX() < 0))
2089 av.getRanges().scrollRight(false);
2091 else if (mouseDragging && (evt.getX() >= getWidth()))
2093 av.getRanges().scrollRight(true);
2100 } catch (Exception ex)
2108 * modify current selection according to a received message.
2111 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2112 HiddenColumns hidden, SelectionSource source)
2114 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2115 // handles selection messages...
2116 // TODO: extend config options to allow user to control if selections may be
2117 // shared between viewports.
2118 boolean iSentTheSelection = (av == source
2119 || (source instanceof AlignViewport
2120 && ((AlignmentViewport) source).getSequenceSetId()
2121 .equals(av.getSequenceSetId())));
2123 if (iSentTheSelection)
2125 // respond to our own event by updating dependent dialogs
2126 if (ap.getCalculationDialog() != null)
2128 ap.getCalculationDialog().validateCalcTypes();
2134 // process further ?
2135 if (!av.followSelection)
2141 * Ignore the selection if there is one of our own pending.
2143 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2149 * Check for selection in a view of which this one is a dna/protein
2152 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2157 // do we want to thread this ? (contention with seqsel and colsel locks, I
2160 * only copy colsel if there is a real intersection between
2161 * sequence selection and this panel's alignment
2163 boolean repaint = false;
2164 boolean copycolsel = false;
2166 SequenceGroup sgroup = null;
2167 if (seqsel != null && seqsel.getSize() > 0)
2169 if (av.getAlignment() == null)
2171 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2172 + " ViewId=" + av.getViewId()
2173 + " 's alignment is NULL! returning immediately.");
2176 sgroup = seqsel.intersect(av.getAlignment(),
2177 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2178 if ((sgroup != null && sgroup.getSize() > 0))
2183 if (sgroup != null && sgroup.getSize() > 0)
2185 av.setSelectionGroup(sgroup);
2189 av.setSelectionGroup(null);
2191 av.isSelectionGroupChanged(true);
2196 // the current selection is unset or from a previous message
2197 // so import the new colsel.
2198 if (colsel == null || colsel.isEmpty())
2200 if (av.getColumnSelection() != null)
2202 av.getColumnSelection().clear();
2208 // TODO: shift colSel according to the intersecting sequences
2209 if (av.getColumnSelection() == null)
2211 av.setColumnSelection(new ColumnSelection(colsel));
2215 av.getColumnSelection().setElementsFrom(colsel,
2216 av.getAlignment().getHiddenColumns());
2219 av.isColSelChanged(true);
2223 if (copycolsel && av.hasHiddenColumns()
2224 && (av.getAlignment().getHiddenColumns() == null))
2226 System.err.println("Bad things");
2228 if (repaint) // always true!
2230 // probably finessing with multiple redraws here
2231 PaintRefresher.Refresh(this, av.getSequenceSetId());
2232 // ap.paintAlignment(false);
2235 // lastly, update dependent dialogs
2236 if (ap.getCalculationDialog() != null)
2238 ap.getCalculationDialog().validateCalcTypes();
2244 * If this panel is a cdna/protein translation view of the selection source,
2245 * tries to map the source selection to a local one, and returns true. Else
2252 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2253 ColumnSelection colsel, HiddenColumns hidden,
2254 SelectionSource source)
2256 if (!(source instanceof AlignViewportI))
2260 final AlignViewportI sourceAv = (AlignViewportI) source;
2261 if (sourceAv.getCodingComplement() != av
2262 && av.getCodingComplement() != sourceAv)
2268 * Map sequence selection
2270 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2271 av.setSelectionGroup(sg);
2272 av.isSelectionGroupChanged(true);
2275 * Map column selection
2277 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2279 ColumnSelection cs = new ColumnSelection();
2280 HiddenColumns hs = new HiddenColumns();
2281 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2282 av.setColumnSelection(cs);
2283 av.getAlignment().setHiddenColumns(hs);
2285 // lastly, update any dependent dialogs
2286 if (ap.getCalculationDialog() != null)
2288 ap.getCalculationDialog().validateCalcTypes();
2291 PaintRefresher.Refresh(this, av.getSequenceSetId());
2298 * @return null or last search results handled by this panel
2300 public SearchResultsI getLastSearchResults()
2302 return lastSearchResults;