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.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.ColumnSelection;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.MappedFeatures;
33 import jalview.datamodel.SearchResultMatchI;
34 import jalview.datamodel.SearchResults;
35 import jalview.datamodel.SearchResultsI;
36 import jalview.datamodel.Sequence;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.io.SequenceAnnotationReport;
41 import jalview.renderer.ResidueShaderI;
42 import jalview.schemes.ResidueProperties;
43 import jalview.structure.SelectionListener;
44 import jalview.structure.SelectionSource;
45 import jalview.structure.SequenceListener;
46 import jalview.structure.StructureSelectionManager;
47 import jalview.structure.VamsasSource;
48 import jalview.util.Comparison;
49 import jalview.util.MappingUtils;
50 import jalview.util.MessageManager;
51 import jalview.util.Platform;
52 import jalview.viewmodel.AlignmentViewport;
53 import jalview.viewmodel.ViewportRanges;
54 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
56 import java.awt.BorderLayout;
57 import java.awt.Color;
59 import java.awt.FontMetrics;
60 import java.awt.Point;
61 import java.awt.event.MouseEvent;
62 import java.awt.event.MouseListener;
63 import java.awt.event.MouseMotionListener;
64 import java.awt.event.MouseWheelEvent;
65 import java.awt.event.MouseWheelListener;
66 import java.util.ArrayList;
67 import java.util.Collections;
68 import java.util.List;
70 import javax.swing.JPanel;
71 import javax.swing.SwingUtilities;
72 import javax.swing.ToolTipManager;
78 * @version $Revision: 1.130 $
80 public class SeqPanel extends JPanel
81 implements MouseListener, MouseMotionListener, MouseWheelListener,
82 SequenceListener, SelectionListener
85 * a class that holds computed mouse position
86 * - column of the alignment (0...)
87 * - sequence offset (0...)
88 * - annotation row offset (0...)
89 * where annotation offset is -1 unless the alignment is shown
90 * in wrapped mode, annotations are shown, and the mouse is
91 * over an annnotation row
96 * alignment column position of cursor (0...)
101 * index in alignment of sequence under cursor,
102 * or nearest above if cursor is not over a sequence
107 * index in annotations array of annotation under the cursor
108 * (only possible in wrapped mode with annotations shown),
109 * or -1 if cursor is not over an annotation row
111 final int annotationIndex;
113 MousePos(int col, int seq, int ann)
117 annotationIndex = ann;
120 boolean isOverAnnotation()
122 return annotationIndex != -1;
126 public boolean equals(Object obj)
128 if (obj == null || !(obj instanceof MousePos))
132 MousePos o = (MousePos) obj;
133 boolean b = (column == o.column && seqIndex == o.seqIndex
134 && annotationIndex == o.annotationIndex);
135 // System.out.println(obj + (b ? "= " : "!= ") + this);
140 * A simple hashCode that ensures that instances that satisfy equals() have
144 public int hashCode()
146 return column + seqIndex + annotationIndex;
150 * toString method for debug output purposes only
153 public String toString()
155 return String.format("c%d:s%d:a%d", column, seqIndex,
160 private static final int MAX_TOOLTIP_LENGTH = 300;
162 public SeqCanvas seqCanvas;
164 public AlignmentPanel ap;
167 * last position for mouseMoved event
169 private MousePos lastMousePosition;
171 protected int editLastRes;
173 protected int editStartSeq;
175 protected AlignViewport av;
177 ScrollThread scrollThread = null;
179 boolean mouseDragging = false;
181 boolean editingSeqs = false;
183 boolean groupEditing = false;
185 // ////////////////////////////////////////
186 // ///Everything below this is for defining the boundary of the rubberband
187 // ////////////////////////////////////////
190 boolean changeEndSeq = false;
192 boolean changeStartSeq = false;
194 boolean changeEndRes = false;
196 boolean changeStartRes = false;
198 SequenceGroup stretchGroup = null;
200 boolean remove = false;
202 Point lastMousePress;
204 boolean mouseWheelPressed = false;
206 StringBuffer keyboardNo1;
208 StringBuffer keyboardNo2;
210 java.net.URL linkImageURL;
212 private final SequenceAnnotationReport seqARep;
214 StringBuilder tooltipText = new StringBuilder();
218 EditCommand editCommand;
220 StructureSelectionManager ssm;
222 SearchResultsI lastSearchResults;
225 * Creates a new SeqPanel object
230 public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
232 linkImageURL = getClass().getResource("/images/link.gif");
233 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
234 ToolTipManager.sharedInstance().registerComponent(this);
235 ToolTipManager.sharedInstance().setInitialDelay(0);
236 ToolTipManager.sharedInstance().setDismissDelay(10000);
238 setBackground(Color.white);
240 seqCanvas = new SeqCanvas(alignPanel);
241 setLayout(new BorderLayout());
242 add(seqCanvas, BorderLayout.CENTER);
244 this.ap = alignPanel;
246 if (!viewport.isDataset())
248 addMouseMotionListener(this);
249 addMouseListener(this);
250 addMouseWheelListener(this);
251 ssm = viewport.getStructureSelectionManager();
252 ssm.addStructureViewerListener(this);
253 ssm.addSelectionListener(this);
257 int startWrapBlock = -1;
259 int wrappedBlock = -1;
262 * Computes the column and sequence row (and possibly annotation row when in
263 * wrapped mode) for the given mouse position
268 MousePos findMousePosition(MouseEvent evt)
270 int col = findColumn(evt);
275 int charHeight = av.getCharHeight();
276 int alignmentHeight = av.getAlignment().getHeight();
277 if (av.getWrapAlignment())
279 seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(),
280 seqCanvas.getHeight());
283 * yPos modulo height of repeating width
285 int yOffsetPx = y % seqCanvas.wrappedRepeatHeightPx;
288 * height of sequences plus space / scale above,
289 * plus gap between sequences and annotations
291 int alignmentHeightPixels = seqCanvas.wrappedSpaceAboveAlignment
292 + alignmentHeight * charHeight
293 + SeqCanvas.SEQS_ANNOTATION_GAP;
294 if (yOffsetPx >= alignmentHeightPixels)
297 * mouse is over annotations; find annotation index, also set
298 * last sequence above (for backwards compatible behaviour)
300 AlignmentAnnotation[] anns = av.getAlignment()
301 .getAlignmentAnnotation();
302 int rowOffsetPx = yOffsetPx - alignmentHeightPixels;
303 annIndex = AnnotationPanel.getRowIndex(rowOffsetPx, anns);
304 seqIndex = alignmentHeight - 1;
309 * mouse is over sequence (or the space above sequences)
311 yOffsetPx -= seqCanvas.wrappedSpaceAboveAlignment;
314 seqIndex = Math.min(yOffsetPx / charHeight, alignmentHeight - 1);
320 ViewportRanges ranges = av.getRanges();
321 seqIndex = Math.min((y / charHeight) + ranges.getStartSeq(),
322 alignmentHeight - 1);
323 seqIndex = Math.min(seqIndex, ranges.getEndSeq());
326 return new MousePos(col, seqIndex, annIndex);
329 * Returns the aligned sequence position (base 0) at the mouse position, or
330 * the closest visible one
335 int findColumn(MouseEvent evt)
340 final int startRes = av.getRanges().getStartRes();
341 final int charWidth = av.getCharWidth();
343 if (av.getWrapAlignment())
345 int hgap = av.getCharHeight();
346 if (av.getScaleAboveWrapped())
348 hgap += av.getCharHeight();
351 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
352 + hgap + seqCanvas.getAnnotationHeight();
355 y = Math.max(0, y - hgap);
356 x -= seqCanvas.getLabelWidthWest();
359 // mouse is over left scale
363 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
368 if (x >= cwidth * charWidth)
370 // mouse is over right scale
374 wrappedBlock = y / cHeight;
375 wrappedBlock += startRes / cwidth;
376 // allow for wrapped view scrolled right (possible from Overview)
377 int startOffset = startRes % cwidth;
378 res = wrappedBlock * cwidth + startOffset
379 + Math.min(cwidth - 1, x / charWidth);
384 * make sure we calculate relative to visible alignment,
385 * rather than right-hand gutter
387 x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth());
388 res = (x / charWidth) + startRes;
389 res = Math.min(res, av.getRanges().getEndRes());
392 if (av.hasHiddenColumns())
394 res = av.getAlignment().getHiddenColumns()
395 .visibleToAbsoluteColumn(res);
402 * When all of a sequence of edits are complete, put the resulting edit list
403 * on the history stack (undo list), and reset flags for editing in progress.
