2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignViewportI;
24 import jalview.bin.Cache;
25 import jalview.commands.EditCommand;
26 import jalview.commands.EditCommand.Action;
27 import jalview.commands.EditCommand.Edit;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.HiddenColumns;
31 import jalview.datamodel.SearchResultMatchI;
32 import jalview.datamodel.SearchResults;
33 import jalview.datamodel.SearchResultsI;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.io.SequenceAnnotationReport;
39 import jalview.renderer.ResidueShaderI;
40 import jalview.schemes.ResidueProperties;
41 import jalview.structure.SelectionListener;
42 import jalview.structure.SelectionSource;
43 import jalview.structure.SequenceListener;
44 import jalview.structure.StructureSelectionManager;
45 import jalview.structure.VamsasSource;
46 import jalview.util.Comparison;
47 import jalview.util.MappingUtils;
48 import jalview.util.MessageManager;
49 import jalview.util.Platform;
50 import jalview.viewmodel.AlignmentViewport;
52 import java.awt.BorderLayout;
53 import java.awt.Color;
55 import java.awt.FontMetrics;
56 import java.awt.Point;
57 import java.awt.event.MouseEvent;
58 import java.awt.event.MouseListener;
59 import java.awt.event.MouseMotionListener;
60 import java.awt.event.MouseWheelEvent;
61 import java.awt.event.MouseWheelListener;
62 import java.util.Collections;
63 import java.util.List;
65 import javax.swing.JPanel;
66 import javax.swing.SwingUtilities;
67 import javax.swing.ToolTipManager;
73 * @version $Revision: 1.130 $
75 public class SeqPanel extends JPanel
76 implements MouseListener, MouseMotionListener, MouseWheelListener,
77 SequenceListener, SelectionListener
79 private static final int MAX_TOOLTIP_LENGTH = 300;
81 public SeqCanvas seqCanvas;
83 public AlignmentPanel ap;
86 * last column position for mouseMoved event
88 private int lastMouseColumn;
91 * last sequence offset for mouseMoved event
93 private int lastMouseSeq;
95 protected int lastres;
97 protected int startseq;
99 protected AlignViewport av;
101 ScrollThread scrollThread = null;
103 boolean mouseDragging = false;
105 boolean editingSeqs = false;
107 boolean groupEditing = false;
109 // ////////////////////////////////////////
110 // ///Everything below this is for defining the boundary of the rubberband
111 // ////////////////////////////////////////
114 boolean changeEndSeq = false;
116 boolean changeStartSeq = false;
118 boolean changeEndRes = false;
120 boolean changeStartRes = false;
122 SequenceGroup stretchGroup = null;
124 boolean remove = false;
126 Point lastMousePress;
128 boolean mouseWheelPressed = false;
130 StringBuffer keyboardNo1;
132 StringBuffer keyboardNo2;
134 java.net.URL linkImageURL;
136 private final SequenceAnnotationReport seqARep;
138 StringBuilder tooltipText = new StringBuilder();
142 EditCommand editCommand;
144 StructureSelectionManager ssm;
146 SearchResultsI lastSearchResults;
149 * Creates a new SeqPanel object
154 public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
156 linkImageURL = getClass().getResource("/images/link.gif");
157 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
158 ToolTipManager.sharedInstance().registerComponent(this);
159 ToolTipManager.sharedInstance().setInitialDelay(0);
160 ToolTipManager.sharedInstance().setDismissDelay(10000);
162 setBackground(Color.white);
164 seqCanvas = new SeqCanvas(alignPanel);
165 setLayout(new BorderLayout());
166 add(seqCanvas, BorderLayout.CENTER);
168 this.ap = alignPanel;
170 if (!viewport.isDataset())
172 addMouseMotionListener(this);
173 addMouseListener(this);
174 addMouseWheelListener(this);
175 ssm = viewport.getStructureSelectionManager();
176 ssm.addStructureViewerListener(this);
177 ssm.addSelectionListener(this);
180 lastMouseColumn = -1;
184 int startWrapBlock = -1;
186 int wrappedBlock = -1;
189 * Returns the aligned sequence position (base 0) at the mouse position, or
190 * the closest visible one
195 int findColumn(MouseEvent evt)
200 int startRes = av.getRanges().getStartRes();
201 if (av.getWrapAlignment())
204 int hgap = av.getCharHeight();
205 if (av.getScaleAboveWrapped())
207 hgap += av.getCharHeight();
210 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
211 + hgap + seqCanvas.getAnnotationHeight();
214 y = Math.max(0, y - hgap);
215 x = Math.max(0, x - seqCanvas.getLabelWidthWest());
217 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
223 wrappedBlock = y / cHeight;
224 wrappedBlock += startRes / cwidth;
225 // allow for wrapped view scrolled right (possible from Overview)
226 int startOffset = startRes % cwidth;
227 res = wrappedBlock * cwidth + startOffset
228 + +Math.min(cwidth - 1, x / av.getCharWidth());
232 if (x > seqCanvas.getX() + seqCanvas.getWidth())
234 // make sure we calculate relative to visible alignment, rather than
236 x = seqCanvas.getX() + seqCanvas.getWidth();
238 res = (x / av.getCharWidth()) + startRes;
239 if (res > av.getRanges().getEndRes())
242 res = av.getRanges().getEndRes();
246 if (av.hasHiddenColumns())
248 res = av.getAlignment().getHiddenColumns()
249 .adjustForHiddenColumns(res);
256 int findSeq(MouseEvent evt)
261 if (av.getWrapAlignment())
263 int hgap = av.getCharHeight();
264 if (av.getScaleAboveWrapped())
266 hgap += av.getCharHeight();
269 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
270 + hgap + seqCanvas.getAnnotationHeight();
274 seq = Math.min((y % cHeight) / av.getCharHeight(),
275 av.getAlignment().getHeight() - 1);
280 (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
281 av.getAlignment().getHeight() - 1);
288 * When all of a sequence of edits are complete, put the resulting edit list
289 * on the history stack (undo list), and reset flags for editing in progress.
