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 .visibleToAbsoluteColumn(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 if (!hidden.isVisible(seqCanvas.cursorX))
368 int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
369 int[] region = hidden.getRegionWithEdgeAtRes(visx);
371 if (region != null) // just in case
376 seqCanvas.cursorX = region[1] + 1;
381 seqCanvas.cursorX = region[0] - 1;
384 seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
387 if (seqCanvas.cursorX >= maxWidth
388 || !hidden.isVisible(seqCanvas.cursorX))
390 seqCanvas.cursorX = original;
394 scrollToVisible(false);
398 * Scroll to make the cursor visible in the viewport.
401 * just jump to the location rather than scrolling
403 void scrollToVisible(boolean jump)
405 if (seqCanvas.cursorX < 0)
407 seqCanvas.cursorX = 0;
409 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
411 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
414 if (seqCanvas.cursorY < 0)
416 seqCanvas.cursorY = 0;
418 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
420 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
425 boolean repaintNeeded = true;
428 // only need to repaint if the viewport did not move, as otherwise it will
430 repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
435 if (av.getWrapAlignment())
437 // scrollToWrappedVisible expects x-value to have hidden cols subtracted
438 int x = av.getAlignment().getHiddenColumns()
439 .absoluteToVisibleColumn(seqCanvas.cursorX);
440 av.getRanges().scrollToWrappedVisible(x);
444 av.getRanges().scrollToVisible(seqCanvas.cursorX,
449 if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
451 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
452 seqCanvas.cursorX, seqCanvas.cursorY);
462 void setSelectionAreaAtCursor(boolean topLeft)
464 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
466 if (av.getSelectionGroup() != null)
468 SequenceGroup sg = av.getSelectionGroup();
469 // Find the top and bottom of this group
470 int min = av.getAlignment().getHeight(), max = 0;
471 for (int i = 0; i < sg.getSize(); i++)
473 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
488 sg.setStartRes(seqCanvas.cursorX);
489 if (sg.getEndRes() < seqCanvas.cursorX)
491 sg.setEndRes(seqCanvas.cursorX);
494 min = seqCanvas.cursorY;
498 sg.setEndRes(seqCanvas.cursorX);
499 if (sg.getStartRes() > seqCanvas.cursorX)
501 sg.setStartRes(seqCanvas.cursorX);
504 max = seqCanvas.cursorY + 1;
509 // Only the user can do this
510 av.setSelectionGroup(null);
514 // Now add any sequences between min and max
515 sg.getSequences(null).clear();
516 for (int i = min; i < max; i++)
518 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
523 if (av.getSelectionGroup() == null)
525 SequenceGroup sg = new SequenceGroup();
526 sg.setStartRes(seqCanvas.cursorX);
527 sg.setEndRes(seqCanvas.cursorX);
528 sg.addSequence(sequence, false);
529 av.setSelectionGroup(sg);
532 ap.paintAlignment(false, false);
536 void insertGapAtCursor(boolean group)
538 groupEditing = group;
539 startseq = seqCanvas.cursorY;
540 lastres = seqCanvas.cursorX;
541 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
545 void deleteGapAtCursor(boolean group)
547 groupEditing = group;
548 startseq = seqCanvas.cursorY;
549 lastres = seqCanvas.cursorX + getKeyboardNo1();
550 editSequence(false, false, seqCanvas.cursorX);
554 void insertNucAtCursor(boolean group, String nuc)
556 // TODO not called - delete?
