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.bin.Jalview;
26 import jalview.commands.EditCommand;
27 import jalview.commands.EditCommand.Action;
28 import jalview.commands.EditCommand.Edit;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.ColumnSelection;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.SearchResultMatchI;
33 import jalview.datamodel.SearchResults;
34 import jalview.datamodel.SearchResultsI;
35 import jalview.datamodel.Sequence;
36 import jalview.datamodel.SequenceFeature;
37 import jalview.datamodel.SequenceGroup;
38 import jalview.datamodel.SequenceI;
39 import jalview.io.SequenceAnnotationReport;
40 import jalview.renderer.ResidueShaderI;
41 import jalview.schemes.ResidueProperties;
42 import jalview.structure.SelectionListener;
43 import jalview.structure.SelectionSource;
44 import jalview.structure.SequenceListener;
45 import jalview.structure.StructureSelectionManager;
46 import jalview.structure.VamsasSource;
47 import jalview.util.Comparison;
48 import jalview.util.MappingUtils;
49 import jalview.util.MessageManager;
50 import jalview.util.Platform;
51 import jalview.viewmodel.AlignmentViewport;
52 import jalview.viewmodel.ViewportRanges;
54 import java.awt.BorderLayout;
55 import java.awt.Color;
57 import java.awt.FontMetrics;
58 import java.awt.Point;
59 import java.awt.event.ActionEvent;
60 import java.awt.event.ActionListener;
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.Collections;
67 import java.util.List;
69 import javax.swing.JLabel;
70 import javax.swing.JPanel;
71 import javax.swing.JToolTip;
72 import javax.swing.SwingUtilities;
73 import javax.swing.Timer;
74 import javax.swing.ToolTipManager;
80 * @version $Revision: 1.130 $
82 public class SeqPanel extends JPanel
83 implements MouseListener, MouseMotionListener, MouseWheelListener,
84 SequenceListener, SelectionListener
86 private static final int MAX_TOOLTIP_LENGTH = 300;
88 public SeqCanvas seqCanvas;
90 public AlignmentPanel ap;
93 * last column position for mouseMoved event
95 private int lastMouseColumn;
98 * last sequence offset for mouseMoved event
100 private int lastMouseSeq;
102 protected int lastres;
104 protected int startseq;
106 protected AlignViewport av;
108 ScrollThread scrollThread = null;
110 boolean mouseDragging = false;
112 boolean editingSeqs = false;
114 boolean groupEditing = false;
116 // ////////////////////////////////////////
117 // ///Everything below this is for defining the boundary of the rubberband
118 // ////////////////////////////////////////
121 boolean changeEndSeq = false;
123 boolean changeStartSeq = false;
125 boolean changeEndRes = false;
127 boolean changeStartRes = false;
129 SequenceGroup stretchGroup = null;
131 boolean remove = false;
133 Point lastMousePress;
135 boolean mouseWheelPressed = false;
137 StringBuffer keyboardNo1;
139 StringBuffer keyboardNo2;
141 java.net.URL linkImageURL;
143 private final SequenceAnnotationReport seqARep;
145 StringBuilder tooltipText = new StringBuilder();
149 EditCommand editCommand;
151 StructureSelectionManager ssm;
153 SearchResultsI lastSearchResults;
156 * Creates a new SeqPanel object
161 public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
163 linkImageURL = getClass().getResource("/images/link.gif");
164 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
165 ToolTipManager.sharedInstance().registerComponent(this);
166 ToolTipManager.sharedInstance().setInitialDelay(0);
167 ToolTipManager.sharedInstance().setDismissDelay(10000);
171 setBackground(Color.white);
173 seqCanvas = new SeqCanvas(alignPanel);
174 setLayout(new BorderLayout());
175 add(seqCanvas, BorderLayout.CENTER);
177 this.ap = alignPanel;
179 if (!viewport.isDataset())
181 addMouseMotionListener(this);
182 addMouseListener(this);
183 addMouseWheelListener(this);
184 ssm = viewport.getStructureSelectionManager();
185 ssm.addStructureViewerListener(this);
186 ssm.addSelectionListener(this);
189 lastMouseColumn = -1;
193 int startWrapBlock = -1;
195 int wrappedBlock = -1;
198 * Returns the aligned sequence position (base 0) at the mouse position, or
199 * the closest visible one
204 int findColumn(MouseEvent evt)
209 int startRes = av.getRanges().getStartRes();
210 if (av.getWrapAlignment())
213 int hgap = av.getCharHeight();
214 if (av.getScaleAboveWrapped())
216 hgap += av.getCharHeight();
219 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
220 + hgap + seqCanvas.getAnnotationHeight();
223 y = Math.max(0, y - hgap);
224 x = Math.max(0, x - seqCanvas.getLabelWidthWest());
226 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
232 wrappedBlock = y / cHeight;
233 wrappedBlock += startRes / cwidth;
234 // allow for wrapped view scrolled right (possible from Overview)
235 int startOffset = startRes % cwidth;
236 res = wrappedBlock * cwidth + startOffset
237 + +Math.min(cwidth - 1, x / av.getCharWidth());
241 if (x > seqCanvas.getX() + seqCanvas.getWidth())
243 // make sure we calculate relative to visible alignment, rather than
245 x = seqCanvas.getX() + seqCanvas.getWidth();
247 res = (x / av.getCharWidth()) + startRes;
248 if (res > av.getRanges().getEndRes())
251 res = av.getRanges().getEndRes();
255 if (av.hasHiddenColumns())
257 res = av.getAlignment().getHiddenColumns()
258 .visibleToAbsoluteColumn(res);
265 int findSeq(MouseEvent evt)
270 if (av.getWrapAlignment())
272 int hgap = av.getCharHeight();
273 if (av.getScaleAboveWrapped())
275 hgap += av.getCharHeight();
278 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
279 + hgap + seqCanvas.getAnnotationHeight();
283 seq = Math.min((y % cHeight) / av.getCharHeight(),
284 av.getAlignment().getHeight() - 1);
289 (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
290 av.getAlignment().getHeight() - 1);
297 * When all of a sequence of edits are complete, put the resulting edit list
298 * on the history stack (undo list), and reset flags for editing in progress.