295 if (editCommand != null && editCommand.getSize() > 0)
297 ap.alignFrame.addHistoryItem(editCommand);
298 av.firePropertyChange("alignment", null,
299 av.getAlignment().getSequences());
304 * Tidy up come what may...
309 groupEditing = false;
318 seqCanvas.cursorY = getKeyboardNo1() - 1;
322 void setCursorColumn()
324 seqCanvas.cursorX = getKeyboardNo1() - 1;
328 void setCursorRowAndColumn()
330 if (keyboardNo2 == null)
332 keyboardNo2 = new StringBuffer();
336 seqCanvas.cursorX = getKeyboardNo1() - 1;
337 seqCanvas.cursorY = getKeyboardNo2() - 1;
342 void setCursorPosition()
344 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
346 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
350 void moveCursor(int dx, int dy)
352 seqCanvas.cursorX += dx;
353 seqCanvas.cursorY += dy;
355 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
357 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
359 int original = seqCanvas.cursorX - dx;
360 int maxWidth = av.getAlignment().getWidth();
362 while (!hidden.isVisible(seqCanvas.cursorX)
363 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
365 seqCanvas.cursorX += dx;
368 if (seqCanvas.cursorX >= maxWidth
369 || !hidden.isVisible(seqCanvas.cursorX))
371 seqCanvas.cursorX = original;
378 void scrollToVisible()
380 if (seqCanvas.cursorX < 0)
382 seqCanvas.cursorX = 0;
384 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
386 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
389 if (seqCanvas.cursorY < 0)
391 seqCanvas.cursorY = 0;
393 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
395 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
399 if (av.getWrapAlignment())
401 av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
405 av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
407 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
408 seqCanvas.cursorX, seqCanvas.cursorY);
413 void setSelectionAreaAtCursor(boolean topLeft)
415 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
417 if (av.getSelectionGroup() != null)
419 SequenceGroup sg = av.getSelectionGroup();
420 // Find the top and bottom of this group
421 int min = av.getAlignment().getHeight(), max = 0;
422 for (int i = 0; i < sg.getSize(); i++)
424 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
439 sg.setStartRes(seqCanvas.cursorX);
440 if (sg.getEndRes() < seqCanvas.cursorX)
442 sg.setEndRes(seqCanvas.cursorX);
445 min = seqCanvas.cursorY;
449 sg.setEndRes(seqCanvas.cursorX);
450 if (sg.getStartRes() > seqCanvas.cursorX)
452 sg.setStartRes(seqCanvas.cursorX);
455 max = seqCanvas.cursorY + 1;
460 // Only the user can do this
461 av.setSelectionGroup(null);
465 // Now add any sequences between min and max
466 sg.getSequences(null).clear();
467 for (int i = min; i < max; i++)
469 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
474 if (av.getSelectionGroup() == null)
476 SequenceGroup sg = new SequenceGroup();
477 sg.setStartRes(seqCanvas.cursorX);
478 sg.setEndRes(seqCanvas.cursorX);
479 sg.addSequence(sequence, false);
480 av.setSelectionGroup(sg);
483 ap.paintAlignment(false, false);
487 void insertGapAtCursor(boolean group)
489 groupEditing = group;
490 startseq = seqCanvas.cursorY;
491 lastres = seqCanvas.cursorX;
492 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
496 void deleteGapAtCursor(boolean group)
498 groupEditing = group;
499 startseq = seqCanvas.cursorY;
500 lastres = seqCanvas.cursorX + getKeyboardNo1();
501 editSequence(false, false, seqCanvas.cursorX);
505 void insertNucAtCursor(boolean group, String nuc)
507 // TODO not called - delete?