557 groupEditing = group;
558 startseq = seqCanvas.cursorY;
559 lastres = seqCanvas.cursorX;
560 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
564 void numberPressed(char value)
566 if (keyboardNo1 == null)
568 keyboardNo1 = new StringBuffer();
571 if (keyboardNo2 != null)
573 keyboardNo2.append(value);
577 keyboardNo1.append(value);
585 if (keyboardNo1 != null)
587 int value = Integer.parseInt(keyboardNo1.toString());
591 } catch (Exception x)
602 if (keyboardNo2 != null)
604 int value = Integer.parseInt(keyboardNo2.toString());
608 } catch (Exception x)
622 public void mouseReleased(MouseEvent evt)
624 boolean didDrag = mouseDragging; // did we come here after a drag
625 mouseDragging = false;
626 mouseWheelPressed = false;
628 if (evt.isPopupTrigger()) // Windows: mouseReleased
637 doMouseReleasedDefineMode(evt, didDrag);
651 public void mousePressed(MouseEvent evt)
653 lastMousePress = evt.getPoint();
655 if (SwingUtilities.isMiddleMouseButton(evt))
657 mouseWheelPressed = true;
661 boolean isControlDown = Platform.isControlDown(evt);
662 if (evt.isShiftDown() || isControlDown)
672 doMousePressedDefineMode(evt);
676 int seq = findSeq(evt);
677 int res = findColumn(evt);
679 if (seq < 0 || res < 0)
684 if ((seq < av.getAlignment().getHeight())
685 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
702 public void mouseOverSequence(SequenceI sequence, int index, int pos)
704 String tmp = sequence.hashCode() + " " + index + " " + pos;
706 if (lastMessage == null || !lastMessage.equals(tmp))
708 // System.err.println("mouseOver Sequence: "+tmp);
709 ssm.mouseOverSequence(sequence, index, pos, av);
715 * Highlight the mapped region described by the search results object (unless
716 * unchanged). This supports highlight of protein while mousing over linked
717 * cDNA and vice versa. The status bar is also updated to show the location of
718 * the start of the highlighted region.
721 public void highlightSequence(SearchResultsI results)
723 if (results == null || results.equals(lastSearchResults))
727 lastSearchResults = results;
729 boolean wasScrolled = false;
731 if (av.isFollowHighlight())
733 // don't allow highlight of protein/cDNA to also scroll a complementary
734 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
735 // over residue to change abruptly, causing highlighted residue in panel 2
736 // to change, causing a scroll in panel 1 etc)
737 ap.setToScrollComplementPanel(false);
738 wasScrolled = ap.scrollToPosition(results, false);
741 seqCanvas.revalidate();
743 ap.setToScrollComplementPanel(true);
746 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
747 if (seqCanvas.highlightSearchResults(results, noFastPaint))
749 setStatusMessage(results);
754 public VamsasSource getVamsasSource()
756 return this.ap == null ? null : this.ap.av;
760 public void updateColours(SequenceI seq, int index)
762 System.out.println("update the seqPanel colours");
767 * Action on mouse movement is to update the status bar to show the current
768 * sequence position, and (if features are shown) to show any features at the
769 * position in a tooltip. Does nothing if the mouse move does not change
775 public void mouseMoved(MouseEvent evt)
779 // This is because MacOSX creates a mouseMoved
780 // If control is down, other platforms will not.
784 final int column = findColumn(evt);
785 final int seq = findSeq(evt);
787 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
792 if (column == lastMouseColumn && seq == lastMouseSeq)
795 * just a pixel move without change of residue
799 lastMouseColumn = column;
802 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
804 if (column >= sequence.getLength())
810 * set status bar message, returning residue position in sequence
812 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
813 final int pos = setStatusMessage(sequence, column, seq);
814 if (ssm != null && !isGapped)
816 mouseOverSequence(sequence, column, pos);
819 tooltipText.setLength(6); // Cuts the buffer back to <html>
821 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
824 for (int g = 0; g < groups.length; g++)
826 if (groups[g].getStartRes() <= column
827 && groups[g].getEndRes() >= column)
829 if (!groups[g].getName().startsWith("JTreeGroup")
830 && !groups[g].getName().startsWith("JGroup"))
832 tooltipText.append(groups[g].getName());
835 if (groups[g].getDescription() != null)
837 tooltipText.append(": " + groups[g].getDescription());
844 * add any features at the position to the tooltip; if over a gap, only
845 * add features that straddle the gap (pos may be the residue before or
848 if (av.isShowSequenceFeatures())
850 List<SequenceFeature> features = ap.getFeatureRenderer()
851 .findFeaturesAtColumn(sequence, column + 1);
852 seqARep.appendFeatures(tooltipText, pos, features,
853 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
855 if (tooltipText.length() == 6) // <html>
857 setToolTipText(null);
862 String textString = tooltipText.toString();
863 if (lastTooltip == null || !lastTooltip.equals(textString))
865 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
867 setToolTipText(formattedTooltipText);
868 lastTooltip = textString;
873 private Point lastp = null;
878 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
881 public Point getToolTipLocation(MouseEvent event)
883 int x = event.getX(), w = getWidth();
884 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
887 if (!event.isShiftDown() || p == null)
889 p = (tooltipText != null && tooltipText.length() > 6)
890 ? new Point(event.getX() + wdth, event.getY() - 20)
894 * TODO: try to modify position region is not obcured by tooltip
902 * set when the current UI interaction has resulted in a change that requires
903 * shading in overviews and structures to be recalculated. this could be
904 * changed to a something more expressive that indicates what actually has
905 * changed, so selective redraws can be applied (ie. only structures, only
908 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
911 * set if av.getSelectionGroup() refers to a group that is defined on the
912 * alignment view, rather than a transient selection
914 // private boolean editingDefinedGroup = false; // TODO: refactor to
915 // avcontroller or viewModel
918 * Sets the status message in alignment panel, showing the sequence number
919 * (index) and id, and residue and residue position if not at a gap, for the
920 * given sequence and column position. Returns the residue position returned
921 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
922 * if at a gapped position.