303 System.out.println("seqPanel endEditing " + editCommand);
307 if (editCommand != null && editCommand.getSize() > 0)
309 ap.alignFrame.addHistoryItem(editCommand);
310 av.firePropertyChange("alignment", null,
311 av.getAlignment().getSequences());
316 * Tidy up come what may...
321 groupEditing = false;
330 seqCanvas.cursorY = getKeyboardNo1() - 1;
331 scrollToVisible(true);
334 void setCursorColumn()
336 seqCanvas.cursorX = getKeyboardNo1() - 1;
337 scrollToVisible(true);
340 void setCursorRowAndColumn()
342 if (keyboardNo2 == null)
344 keyboardNo2 = new StringBuffer();
348 seqCanvas.cursorX = getKeyboardNo1() - 1;
349 seqCanvas.cursorY = getKeyboardNo2() - 1;
350 scrollToVisible(true);
354 void setCursorPosition()
356 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
358 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
359 scrollToVisible(true);
362 void moveCursor(int dx, int dy)
364 seqCanvas.cursorX += dx;
365 seqCanvas.cursorY += dy;
367 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
369 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
371 int original = seqCanvas.cursorX - dx;
372 int maxWidth = av.getAlignment().getWidth();
374 if (!hidden.isVisible(seqCanvas.cursorX))
376 int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
377 int[] region = hidden.getRegionWithEdgeAtRes(visx);
379 if (region != null) // just in case
384 seqCanvas.cursorX = region[1] + 1;
389 seqCanvas.cursorX = region[0] - 1;
392 seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
395 if (seqCanvas.cursorX >= maxWidth
396 || !hidden.isVisible(seqCanvas.cursorX))
398 seqCanvas.cursorX = original;
402 scrollToVisible(false);
406 * Scroll to make the cursor visible in the viewport.
409 * just jump to the location rather than scrolling
411 void scrollToVisible(boolean jump)
413 if (seqCanvas.cursorX < 0)
415 seqCanvas.cursorX = 0;
417 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
419 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
422 if (seqCanvas.cursorY < 0)
424 seqCanvas.cursorY = 0;
426 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
428 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
433 boolean repaintNeeded = true;
436 // only need to repaint if the viewport did not move, as otherwise it will
438 repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
443 if (av.getWrapAlignment())
445 // scrollToWrappedVisible expects x-value to have hidden cols subtracted
446 int x = av.getAlignment().getHiddenColumns()
447 .absoluteToVisibleColumn(seqCanvas.cursorX);
448 av.getRanges().scrollToWrappedVisible(x);
452 av.getRanges().scrollToVisible(seqCanvas.cursorX,
457 if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
459 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
460 seqCanvas.cursorX, seqCanvas.cursorY);
470 void setSelectionAreaAtCursor(boolean topLeft)
472 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
474 if (av.getSelectionGroup() != null)
476 SequenceGroup sg = av.getSelectionGroup();
477 // Find the top and bottom of this group
478 int min = av.getAlignment().getHeight(), max = 0;
479 for (int i = 0; i < sg.getSize(); i++)
481 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
496 sg.setStartRes(seqCanvas.cursorX);
497 if (sg.getEndRes() < seqCanvas.cursorX)
499 sg.setEndRes(seqCanvas.cursorX);
502 min = seqCanvas.cursorY;
506 sg.setEndRes(seqCanvas.cursorX);
507 if (sg.getStartRes() > seqCanvas.cursorX)
509 sg.setStartRes(seqCanvas.cursorX);
512 max = seqCanvas.cursorY + 1;
517 // Only the user can do this
518 av.setSelectionGroup(null);
522 // Now add any sequences between min and max
523 sg.getSequences(null).clear();
524 for (int i = min; i < max; i++)
526 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
531 if (av.getSelectionGroup() == null)
533 SequenceGroup sg = new SequenceGroup();
534 sg.setStartRes(seqCanvas.cursorX);
535 sg.setEndRes(seqCanvas.cursorX);
536 sg.addSequence(sequence, false);
537 av.setSelectionGroup(sg);
540 ap.paintAlignment(false, false);
544 void insertGapAtCursor(boolean group)
546 groupEditing = group;
547 startseq = seqCanvas.cursorY;
548 lastres = seqCanvas.cursorX;
549 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
553 void deleteGapAtCursor(boolean group)
555 groupEditing = group;
556 startseq = seqCanvas.cursorY;
557 lastres = seqCanvas.cursorX + getKeyboardNo1();
558 editSequence(false, false, seqCanvas.cursorX);
562 void insertNucAtCursor(boolean group, String nuc)
564 // TODO not called - delete?