409 if (editCommand != null && editCommand.getSize() > 0)
411 ap.alignFrame.addHistoryItem(editCommand);
412 av.firePropertyChange("alignment", null,
413 av.getAlignment().getSequences());
418 * Tidy up come what may...
423 groupEditing = false;
432 seqCanvas.cursorY = getKeyboardNo1() - 1;
433 scrollToVisible(true);
436 void setCursorColumn()
438 seqCanvas.cursorX = getKeyboardNo1() - 1;
439 scrollToVisible(true);
442 void setCursorRowAndColumn()
444 if (keyboardNo2 == null)
446 keyboardNo2 = new StringBuffer();
450 seqCanvas.cursorX = getKeyboardNo1() - 1;
451 seqCanvas.cursorY = getKeyboardNo2() - 1;
452 scrollToVisible(true);
456 void setCursorPosition()
458 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
460 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
461 scrollToVisible(true);
464 void moveCursor(int dx, int dy)
466 seqCanvas.cursorX += dx;
467 seqCanvas.cursorY += dy;
469 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
471 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
473 int original = seqCanvas.cursorX - dx;
474 int maxWidth = av.getAlignment().getWidth();
476 if (!hidden.isVisible(seqCanvas.cursorX))
478 int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
479 int[] region = hidden.getRegionWithEdgeAtRes(visx);
481 if (region != null) // just in case
486 seqCanvas.cursorX = region[1] + 1;
491 seqCanvas.cursorX = region[0] - 1;
494 seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
497 if (seqCanvas.cursorX >= maxWidth
498 || !hidden.isVisible(seqCanvas.cursorX))
500 seqCanvas.cursorX = original;
504 scrollToVisible(false);
508 * Scroll to make the cursor visible in the viewport.
511 * just jump to the location rather than scrolling
513 void scrollToVisible(boolean jump)
515 if (seqCanvas.cursorX < 0)
517 seqCanvas.cursorX = 0;
519 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
521 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
524 if (seqCanvas.cursorY < 0)
526 seqCanvas.cursorY = 0;
528 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
530 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
535 boolean repaintNeeded = true;
538 // only need to repaint if the viewport did not move, as otherwise it will
540 repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
545 if (av.getWrapAlignment())
547 // scrollToWrappedVisible expects x-value to have hidden cols subtracted
548 int x = av.getAlignment().getHiddenColumns()
549 .absoluteToVisibleColumn(seqCanvas.cursorX);
550 av.getRanges().scrollToWrappedVisible(x);
554 av.getRanges().scrollToVisible(seqCanvas.cursorX,
559 if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
561 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
562 seqCanvas.cursorX, seqCanvas.cursorY);
572 void setSelectionAreaAtCursor(boolean topLeft)
574 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
576 if (av.getSelectionGroup() != null)
578 SequenceGroup sg = av.getSelectionGroup();
579 // Find the top and bottom of this group
580 int min = av.getAlignment().getHeight(), max = 0;
581 for (int i = 0; i < sg.getSize(); i++)
583 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
598 sg.setStartRes(seqCanvas.cursorX);
599 if (sg.getEndRes() < seqCanvas.cursorX)
601 sg.setEndRes(seqCanvas.cursorX);
604 min = seqCanvas.cursorY;
608 sg.setEndRes(seqCanvas.cursorX);
609 if (sg.getStartRes() > seqCanvas.cursorX)
611 sg.setStartRes(seqCanvas.cursorX);
614 max = seqCanvas.cursorY + 1;
619 // Only the user can do this
620 av.setSelectionGroup(null);
624 // Now add any sequences between min and max
625 sg.getSequences(null).clear();
626 for (int i = min; i < max; i++)
628 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
633 if (av.getSelectionGroup() == null)
635 SequenceGroup sg = new SequenceGroup();
636 sg.setStartRes(seqCanvas.cursorX);
637 sg.setEndRes(seqCanvas.cursorX);
638 sg.addSequence(sequence, false);
639 av.setSelectionGroup(sg);
642 ap.paintAlignment(false, false);
646 void insertGapAtCursor(boolean group)
648 groupEditing = group;
649 editStartSeq = seqCanvas.cursorY;
650 editLastRes = seqCanvas.cursorX;
651 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
655 void deleteGapAtCursor(boolean group)
657 groupEditing = group;
658 editStartSeq = seqCanvas.cursorY;
659 editLastRes = seqCanvas.cursorX + getKeyboardNo1();
660 editSequence(false, false, seqCanvas.cursorX);
664 void insertNucAtCursor(boolean group, String nuc)
666 // TODO not called - delete?