925 * aligned sequence object
929 * index of sequence in alignment
930 * @return sequence position of residue at column, or adjacent residue if at a
933 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
935 char sequenceChar = sequence.getCharAt(column);
936 int pos = sequence.findPosition(column);
937 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
943 * Builds the status message for the current cursor location and writes it to
944 * the status bar, for example
947 * Sequence 3 ID: FER1_SOLLC
948 * Sequence 5 ID: FER1_PEA Residue: THR (4)
949 * Sequence 5 ID: FER1_PEA Residue: B (3)
950 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
955 * sequence position in the alignment (1..)
956 * @param sequenceChar
957 * the character under the cursor
959 * the sequence residue position (if not over a gap)
961 protected void setStatusMessage(SequenceI sequence, int seqIndex,
962 char sequenceChar, int residuePos)
964 StringBuilder text = new StringBuilder(32);
967 * Sequence number (if known), and sequence name.
969 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
970 text.append("Sequence").append(seqno).append(" ID: ")
971 .append(sequence.getName());
973 String residue = null;
976 * Try to translate the display character to residue name (null for gap).
978 boolean isGapped = Comparison.isGap(sequenceChar);
982 boolean nucleotide = av.getAlignment().isNucleotide();
983 String displayChar = String.valueOf(sequenceChar);
986 residue = ResidueProperties.nucleotideName.get(displayChar);
990 residue = "X".equalsIgnoreCase(displayChar) ? "X"
991 : ("*".equals(displayChar) ? "STOP"
992 : ResidueProperties.aa2Triplet.get(displayChar));
994 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
995 .append(": ").append(residue == null ? displayChar : residue);
997 text.append(" (").append(Integer.toString(residuePos)).append(")");
999 ap.alignFrame.statusBar.setText(text.toString());
1003 * Set the status bar message to highlight the first matched position in
1008 private void setStatusMessage(SearchResultsI results)
1010 AlignmentI al = this.av.getAlignment();
1011 int sequenceIndex = al.findIndex(results);
1012 if (sequenceIndex == -1)
1016 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
1017 for (SearchResultMatchI m : results.getResults())
1019 SequenceI seq = m.getSequence();
1020 if (seq.getDatasetSequence() != null)
1022 seq = seq.getDatasetSequence();
1027 int start = m.getStart();
1028 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1039 public void mouseDragged(MouseEvent evt)
1041 if (mouseWheelPressed)
1043 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1044 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1046 int oldWidth = av.getCharWidth();
1048 // Which is bigger, left-right or up-down?