565 groupEditing = group;
566 startseq = seqCanvas.cursorY;
567 lastres = seqCanvas.cursorX;
568 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
572 void numberPressed(char value)
574 if (keyboardNo1 == null)
576 keyboardNo1 = new StringBuffer();
579 if (keyboardNo2 != null)
581 keyboardNo2.append(value);
585 keyboardNo1.append(value);
593 if (keyboardNo1 != null)
595 int value = Integer.parseInt(keyboardNo1.toString());
599 } catch (Exception x)
610 if (keyboardNo2 != null)
612 int value = Integer.parseInt(keyboardNo2.toString());
616 } catch (Exception x)
630 public void mouseReleased(MouseEvent evt)
633 System.out.println("seqPanel mouse evt release " + evt.isShiftDown() + " " + mouseDragging + " " + editingSeqs);
636 boolean didDrag = mouseDragging; // did we come here after a drag
637 mouseDragging = false;
638 mouseWheelPressed = false;
640 if (evt.isPopupTrigger()) // Windows: mouseReleased
653 doMouseReleasedDefineMode(evt, didDrag);
664 public void mousePressed(MouseEvent evt)
666 System.out.println("seqPanel mouse evt " + evt.isShiftDown());
667 lastMousePress = evt.getPoint();
669 if (SwingUtilities.isMiddleMouseButton(evt))
671 mouseWheelPressed = true;
675 boolean isControlDown = Platform.isControlDown(evt);
676 if (evt.isShiftDown() || isControlDown)
686 doMousePressedDefineMode(evt);
690 int seq = findSeq(evt);
691 int res = findColumn(evt);
693 if (seq < 0 || res < 0)
698 if ((seq < av.getAlignment().getHeight())
699 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
715 private String formattedTooltipText;
718 public void mouseOverSequence(SequenceI sequence, int index, int pos)
720 String tmp = sequence.hashCode() + " " + index + " " + pos;
722 if (lastMessage == null || !lastMessage.equals(tmp))
724 // System.err.println("mouseOver Sequence: "+tmp);
725 ssm.mouseOverSequence(sequence, index, pos, av);
731 * Highlight the mapped region described by the search results object (unless
732 * unchanged). This supports highlight of protein while mousing over linked
733 * cDNA and vice versa. The status bar is also updated to show the location of
734 * the start of the highlighted region.
737 public void highlightSequence(SearchResultsI results)
739 if (results == null || results.equals(lastSearchResults))
743 lastSearchResults = results;
745 boolean wasScrolled = false;
747 if (av.isFollowHighlight())
749 // don't allow highlight of protein/cDNA to also scroll a complementary
750 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
751 // over residue to change abruptly, causing highlighted residue in panel 2
752 // to change, causing a scroll in panel 1 etc)
753 ap.setToScrollComplementPanel(false);
754 wasScrolled = ap.scrollToPosition(results, false);
757 seqCanvas.revalidate();
759 ap.setToScrollComplementPanel(true);
762 boolean fastPaint = !(wasScrolled && av.getWrapAlignment());
763 if (seqCanvas.highlightSearchResults(results, fastPaint))
765 setStatusMessage(results);
770 public VamsasSource getVamsasSource()
772 return this.ap == null ? null : this.ap.av;
776 public void updateColours(SequenceI seq, int index)
778 System.out.println("update the seqPanel colours");
783 * Action on mouse movement is to update the status bar to show the current
784 * sequence position, and (if features are shown) to show any features at the
785 * position in a tooltip. Does nothing if the mouse move does not change
791 public void mouseMoved(MouseEvent evt)
795 // This is because MacOSX creates a mouseMoved
796 // If control is down, other platforms will not.
800 final int column = findColumn(evt);
801 final int seq = findSeq(evt);
803 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
808 if (column == lastMouseColumn && seq == lastMouseSeq)
811 * just a pixel move without change of residue
815 lastMouseColumn = column;
818 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
820 if (column >= sequence.getLength())
826 * set status bar message, returning residue position in sequence
828 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
829 final int pos = setStatusMessage(sequence, column, seq);
830 if (ssm != null && !isGapped)
832 mouseOverSequence(sequence, column, pos);
835 tooltipText.setLength(6); // Cuts the buffer back to <html>
837 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
840 for (int g = 0; g < groups.length; g++)
842 if (groups[g].getStartRes() <= column
843 && groups[g].getEndRes() >= column)
845 if (!groups[g].getName().startsWith("JTreeGroup")
846 && !groups[g].getName().startsWith("JGroup"))
848 tooltipText.append(groups[g].getName());
851 if (groups[g].getDescription() != null)
853 tooltipText.append(": " + groups[g].getDescription());
860 * add any features at the position to the tooltip; if over a gap, only
861 * add features that straddle the gap (pos may be the residue before or
864 if (av.isShowSequenceFeatures())
866 List<SequenceFeature> features = ap.getFeatureRenderer()
867 .findFeaturesAtColumn(sequence, column + 1);
868 seqARep.appendFeatures(tooltipText, pos, features,
869 this.ap.getSeqPanel().seqCanvas.fr);
871 if (tooltipText.length() == 6) // <html>
873 setToolTipText(null);
878 if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
880 tooltipText.setLength(MAX_TOOLTIP_LENGTH);
881 tooltipText.append("...");
883 String textString = tooltipText.toString();
884 if (lastTooltip == null || !lastTooltip.equals(textString))
886 formattedTooltipText = JvSwingUtils.wrapTooltip(true,
888 setToolTipText(formattedTooltipText);
890 lastTooltip = textString;
896 private Point lastp = null;
898 private JToolTip tempTip = new JLabel().createToolTip();
903 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
906 public Point getToolTipLocation(MouseEvent event)
910 if (tooltipText == null || tooltipText.length() == 6)
913 if (lastp != null && event.isShiftDown())
917 int x = event.getX();
918 int y = event.getY();
921 tempTip.setTipText(formattedTooltipText);
922 int tipWidth = (int) tempTip.getPreferredSize().getWidth();
924 // was x += (w - x < 200) ? -(w / 2) : 5;
925 x = (x + tipWidth < w ? x + 10 : w - tipWidth);
926 p = new Point(x, y + 20); // BH 2018 was - 20?