667 groupEditing = group;
668 editStartSeq = seqCanvas.cursorY;
669 editLastRes = seqCanvas.cursorX;
670 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
674 void numberPressed(char value)
676 if (keyboardNo1 == null)
678 keyboardNo1 = new StringBuffer();
681 if (keyboardNo2 != null)
683 keyboardNo2.append(value);
687 keyboardNo1.append(value);
695 if (keyboardNo1 != null)
697 int value = Integer.parseInt(keyboardNo1.toString());
701 } catch (Exception x)
712 if (keyboardNo2 != null)
714 int value = Integer.parseInt(keyboardNo2.toString());
718 } catch (Exception x)
732 public void mouseReleased(MouseEvent evt)
734 MousePos pos = findMousePosition(evt);
735 if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
740 boolean didDrag = mouseDragging; // did we come here after a drag
741 mouseDragging = false;
742 mouseWheelPressed = false;
744 if (evt.isPopupTrigger()) // Windows: mouseReleased
746 showPopupMenu(evt, pos);
757 doMouseReleasedDefineMode(evt, didDrag);
768 public void mousePressed(MouseEvent evt)
770 lastMousePress = evt.getPoint();
771 MousePos pos = findMousePosition(evt);
772 if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
777 if (SwingUtilities.isMiddleMouseButton(evt))
779 mouseWheelPressed = true;
783 boolean isControlDown = Platform.isControlDown(evt);
784 if (evt.isShiftDown() || isControlDown)
794 doMousePressedDefineMode(evt, pos);
798 int seq = pos.seqIndex;
799 int res = pos.column;
801 if ((seq < av.getAlignment().getHeight())
802 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
819 public void mouseOverSequence(SequenceI sequence, int index, int pos)
821 String tmp = sequence.hashCode() + " " + index + " " + pos;
823 if (lastMessage == null || !lastMessage.equals(tmp))
825 // System.err.println("mouseOver Sequence: "+tmp);
826 ssm.mouseOverSequence(sequence, index, pos, av);
832 * Highlight the mapped region described by the search results object (unless
833 * unchanged). This supports highlight of protein while mousing over linked
834 * cDNA and vice versa. The status bar is also updated to show the location of
835 * the start of the highlighted region.
838 public String highlightSequence(SearchResultsI results)
840 if (results == null || results.equals(lastSearchResults))
844 lastSearchResults = results;
846 boolean wasScrolled = false;
848 if (av.isFollowHighlight())
850 // don't allow highlight of protein/cDNA to also scroll a complementary
851 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
852 // over residue to change abruptly, causing highlighted residue in panel 2
853 // to change, causing a scroll in panel 1 etc)
854 ap.setToScrollComplementPanel(false);
855 wasScrolled = ap.scrollToPosition(results);
858 seqCanvas.revalidate();
860 ap.setToScrollComplementPanel(true);
863 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
864 if (seqCanvas.highlightSearchResults(results, noFastPaint))
866 setStatusMessage(results);
868 return results.isEmpty() ? null : getHighlightInfo(results);
872 * temporary hack: answers a message suitable to show on structure hover
873 * label. This is normally null. It is a peptide variation description if
875 * <li>results are a single residue in a protein alignment</li>
876 * <li>there is a mapping to a coding sequence (codon)</li>
877 * <li>there are one or more SNP variant features on the codon</li>
879 * in which case the answer is of the format (e.g.) "p.Glu388Asp"
884 private String getHighlightInfo(SearchResultsI results)
887 * ideally, just find mapped CDS (as we don't care about render style here);
888 * for now, go via split frame complement's FeatureRenderer
890 AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
891 if (complement == null)
895 AlignFrame af = Desktop.getAlignFrameFor(complement);
896 FeatureRendererModel fr2 = af.getFeatureRenderer();
898 int j = results.getSize();
899 List<String> infos = new ArrayList<>();
900 for (int i = 0; i < j; i++)
902 SearchResultMatchI match = results.getResults().get(i);
903 int pos = match.getStart();
904 if (pos == match.getEnd())
906 SequenceI seq = match.getSequence();
907 SequenceI ds = seq.getDatasetSequence() == null ? seq
908 : seq.getDatasetSequence();
909 MappedFeatures mf = fr2
910 .findComplementFeaturesAtResidue(ds, pos);
913 for (SequenceFeature sf : mf.features)
915 String pv = mf.findProteinVariants(sf);
916 if (pv.length() > 0 && !infos.contains(pv))
929 StringBuilder sb = new StringBuilder();
930 for (String info : infos)
938 return sb.toString();
942 public VamsasSource getVamsasSource()
944 return this.ap == null ? null : this.ap.av;
948 public void updateColours(SequenceI seq, int index)
950 System.out.println("update the seqPanel colours");
955 * Action on mouse movement is to update the status bar to show the current
956 * sequence position, and (if features are shown) to show any features at the
957 * position in a tooltip. Does nothing if the mouse move does not change
963 public void mouseMoved(MouseEvent evt)
967 // This is because MacOSX creates a mouseMoved
968 // If control is down, other platforms will not.
972 final MousePos mousePos = findMousePosition(evt);
973 if (mousePos.equals(lastMousePosition))
976 * just a pixel move without change of 'cell'
980 lastMousePosition = mousePos;
982 if (mousePos.isOverAnnotation())
984 mouseMovedOverAnnotation(mousePos);
987 final int seq = mousePos.seqIndex;
989 final int column = mousePos.column;
990 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
992 lastMousePosition = null;
993 setToolTipText(null);
995 ap.alignFrame.setStatus("");
999 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1001 if (column >= sequence.getLength())
1007 * set status bar message, returning residue position in sequence
1009 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
1010 final int pos = setStatusMessage(sequence, column, seq);
1011 if (ssm != null && !isGapped)
1013 mouseOverSequence(sequence, column, pos);
1016 tooltipText.setLength(6); // Cuts the buffer back to <html>
1018 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
1021 for (int g = 0; g < groups.length; g++)
1023 if (groups[g].getStartRes() <= column
1024 && groups[g].getEndRes() >= column)
1026 if (!groups[g].getName().startsWith("JTreeGroup")
1027 && !groups[g].getName().startsWith("JGroup"))
1029 tooltipText.append(groups[g].getName());
1032 if (groups[g].getDescription() != null)
1034 tooltipText.append(": " + groups[g].getDescription());
1041 * add any features at the position to the tooltip; if over a gap, only
1042 * add features that straddle the gap (pos may be the residue before or
1045 if (av.isShowSequenceFeatures())
1047 List<SequenceFeature> features = ap.getFeatureRenderer()
1048 .findFeaturesAtColumn(sequence, column + 1);
1049 seqARep.appendFeatures(tooltipText, pos, features,
1050 this.ap.getSeqPanel().seqCanvas.fr);
1053 * add features in CDS/protein complement at the corresponding
1054 * position if configured to do so
1056 if (av.isShowComplementFeatures())
1058 if (!Comparison.isGap(sequence.getCharAt(column)))
1060 AlignViewportI complement = ap.getAlignViewport()
1061 .getCodingComplement();
1062 AlignFrame af = Desktop.getAlignFrameFor(complement);
1063 FeatureRendererModel fr2 = af.getFeatureRenderer();
1064 MappedFeatures mf = fr2.findComplementFeaturesAtResidue(sequence,
1068 seqARep.appendFeatures(tooltipText, pos, mf, fr2);
1073 if (tooltipText.length() == 6) // <html>
1075 setToolTipText(null);
1080 if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
1082 tooltipText.setLength(MAX_TOOLTIP_LENGTH);