1049 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1050 .abs(evt.getX() - lastMousePress.getX()))
1053 * on drag up or down, decrement or increment font size
1055 int fontSize = av.font.getSize();
1056 boolean fontChanged = false;
1058 if (evt.getY() < lastMousePress.getY())
1063 else if (evt.getY() > lastMousePress.getY())
1076 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1078 av.setFont(newFont, true);
1079 av.setCharWidth(oldWidth);
1083 ap.av.getCodingComplement().setFont(newFont, true);
1084 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1085 .getSplitViewContainer();
1086 splitFrame.adjustLayout();
1087 splitFrame.repaint();
1094 * on drag left or right, decrement or increment character width
1097 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1099 newWidth = av.getCharWidth() - 1;
1100 av.setCharWidth(newWidth);
1102 else if (evt.getX() > lastMousePress.getX())
1104 newWidth = av.getCharWidth() + 1;
1105 av.setCharWidth(newWidth);
1109 ap.paintAlignment(false, false);
1113 * need to ensure newWidth is set on cdna, regardless of which
1114 * panel the mouse drag happened in; protein will compute its
1115 * character width as 1:1 or 3:1
1117 av.getCodingComplement().setCharWidth(newWidth);
1118 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1119 .getSplitViewContainer();
1120 splitFrame.adjustLayout();
1121 splitFrame.repaint();
1126 FontMetrics fm = getFontMetrics(av.getFont());
1127 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1129 lastMousePress = evt.getPoint();
1136 doMouseDraggedDefineMode(evt);
1140 int res = findColumn(evt);
1147 if ((lastres == -1) || (lastres == res))
1152 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1154 // dragLeft, delete gap
1155 editSequence(false, false, res);
1159 editSequence(true, false, res);
1162 mouseDragging = true;
1163 if ((scrollThread != null) && (scrollThread.isRunning()))
1165 scrollThread.setEvent(evt);
1169 // TODO: Make it more clever than many booleans
1170 synchronized void editSequence(boolean insertGap, boolean editSeq,
1174 int fixedRight = -1;
1175 boolean fixedColumns = false;
1176 SequenceGroup sg = av.getSelectionGroup();
1178 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1180 // No group, but the sequence may represent a group
1181 if (!groupEditing && av.hasHiddenRows())
1183 if (av.isHiddenRepSequence(seq))
1185 sg = av.getRepresentedSequences(seq);
1186 groupEditing = true;
1190 StringBuilder message = new StringBuilder(64);
1193 message.append("Edit group:");
1194 if (editCommand == null)
1196 editCommand = new EditCommand(
1197 MessageManager.getString("action.edit_group"));
1202 message.append("Edit sequence: " + seq.getName());
1203 String label = seq.getName();
1204 if (label.length() > 10)
1206 label = label.substring(0, 10);
1208 if (editCommand == null)
1210 editCommand = new EditCommand(MessageManager
1211 .formatMessage("label.edit_params", new String[]
1218 message.append(" insert ");
1222 message.append(" delete ");
1225 message.append(Math.abs(startres - lastres) + " gaps.");
1226 ap.alignFrame.statusBar.setText(message.toString());
1228 // Are we editing within a selection group?
1229 if (groupEditing || (sg != null
1230 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1232 fixedColumns = true;
1234 // sg might be null as the user may only see 1 sequence,
1235 // but the sequence represents a group
1238 if (!av.isHiddenRepSequence(seq))
1243 sg = av.getRepresentedSequences(seq);
1246 fixedLeft = sg.getStartRes();
1247 fixedRight = sg.getEndRes();
1249 if ((startres < fixedLeft && lastres >= fixedLeft)
1250 || (startres >= fixedLeft && lastres < fixedLeft)
1251 || (startres > fixedRight && lastres <= fixedRight)
1252 || (startres <= fixedRight && lastres > fixedRight))
1258 if (fixedLeft > startres)
1260 fixedRight = fixedLeft - 1;
1263 else if (fixedRight < startres)
1265 fixedLeft = fixedRight;
1270 if (av.hasHiddenColumns())
1272 fixedColumns = true;
1273 int y1 = av.getAlignment().getHiddenColumns()
1274 .getNextHiddenBoundary(true, startres);
1275 int y2 = av.getAlignment().getHiddenColumns()
1276 .getNextHiddenBoundary(false, startres);
1278 if ((insertGap && startres > y1 && lastres < y1)
1279 || (!insertGap && startres < y2 && lastres > y2))
1285 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1286 // Selection spans a hidden region
1287 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1295 fixedRight = y2 - 1;
1302 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1303 int g, groupSize = vseqs.size();
1304 SequenceI[] groupSeqs = new SequenceI[groupSize];
1305 for (g = 0; g < groupSeqs.length; g++)
1307 groupSeqs[g] = vseqs.get(g);
1313 // If the user has selected the whole sequence, and is dragging to
1314 // the right, we can still extend the alignment and selectionGroup
1315 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1316 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1318 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1319 fixedRight = sg.getEndRes();
1322 // Is it valid with fixed columns??
