2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignViewportI;
24 import jalview.bin.Cache;
25 import jalview.commands.EditCommand;
26 import jalview.commands.EditCommand.Action;
27 import jalview.commands.EditCommand.Edit;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.HiddenColumns;
31 import jalview.datamodel.SearchResultMatchI;
32 import jalview.datamodel.SearchResults;
33 import jalview.datamodel.SearchResultsI;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.io.SequenceAnnotationReport;
39 import jalview.renderer.ResidueShaderI;
40 import jalview.schemes.ResidueProperties;
41 import jalview.structure.SelectionListener;
42 import jalview.structure.SelectionSource;
43 import jalview.structure.SequenceListener;
44 import jalview.structure.StructureSelectionManager;
45 import jalview.structure.VamsasSource;
46 import jalview.util.Comparison;
47 import jalview.util.MappingUtils;
48 import jalview.util.MessageManager;
49 import jalview.util.Platform;
50 import jalview.viewmodel.AlignmentViewport;
52 import java.awt.BorderLayout;
53 import java.awt.Color;
55 import java.awt.FontMetrics;
56 import java.awt.Point;
57 import java.awt.event.MouseEvent;
58 import java.awt.event.MouseListener;
59 import java.awt.event.MouseMotionListener;
60 import java.awt.event.MouseWheelEvent;
61 import java.awt.event.MouseWheelListener;
62 import java.util.ArrayList;
63 import java.util.Collections;
64 import java.util.List;
66 import javax.swing.JPanel;
67 import javax.swing.SwingUtilities;
68 import javax.swing.ToolTipManager;
74 * @version $Revision: 1.130 $
76 public class SeqPanel extends JPanel
77 implements MouseListener, MouseMotionListener, MouseWheelListener,
78 SequenceListener, SelectionListener
82 public SeqCanvas seqCanvas;
85 public AlignmentPanel ap;
88 * last column position for mouseMoved event
90 private int lastMouseColumn;
93 * last sequence offset for mouseMoved event
95 private int lastMouseSeq;
97 protected int lastres;
99 protected int startseq;
101 protected AlignViewport av;
103 ScrollThread scrollThread = null;
105 boolean mouseDragging = false;
107 boolean editingSeqs = false;
109 boolean groupEditing = false;
111 // ////////////////////////////////////////
112 // ///Everything below this is for defining the boundary of the rubberband
113 // ////////////////////////////////////////
116 boolean changeEndSeq = false;
118 boolean changeStartSeq = false;
120 boolean changeEndRes = false;
122 boolean changeStartRes = false;
124 SequenceGroup stretchGroup = null;
126 boolean remove = false;
128 Point lastMousePress;
130 boolean mouseWheelPressed = false;
132 StringBuffer keyboardNo1;
134 StringBuffer keyboardNo2;
136 java.net.URL linkImageURL;
138 private final SequenceAnnotationReport seqARep;
140 StringBuilder tooltipText = new StringBuilder();
144 EditCommand editCommand;
146 StructureSelectionManager ssm;
148 SearchResultsI lastSearchResults;
151 * Creates a new SeqPanel object.