1083 tooltipText.append("...");
1085 String textString = tooltipText.toString();
1086 if (lastTooltip == null || !lastTooltip.equals(textString))
1088 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
1090 setToolTipText(formattedTooltipText);
1091 lastTooltip = textString;
1097 * When the view is in wrapped mode, and the mouse is over an annotation row,
1098 * shows the corresponding tooltip and status message (if any)
1103 protected void mouseMovedOverAnnotation(MousePos pos)
1105 final int column = pos.column;
1106 final int rowIndex = pos.annotationIndex;
1108 if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation()
1113 AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
1115 String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
1117 setToolTipText(tooltip);
1118 lastTooltip = tooltip;
1120 String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column,
1122 ap.alignFrame.setStatus(msg);
1125 private Point lastp = null;
1130 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
1133 public Point getToolTipLocation(MouseEvent event)
1135 if (tooltipText == null || tooltipText.length() <= 6)
1141 int x = event.getX();
1143 // switch sides when tooltip is too close to edge
1144 int wdth = (w - x < 200) ? -(w / 2) : 5;
1146 if (!event.isShiftDown() || p == null)
1148 p = new Point(event.getX() + wdth, event.getY() - 20);
1152 * TODO: try to set position so region is not obscured by tooltip
1160 * set when the current UI interaction has resulted in a change that requires
1161 * shading in overviews and structures to be recalculated. this could be
1162 * changed to a something more expressive that indicates what actually has
1163 * changed, so selective redraws can be applied (ie. only structures, only
1166 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
1169 * set if av.getSelectionGroup() refers to a group that is defined on the
1170 * alignment view, rather than a transient selection
1172 // private boolean editingDefinedGroup = false; // TODO: refactor to
1173 // avcontroller or viewModel
1176 * Sets the status message in alignment panel, showing the sequence number
1177 * (index) and id, and residue and residue position if not at a gap, for the
1178 * given sequence and column position. Returns the residue position returned
1179 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
1180 * if at a gapped position.
1183 * aligned sequence object
1187 * index of sequence in alignment
1188 * @return sequence position of residue at column, or adjacent residue if at a
1191 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
1193 char sequenceChar = sequence.getCharAt(column);
1194 int pos = sequence.findPosition(column);
1195 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
1201 * Builds the status message for the current cursor location and writes it to
1202 * the status bar, for example
1205 * Sequence 3 ID: FER1_SOLLC
1206 * Sequence 5 ID: FER1_PEA Residue: THR (4)
1207 * Sequence 5 ID: FER1_PEA Residue: B (3)
1208 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
1213 * sequence position in the alignment (1..)
1214 * @param sequenceChar
1215 * the character under the cursor
1217 * the sequence residue position (if not over a gap)
1219 protected void setStatusMessage(SequenceI sequence, int seqIndex,
1220 char sequenceChar, int residuePos)
1222 StringBuilder text = new StringBuilder(32);
1225 * Sequence number (if known), and sequence name.
1227 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
1228 text.append("Sequence").append(seqno).append(" ID: ")
1229 .append(sequence.getName());
1231 String residue = null;
1234 * Try to translate the display character to residue name (null for gap).
1236 boolean isGapped = Comparison.isGap(sequenceChar);
1240 boolean nucleotide = av.getAlignment().isNucleotide();
1241 String displayChar = String.valueOf(sequenceChar);
1244 residue = ResidueProperties.nucleotideName.get(displayChar);
1248 residue = "X".equalsIgnoreCase(displayChar) ? "X"
1249 : ("*".equals(displayChar) ? "STOP"
1250 : ResidueProperties.aa2Triplet.get(displayChar));
1252 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
1253 .append(": ").append(residue == null ? displayChar : residue);
1255 text.append(" (").append(Integer.toString(residuePos)).append(")");
1257 ap.alignFrame.setStatus(text.toString());
1261 * Set the status bar message to highlight the first matched position in
1266 private void setStatusMessage(SearchResultsI results)
1268 AlignmentI al = this.av.getAlignment();
1269 int sequenceIndex = al.findIndex(results);
1270 if (sequenceIndex == -1)
1274 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
1275 for (SearchResultMatchI m : results.getResults())
1277 SequenceI seq = m.getSequence();
1278 if (seq.getDatasetSequence() != null)
1280 seq = seq.getDatasetSequence();
1285 int start = m.getStart();
1286 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1297 public void mouseDragged(MouseEvent evt)
1299 MousePos pos = findMousePosition(evt);
1300 if (pos.isOverAnnotation() || pos.column == -1)
1305 if (mouseWheelPressed)
1307 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1308 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1310 int oldWidth = av.getCharWidth();
1312 // Which is bigger, left-right or up-down?
1313 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1314 .abs(evt.getX() - lastMousePress.getX()))
1317 * on drag up or down, decrement or increment font size
1319 int fontSize = av.font.getSize();
1320 boolean fontChanged = false;
1322 if (evt.getY() < lastMousePress.getY())
1327 else if (evt.getY() > lastMousePress.getY())
1340 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1342 av.setFont(newFont, true);
1343 av.setCharWidth(oldWidth);
1347 ap.av.getCodingComplement().setFont(newFont, true);
1348 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1349 .getSplitViewContainer();
1350 splitFrame.adjustLayout();
1351 splitFrame.repaint();
1358 * on drag left or right, decrement or increment character width
1361 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1363 newWidth = av.getCharWidth() - 1;
1364 av.setCharWidth(newWidth);
1366 else if (evt.getX() > lastMousePress.getX())
1368 newWidth = av.getCharWidth() + 1;
1369 av.setCharWidth(newWidth);
1373 ap.paintAlignment(false, false);
1377 * need to ensure newWidth is set on cdna, regardless of which
1378 * panel the mouse drag happened in; protein will compute its
1379 * character width as 1:1 or 3:1
1381 av.getCodingComplement().setCharWidth(newWidth);
1382 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1383 .getSplitViewContainer();
1384 splitFrame.adjustLayout();
1385 splitFrame.repaint();
1390 FontMetrics fm = getFontMetrics(av.getFont());
1391 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1393 lastMousePress = evt.getPoint();
1400 dragStretchGroup(evt);
1404 int res = pos.column;
1411 if ((editLastRes == -1) || (editLastRes == res))
1416 if ((res < av.getAlignment().getWidth()) && (res < editLastRes))
1418 // dragLeft, delete gap
1419 editSequence(false, false, res);
1423 editSequence(true, false, res);
1426 mouseDragging = true;
1427 if (scrollThread != null)
1429 scrollThread.setMousePosition(evt.getPoint());
1434 * Edits the sequence to insert or delete one or more gaps, in response to a
1435 * mouse drag or cursor mode command. The number of inserts/deletes may be
1436 * specified with the cursor command, or else depends on the mouse event
1437 * (normally one column, but potentially more for a fast mouse drag).