1323 // Find the next gap before the end
1324 // of the visible region boundary
1325 boolean blank = false;
1326 for (; fixedRight > lastres; fixedRight--)
1330 for (g = 0; g < groupSize; g++)
1332 for (int j = 0; j < startres - lastres; j++)
1334 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1349 if (sg.getSize() == av.getAlignment().getHeight())
1351 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1353 .getNextHiddenBoundary(false, startres)))
1359 int alWidth = av.getAlignment().getWidth();
1360 if (av.hasHiddenRows())
1362 int hwidth = av.getAlignment().getHiddenSequences()
1364 if (hwidth > alWidth)
1369 // We can still insert gaps if the selectionGroup
1370 // contains all the sequences
1371 sg.setEndRes(sg.getEndRes() + startres - lastres);
1372 fixedRight = alWidth + startres - lastres;
1383 else if (!insertGap)
1385 // / Are we able to delete?
1386 // ie are all columns blank?
1388 for (g = 0; g < groupSize; g++)
1390 for (int j = startres; j < lastres; j++)
1392 if (groupSeqs[g].getLength() <= j)
1397 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1399 // Not a gap, block edit not valid
1409 // dragging to the right
1410 if (fixedColumns && fixedRight != -1)
1412 for (int j = lastres; j < startres; j++)
1414 insertChar(j, groupSeqs, fixedRight);
1419 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1420 startres - lastres);
1425 // dragging to the left
1426 if (fixedColumns && fixedRight != -1)
1428 for (int j = lastres; j > startres; j--)
1430 deleteChar(startres, groupSeqs, fixedRight);
1435 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1436 lastres - startres);
1442 // ///Editing a single sequence///////////
1446 // dragging to the right
1447 if (fixedColumns && fixedRight != -1)
1449 for (int j = lastres; j < startres; j++)
1451 insertChar(j, new SequenceI[] { seq }, fixedRight);
1456 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1457 startres - lastres);
1464 // dragging to the left
1465 if (fixedColumns && fixedRight != -1)
1467 for (int j = lastres; j > startres; j--)
1469 if (!Comparison.isGap(seq.getCharAt(startres)))
1474 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1479 // could be a keyboard edit trying to delete none gaps
1481 for (int m = startres; m < lastres; m++)
1483 if (!Comparison.isGap(seq.getCharAt(m)))
1492 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1498 {// insertGap==false AND editSeq==TRUE;
1499 if (fixedColumns && fixedRight != -1)
1501 for (int j = lastres; j < startres; j++)
1503 insertChar(j, new SequenceI[] { seq }, fixedRight);
1508 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1509 startres - lastres);
1516 seqCanvas.repaint();
1519 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1521 int blankColumn = fixedColumn;
1522 for (int s = 0; s < seq.length; s++)
1524 // Find the next gap before the end of the visible region boundary
1525 // If lastCol > j, theres a boundary after the gap insertion
1527 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1529 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1531 // Theres a space, so break and insert the gap
1536 if (blankColumn <= j)
1538 blankColumn = fixedColumn;
1544 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1546 appendEdit(Action.INSERT_GAP, seq, j, 1);
1551 * Helper method to add and perform one edit action.
1558 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1562 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1563 av.getAlignment().getGapCharacter());
1565 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1568 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1571 appendEdit(Action.DELETE_GAP, seq, j, 1);
1573 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1583 public void mouseEntered(MouseEvent e)
1590 if ((scrollThread != null) && (scrollThread.isRunning()))
1592 scrollThread.stopScrolling();
1593 scrollThread = null;
1604 public void mouseExited(MouseEvent e)
1606 if (av.getWrapAlignment())
1611 if (mouseDragging && scrollThread == null)
1613 scrollThread = new ScrollThread();
1618 * Handler for double-click on a position with one or more sequence features.
1619 * Opens the Amend Features dialog to allow feature details to be amended, or
1620 * the feature deleted.