928 * TODO: try to modify position region is not obcured by tooltip
939 * set when the current UI interaction has resulted in a change that requires
940 * shading in overviews and structures to be recalculated. this could be
941 * changed to a something more expressive that indicates what actually has
942 * changed, so selective redraws can be applied (ie. only structures, only
945 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
948 * set if av.getSelectionGroup() refers to a group that is defined on the
949 * alignment view, rather than a transient selection
951 // private boolean editingDefinedGroup = false; // TODO: refactor to
952 // avcontroller or viewModel
955 * Sets the status message in alignment panel, showing the sequence number
956 * (index) and id, and residue and residue position if not at a gap, for the
957 * given sequence and column position. Returns the residue position returned
958 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
959 * if at a gapped position.
962 * aligned sequence object
966 * index of sequence in alignment
967 * @return sequence position of residue at column, or adjacent residue if at a
970 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
972 char sequenceChar = sequence.getCharAt(column);
973 int pos = sequence.findPosition(column);
974 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
980 * Builds the status message for the current cursor location and writes it to
981 * the status bar, for example
984 * Sequence 3 ID: FER1_SOLLC
985 * Sequence 5 ID: FER1_PEA Residue: THR (4)
986 * Sequence 5 ID: FER1_PEA Residue: B (3)
987 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
992 * sequence position in the alignment (1..)
993 * @param sequenceChar
994 * the character under the cursor
996 * the sequence residue position (if not over a gap)
998 protected void setStatusMessage(SequenceI sequence, int seqIndex,
999 char sequenceChar, int residuePos)
1001 StringBuilder text = new StringBuilder(32);
1004 * Sequence number (if known), and sequence name.
1006 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
1007 text.append("Sequence").append(seqno).append(" ID: ")
1008 .append(sequence.getName());
1010 String residue = null;
1013 * Try to translate the display character to residue name (null for gap).
1015 boolean isGapped = Comparison.isGap(sequenceChar);
1019 boolean nucleotide = av.getAlignment().isNucleotide();
1020 String displayChar = String.valueOf(sequenceChar);
1023 residue = ResidueProperties.nucleotideName.get(displayChar);
1027 residue = "X".equalsIgnoreCase(displayChar) ? "X"
1028 : ("*".equals(displayChar) ? "STOP"
1029 : ResidueProperties.aa2Triplet.get(displayChar));
1031 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
1032 .append(": ").append(residue == null ? displayChar : residue);
1034 text.append(" (").append(Integer.toString(residuePos)).append(")");
1036 ap.alignFrame.setStatus(text.toString());
1040 * Set the status bar message to highlight the first matched position in
1045 private void setStatusMessage(SearchResultsI results)
1047 AlignmentI al = this.av.getAlignment();
1048 int sequenceIndex = al.findIndex(results);
1049 if (sequenceIndex == -1)
1053 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
1054 for (SearchResultMatchI m : results.getResults())
1056 SequenceI seq = m.getSequence();
1057 if (seq.getDatasetSequence() != null)
1059 seq = seq.getDatasetSequence();
1064 int start = m.getStart();
1065 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1076 public void mouseDragged(MouseEvent evt)
1078 if (mouseWheelPressed)
1080 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1081 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1083 int oldWidth = av.getCharWidth();
1085 // Which is bigger, left-right or up-down?
1086 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1087 .abs(evt.getX() - lastMousePress.getX()))
1090 * on drag up or down, decrement or increment font size
1092 int fontSize = av.font.getSize();
1093 boolean fontChanged = false;
1095 if (evt.getY() < lastMousePress.getY())
1100 else if (evt.getY() > lastMousePress.getY())
1113 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1115 av.setFont(newFont, true);
1116 av.setCharWidth(oldWidth);
1120 ap.av.getCodingComplement().setFont(newFont, true);
1121 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1122 .getSplitViewContainer();
1123 splitFrame.adjustLayout();
1124 splitFrame.repaint();
1131 * on drag left or right, decrement or increment character width
1134 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1136 newWidth = av.getCharWidth() - 1;
1137 av.setCharWidth(newWidth);
1139 else if (evt.getX() > lastMousePress.getX())
1141 newWidth = av.getCharWidth() + 1;
1142 av.setCharWidth(newWidth);
1145 System.out.println("seqPanel mouse evt " + evt.isShiftDown() + " " + newWidth);
1149 ap.paintAlignment(false, false);
1153 * need to ensure newWidth is set on cdna, regardless of which
1154 * panel the mouse drag happened in; protein will compute its
1155 * character width as 1:1 or 3:1
1157 av.getCodingComplement().setCharWidth(newWidth);
1158 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1159 .getSplitViewContainer();
1160 splitFrame.adjustLayout();
1161 splitFrame.repaint();
1166 FontMetrics fm = getFontMetrics(av.getFont());
1167 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1169 lastMousePress = evt.getPoint();
1176 doMouseDraggedDefineMode(evt);
1180 int res = findColumn(evt);
1187 if ((lastres == -1) || (lastres == res))
1192 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1194 // dragLeft, delete gap
1195 editSequence(false, false, res);
1199 editSequence(true, false, res);
1202 mouseDragging = true;
1203 if (scrollThread != null)
1205 scrollThread.setMousePosition(evt.getPoint());
1209 // TODO: Make it more clever than many booleans
1210 synchronized void editSequence(boolean insertGap, boolean editSeq,
1214 int fixedRight = -1;
1215 boolean fixedColumns = false;
1216 SequenceGroup sg = av.getSelectionGroup();
1218 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1220 // No group, but the sequence may represent a group
1221 if (!groupEditing && av.hasHiddenRows())
1223 if (av.isHiddenRepSequence(seq))
1225 sg = av.getRepresentedSequences(seq);
1226 groupEditing = true;
1230 StringBuilder message = new StringBuilder(64);
1233 message.append("Edit group:");
1234 if (editCommand == null)
1236 editCommand = new EditCommand(
1237 MessageManager.getString("action.edit_group"));
1242 message.append("Edit sequence: " + seq.getName());
1243 String label = seq.getName();
1244 if (label.length() > 10)
1246 label = label.substring(0, 10);
1248 if (editCommand == null)
1250 editCommand = new EditCommand(MessageManager
1251 .formatMessage("label.edit_params", new String[]
1258 message.append(" insert ");
1262 message.append(" delete ");
1265 message.append(Math.abs(startres - lastres) + " gaps.");
1266 ap.alignFrame.setStatus(message.toString());
1268 // Are we editing within a selection group?