508 groupEditing = group;
509 startseq = seqCanvas.cursorY;
510 lastres = seqCanvas.cursorX;
511 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
515 void numberPressed(char value)
517 if (keyboardNo1 == null)
519 keyboardNo1 = new StringBuffer();
522 if (keyboardNo2 != null)
524 keyboardNo2.append(value);
528 keyboardNo1.append(value);
536 if (keyboardNo1 != null)
538 int value = Integer.parseInt(keyboardNo1.toString());
542 } catch (Exception x)
553 if (keyboardNo2 != null)
555 int value = Integer.parseInt(keyboardNo2.toString());
559 } catch (Exception x)
573 public void mouseReleased(MouseEvent evt)
575 boolean didDrag = mouseDragging; // did we come here after a drag
576 mouseDragging = false;
577 mouseWheelPressed = false;
579 if (evt.isPopupTrigger()) // Windows: mouseReleased
588 doMouseReleasedDefineMode(evt, didDrag);
602 public void mousePressed(MouseEvent evt)
604 lastMousePress = evt.getPoint();
606 if (SwingUtilities.isMiddleMouseButton(evt))
608 mouseWheelPressed = true;
612 boolean isControlDown = Platform.isControlDown(evt);
613 if (evt.isShiftDown() || isControlDown)
623 doMousePressedDefineMode(evt);
627 int seq = findSeq(evt);
628 int res = findColumn(evt);
630 if (seq < 0 || res < 0)
635 if ((seq < av.getAlignment().getHeight())
636 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
653 public void mouseOverSequence(SequenceI sequence, int index, int pos)
655 String tmp = sequence.hashCode() + " " + index + " " + pos;
657 if (lastMessage == null || !lastMessage.equals(tmp))
659 // System.err.println("mouseOver Sequence: "+tmp);
660 ssm.mouseOverSequence(sequence, index, pos, av);
666 * Highlight the mapped region described by the search results object (unless
667 * unchanged). This supports highlight of protein while mousing over linked
668 * cDNA and vice versa. The status bar is also updated to show the location of
669 * the start of the highlighted region.
672 public void highlightSequence(SearchResultsI results)
674 if (results == null || results.equals(lastSearchResults))
678 lastSearchResults = results;
680 boolean wasScrolled = false;
682 if (av.isFollowHighlight())
684 // don't allow highlight of protein/cDNA to also scroll a complementary
685 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
686 // over residue to change abruptly, causing highlighted residue in panel 2
687 // to change, causing a scroll in panel 1 etc)
688 ap.setToScrollComplementPanel(false);
689 wasScrolled = ap.scrollToPosition(results, false);
692 seqCanvas.revalidate();
694 ap.setToScrollComplementPanel(true);
697 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
698 if (seqCanvas.highlightSearchResults(results, noFastPaint))
700 setStatusMessage(results);
705 public VamsasSource getVamsasSource()
707 return this.ap == null ? null : this.ap.av;
711 public void updateColours(SequenceI seq, int index)
713 System.out.println("update the seqPanel colours");
718 * Action on mouse movement is to update the status bar to show the current
719 * sequence position, and (if features are shown) to show any features at the
720 * position in a tooltip. Does nothing if the mouse move does not change
726 public void mouseMoved(MouseEvent evt)
730 // This is because MacOSX creates a mouseMoved
731 // If control is down, other platforms will not.
735 final int column = findColumn(evt);
736 final int seq = findSeq(evt);
738 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
743 if (column == lastMouseColumn && seq == lastMouseSeq)
746 * just a pixel move without change of residue
750 lastMouseColumn = column;
753 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
755 if (column >= sequence.getLength())
761 * set status bar message, returning residue position in sequence
763 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
764 final int pos = setStatusMessage(sequence, column, seq);
765 if (ssm != null && !isGapped)
767 mouseOverSequence(sequence, column, pos);
770 tooltipText.setLength(6); // Cuts the buffer back to <html>
772 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
775 for (int g = 0; g < groups.length; g++)
777 if (groups[g].getStartRes() <= column
778 && groups[g].getEndRes() >= column)
780 if (!groups[g].getName().startsWith("JTreeGroup")
781 && !groups[g].getName().startsWith("JGroup"))
783 tooltipText.append(groups[g].getName());
786 if (groups[g].getDescription() != null)
788 tooltipText.append(": " + groups[g].getDescription());
795 * add any features at the position to the tooltip; if over a gap, only
796 * add features that straddle the gap (pos may be the residue before or
799 if (av.isShowSequenceFeatures())
801 List<SequenceFeature> features = ap.getFeatureRenderer()
802 .findFeaturesAtColumn(sequence, column + 1);
803 seqARep.appendFeatures(tooltipText, pos, features,
804 this.ap.getSeqPanel().seqCanvas.fr);
806 if (tooltipText.length() == 6) // <html>
808 setToolTipText(null);
813 if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
815 tooltipText.setLength(MAX_TOOLTIP_LENGTH);
816 tooltipText.append("...");
818 String textString = tooltipText.toString();
819 if (lastTooltip == null || !lastTooltip.equals(textString))
821 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
823 setToolTipText(formattedTooltipText);
824 lastTooltip = textString;
829 private Point lastp = null;
834 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
837 public Point getToolTipLocation(MouseEvent event)
839 int x = event.getX(), w = getWidth();
840 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
843 if (!event.isShiftDown() || p == null)
845 p = (tooltipText != null && tooltipText.length() > 6)
846 ? new Point(event.getX() + wdth, event.getY() - 20)
850 * TODO: try to modify position region is not obcured by tooltip
858 * set when the current UI interaction has resulted in a change that requires
859 * shading in overviews and structures to be recalculated. this could be
860 * changed to a something more expressive that indicates what actually has
861 * changed, so selective redraws can be applied (ie. only structures, only
864 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
867 * set if av.getSelectionGroup() refers to a group that is defined on the
868 * alignment view, rather than a transient selection
870 // private boolean editingDefinedGroup = false; // TODO: refactor to
871 // avcontroller or viewModel
874 * Sets the status message in alignment panel, showing the sequence number
875 * (index) and id, and residue and residue position if not at a gap, for the
876 * given sequence and column position. Returns the residue position returned
877 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
878 * if at a gapped position.