158 public SeqPanel(AlignViewport av, AlignmentPanel ap)
160 linkImageURL = getClass().getResource("/images/link.gif");
161 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
162 ToolTipManager.sharedInstance().registerComponent(this);
163 ToolTipManager.sharedInstance().setInitialDelay(0);
164 ToolTipManager.sharedInstance().setDismissDelay(10000);
166 setBackground(Color.white);
168 seqCanvas = new SeqCanvas(ap);
169 setLayout(new BorderLayout());
170 add(seqCanvas, BorderLayout.CENTER);
176 addMouseMotionListener(this);
177 addMouseListener(this);
178 addMouseWheelListener(this);
179 ssm = av.getStructureSelectionManager();
180 ssm.addStructureViewerListener(this);
181 ssm.addSelectionListener(this);
184 lastMouseColumn = -1;
188 int startWrapBlock = -1;
190 int wrappedBlock = -1;
193 * Returns the aligned sequence position (base 0) at the mouse position, or
194 * the closest visible one
199 int findColumn(MouseEvent evt)
204 int startRes = av.getRanges().getStartRes();
205 if (av.getWrapAlignment())
208 int hgap = av.getCharHeight();
209 if (av.getScaleAboveWrapped())
211 hgap += av.getCharHeight();
214 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
215 + hgap + seqCanvas.getAnnotationHeight();
219 x = Math.max(0, x - seqCanvas.labelWidthWest);
221 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
227 wrappedBlock = y / cHeight;
228 wrappedBlock += startRes / cwidth;
229 // allow for wrapped view scrolled right (possible from Overview)
230 int startOffset = startRes % cwidth;
231 res = wrappedBlock * cwidth + startOffset
232 + +Math.min(cwidth - 1, x / av.getCharWidth());
236 if (x > seqCanvas.getX() + seqCanvas.getWidth())
238 // make sure we calculate relative to visible alignment, rather than
240 x = seqCanvas.getX() + seqCanvas.getWidth();
242 res = (x / av.getCharWidth()) + startRes;
243 if (res > av.getRanges().getEndRes())
246 res = av.getRanges().getEndRes();
250 if (av.hasHiddenColumns())
252 res = av.getAlignment().getHiddenColumns()
253 .adjustForHiddenColumns(res);
260 int findSeq(MouseEvent evt)
265 if (av.getWrapAlignment())
267 int hgap = av.getCharHeight();
268 if (av.getScaleAboveWrapped())
270 hgap += av.getCharHeight();
273 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
274 + hgap + seqCanvas.getAnnotationHeight();
278 seq = Math.min((y % cHeight) / av.getCharHeight(),
279 av.getAlignment().getHeight() - 1);
284 (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
285 av.getAlignment().getHeight() - 1);
292 * When all of a sequence of edits are complete, put the resulting edit list
293 * on the history stack (undo list), and reset flags for editing in progress.
299 if (editCommand != null && editCommand.getSize() > 0)
301 ap.alignFrame.addHistoryItem(editCommand);
302 av.firePropertyChange("alignment", null,
303 av.getAlignment().getSequences());
308 * Tidy up come what may...
313 groupEditing = false;
322 seqCanvas.cursorY = getKeyboardNo1() - 1;
326 void setCursorColumn()
328 seqCanvas.cursorX = getKeyboardNo1() - 1;
332 void setCursorRowAndColumn()
334 if (keyboardNo2 == null)
336 keyboardNo2 = new StringBuffer();
340 seqCanvas.cursorX = getKeyboardNo1() - 1;
341 seqCanvas.cursorY = getKeyboardNo2() - 1;
346 void setCursorPosition()
348 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
350 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
354 void moveCursor(int dx, int dy)
356 seqCanvas.cursorX += dx;
357 seqCanvas.cursorY += dy;
359 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
361 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
363 int original = seqCanvas.cursorX - dx;
364 int maxWidth = av.getAlignment().getWidth();
366 while (!hidden.isVisible(seqCanvas.cursorX)
367 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
369 seqCanvas.cursorX += dx;
372 if (seqCanvas.cursorX >= maxWidth
373 || !hidden.isVisible(seqCanvas.cursorX))
375 seqCanvas.cursorX = original;
382 void scrollToVisible()
384 if (seqCanvas.cursorX < 0)
386 seqCanvas.cursorX = 0;
388 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