1269 if (groupEditing || (sg != null
1270 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1272 fixedColumns = true;
1274 // sg might be null as the user may only see 1 sequence,
1275 // but the sequence represents a group
1278 if (!av.isHiddenRepSequence(seq))
1283 sg = av.getRepresentedSequences(seq);
1286 fixedLeft = sg.getStartRes();
1287 fixedRight = sg.getEndRes();
1289 if ((startres < fixedLeft && lastres >= fixedLeft)
1290 || (startres >= fixedLeft && lastres < fixedLeft)
1291 || (startres > fixedRight && lastres <= fixedRight)
1292 || (startres <= fixedRight && lastres > fixedRight))
1298 if (fixedLeft > startres)
1300 fixedRight = fixedLeft - 1;
1303 else if (fixedRight < startres)
1305 fixedLeft = fixedRight;
1310 if (av.hasHiddenColumns())
1312 fixedColumns = true;
1313 int y1 = av.getAlignment().getHiddenColumns()
1314 .getNextHiddenBoundary(true, startres);
1315 int y2 = av.getAlignment().getHiddenColumns()
1316 .getNextHiddenBoundary(false, startres);
1318 if ((insertGap && startres > y1 && lastres < y1)
1319 || (!insertGap && startres < y2 && lastres > y2))
1325 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1326 // Selection spans a hidden region
1327 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1335 fixedRight = y2 - 1;
1342 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1343 int g, groupSize = vseqs.size();
1344 SequenceI[] groupSeqs = new SequenceI[groupSize];
1345 for (g = 0; g < groupSeqs.length; g++)
1347 groupSeqs[g] = vseqs.get(g);
1353 // If the user has selected the whole sequence, and is dragging to
1354 // the right, we can still extend the alignment and selectionGroup
1355 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1356 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1358 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1359 fixedRight = sg.getEndRes();
1362 // Is it valid with fixed columns??
1363 // Find the next gap before the end
1364 // of the visible region boundary
1365 boolean blank = false;
1366 for (; fixedRight > lastres; fixedRight--)
1370 for (g = 0; g < groupSize; g++)
1372 for (int j = 0; j < startres - lastres; j++)
1374 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1389 if (sg.getSize() == av.getAlignment().getHeight())
1391 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1393 .getNextHiddenBoundary(false, startres)))
1399 int alWidth = av.getAlignment().getWidth();
1400 if (av.hasHiddenRows())
1402 int hwidth = av.getAlignment().getHiddenSequences()
1404 if (hwidth > alWidth)
1409 // We can still insert gaps if the selectionGroup
1410 // contains all the sequences
1411 sg.setEndRes(sg.getEndRes() + startres - lastres);
1412 fixedRight = alWidth + startres - lastres;
1423 else if (!insertGap)
1425 // / Are we able to delete?
1426 // ie are all columns blank?
1428 for (g = 0; g < groupSize; g++)
1430 for (int j = startres; j < lastres; j++)
1432 if (groupSeqs[g].getLength() <= j)
1437 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1439 // Not a gap, block edit not valid
1449 // dragging to the right
1450 if (fixedColumns && fixedRight != -1)
1452 for (int j = lastres; j < startres; j++)
1454 insertChar(j, groupSeqs, fixedRight);
1459 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1460 startres - lastres);
1465 // dragging to the left
1466 if (fixedColumns && fixedRight != -1)
1468 for (int j = lastres; j > startres; j--)
1470 deleteChar(startres, groupSeqs, fixedRight);
1475 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1476 lastres - startres);
1482 // ///Editing a single sequence///////////
1486 // dragging to the right
1487 if (fixedColumns && fixedRight != -1)
1489 for (int j = lastres; j < startres; j++)
1491 insertChar(j, new SequenceI[] { seq }, fixedRight);
1496 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1497 startres - lastres);
1504 // dragging to the left
1505 if (fixedColumns && fixedRight != -1)
1507 for (int j = lastres; j > startres; j--)
1509 if (!Comparison.isGap(seq.getCharAt(startres)))
1514 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1519 // could be a keyboard edit trying to delete none gaps
1521 for (int m = startres; m < lastres; m++)
1523 if (!Comparison.isGap(seq.getCharAt(m)))
1532 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1538 {// insertGap==false AND editSeq==TRUE;
1539 if (fixedColumns && fixedRight != -1)
1541 for (int j = lastres; j < startres; j++)
1543 insertChar(j, new SequenceI[] { seq }, fixedRight);
1548 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1549 startres - lastres);
1556 seqCanvas.repaint();
1559 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1561 int blankColumn = fixedColumn;
1562 for (int s = 0; s < seq.length; s++)
1564 // Find the next gap before the end of the visible region boundary
1565 // If lastCol > j, theres a boundary after the gap insertion
1567 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1569 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1571 // Theres a space, so break and insert the gap
1576 if (blankColumn <= j)
1578 blankColumn = fixedColumn;
1584 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1586 appendEdit(Action.INSERT_GAP, seq, j, 1);
1591 * Helper method to add and perform one edit action.