881 * aligned sequence object
885 * index of sequence in alignment
886 * @return sequence position of residue at column, or adjacent residue if at a
889 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
891 char sequenceChar = sequence.getCharAt(column);
892 int pos = sequence.findPosition(column);
893 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
899 * Builds the status message for the current cursor location and writes it to
900 * the status bar, for example
903 * Sequence 3 ID: FER1_SOLLC
904 * Sequence 5 ID: FER1_PEA Residue: THR (4)
905 * Sequence 5 ID: FER1_PEA Residue: B (3)
906 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
911 * sequence position in the alignment (1..)
912 * @param sequenceChar
913 * the character under the cursor
915 * the sequence residue position (if not over a gap)
917 protected void setStatusMessage(SequenceI sequence, int seqIndex,
918 char sequenceChar, int residuePos)
920 StringBuilder text = new StringBuilder(32);
923 * Sequence number (if known), and sequence name.
925 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
926 text.append("Sequence").append(seqno).append(" ID: ")
927 .append(sequence.getName());
929 String residue = null;
932 * Try to translate the display character to residue name (null for gap).
934 boolean isGapped = Comparison.isGap(sequenceChar);
938 boolean nucleotide = av.getAlignment().isNucleotide();
939 String displayChar = String.valueOf(sequenceChar);
942 residue = ResidueProperties.nucleotideName.get(displayChar);
946 residue = "X".equalsIgnoreCase(displayChar) ? "X"
947 : ("*".equals(displayChar) ? "STOP"
948 : ResidueProperties.aa2Triplet.get(displayChar));
950 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
951 .append(": ").append(residue == null ? displayChar : residue);
953 text.append(" (").append(Integer.toString(residuePos)).append(")");
955 ap.alignFrame.statusBar.setText(text.toString());
959 * Set the status bar message to highlight the first matched position in
964 private void setStatusMessage(SearchResultsI results)
966 AlignmentI al = this.av.getAlignment();
967 int sequenceIndex = al.findIndex(results);
968 if (sequenceIndex == -1)
972 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
973 for (SearchResultMatchI m : results.getResults())
975 SequenceI seq = m.getSequence();
976 if (seq.getDatasetSequence() != null)
978 seq = seq.getDatasetSequence();
983 int start = m.getStart();
984 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
995 public void mouseDragged(MouseEvent evt)
997 if (mouseWheelPressed)
999 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1000 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1002 int oldWidth = av.getCharWidth();
1004 // Which is bigger, left-right or up-down?
1005 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1006 .abs(evt.getX() - lastMousePress.getX()))
1009 * on drag up or down, decrement or increment font size
1011 int fontSize = av.font.getSize();
1012 boolean fontChanged = false;
1014 if (evt.getY() < lastMousePress.getY())
1019 else if (evt.getY() > lastMousePress.getY())
1032 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1034 av.setFont(newFont, true);
1035 av.setCharWidth(oldWidth);
1039 ap.av.getCodingComplement().setFont(newFont, true);
1040 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1041 .getSplitViewContainer();
1042 splitFrame.adjustLayout();
1043 splitFrame.repaint();
1050 * on drag left or right, decrement or increment character width
1053 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1055 newWidth = av.getCharWidth() - 1;
1056 av.setCharWidth(newWidth);
1058 else if (evt.getX() > lastMousePress.getX())
1060 newWidth = av.getCharWidth() + 1;
1061 av.setCharWidth(newWidth);
1065 ap.paintAlignment(false, false);
1069 * need to ensure newWidth is set on cdna, regardless of which
1070 * panel the mouse drag happened in; protein will compute its
1071 * character width as 1:1 or 3:1
1073 av.getCodingComplement().setCharWidth(newWidth);
1074 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1075 .getSplitViewContainer();
1076 splitFrame.adjustLayout();
1077 splitFrame.repaint();
1082 FontMetrics fm = getFontMetrics(av.getFont());
1083 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1085 lastMousePress = evt.getPoint();
1092 doMouseDraggedDefineMode(evt);
1096 int res = findColumn(evt);