1623 public void mouseClicked(MouseEvent evt)
1625 SequenceGroup sg = null;
1626 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1627 if (evt.getClickCount() > 1)
1629 sg = av.getSelectionGroup();
1630 if (sg != null && sg.getSize() == 1
1631 && sg.getEndRes() - sg.getStartRes() < 2)
1633 av.setSelectionGroup(null);
1636 int column = findColumn(evt);
1639 * find features at the position (if not gapped), or straddling
1640 * the position (if at a gap)
1642 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1643 .findFeaturesAtColumn(sequence, column + 1);
1645 if (!features.isEmpty())
1648 * highlight the first feature at the position on the alignment
1650 SearchResultsI highlight = new SearchResults();
1651 highlight.addResult(sequence, features.get(0).getBegin(), features
1653 seqCanvas.highlightSearchResults(highlight, false);
1656 * open the Amend Features dialog; clear highlighting afterwards,
1657 * whether changes were made or not
1659 List<SequenceI> seqs = Collections.singletonList(sequence);
1660 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1662 av.setSearchResults(null); // clear highlighting
1663 seqCanvas.repaint(); // draw new/amended features
1669 public void mouseWheelMoved(MouseWheelEvent e)
1672 double wheelRotation = e.getPreciseWheelRotation();
1673 if (wheelRotation > 0)
1675 if (e.isShiftDown())
1677 av.getRanges().scrollRight(true);
1682 av.getRanges().scrollUp(false);
1685 else if (wheelRotation < 0)
1687 if (e.isShiftDown())
1689 av.getRanges().scrollRight(false);
1693 av.getRanges().scrollUp(true);
1698 * update status bar and tooltip for new position
1699 * (need to synthesize a mouse movement to refresh tooltip)
1702 ToolTipManager.sharedInstance().mouseMoved(e);
1711 public void doMousePressedDefineMode(MouseEvent evt)
1713 final int res = findColumn(evt);
1714 final int seq = findSeq(evt);
1716 updateOverviewAndStructs = false;
1718 startWrapBlock = wrappedBlock;
1720 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1722 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1723 MessageManager.getString(
1724 "label.cannot_edit_annotations_in_wrapped_view"),
1725 MessageManager.getString("label.wrapped_view_no_edit"),
1726 JvOptionPane.WARNING_MESSAGE);
1730 if (seq < 0 || res < 0)
1735 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1737 if ((sequence == null) || (res > sequence.getLength()))
1742 stretchGroup = av.getSelectionGroup();
1744 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1746 stretchGroup = av.getAlignment().findGroup(sequence, res);
1747 if (stretchGroup != null)
1749 // only update the current selection if the popup menu has a group to
1751 av.setSelectionGroup(stretchGroup);
1755 if (evt.isPopupTrigger()) // Mac: mousePressed
1762 * defer right-mouse click handling to mouseReleased on Windows
1763 * (where isPopupTrigger() will answer true)
1764 * NB isRightMouseButton is also true for Cmd-click on Mac
1766 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1773 seqCanvas.cursorX = findColumn(evt);
1774 seqCanvas.cursorY = findSeq(evt);
1775 seqCanvas.repaint();
1779 if (stretchGroup == null)
1781 createStretchGroup(res, sequence);
1784 if (stretchGroup != null)
1786 stretchGroup.addPropertyChangeListener(seqCanvas);
1789 seqCanvas.repaint();
1792 private void createStretchGroup(int res, SequenceI sequence)
1794 // Only if left mouse button do we want to change group sizes
1795 // define a new group here
1796 SequenceGroup sg = new SequenceGroup();
1797 sg.setStartRes(res);
1799 sg.addSequence(sequence, false);
1800 av.setSelectionGroup(sg);
1803 if (av.getConservationSelected())
1805 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1809 if (av.getAbovePIDThreshold())
1811 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1814 // TODO: stretchGroup will always be not null. Is this a merge error ?
1815 // or is there a threading issue here?