1598 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1602 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1603 av.getAlignment().getGapCharacter());
1605 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1608 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1611 appendEdit(Action.DELETE_GAP, seq, j, 1);
1613 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1617 * On reentering the panel, stops any scrolling that was started on dragging
1623 public void mouseEntered(MouseEvent e)
1633 * On leaving the panel, if the mouse is being dragged, starts a thread to
1634 * scroll it until the mouse is released (in unwrapped mode only)
1639 public void mouseExited(MouseEvent e)
1643 startScrolling(e.getPoint());
1648 * Handler for double-click on a position with one or more sequence features.
1649 * Opens the Amend Features dialog to allow feature details to be amended, or
1650 * the feature deleted.
1653 public void mouseClicked(MouseEvent evt)
1655 SequenceGroup sg = null;
1656 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1657 if (evt.getClickCount() > 1)
1659 sg = av.getSelectionGroup();
1660 if (sg != null && sg.getSize() == 1
1661 && sg.getEndRes() - sg.getStartRes() < 2)
1663 av.setSelectionGroup(null);
1666 int column = findColumn(evt);
1669 * find features at the position (if not gapped), or straddling
1670 * the position (if at a gap)
1672 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1673 .findFeaturesAtColumn(sequence, column + 1);
1675 if (!features.isEmpty())
1678 * highlight the first feature at the position on the alignment
1680 SearchResultsI highlight = new SearchResults();
1681 highlight.addResult(sequence, features.get(0).getBegin(), features
1683 seqCanvas.highlightSearchResults(highlight, true);
1686 * open the Amend Features dialog
1688 new FeatureEditor(ap, Collections.singletonList(sequence), features,
1689 false).showDialog();
1695 public void mouseWheelMoved(MouseWheelEvent e)
1698 double wheelRotation = e.getPreciseWheelRotation();
1699 if (wheelRotation > 0)
1701 if (e.isShiftDown())
1703 av.getRanges().scrollRight(true);
1708 av.getRanges().scrollUp(false);
1711 else if (wheelRotation < 0)
1713 if (e.isShiftDown())
1715 av.getRanges().scrollRight(false);
1719 av.getRanges().scrollUp(true);
1724 * update status bar and tooltip for new position
1725 * (need to synthesize a mouse movement to refresh tooltip)
1728 ToolTipManager.sharedInstance().mouseMoved(e);
1737 public void doMousePressedDefineMode(MouseEvent evt)
1739 final int res = findColumn(evt);
1740 final int seq = findSeq(evt);
1742 updateOverviewAndStructs = false;
1744 startWrapBlock = wrappedBlock;
1746 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1748 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1749 MessageManager.getString(
1750 "label.cannot_edit_annotations_in_wrapped_view"),
1751 MessageManager.getString("label.wrapped_view_no_edit"),
1752 JvOptionPane.WARNING_MESSAGE);
1756 if (seq < 0 || res < 0)
1761 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1763 if ((sequence == null) || (res > sequence.getLength()))
1768 stretchGroup = av.getSelectionGroup();
1770 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1772 stretchGroup = av.getAlignment().findGroup(sequence, res);
1773 if (stretchGroup != null)
1775 // only update the current selection if the popup menu has a group to
1777 av.setSelectionGroup(stretchGroup);
1781 if (evt.isPopupTrigger()) // Mac: mousePressed
1788 * defer right-mouse click handling to mouseReleased on Windows
1789 * (where isPopupTrigger() will answer true)
1790 * NB isRightMouseButton is also true for Cmd-click on Mac
1792 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1799 seqCanvas.cursorX = findColumn(evt);
1800 seqCanvas.cursorY = findSeq(evt);
1801 seqCanvas.repaint();
1805 if (stretchGroup == null)
1807 createStretchGroup(res, sequence);
1810 if (stretchGroup != null)
1812 stretchGroup.addPropertyChangeListener(seqCanvas);
1815 seqCanvas.repaint();
1818 private void createStretchGroup(int res, SequenceI sequence)
1820 // Only if left mouse button do we want to change group sizes
1821 // define a new group here
1822 SequenceGroup sg = new SequenceGroup();
1823 sg.setStartRes(res);
1825 sg.addSequence(sequence, false);
1826 av.setSelectionGroup(sg);
1829 if (av.getConservationSelected())
1831 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1835 if (av.getAbovePIDThreshold())
1837 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1840 // TODO: stretchGroup will always be not null. Is this a merge error ?
1841 // or is there a threading issue here?