1103 if ((lastres == -1) || (lastres == res))
1108 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1110 // dragLeft, delete gap
1111 editSequence(false, false, res);
1115 editSequence(true, false, res);
1118 mouseDragging = true;
1119 if ((scrollThread != null) && (scrollThread.isRunning()))
1121 scrollThread.setEvent(evt);
1125 // TODO: Make it more clever than many booleans
1126 synchronized void editSequence(boolean insertGap, boolean editSeq,
1130 int fixedRight = -1;
1131 boolean fixedColumns = false;
1132 SequenceGroup sg = av.getSelectionGroup();
1134 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1136 // No group, but the sequence may represent a group
1137 if (!groupEditing && av.hasHiddenRows())
1139 if (av.isHiddenRepSequence(seq))
1141 sg = av.getRepresentedSequences(seq);
1142 groupEditing = true;
1146 StringBuilder message = new StringBuilder(64);
1149 message.append("Edit group:");
1150 if (editCommand == null)
1152 editCommand = new EditCommand(
1153 MessageManager.getString("action.edit_group"));
1158 message.append("Edit sequence: " + seq.getName());
1159 String label = seq.getName();
1160 if (label.length() > 10)
1162 label = label.substring(0, 10);
1164 if (editCommand == null)
1166 editCommand = new EditCommand(MessageManager
1167 .formatMessage("label.edit_params", new String[]
1174 message.append(" insert ");
1178 message.append(" delete ");
1181 message.append(Math.abs(startres - lastres) + " gaps.");
1182 ap.alignFrame.statusBar.setText(message.toString());
1184 // Are we editing within a selection group?
1185 if (groupEditing || (sg != null
1186 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1188 fixedColumns = true;
1190 // sg might be null as the user may only see 1 sequence,
1191 // but the sequence represents a group
1194 if (!av.isHiddenRepSequence(seq))
1199 sg = av.getRepresentedSequences(seq);
1202 fixedLeft = sg.getStartRes();
1203 fixedRight = sg.getEndRes();
1205 if ((startres < fixedLeft && lastres >= fixedLeft)
1206 || (startres >= fixedLeft && lastres < fixedLeft)
1207 || (startres > fixedRight && lastres <= fixedRight)
1208 || (startres <= fixedRight && lastres > fixedRight))
1214 if (fixedLeft > startres)
1216 fixedRight = fixedLeft - 1;
1219 else if (fixedRight < startres)
1221 fixedLeft = fixedRight;
1226 if (av.hasHiddenColumns())
1228 fixedColumns = true;
1229 int y1 = av.getAlignment().getHiddenColumns()
1230 .getHiddenBoundaryLeft(startres);
1231 int y2 = av.getAlignment().getHiddenColumns()
1232 .getHiddenBoundaryRight(startres);
1234 if ((insertGap && startres > y1 && lastres < y1)
1235 || (!insertGap && startres < y2 && lastres > y2))
1241 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1242 // Selection spans a hidden region
1243 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1251 fixedRight = y2 - 1;
1258 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1259 int g, groupSize = vseqs.size();
1260 SequenceI[] groupSeqs = new SequenceI[groupSize];
1261 for (g = 0; g < groupSeqs.length; g++)
1263 groupSeqs[g] = vseqs.get(g);
1269 // If the user has selected the whole sequence, and is dragging to
1270 // the right, we can still extend the alignment and selectionGroup
1271 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1272 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1274 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1275 fixedRight = sg.getEndRes();
1278 // Is it valid with fixed columns??
1279 // Find the next gap before the end
1280 // of the visible region boundary
1281 boolean blank = false;
1282 for (; fixedRight > lastres; fixedRight--)
1286 for (g = 0; g < groupSize; g++)
1288 for (int j = 0; j < startres - lastres; j++)
1290 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1305 if (sg.getSize() == av.getAlignment().getHeight())
1307 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1308 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1314 int alWidth = av.getAlignment().getWidth();
1315 if (av.hasHiddenRows())
1317 int hwidth = av.getAlignment().getHiddenSequences()
1319 if (hwidth > alWidth)
1324 // We can still insert gaps if the selectionGroup
1325 // contains all the sequences
1326 sg.setEndRes(sg.getEndRes() + startres - lastres);
1327 fixedRight = alWidth + startres - lastres;
1338 else if (!insertGap)
1340 // / Are we able to delete?
1341 // ie are all columns blank?