1439 * Delete gaps is limited to the number of gaps left of the cursor position
1440 * (mouse drag), or at or right of the cursor position (cursor mode).
1442 * In group editing mode (Ctrl or Cmd down), the edit acts on all sequences in
1443 * the current selection group.
1445 * In locked editing mode (with a selection group present), inserts/deletions
1446 * within the selection group are limited to its boundaries (and edits outside
1447 * the group stop at its border).
1450 * true to insert gaps, false to delete gaps
1452 * (unused parameter)
1454 * the column at which to perform the action; the number of columns
1455 * affected depends on <code>this.editLastRes</code> (cursor column
1458 synchronized void editSequence(boolean insertGap, boolean editSeq,
1462 int fixedRight = -1;
1463 boolean fixedColumns = false;
1464 SequenceGroup sg = av.getSelectionGroup();
1466 final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
1468 // No group, but the sequence may represent a group
1469 if (!groupEditing && av.hasHiddenRows())
1471 if (av.isHiddenRepSequence(seq))
1473 sg = av.getRepresentedSequences(seq);
1474 groupEditing = true;
1478 StringBuilder message = new StringBuilder(64); // for status bar
1481 * make a name for the edit action, for
1482 * status bar message and Undo/Redo menu
1484 String label = null;
1487 message.append("Edit group:");
1488 label = MessageManager.getString("action.edit_group");
1492 message.append("Edit sequence: " + seq.getName());
1493 label = seq.getName();
1494 if (label.length() > 10)
1496 label = label.substring(0, 10);
1498 label = MessageManager.formatMessage("label.edit_params",
1504 * initialise the edit command if there is not
1505 * already one being extended
1507 if (editCommand == null)
1509 editCommand = new EditCommand(label);
1514 message.append(" insert ");
1518 message.append(" delete ");
1521 message.append(Math.abs(startres - editLastRes) + " gaps.");
1522 ap.alignFrame.setStatus(message.toString());
1525 * is there a selection group containing the sequence being edited?
1526 * if so the boundary of the group is the limit of the edit
1527 * (but the edit may be inside or outside the selection group)
1529 boolean inSelectionGroup = sg != null
1530 && sg.getSequences(av.getHiddenRepSequences()).contains(seq);
1531 if (groupEditing || inSelectionGroup)
1533 fixedColumns = true;
1535 // sg might be null as the user may only see 1 sequence,
1536 // but the sequence represents a group
1539 if (!av.isHiddenRepSequence(seq))
1544 sg = av.getRepresentedSequences(seq);
1547 fixedLeft = sg.getStartRes();
1548 fixedRight = sg.getEndRes();
1550 if ((startres < fixedLeft && editLastRes >= fixedLeft)
1551 || (startres >= fixedLeft && editLastRes < fixedLeft)
1552 || (startres > fixedRight && editLastRes <= fixedRight)
1553 || (startres <= fixedRight && editLastRes > fixedRight))
1559 if (fixedLeft > startres)
1561 fixedRight = fixedLeft - 1;
1564 else if (fixedRight < startres)
1566 fixedLeft = fixedRight;
1571 if (av.hasHiddenColumns())
1573 fixedColumns = true;
1574 int y1 = av.getAlignment().getHiddenColumns()
1575 .getNextHiddenBoundary(true, startres);
1576 int y2 = av.getAlignment().getHiddenColumns()
1577 .getNextHiddenBoundary(false, startres);
1579 if ((insertGap && startres > y1 && editLastRes < y1)
1580 || (!insertGap && startres < y2 && editLastRes > y2))
1586 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1587 // Selection spans a hidden region
1588 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1596 fixedRight = y2 - 1;
1601 boolean success = doEditSequence(insertGap, editSeq, startres,
1602 fixedRight, fixedColumns, sg);
1605 * report what actually happened (might be less than
1606 * what was requested), by inspecting the edit commands added
1608 String msg = getEditStatusMessage(editCommand);
1609 ap.alignFrame.setStatus(msg == null ? " " : msg);
1615 editLastRes = startres;
1616 seqCanvas.repaint();
1620 * A helper method that performs the requested editing to insert or delete
1621 * gaps (if possible). Answers true if the edit was successful, false if could
1622 * only be performed in part or not at all. Failure may occur in 'locked edit'
1623 * mode, when an insertion requires a matching gapped position (or column) to
1624 * delete, and deletion requires an adjacent gapped position (or column) to
1628 * true if inserting gap(s), false if deleting
1630 * (unused parameter, currently always false)
1632 * the column at which to perform the edit
1634 * fixed right boundary column of a locked edit (within or to the
1635 * left of a selection group)
1636 * @param fixedColumns
1637 * true if this is a locked edit
1639 * the sequence group (if group edit is being performed)
1642 protected boolean doEditSequence(final boolean insertGap,
1643 final boolean editSeq, final int startres, int fixedRight,
1644 final boolean fixedColumns, final SequenceGroup sg)
1646 final SequenceI seq = av.getAlignment().getSequenceAt(editStartSeq);
1647 SequenceI[] seqs = new SequenceI[] { seq };
1651 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1652 int g, groupSize = vseqs.size();
1653 SequenceI[] groupSeqs = new SequenceI[groupSize];
1654 for (g = 0; g < groupSeqs.length; g++)
1656 groupSeqs[g] = vseqs.get(g);
1662 // If the user has selected the whole sequence, and is dragging to
1663 // the right, we can still extend the alignment and selectionGroup
1664 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1665 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1668 av.getAlignment().getWidth() + startres - editLastRes);
1669 fixedRight = sg.getEndRes();
1672 // Is it valid with fixed columns??
1673 // Find the next gap before the end
1674 // of the visible region boundary
1675 boolean blank = false;
1676 for (; fixedRight > editLastRes; fixedRight--)
1680 for (g = 0; g < groupSize; g++)
1682 for (int j = 0; j < startres - editLastRes; j++)
1685 .isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1700 if (sg.getSize() == av.getAlignment().getHeight())
1702 if ((av.hasHiddenColumns()
1703 && startres < av.getAlignment().getHiddenColumns()
1704 .getNextHiddenBoundary(false, startres)))
1709 int alWidth = av.getAlignment().getWidth();
1710 if (av.hasHiddenRows())
1712 int hwidth = av.getAlignment().getHiddenSequences()
1714 if (hwidth > alWidth)
1719 // We can still insert gaps if the selectionGroup
1720 // contains all the sequences
1721 sg.setEndRes(sg.getEndRes() + startres - editLastRes);
1722 fixedRight = alWidth + startres - editLastRes;
1732 else if (!insertGap)
1734 // / Are we able to delete?