390 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
393 if (seqCanvas.cursorY < 0)
395 seqCanvas.cursorY = 0;
397 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
399 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
403 if (av.getWrapAlignment())
405 av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
409 av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
411 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
412 seqCanvas.cursorX, seqCanvas.cursorY);
417 void setSelectionAreaAtCursor(boolean topLeft)
419 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
421 if (av.getSelectionGroup() != null)
423 SequenceGroup sg = av.getSelectionGroup();
424 // Find the top and bottom of this group
425 int min = av.getAlignment().getHeight(), max = 0;
426 for (int i = 0; i < sg.getSize(); i++)
428 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
443 sg.setStartRes(seqCanvas.cursorX);
444 if (sg.getEndRes() < seqCanvas.cursorX)
446 sg.setEndRes(seqCanvas.cursorX);
449 min = seqCanvas.cursorY;
453 sg.setEndRes(seqCanvas.cursorX);
454 if (sg.getStartRes() > seqCanvas.cursorX)
456 sg.setStartRes(seqCanvas.cursorX);
459 max = seqCanvas.cursorY + 1;
464 // Only the user can do this
465 av.setSelectionGroup(null);
469 // Now add any sequences between min and max
470 sg.getSequences(null).clear();
471 for (int i = min; i < max; i++)
473 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
478 if (av.getSelectionGroup() == null)
480 SequenceGroup sg = new SequenceGroup();
481 sg.setStartRes(seqCanvas.cursorX);
482 sg.setEndRes(seqCanvas.cursorX);
483 sg.addSequence(sequence, false);
484 av.setSelectionGroup(sg);
487 ap.paintAlignment(false, false);
491 void insertGapAtCursor(boolean group)
493 groupEditing = group;
494 startseq = seqCanvas.cursorY;
495 lastres = seqCanvas.cursorX;
496 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
500 void deleteGapAtCursor(boolean group)
502 groupEditing = group;
503 startseq = seqCanvas.cursorY;
504 lastres = seqCanvas.cursorX + getKeyboardNo1();
505 editSequence(false, false, seqCanvas.cursorX);
509 void insertNucAtCursor(boolean group, String nuc)
511 // TODO not called - delete?
512 groupEditing = group;
513 startseq = seqCanvas.cursorY;
514 lastres = seqCanvas.cursorX;
515 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
519 void numberPressed(char value)
521 if (keyboardNo1 == null)
523 keyboardNo1 = new StringBuffer();
526 if (keyboardNo2 != null)
528 keyboardNo2.append(value);
532 keyboardNo1.append(value);
540 if (keyboardNo1 != null)
542 int value = Integer.parseInt(keyboardNo1.toString());
546 } catch (Exception x)
557 if (keyboardNo2 != null)
559 int value = Integer.parseInt(keyboardNo2.toString());
563 } catch (Exception x)
577 public void mouseReleased(MouseEvent evt)
579 boolean didDrag = mouseDragging; // did we come here after a drag
580 mouseDragging = false;
581 mouseWheelPressed = false;
583 if (evt.isPopupTrigger()) // Windows: mouseReleased
592 doMouseReleasedDefineMode(evt, didDrag);
606 public void mousePressed(MouseEvent evt)
608 lastMousePress = evt.getPoint();
610 if (SwingUtilities.isMiddleMouseButton(evt))
612 mouseWheelPressed = true;
616 boolean isControlDown = Platform.isControlDown(evt);
617 if (evt.isShiftDown() || isControlDown)
627 doMousePressedDefineMode(evt);
631 int seq = findSeq(evt);
632 int res = findColumn(evt);
634 if (seq < 0 || res < 0)
639 if ((seq < av.getAlignment().getHeight())
640 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
657 public void mouseOverSequence(SequenceI sequence, int index, int pos)
659 String tmp = sequence.hashCode() + " " + index + " " + pos;
661 if (lastMessage == null || !lastMessage.equals(tmp))
663 // System.err.println("mouseOver Sequence: "+tmp);
664 ssm.mouseOverSequence(sequence, index, pos, av);
670 * Highlight the mapped region described by the search results object (unless
671 * unchanged). This supports highlight of protein while mousing over linked
672 * cDNA and vice versa. The status bar is also updated to show the location of
673 * the start of the highlighted region.