1343 for (g = 0; g < groupSize; g++)
1345 for (int j = startres; j < lastres; j++)
1347 if (groupSeqs[g].getLength() <= j)
1352 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1354 // Not a gap, block edit not valid
1364 // dragging to the right
1365 if (fixedColumns && fixedRight != -1)
1367 for (int j = lastres; j < startres; j++)
1369 insertChar(j, groupSeqs, fixedRight);
1374 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1375 startres - lastres);
1380 // dragging to the left
1381 if (fixedColumns && fixedRight != -1)
1383 for (int j = lastres; j > startres; j--)
1385 deleteChar(startres, groupSeqs, fixedRight);
1390 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1391 lastres - startres);
1397 // ///Editing a single sequence///////////
1401 // dragging to the right
1402 if (fixedColumns && fixedRight != -1)
1404 for (int j = lastres; j < startres; j++)
1406 insertChar(j, new SequenceI[] { seq }, fixedRight);
1411 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1412 startres - lastres);
1419 // dragging to the left
1420 if (fixedColumns && fixedRight != -1)
1422 for (int j = lastres; j > startres; j--)
1424 if (!Comparison.isGap(seq.getCharAt(startres)))
1429 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1434 // could be a keyboard edit trying to delete none gaps
1436 for (int m = startres; m < lastres; m++)
1438 if (!Comparison.isGap(seq.getCharAt(m)))
1447 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1453 {// insertGap==false AND editSeq==TRUE;
1454 if (fixedColumns && fixedRight != -1)
1456 for (int j = lastres; j < startres; j++)
1458 insertChar(j, new SequenceI[] { seq }, fixedRight);
1463 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1464 startres - lastres);
1471 seqCanvas.repaint();
1474 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1476 int blankColumn = fixedColumn;
1477 for (int s = 0; s < seq.length; s++)
1479 // Find the next gap before the end of the visible region boundary
1480 // If lastCol > j, theres a boundary after the gap insertion
1482 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1484 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1486 // Theres a space, so break and insert the gap
1491 if (blankColumn <= j)
1493 blankColumn = fixedColumn;
1499 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1501 appendEdit(Action.INSERT_GAP, seq, j, 1);
1506 * Helper method to add and perform one edit action.
1513 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1517 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1518 av.getAlignment().getGapCharacter());
1520 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1523 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1526 appendEdit(Action.DELETE_GAP, seq, j, 1);
1528 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1538 public void mouseEntered(MouseEvent e)
1545 if ((scrollThread != null) && (scrollThread.isRunning()))
1547 scrollThread.stopScrolling();
1548 scrollThread = null;
1559 public void mouseExited(MouseEvent e)
1561 if (av.getWrapAlignment())
1566 if (mouseDragging && scrollThread == null)
1568 scrollThread = new ScrollThread();
1573 * Handler for double-click on a position with one or more sequence features.
1574 * Opens the Amend Features dialog to allow feature details to be amended, or
1575 * the feature deleted.
1578 public void mouseClicked(MouseEvent evt)
1580 SequenceGroup sg = null;
1581 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1582 if (evt.getClickCount() > 1)
1584 sg = av.getSelectionGroup();
1585 if (sg != null && sg.getSize() == 1
1586 && sg.getEndRes() - sg.getStartRes() < 2)
1588 av.setSelectionGroup(null);
1591 int column = findColumn(evt);
1594 * find features at the position (if not gapped), or straddling
1595 * the position (if at a gap)
1597 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1598 .findFeaturesAtColumn(sequence, column + 1);
1600 if (!features.isEmpty())
1603 * highlight the first feature at the position on the alignment
1605 SearchResultsI highlight = new SearchResults();
1606 highlight.addResult(sequence, features.get(0).getBegin(), features
1608 seqCanvas.highlightSearchResults(highlight, false);
1611 * open the Amend Features dialog; clear highlighting afterwards,
1612 * whether changes were made or not
1614 List<SequenceI> seqs = Collections.singletonList(sequence);
1615 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1617 av.setSearchResults(null); // clear highlighting
1618 seqCanvas.repaint(); // draw new/amended features
1624 public void mouseWheelMoved(MouseWheelEvent e)
1627 if (e.getWheelRotation() > 0)
1629 if (e.isShiftDown())
1631 av.getRanges().scrollRight(true);
1636 av.getRanges().scrollUp(false);
1641 if (e.isShiftDown())
1643 av.getRanges().scrollRight(false);
1647 av.getRanges().scrollUp(true);
1652 * update status bar and tooltip for new position
1653 * (need to synthesize a mouse movement to refresh tooltip)
1656 ToolTipManager.sharedInstance().mouseMoved(e);
1665 public void doMousePressedDefineMode(MouseEvent evt)
1667 final int res = findColumn(evt);
1668 final int seq = findSeq(evt);
1670 updateOverviewAndStructs = false;
1672 startWrapBlock = wrappedBlock;
1674 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1676 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1677 MessageManager.getString(
1678 "label.cannot_edit_annotations_in_wrapped_view"),
1679 MessageManager.getString("label.wrapped_view_no_edit"),
1680 JvOptionPane.WARNING_MESSAGE);
1684 if (seq < 0 || res < 0)
1689 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1691 if ((sequence == null) || (res > sequence.getLength()))
1696 stretchGroup = av.getSelectionGroup();
1698 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1700 stretchGroup = av.getAlignment().findGroup(sequence, res);
1701 if (stretchGroup != null)
1703 // only update the current selection if the popup menu has a group to
1705 av.setSelectionGroup(stretchGroup);
1709 if (evt.isPopupTrigger()) // Mac: mousePressed
1716 * defer right-mouse click handling to mouseReleased on Windows
1717 * (where isPopupTrigger() will answer true)
1718 * NB isRightMouseButton is also true for Cmd-click on Mac
1720 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1727 seqCanvas.cursorX = findColumn(evt);
1728 seqCanvas.cursorY = findSeq(evt);
1729 seqCanvas.repaint();
1733 if (stretchGroup == null)
1735 createStretchGroup(res, sequence);
1738 if (stretchGroup != null)
1740 stretchGroup.addPropertyChangeListener(seqCanvas);
1743 seqCanvas.repaint();
1746 private void createStretchGroup(int res, SequenceI sequence)
1748 // Only if left mouse button do we want to change group sizes
1749 // define a new group here
1750 SequenceGroup sg = new SequenceGroup();
1751 sg.setStartRes(res);
1753 sg.addSequence(sequence, false);
1754 av.setSelectionGroup(sg);
1757 if (av.getConservationSelected())
1759 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1763 if (av.getAbovePIDThreshold())
1765 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1768 // TODO: stretchGroup will always be not null. Is this a merge error ?