1735 // ie are all columns blank?
1737 for (g = 0; g < groupSize; g++)
1739 for (int j = startres; j < editLastRes; j++)
1741 if (groupSeqs[g].getLength() <= j)
1746 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1748 // Not a gap, block edit not valid
1757 // dragging to the right
1758 if (fixedColumns && fixedRight != -1)
1760 for (int j = editLastRes; j < startres; j++)
1762 insertGap(j, groupSeqs, fixedRight);
1767 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1768 startres - editLastRes, false);
1773 // dragging to the left
1774 if (fixedColumns && fixedRight != -1)
1776 for (int j = editLastRes; j > startres; j--)
1778 deleteChar(startres, groupSeqs, fixedRight);
1783 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1784 editLastRes - startres, false);
1791 * editing a single sequence
1795 // dragging to the right
1796 if (fixedColumns && fixedRight != -1)
1798 for (int j = editLastRes; j < startres; j++)
1800 if (!insertGap(j, seqs, fixedRight))
1803 * e.g. cursor mode command specified
1804 * more inserts than are possible
1812 appendEdit(Action.INSERT_GAP, seqs, editLastRes,
1813 startres - editLastRes, false);
1820 // dragging to the left
1821 if (fixedColumns && fixedRight != -1)
1823 for (int j = editLastRes; j > startres; j--)
1825 if (!Comparison.isGap(seq.getCharAt(startres)))
1829 deleteChar(startres, seqs, fixedRight);
1834 // could be a keyboard edit trying to delete none gaps
1836 for (int m = startres; m < editLastRes; m++)
1838 if (!Comparison.isGap(seq.getCharAt(m)))
1846 appendEdit(Action.DELETE_GAP, seqs, startres, max, false);
1851 {// insertGap==false AND editSeq==TRUE;
1852 if (fixedColumns && fixedRight != -1)
1854 for (int j = editLastRes; j < startres; j++)
1856 insertGap(j, seqs, fixedRight);
1861 appendEdit(Action.INSERT_NUC, seqs, editLastRes,
1862 startres - editLastRes, false);
1872 * Constructs an informative status bar message while dragging to insert or
1873 * delete gaps. Answers null if inserts and deletes cancel out.
1875 * @param editCommand
1876 * a command containing the list of individual edits
1879 protected static String getEditStatusMessage(EditCommand editCommand)
1881 if (editCommand == null)
1887 * add any inserts, and subtract any deletes,
1888 * not counting those auto-inserted when doing a 'locked edit'
1889 * (so only counting edits 'under the cursor')
1892 for (Edit cmd : editCommand.getEdits())
1894 if (!cmd.isSystemGenerated())
1896 count += cmd.getAction() == Action.INSERT_GAP ? cmd.getNumber()
1904 * inserts and deletes cancel out
1909 String msgKey = count > 1 ? "label.insert_gaps"
1910 : (count == 1 ? "label.insert_gap"
1911 : (count == -1 ? "label.delete_gap"
1912 : "label.delete_gaps"));
1913 count = Math.abs(count);
1915 return MessageManager.formatMessage(msgKey, String.valueOf(count));
1919 * Inserts one gap at column j, deleting the right-most gapped column up to
1920 * (and including) fixedColumn. Returns true if the edit is successful, false
1921 * if no blank column is available to allow the insertion to be balanced by a
1926 * @param fixedColumn
1929 boolean insertGap(int j, SequenceI[] seq, int fixedColumn)
1931 int blankColumn = fixedColumn;
1932 for (int s = 0; s < seq.length; s++)
1934 // Find the next gap before the end of the visible region boundary
1935 // If lastCol > j, theres a boundary after the gap insertion
1937 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1939 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1941 // Theres a space, so break and insert the gap
1946 if (blankColumn <= j)
1948 blankColumn = fixedColumn;
1954 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1, true);
1956 appendEdit(Action.INSERT_GAP, seq, j, 1, false);
1962 * Helper method to add and perform one edit action
1968 * @param systemGenerated
1969 * true if the edit is a 'balancing' delete (or insert) to match a
1970 * user's insert (or delete) in a locked editing region
1972 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1973 int count, boolean systemGenerated)
1976 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1977 av.getAlignment().getGapCharacter());
1978 edit.setSystemGenerated(systemGenerated);
1980 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1984 * Deletes the character at column j, and inserts a gap at fixedColumn, in
1985 * each of the given sequences. The caller should ensure that all sequences
1986 * are gapped in column j.
1990 * @param fixedColumn
1992 void deleteChar(int j, SequenceI[] seqs, int fixedColumn)
1994 appendEdit(Action.DELETE_GAP, seqs, j, 1, false);
1996 appendEdit(Action.INSERT_GAP, seqs, fixedColumn, 1, true);
2000 * On reentering the panel, stops any scrolling that was started on dragging
2006 public void mouseEntered(MouseEvent e)
2016 * On leaving the panel, if the mouse is being dragged, starts a thread to
2017 * scroll it until the mouse is released (in unwrapped mode only)
2022 public void mouseExited(MouseEvent e)
2024 lastMousePosition = null;
2025 ap.alignFrame.setStatus(" ");
2026 if (av.getWrapAlignment())
2031 if (mouseDragging && scrollThread == null)
2033 scrollThread = new ScrollThread();
2038 * Handler for double-click on a position with one or more sequence features.
2039 * Opens the Amend Features dialog to allow feature details to be amended, or
2040 * the feature deleted.