1842 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1844 // Edit end res position of selected group
1845 changeEndRes = true;
1847 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1849 // Edit end res position of selected group
1850 changeStartRes = true;
1852 stretchGroup.getWidth();
1857 * Build and show a pop-up menu at the right-click mouse position
1863 void showPopupMenu(MouseEvent evt)
1865 final int column = findColumn(evt);
1866 final int seq = findSeq(evt);
1867 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1868 List<SequenceFeature> features = ap.getFeatureRenderer()
1869 .findFeaturesAtColumn(sequence, column + 1);
1871 PopupMenu pop = new PopupMenu(ap, null, features);
1872 pop.show(this, evt.getX(), evt.getY());
1876 * Update the display after mouse up on a selection or group
1879 * mouse released event details
1881 * true if this event is happening after a mouse drag (rather than a
1884 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1886 if (stretchGroup == null)
1891 stretchGroup.removePropertyChangeListener(seqCanvas);
1893 // always do this - annotation has own state
1894 // but defer colourscheme update until hidden sequences are passed in
1895 boolean vischange = stretchGroup.recalcConservation(true);
1896 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1898 if (stretchGroup.cs != null)
1900 stretchGroup.cs.alignmentChanged(stretchGroup,
1901 av.getHiddenRepSequences());
1903 ResidueShaderI groupColourScheme = stretchGroup
1904 .getGroupColourScheme();
1905 String name = stretchGroup.getName();
1906 if (stretchGroup.cs.conservationApplied())
1908 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1910 if (stretchGroup.cs.getThreshold() > 0)
1912 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1915 PaintRefresher.Refresh(this, av.getSequenceSetId());
1916 // TODO: structure colours only need updating if stretchGroup used to or now
1917 // does contain sequences with structure views
1918 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1919 updateOverviewAndStructs = false;
1920 changeEndRes = false;
1921 changeStartRes = false;
1922 stretchGroup = null;
1932 public void doMouseDraggedDefineMode(MouseEvent evt)
1934 int res = findColumn(evt);
1935 int y = findSeq(evt);
1937 if (wrappedBlock != startWrapBlock)
1942 if (stretchGroup == null)
1947 res = Math.min(res, av.getAlignment().getWidth()-1);
1949 if (stretchGroup.getEndRes() == res)
1951 // Edit end res position of selected group
1952 changeEndRes = true;
1954 else if (stretchGroup.getStartRes() == res)
1956 // Edit start res position of selected group
1957 changeStartRes = true;
1960 if (res < av.getRanges().getStartRes())
1962 res = av.getRanges().getStartRes();
1967 if (res > (stretchGroup.getStartRes() - 1))
1969 stretchGroup.setEndRes(res);
1970 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1973 else if (changeStartRes)
1975 if (res < (stretchGroup.getEndRes() + 1))
1977 stretchGroup.setStartRes(res);
1978 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1982 int dragDirection = 0;
1988 else if (y < oldSeq)
1993 while ((y != oldSeq) && (oldSeq > -1)
1994 && (y < av.getAlignment().getHeight()))
1996 // This routine ensures we don't skip any sequences, as the
1997 // selection is quite slow.
1998 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
2000 oldSeq += dragDirection;
2007 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
2009 if (stretchGroup.getSequences(null).contains(nextSeq))
2011 stretchGroup.deleteSequence(seq, false);
2012 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2018 stretchGroup.addSequence(seq, false);
2021 stretchGroup.addSequence(nextSeq, false);
2022 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
2031 mouseDragging = true;
2033 if (scrollThread != null)
2035 scrollThread.setMousePosition(evt.getPoint());
2040 * Stops the scroll thread if it is running
2042 void stopScrolling()
2044 if (scrollThread != null)
2046 scrollThread.stopScrolling();
2047 scrollThread = null;
2049 mouseDragging = false;
2053 * Starts a thread to scroll the alignment, towards a given mouse position
2054 * outside the panel bounds, unless the alignment is in wrapped mode
2058 void startScrolling(Point mousePos)
2061 * set this.mouseDragging in case this was called from
2062 * a drag in ScalePanel or AnnotationPanel
2064 mouseDragging = true;
2065 if (!av.getWrapAlignment() && scrollThread == null)
2067 scrollThread = new ScrollThread();
2068 scrollThread.setMousePosition(mousePos);
2069 if (!Jalview.isJS())
2072 * Java - run in a new thread
2074 scrollThread.start();
2079 * Javascript - run every 20ms until scrolling stopped
2080 * or reaches the limit of scrollable alignment
2082 // java.util.Timer version:
2083 // Timer t = new Timer("ScrollThreadTimer", true);
2084 // TimerTask task = new TimerTask()
2087 // public void run()
2089 // if (!scrollThread.scrollOnce())
2095 // t.schedule(task, 20, 20);
2096 Timer t = new Timer(20, new ActionListener()
2099 public void actionPerformed(ActionEvent e)
2101 if (scrollThread != null)
2103 // if (!scrollOnce() {t.stop();}) gives compiler error :-(
2104 scrollThread.scrollOnce();
2108 t.addActionListener(new ActionListener()
2111 public void actionPerformed(ActionEvent e)
2113 if (scrollThread == null)
2115 // finished and nulled itself
2126 * Performs scrolling of the visible alignment left, right, up or down, until
2127 * scrolling is stopped by calling stopScrolling, mouse drag is ended, or the
2128 * limit of the alignment is reached
2130 class ScrollThread extends Thread
2132 private Point mousePos;
2134 private volatile boolean keepRunning = true;
2139 public ScrollThread()
2141 setName("SeqPanel$ScrollThread");
2145 * Sets the position of the mouse that determines the direction of the
2146 * scroll to perform. If this is called as the mouse moves, scrolling should
2147 * respond accordingly. For example, if the mouse is dragged right, scroll
2148 * right should start; if the drag continues down, scroll down should also
2153 public void setMousePosition(Point p)
2159 * Sets a flag that will cause the thread to exit
2161 public void stopScrolling()
2163 keepRunning = false;
2167 * Scrolls the alignment left or right, and/or up or down, depending on the
2168 * last notified mouse position, until the limit of the alignment is
2169 * reached, or a flag is set to stop the scroll
2176 if (mousePos != null)
2178 keepRunning = scrollOnce();
2183 } catch (Exception ex)
2187 SeqPanel.this.scrollThread = null;
2193 * <li>one row up, if the mouse is above the panel</li>
2194 * <li>one row down, if the mouse is below the panel</li>
2195 * <li>one column left, if the mouse is left of the panel</li>
2196 * <li>one column right, if the mouse is right of the panel</li>
2198 * Answers true if a scroll was performed, false if not - meaning either
2199 * that the mouse position is within the panel, or the edge of the alignment
2202 boolean scrollOnce()
2205 * quit after mouseUp ensures interrupt in JalviewJS
2212 boolean scrolled = false;
2213 ViewportRanges ranges = SeqPanel.this.av.getRanges();
2220 // mouse is above this panel - try scroll up
2221 scrolled = ranges.scrollUp(true);
2223 else if (mousePos.y >= getHeight())
2225 // mouse is below this panel - try scroll down
2226 scrolled = ranges.scrollUp(false);
2230 * scroll left or right
2234 scrolled |= ranges.scrollRight(false);
2236 else if (mousePos.x >= getWidth())
2238 scrolled |= ranges.scrollRight(true);
2245 * modify current selection according to a received message.