1769 // or is there a threading issue here?
1770 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1772 // Edit end res position of selected group
1773 changeEndRes = true;
1775 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1777 // Edit end res position of selected group
1778 changeStartRes = true;
1780 stretchGroup.getWidth();
1785 * Build and show a pop-up menu at the right-click mouse position
1791 void showPopupMenu(MouseEvent evt)
1793 final int column = findColumn(evt);
1794 final int seq = findSeq(evt);
1795 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1796 List<SequenceFeature> features = ap.getFeatureRenderer()
1797 .findFeaturesAtColumn(sequence, column + 1);
1799 PopupMenu pop = new PopupMenu(ap, null, features);
1800 pop.show(this, evt.getX(), evt.getY());
1804 * Update the display after mouse up on a selection or group
1807 * mouse released event details
1809 * true if this event is happening after a mouse drag (rather than a
1812 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1814 if (stretchGroup == null)
1819 stretchGroup.removePropertyChangeListener(seqCanvas);
1821 // always do this - annotation has own state
1822 // but defer colourscheme update until hidden sequences are passed in
1823 boolean vischange = stretchGroup.recalcConservation(true);
1824 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1826 if (stretchGroup.cs != null)
1828 stretchGroup.cs.alignmentChanged(stretchGroup,
1829 av.getHiddenRepSequences());
1831 ResidueShaderI groupColourScheme = stretchGroup
1832 .getGroupColourScheme();
1833 String name = stretchGroup.getName();
1834 if (stretchGroup.cs.conservationApplied())
1836 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1838 if (stretchGroup.cs.getThreshold() > 0)
1840 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1843 PaintRefresher.Refresh(this, av.getSequenceSetId());
1844 // TODO: structure colours only need updating if stretchGroup used to or now
1845 // does contain sequences with structure views
1846 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1847 updateOverviewAndStructs = false;
1848 changeEndRes = false;
1849 changeStartRes = false;
1850 stretchGroup = null;
1860 public void doMouseDraggedDefineMode(MouseEvent evt)
1862 int res = findColumn(evt);
1863 int y = findSeq(evt);
1865 if (wrappedBlock != startWrapBlock)
1870 if (stretchGroup == null)
1875 if (res >= av.getAlignment().getWidth())
1877 res = av.getAlignment().getWidth() - 1;
1880 if (stretchGroup.getEndRes() == res)
1882 // Edit end res position of selected group
1883 changeEndRes = true;
1885 else if (stretchGroup.getStartRes() == res)
1887 // Edit start res position of selected group
1888 changeStartRes = true;
1891 if (res < av.getRanges().getStartRes())
1893 res = av.getRanges().getStartRes();
1898 if (res > (stretchGroup.getStartRes() - 1))
1900 stretchGroup.setEndRes(res);
1901 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1904 else if (changeStartRes)
1906 if (res < (stretchGroup.getEndRes() + 1))
1908 stretchGroup.setStartRes(res);
1909 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1913 int dragDirection = 0;
1919 else if (y < oldSeq)
1924 while ((y != oldSeq) && (oldSeq > -1)
1925 && (y < av.getAlignment().getHeight()))
1927 // This routine ensures we don't skip any sequences, as the
1928 // selection is quite slow.