2043 public void mouseClicked(MouseEvent evt)
2045 SequenceGroup sg = null;
2046 MousePos pos = findMousePosition(evt);
2047 if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
2052 if (evt.getClickCount() > 1)
2054 sg = av.getSelectionGroup();
2055 if (sg != null && sg.getSize() == 1
2056 && sg.getEndRes() - sg.getStartRes() < 2)
2058 av.setSelectionGroup(null);
2061 int column = pos.column;
2064 * find features at the position (if not gapped), or straddling
2065 * the position (if at a gap)
2067 SequenceI sequence = av.getAlignment().getSequenceAt(pos.seqIndex);
2068 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
2069 .findFeaturesAtColumn(sequence, column + 1);
2071 if (!features.isEmpty())
2074 * highlight the first feature at the position on the alignment
2076 SearchResultsI highlight = new SearchResults();
2077 highlight.addResult(sequence, features.get(0).getBegin(), features
2079 seqCanvas.highlightSearchResults(highlight, false);
2082 * open the Amend Features dialog; clear highlighting afterwards,
2083 * whether changes were made or not
2085 List<SequenceI> seqs = Collections.singletonList(sequence);
2086 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
2088 av.setSearchResults(null); // clear highlighting
2089 seqCanvas.repaint(); // draw new/amended features
2095 public void mouseWheelMoved(MouseWheelEvent e)
2098 double wheelRotation = e.getPreciseWheelRotation();
2099 if (wheelRotation > 0)
2101 if (e.isShiftDown())
2103 av.getRanges().scrollRight(true);
2108 av.getRanges().scrollUp(false);
2111 else if (wheelRotation < 0)
2113 if (e.isShiftDown())
2115 av.getRanges().scrollRight(false);
2119 av.getRanges().scrollUp(true);
2124 * update status bar and tooltip for new position
2125 * (need to synthesize a mouse movement to refresh tooltip)
2128 ToolTipManager.sharedInstance().mouseMoved(e);
2137 protected void doMousePressedDefineMode(MouseEvent evt, MousePos pos)
2139 if (pos.isOverAnnotation() || pos.seqIndex == -1 || pos.column == -1)
2144 final int res = pos.column;
2145 final int seq = pos.seqIndex;
2147 updateOverviewAndStructs = false;
2149 startWrapBlock = wrappedBlock;
2151 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
2153 if ((sequence == null) || (res > sequence.getLength()))
2158 stretchGroup = av.getSelectionGroup();
2160 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
2162 stretchGroup = av.getAlignment().findGroup(sequence, res);
2163 if (stretchGroup != null)
2165 // only update the current selection if the popup menu has a group to
2167 av.setSelectionGroup(stretchGroup);
2171 if (evt.isPopupTrigger()) // Mac: mousePressed
2173 showPopupMenu(evt, pos);
2178 * defer right-mouse click handling to mouseReleased on Windows
2179 * (where isPopupTrigger() will answer true)
2180 * NB isRightMouseButton is also true for Cmd-click on Mac
2182 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
2189 seqCanvas.cursorX = res;
2190 seqCanvas.cursorY = seq;
2191 seqCanvas.repaint();
2195 if (stretchGroup == null)
2197 createStretchGroup(res, sequence);
2200 if (stretchGroup != null)
2202 stretchGroup.addPropertyChangeListener(seqCanvas);
2205 seqCanvas.repaint();
2208 private void createStretchGroup(int res, SequenceI sequence)
2210 // Only if left mouse button do we want to change group sizes
2211 // define a new group here
2212 SequenceGroup sg = new SequenceGroup();
2213 sg.setStartRes(res);
2215 sg.addSequence(sequence, false);
2216 av.setSelectionGroup(sg);
2219 if (av.getConservationSelected())
2221 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
2225 if (av.getAbovePIDThreshold())
2227 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
2230 // TODO: stretchGroup will always be not null. Is this a merge error ?
2231 // or is there a threading issue here?
2232 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
2234 // Edit end res position of selected group
2235 changeEndRes = true;
2237 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
2239 // Edit end res position of selected group
2240 changeStartRes = true;
2242 stretchGroup.getWidth();
2247 * Build and show a pop-up menu at the right-click mouse position
2252 void showPopupMenu(MouseEvent evt, MousePos pos)
2254 final int column = pos.column;
2255 final int seq = pos.seqIndex;
2256 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
2257 if (sequence != null)
2259 PopupMenu pop = new PopupMenu(ap, sequence, column);
2260 pop.show(this, evt.getX(), evt.getY());
2265 * Update the display after mouse up on a selection or group
2268 * mouse released event details
2270 * true if this event is happening after a mouse drag (rather than a
2273 protected void doMouseReleasedDefineMode(MouseEvent evt,
2276 if (stretchGroup == null)
2281 stretchGroup.removePropertyChangeListener(seqCanvas);
2283 // always do this - annotation has own state
2284 // but defer colourscheme update until hidden sequences are passed in
2285 boolean vischange = stretchGroup.recalcConservation(true);
2286 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
2288 if (stretchGroup.cs != null)
2292 stretchGroup.cs.alignmentChanged(stretchGroup,
2293 av.getHiddenRepSequences());
2296 ResidueShaderI groupColourScheme = stretchGroup
2297 .getGroupColourScheme();
2298 String name = stretchGroup.getName();
2299 if (stretchGroup.cs.conservationApplied())
2301 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
2303 if (stretchGroup.cs.getThreshold() > 0)
2305 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
2308 PaintRefresher.Refresh(this, av.getSequenceSetId());
2309 // TODO: structure colours only need updating if stretchGroup used to or now
2310 // does contain sequences with structure views
2311 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
2312 updateOverviewAndStructs = false;
2313 changeEndRes = false;
2314 changeStartRes = false;
2315 stretchGroup = null;
2320 * Resizes the borders of a selection group depending on the direction of
2325 protected void dragStretchGroup(MouseEvent evt)
2327 if (stretchGroup == null)
2332 MousePos pos = findMousePosition(evt);
2333 if (pos.isOverAnnotation() || pos.column == -1 || pos.seqIndex == -1)
2338 int res = pos.column;
2339 int y = pos.seqIndex;
2341 if (wrappedBlock != startWrapBlock)
2346 res = Math.min(res, av.getAlignment().getWidth()-1);
2348 if (stretchGroup.getEndRes() == res)
2350 // Edit end res position of selected group
2351 changeEndRes = true;
2353 else if (stretchGroup.getStartRes() == res)
2355 // Edit start res position of selected group
2356 changeStartRes = true;
2359 if (res < av.getRanges().getStartRes())
2361 res = av.getRanges().getStartRes();
2366 if (res > (stretchGroup.getStartRes() - 1))
2368 stretchGroup.setEndRes(res);
2369 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2372 else if (changeStartRes)
2374 if (res < (stretchGroup.getEndRes() + 1))
2376 stretchGroup.setStartRes(res);
2377 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2381 int dragDirection = 0;
2387 else if (y < oldSeq)
2392 while ((y != oldSeq) && (oldSeq > -1)
2393 && (y < av.getAlignment().getHeight()))
2395 // This routine ensures we don't skip any sequences, as the
2396 // selection is quite slow.