676 public void highlightSequence(SearchResultsI results)
678 if (results == null || results.equals(lastSearchResults))
682 lastSearchResults = results;
684 boolean wasScrolled = false;
686 if (av.isFollowHighlight())
688 // don't allow highlight of protein/cDNA to also scroll a complementary
689 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
690 // over residue to change abruptly, causing highlighted residue in panel 2
691 // to change, causing a scroll in panel 1 etc)
692 ap.setToScrollComplementPanel(false);
693 wasScrolled = ap.scrollToPosition(results, false);
696 seqCanvas.revalidate();
698 ap.setToScrollComplementPanel(true);
701 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
702 if (seqCanvas.highlightSearchResults(results, noFastPaint))
704 setStatusMessage(results);
709 public VamsasSource getVamsasSource()
711 return this.ap == null ? null : this.ap.av;
715 public void updateColours(SequenceI seq, int index)
717 System.out.println("update the seqPanel colours");
728 public void mouseMoved(MouseEvent evt)
732 // This is because MacOSX creates a mouseMoved
733 // If control is down, other platforms will not.
737 final int column = findColumn(evt);
738 int seq = findSeq(evt);
739 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
744 if (column == lastMouseColumn && seq == lastMouseSeq)
747 * just a pixel move without change of residue
751 lastMouseColumn = column;
754 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
756 if (column >= sequence.getLength())
762 * set status bar message, returning residue position in sequence
764 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
765 final int pos = setStatusMessage(sequence, column, seq);
766 if (ssm != null && !isGapped)
768 mouseOverSequence(sequence, column, pos);
771 tooltipText.setLength(6); // Cuts the buffer back to <html>
773 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
776 for (int g = 0; g < groups.length; g++)
778 if (groups[g].getStartRes() <= column
779 && groups[g].getEndRes() >= column)
781 if (!groups[g].getName().startsWith("JTreeGroup")
782 && !groups[g].getName().startsWith("JGroup"))
784 tooltipText.append(groups[g].getName());
787 if (groups[g].getDescription() != null)
789 tooltipText.append(": " + groups[g].getDescription());
796 * add any features at the position to the tooltip; if over a gap, only
797 * add features that straddle the gap (pos may be the residue before or
800 if (av.isShowSequenceFeatures())
802 List<SequenceFeature> features = ap.getFeatureRenderer()
803 .findFeaturesAtColumn(sequence, column + 1);
804 seqARep.appendFeatures(tooltipText, pos, features,
805 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
807 if (tooltipText.length() == 6) // <html>
809 setToolTipText(null);
814 String textString = tooltipText.toString();
815 if (lastTooltip == null || !lastTooltip.equals(textString))
817 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
819 setToolTipText(formattedTooltipText);
820 lastTooltip = textString;
825 private Point lastp = null;
830 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
833 public Point getToolTipLocation(MouseEvent event)
835 int x = event.getX(), w = getWidth();
836 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
839 if (!event.isShiftDown() || p == null)
841 p = (tooltipText != null && tooltipText.length() > 6)
842 ? new Point(event.getX() + wdth, event.getY() - 20)
846 * TODO: try to modify position region is not obcured by tooltip
854 * set when the current UI interaction has resulted in a change that requires
855 * shading in overviews and structures to be recalculated. this could be
856 * changed to a something more expressive that indicates what actually has
857 * changed, so selective redraws can be applied (ie. only structures, only
860 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
863 * set if av.getSelectionGroup() refers to a group that is defined on the
864 * alignment view, rather than a transient selection
866 // private boolean editingDefinedGroup = false; // TODO: refactor to
867 // avcontroller or viewModel
870 * Sets the status message in alignment panel, showing the sequence number
871 * (index) and id, and residue and residue position if not at a gap, for the
872 * given sequence and column position. Returns the residue position returned
873 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
874 * if at a gapped position.