1929 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1931 oldSeq += dragDirection;
1938 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1940 if (stretchGroup.getSequences(null).contains(nextSeq))
1942 stretchGroup.deleteSequence(seq, false);
1943 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1949 stretchGroup.addSequence(seq, false);
1952 stretchGroup.addSequence(nextSeq, false);
1953 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1962 mouseDragging = true;
1964 if ((scrollThread != null) && (scrollThread.isRunning()))
1966 scrollThread.setEvent(evt);
1970 void scrollCanvas(MouseEvent evt)
1974 if ((scrollThread != null) && (scrollThread.isRunning()))
1976 scrollThread.stopScrolling();
1977 scrollThread = null;
1979 mouseDragging = false;
1983 if (scrollThread == null)
1985 scrollThread = new ScrollThread();
1988 mouseDragging = true;
1989 scrollThread.setEvent(evt);
1994 // this class allows scrolling off the bottom of the visible alignment
1995 class ScrollThread extends Thread
1999 private volatile boolean threadRunning = true;
2001 public ScrollThread()
2006 public void setEvent(MouseEvent e)
2011 public void stopScrolling()
2013 threadRunning = false;
2016 public boolean isRunning()
2018 return threadRunning;
2024 while (threadRunning)
2028 if (mouseDragging && (evt.getY() < 0)
2029 && (av.getRanges().getStartSeq() > 0))
2031 av.getRanges().scrollUp(true);
2034 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2035 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2037 av.getRanges().scrollUp(false);
2040 if (mouseDragging && (evt.getX() < 0))
2042 av.getRanges().scrollRight(false);
2044 else if (mouseDragging && (evt.getX() >= getWidth()))
2046 av.getRanges().scrollRight(true);
2053 } catch (Exception ex)
2061 * modify current selection according to a received message.
2064 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2065 HiddenColumns hidden, SelectionSource source)
2067 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2068 // handles selection messages...
2069 // TODO: extend config options to allow user to control if selections may be
2070 // shared between viewports.
2071 boolean iSentTheSelection = (av == source
2072 || (source instanceof AlignViewport
2073 && ((AlignmentViewport) source).getSequenceSetId()
2074 .equals(av.getSequenceSetId())));
2076 if (iSentTheSelection)
2078 // respond to our own event by updating dependent dialogs
2079 if (ap.getCalculationDialog() != null)
2081 ap.getCalculationDialog().validateCalcTypes();
2087 // process further ?
2088 if (!av.followSelection)
2094 * Ignore the selection if there is one of our own pending.
2096 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2102 * Check for selection in a view of which this one is a dna/protein
2105 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2110 // do we want to thread this ? (contention with seqsel and colsel locks, I
2113 * only copy colsel if there is a real intersection between
2114 * sequence selection and this panel's alignment
2116 boolean repaint = false;
2117 boolean copycolsel = false;
2119 SequenceGroup sgroup = null;
2120 if (seqsel != null && seqsel.getSize() > 0)
2122 if (av.getAlignment() == null)
2124 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2125 + " ViewId=" + av.getViewId()
2126 + " 's alignment is NULL! returning immediately.");
2129 sgroup = seqsel.intersect(av.getAlignment(),
2130 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2131 if ((sgroup != null && sgroup.getSize() > 0))
2136 if (sgroup != null && sgroup.getSize() > 0)
2138 av.setSelectionGroup(sgroup);
2142 av.setSelectionGroup(null);
2144 av.isSelectionGroupChanged(true);
2149 // the current selection is unset or from a previous message
2150 // so import the new colsel.
2151 if (colsel == null || colsel.isEmpty())
2153 if (av.getColumnSelection() != null)
2155 av.getColumnSelection().clear();
2161 // TODO: shift colSel according to the intersecting sequences
2162 if (av.getColumnSelection() == null)
2164 av.setColumnSelection(new ColumnSelection(colsel));
2168 av.getColumnSelection().setElementsFrom(colsel,
2169 av.getAlignment().getHiddenColumns());
2172 av.isColSelChanged(true);
2176 if (copycolsel && av.hasHiddenColumns()
2177 && (av.getAlignment().getHiddenColumns() == null))
2179 System.err.println("Bad things");
2181 if (repaint) // always true!
2183 // probably finessing with multiple redraws here
2184 PaintRefresher.Refresh(this, av.getSequenceSetId());
2185 // ap.paintAlignment(false);
2188 // lastly, update dependent dialogs
2189 if (ap.getCalculationDialog() != null)
2191 ap.getCalculationDialog().validateCalcTypes();
2197 * If this panel is a cdna/protein translation view of the selection source,
2198 * tries to map the source selection to a local one, and returns true. Else
2205 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2206 ColumnSelection colsel, HiddenColumns hidden,
2207 SelectionSource source)
2209 if (!(source instanceof AlignViewportI))
2213 final AlignViewportI sourceAv = (AlignViewportI) source;
2214 if (sourceAv.getCodingComplement() != av
2215 && av.getCodingComplement() != sourceAv)
2221 * Map sequence selection
2223 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2224 av.setSelectionGroup(sg);
2225 av.isSelectionGroupChanged(true);
2228 * Map column selection
2230 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2232 ColumnSelection cs = new ColumnSelection();
2233 HiddenColumns hs = new HiddenColumns();
2234 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2235 av.setColumnSelection(cs);
2236 av.getAlignment().setHiddenColumns(hs);
2238 // lastly, update any dependent dialogs
2239 if (ap.getCalculationDialog() != null)
2241 ap.getCalculationDialog().validateCalcTypes();
2244 PaintRefresher.Refresh(this, av.getSequenceSetId());