2248 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2249 HiddenColumns hidden, SelectionSource source)
2251 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2252 // handles selection messages...
2253 // TODO: extend config options to allow user to control if selections may be
2254 // shared between viewports.
2255 boolean iSentTheSelection = (av == source
2256 || (source instanceof AlignViewport
2257 && ((AlignmentViewport) source).getSequenceSetId()
2258 .equals(av.getSequenceSetId())));
2260 if (iSentTheSelection)
2262 // respond to our own event by updating dependent dialogs
2263 if (ap.getCalculationDialog() != null)
2265 ap.getCalculationDialog().validateCalcTypes();
2271 // process further ?
2272 if (!av.followSelection)
2278 * Ignore the selection if there is one of our own pending.
2280 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2286 * Check for selection in a view of which this one is a dna/protein
2289 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2294 // do we want to thread this ? (contention with seqsel and colsel locks, I
2297 * only copy colsel if there is a real intersection between
2298 * sequence selection and this panel's alignment
2300 boolean repaint = false;
2301 boolean copycolsel = false;
2303 SequenceGroup sgroup = null;
2304 if (seqsel != null && seqsel.getSize() > 0)
2306 if (av.getAlignment() == null)
2308 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2309 + " ViewId=" + av.getViewId()
2310 + " 's alignment is NULL! returning immediately.");
2313 sgroup = seqsel.intersect(av.getAlignment(),
2314 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2315 if ((sgroup != null && sgroup.getSize() > 0))
2320 if (sgroup != null && sgroup.getSize() > 0)
2322 av.setSelectionGroup(sgroup);
2326 av.setSelectionGroup(null);
2328 av.isSelectionGroupChanged(true);
2333 // the current selection is unset or from a previous message
2334 // so import the new colsel.
2335 if (colsel == null || colsel.isEmpty())
2337 if (av.getColumnSelection() != null)
2339 av.getColumnSelection().clear();
2345 // TODO: shift colSel according to the intersecting sequences
2346 if (av.getColumnSelection() == null)
2348 av.setColumnSelection(new ColumnSelection(colsel));
2352 av.getColumnSelection().setElementsFrom(colsel,
2353 av.getAlignment().getHiddenColumns());
2356 av.isColSelChanged(true);
2360 if (copycolsel && av.hasHiddenColumns()
2361 && (av.getAlignment().getHiddenColumns() == null))
2363 System.err.println("Bad things");
2365 if (repaint) // always true!
2367 // probably finessing with multiple redraws here
2368 PaintRefresher.Refresh(this, av.getSequenceSetId());
2369 // ap.paintAlignment(false);
2372 // lastly, update dependent dialogs
2373 if (ap.getCalculationDialog() != null)
2375 ap.getCalculationDialog().validateCalcTypes();
2381 * If this panel is a cdna/protein translation view of the selection source,
2382 * tries to map the source selection to a local one, and returns true. Else
2389 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2390 ColumnSelection colsel, HiddenColumns hidden,
2391 SelectionSource source)
2393 if (!(source instanceof AlignViewportI))
2397 final AlignViewportI sourceAv = (AlignViewportI) source;
2398 if (sourceAv.getCodingComplement() != av
2399 && av.getCodingComplement() != sourceAv)
2405 * Map sequence selection
2407 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2408 av.setSelectionGroup(sg);
2409 av.isSelectionGroupChanged(true);
2412 * Map column selection
2414 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2416 ColumnSelection cs = new ColumnSelection();
2417 HiddenColumns hs = new HiddenColumns();
2418 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2419 av.setColumnSelection(cs);
2420 av.getAlignment().setHiddenColumns(hs);
2422 // lastly, update any dependent dialogs
2423 if (ap.getCalculationDialog() != null)
2425 ap.getCalculationDialog().validateCalcTypes();
2428 PaintRefresher.Refresh(this, av.getSequenceSetId());
2435 * @return null or last search results handled by this panel
2437 public SearchResultsI getLastSearchResults()
2439 return lastSearchResults;