1816 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1818 // Edit end res position of selected group
1819 changeEndRes = true;
1821 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1823 // Edit end res position of selected group
1824 changeStartRes = true;
1826 stretchGroup.getWidth();
1831 * Build and show a pop-up menu at the right-click mouse position
1837 void showPopupMenu(MouseEvent evt)
1839 final int column = findColumn(evt);
1840 final int seq = findSeq(evt);
1841 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1842 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1843 .findFeaturesAtColumn(sequence, column + 1);
1844 List<String> links = new ArrayList<>();
1845 for (SequenceFeature sf : allFeatures)
1847 if (sf.links != null)
1849 for (String link : sf.links)
1856 PopupMenu pop = new PopupMenu(ap, null, links);
1857 pop.show(this, evt.getX(), evt.getY());
1861 * Update the display after mouse up on a selection or group
1864 * mouse released event details
1866 * true if this event is happening after a mouse drag (rather than a
1869 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1871 if (stretchGroup == null)
1876 stretchGroup.removePropertyChangeListener(seqCanvas);
1878 // always do this - annotation has own state
1879 // but defer colourscheme update until hidden sequences are passed in
1880 boolean vischange = stretchGroup.recalcConservation(true);
1881 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1883 if (stretchGroup.cs != null)
1885 stretchGroup.cs.alignmentChanged(stretchGroup,
1886 av.getHiddenRepSequences());
1888 ResidueShaderI groupColourScheme = stretchGroup
1889 .getGroupColourScheme();
1890 String name = stretchGroup.getName();
1891 if (stretchGroup.cs.conservationApplied())
1893 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1895 if (stretchGroup.cs.getThreshold() > 0)
1897 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1900 PaintRefresher.Refresh(this, av.getSequenceSetId());
1901 // TODO: structure colours only need updating if stretchGroup used to or now
1902 // does contain sequences with structure views
1903 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1904 updateOverviewAndStructs = false;
1905 changeEndRes = false;
1906 changeStartRes = false;
1907 stretchGroup = null;
1917 public void doMouseDraggedDefineMode(MouseEvent evt)
1919 int res = findColumn(evt);
1920 int y = findSeq(evt);
1922 if (wrappedBlock != startWrapBlock)
1927 if (stretchGroup == null)
1932 if (res >= av.getAlignment().getWidth())
1934 res = av.getAlignment().getWidth() - 1;
1937 if (stretchGroup.getEndRes() == res)
1939 // Edit end res position of selected group
1940 changeEndRes = true;
1942 else if (stretchGroup.getStartRes() == res)
1944 // Edit start res position of selected group
1945 changeStartRes = true;
1948 if (res < av.getRanges().getStartRes())
1950 res = av.getRanges().getStartRes();
1955 if (res > (stretchGroup.getStartRes() - 1))
1957 stretchGroup.setEndRes(res);
1958 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1961 else if (changeStartRes)
1963 if (res < (stretchGroup.getEndRes() + 1))
1965 stretchGroup.setStartRes(res);
1966 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1970 int dragDirection = 0;
1976 else if (y < oldSeq)
1981 while ((y != oldSeq) && (oldSeq > -1)
1982 && (y < av.getAlignment().getHeight()))
1984 // This routine ensures we don't skip any sequences, as the
1985 // selection is quite slow.
1986 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1988 oldSeq += dragDirection;
1995 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1997 if (stretchGroup.getSequences(null).contains(nextSeq))
1999 stretchGroup.deleteSequence(seq, false);
2000 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2006 stretchGroup.addSequence(seq, false);
2009 stretchGroup.addSequence(nextSeq, false);
2010 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2019 mouseDragging = true;
2021 if ((scrollThread != null) && (scrollThread.isRunning()))
2023 scrollThread.setEvent(evt);
2027 void scrollCanvas(MouseEvent evt)
2031 if ((scrollThread != null) && (scrollThread.isRunning()))
2033 scrollThread.stopScrolling();
2034 scrollThread = null;
2036 mouseDragging = false;
2040 if (scrollThread == null)
2042 scrollThread = new ScrollThread();
2045 mouseDragging = true;
2046 scrollThread.setEvent(evt);
2051 // this class allows scrolling off the bottom of the visible alignment
2052 class ScrollThread extends Thread
2056 private volatile boolean threadRunning = true;
2058 public ScrollThread()
2063 public void setEvent(MouseEvent e)
2068 public void stopScrolling()
2070 threadRunning = false;
2073 public boolean isRunning()
2075 return threadRunning;
2081 while (threadRunning)
2085 if (mouseDragging && (evt.getY() < 0)
2086 && (av.getRanges().getStartSeq() > 0))
2088 av.getRanges().scrollUp(true);
2091 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2092 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2094 av.getRanges().scrollUp(false);
2097 if (mouseDragging && (evt.getX() < 0))
2099 av.getRanges().scrollRight(false);
2101 else if (mouseDragging && (evt.getX() >= getWidth()))
2103 av.getRanges().scrollRight(true);
2110 } catch (Exception ex)
2118 * modify current selection according to a received message.