2397 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
2399 oldSeq += dragDirection;
2406 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
2408 if (stretchGroup.getSequences(null).contains(nextSeq))
2410 stretchGroup.deleteSequence(seq, false);
2411 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2417 stretchGroup.addSequence(seq, false);
2420 stretchGroup.addSequence(nextSeq, false);
2421 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2430 mouseDragging = true;
2432 if (scrollThread != null)
2434 scrollThread.setMousePosition(evt.getPoint());
2438 * construct a status message showing the range of the selection
2440 StringBuilder status = new StringBuilder(64);
2441 List<SequenceI> seqs = stretchGroup.getSequences();
2442 String name = seqs.get(0).getName();
2443 if (name.length() > 20)
2445 name = name.substring(0, 20);
2447 status.append(name).append(" - ");
2448 name = seqs.get(seqs.size() - 1).getName();
2449 if (name.length() > 20)
2451 name = name.substring(0, 20);
2453 status.append(name).append(" ");
2454 int startRes = stretchGroup.getStartRes();
2455 status.append(" cols ").append(String.valueOf(startRes + 1))
2457 int endRes = stretchGroup.getEndRes();
2458 status.append(String.valueOf(endRes + 1));
2459 status.append(" (").append(String.valueOf(seqs.size())).append(" x ")
2460 .append(String.valueOf(endRes - startRes + 1)).append(")");
2461 ap.alignFrame.setStatus(status.toString());
2465 * Stops the scroll thread if it is running
2467 void stopScrolling()
2469 if (scrollThread != null)
2471 scrollThread.stopScrolling();
2472 scrollThread = null;
2474 mouseDragging = false;
2478 * Starts a thread to scroll the alignment, towards a given mouse position
2479 * outside the panel bounds
2483 void startScrolling(Point mousePos)
2485 if (scrollThread == null)
2487 scrollThread = new ScrollThread();
2490 mouseDragging = true;
2491 scrollThread.setMousePosition(mousePos);
2495 * Performs scrolling of the visible alignment left, right, up or down
2497 class ScrollThread extends Thread
2499 private Point mousePos;
2501 private volatile boolean threadRunning = true;
2506 public ScrollThread()
2508 setName("SeqPanel$ScrollThread");
2513 * Sets the position of the mouse that determines the direction of the
2518 public void setMousePosition(Point p)
2524 * Sets a flag that will cause the thread to exit
2526 public void stopScrolling()
2528 threadRunning = false;
2532 * Scrolls the alignment left or right, and/or up or down, depending on the
2533 * last notified mouse position, until the limit of the alignment is
2534 * reached, or a flag is set to stop the scroll
2539 while (threadRunning && mouseDragging)
2541 if (mousePos != null)
2543 boolean scrolled = false;
2544 ViewportRanges ranges = SeqPanel.this.av.getRanges();
2551 // mouse is above this panel - try scroll up
2552 scrolled = ranges.scrollUp(true);
2554 else if (mousePos.y >= getHeight())
2556 // mouse is below this panel - try scroll down
2557 scrolled = ranges.scrollUp(false);
2561 * scroll left or right
2565 scrolled |= ranges.scrollRight(false);
2567 else if (mousePos.x >= getWidth())
2569 scrolled |= ranges.scrollRight(true);
2574 * we have reached the limit of the visible alignment - quit
2576 threadRunning = false;
2577 SeqPanel.this.ap.repaint();
2584 } catch (Exception ex)
2592 * modify current selection according to a received message.
2595 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2596 HiddenColumns hidden, SelectionSource source)
2598 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2599 // handles selection messages...
2600 // TODO: extend config options to allow user to control if selections may be
2601 // shared between viewports.
2602 boolean iSentTheSelection = (av == source
2603 || (source instanceof AlignViewport
2604 && ((AlignmentViewport) source).getSequenceSetId()
2605 .equals(av.getSequenceSetId())));
2607 if (iSentTheSelection)
2609 // respond to our own event by updating dependent dialogs
2610 if (ap.getCalculationDialog() != null)
2612 ap.getCalculationDialog().validateCalcTypes();
2618 // process further ?
2619 if (!av.followSelection)
2625 * Ignore the selection if there is one of our own pending.
2627 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2633 * Check for selection in a view of which this one is a dna/protein
2636 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2641 // do we want to thread this ? (contention with seqsel and colsel locks, I
2644 * only copy colsel if there is a real intersection between
2645 * sequence selection and this panel's alignment
2647 boolean repaint = false;
2648 boolean copycolsel = false;
2650 SequenceGroup sgroup = null;
2651 if (seqsel != null && seqsel.getSize() > 0)
2653 if (av.getAlignment() == null)
2655 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2656 + " ViewId=" + av.getViewId()
2657 + " 's alignment is NULL! returning immediately.");
2660 sgroup = seqsel.intersect(av.getAlignment(),
2661 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2662 if ((sgroup != null && sgroup.getSize() > 0))
2667 if (sgroup != null && sgroup.getSize() > 0)
2669 av.setSelectionGroup(sgroup);
2673 av.setSelectionGroup(null);
2675 av.isSelectionGroupChanged(true);
2680 // the current selection is unset or from a previous message
2681 // so import the new colsel.
2682 if (colsel == null || colsel.isEmpty())
2684 if (av.getColumnSelection() != null)
2686 av.getColumnSelection().clear();
2692 // TODO: shift colSel according to the intersecting sequences
2693 if (av.getColumnSelection() == null)
2695 av.setColumnSelection(new ColumnSelection(colsel));
2699 av.getColumnSelection().setElementsFrom(colsel,
2700 av.getAlignment().getHiddenColumns());
2703 av.isColSelChanged(true);
2707 if (copycolsel && av.hasHiddenColumns()
2708 && (av.getAlignment().getHiddenColumns() == null))
2710 System.err.println("Bad things");
2712 if (repaint) // always true!
2714 // probably finessing with multiple redraws here
2715 PaintRefresher.Refresh(this, av.getSequenceSetId());
2716 // ap.paintAlignment(false);
2719 // lastly, update dependent dialogs
2720 if (ap.getCalculationDialog() != null)
2722 ap.getCalculationDialog().validateCalcTypes();
2728 * If this panel is a cdna/protein translation view of the selection source,
2729 * tries to map the source selection to a local one, and returns true. Else
2736 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2737 ColumnSelection colsel, HiddenColumns hidden,
2738 SelectionSource source)
2740 if (!(source instanceof AlignViewportI))
2744 final AlignViewportI sourceAv = (AlignViewportI) source;
2745 if (sourceAv.getCodingComplement() != av
2746 && av.getCodingComplement() != sourceAv)
2752 * Map sequence selection
2754 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2755 av.setSelectionGroup(sg);
2756 av.isSelectionGroupChanged(true);
2759 * Map column selection
2761 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2763 ColumnSelection cs = new ColumnSelection();
2764 HiddenColumns hs = new HiddenColumns();
2765 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2766 av.setColumnSelection(cs);
2767 boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs);
2769 // lastly, update any dependent dialogs
2770 if (ap.getCalculationDialog() != null)
2772 ap.getCalculationDialog().validateCalcTypes();
2776 * repaint alignment, and also Overview or Structure
2777 * if hidden column selection has changed
2779 ap.paintAlignment(hiddenChanged, hiddenChanged);
2786 * @return null or last search results handled by this panel
2788 public SearchResultsI getLastSearchResults()
2790 return lastSearchResults;