2121 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2122 HiddenColumns hidden, SelectionSource source)
2124 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2125 // handles selection messages...
2126 // TODO: extend config options to allow user to control if selections may be
2127 // shared between viewports.
2128 boolean iSentTheSelection = (av == source
2129 || (source instanceof AlignViewport
2130 && ((AlignmentViewport) source).getSequenceSetId()
2131 .equals(av.getSequenceSetId())));
2133 if (iSentTheSelection)
2135 // respond to our own event by updating dependent dialogs
2136 if (ap.getCalculationDialog() != null)
2138 ap.getCalculationDialog().validateCalcTypes();
2144 // process further ?
2145 if (!av.followSelection)
2151 * Ignore the selection if there is one of our own pending.
2153 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2159 * Check for selection in a view of which this one is a dna/protein
2162 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2167 // do we want to thread this ? (contention with seqsel and colsel locks, I
2170 * only copy colsel if there is a real intersection between
2171 * sequence selection and this panel's alignment
2173 boolean repaint = false;
2174 boolean copycolsel = false;
2176 SequenceGroup sgroup = null;
2177 if (seqsel != null && seqsel.getSize() > 0)
2179 if (av.getAlignment() == null)
2181 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2182 + " ViewId=" + av.getViewId()
2183 + " 's alignment is NULL! returning immediately.");
2186 sgroup = seqsel.intersect(av.getAlignment(),
2187 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2188 if ((sgroup != null && sgroup.getSize() > 0))
2193 if (sgroup != null && sgroup.getSize() > 0)
2195 av.setSelectionGroup(sgroup);
2199 av.setSelectionGroup(null);
2201 av.isSelectionGroupChanged(true);
2206 // the current selection is unset or from a previous message
2207 // so import the new colsel.
2208 if (colsel == null || colsel.isEmpty())
2210 if (av.getColumnSelection() != null)
2212 av.getColumnSelection().clear();
2218 // TODO: shift colSel according to the intersecting sequences
2219 if (av.getColumnSelection() == null)
2221 av.setColumnSelection(new ColumnSelection(colsel));
2225 av.getColumnSelection().setElementsFrom(colsel,
2226 av.getAlignment().getHiddenColumns());
2229 av.isColSelChanged(true);
2233 if (copycolsel && av.hasHiddenColumns()
2234 && (av.getAlignment().getHiddenColumns() == null))
2236 System.err.println("Bad things");
2238 if (repaint) // always true!
2240 // probably finessing with multiple redraws here
2241 PaintRefresher.Refresh(this, av.getSequenceSetId());
2242 // ap.paintAlignment(false);
2245 // lastly, update dependent dialogs
2246 if (ap.getCalculationDialog() != null)
2248 ap.getCalculationDialog().validateCalcTypes();
2254 * If this panel is a cdna/protein translation view of the selection source,
2255 * tries to map the source selection to a local one, and returns true. Else
2262 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2263 ColumnSelection colsel, HiddenColumns hidden,
2264 SelectionSource source)
2266 if (!(source instanceof AlignViewportI))
2270 final AlignViewportI sourceAv = (AlignViewportI) source;
2271 if (sourceAv.getCodingComplement() != av
2272 && av.getCodingComplement() != sourceAv)
2278 * Map sequence selection
2280 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2281 av.setSelectionGroup(sg);
2282 av.isSelectionGroupChanged(true);
2285 * Map column selection
2287 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2289 ColumnSelection cs = new ColumnSelection();
2290 HiddenColumns hs = new HiddenColumns();
2291 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2292 av.setColumnSelection(cs);
2293 av.getAlignment().setHiddenColumns(hs);
2295 // lastly, update any dependent dialogs
2296 if (ap.getCalculationDialog() != null)
2298 ap.getCalculationDialog().validateCalcTypes();
2301 PaintRefresher.Refresh(this, av.getSequenceSetId());
2308 * @return null or last search results handled by this panel
2310 public SearchResultsI getLastSearchResults()
2312 return lastSearchResults;