877 * aligned sequence object
881 * index of sequence in alignment
882 * @return sequence position of residue at column, or adjacent residue if at a
885 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
887 char sequenceChar = sequence.getCharAt(column);
888 int pos = sequence.findPosition(column);
889 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
895 * Builds the status message for the current cursor location and writes it to
896 * the status bar, for example
899 * Sequence 3 ID: FER1_SOLLC
900 * Sequence 5 ID: FER1_PEA Residue: THR (4)
901 * Sequence 5 ID: FER1_PEA Residue: B (3)
902 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
907 * sequence position in the alignment (1..)
908 * @param sequenceChar
909 * the character under the cursor
911 * the sequence residue position (if not over a gap)
913 protected void setStatusMessage(SequenceI sequence, int seqIndex,
914 char sequenceChar, int residuePos)
916 StringBuilder text = new StringBuilder(32);
919 * Sequence number (if known), and sequence name.
921 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
922 text.append("Sequence").append(seqno).append(" ID: ")
923 .append(sequence.getName());
925 String residue = null;
928 * Try to translate the display character to residue name (null for gap).
930 boolean isGapped = Comparison.isGap(sequenceChar);
934 boolean nucleotide = av.getAlignment().isNucleotide();
935 String displayChar = String.valueOf(sequenceChar);
938 residue = ResidueProperties.nucleotideName.get(displayChar);
942 residue = "X".equalsIgnoreCase(displayChar) ? "X"
943 : ("*".equals(displayChar) ? "STOP"
944 : ResidueProperties.aa2Triplet.get(displayChar));
946 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
947 .append(": ").append(residue == null ? displayChar : residue);
949 text.append(" (").append(Integer.toString(residuePos)).append(")");
951 ap.alignFrame.statusBar.setText(text.toString());
955 * Set the status bar message to highlight the first matched position in
960 private void setStatusMessage(SearchResultsI results)
962 AlignmentI al = this.av.getAlignment();
963 int sequenceIndex = al.findIndex(results);
964 if (sequenceIndex == -1)
968 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
969 for (SearchResultMatchI m : results.getResults())
971 SequenceI seq = m.getSequence();
972 if (seq.getDatasetSequence() != null)
974 seq = seq.getDatasetSequence();
979 int start = m.getStart();
980 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
991 public void mouseDragged(MouseEvent evt)
993 if (mouseWheelPressed)
995 boolean inSplitFrame = ap.av.getCodingComplement() != null;
996 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
998 int oldWidth = av.getCharWidth();
1000 // Which is bigger, left-right or up-down?
1001 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1002 .abs(evt.getX() - lastMousePress.getX()))
1005 * on drag up or down, decrement or increment font size
1007 int fontSize = av.font.getSize();
1008 boolean fontChanged = false;
1010 if (evt.getY() < lastMousePress.getY())
1015 else if (evt.getY() > lastMousePress.getY())
1028 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1030 av.setFont(newFont, true);
1031 av.setCharWidth(oldWidth);
1035 ap.av.getCodingComplement().setFont(newFont, true);
1036 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1037 .getSplitViewContainer();
1038 splitFrame.adjustLayout();
1039 splitFrame.repaint();
1046 * on drag left or right, decrement or increment character width
1049 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1051 newWidth = av.getCharWidth() - 1;
1052 av.setCharWidth(newWidth);
1054 else if (evt.getX() > lastMousePress.getX())
1056 newWidth = av.getCharWidth() + 1;
1057 av.setCharWidth(newWidth);
1061 ap.paintAlignment(false, false);
1065 * need to ensure newWidth is set on cdna, regardless of which
1066 * panel the mouse drag happened in; protein will compute its
1067 * character width as 1:1 or 3:1
1069 av.getCodingComplement().setCharWidth(newWidth);
1070 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1071 .getSplitViewContainer();
1072 splitFrame.adjustLayout();
1073 splitFrame.repaint();
1078 FontMetrics fm = getFontMetrics(av.getFont());
1079 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1081 lastMousePress = evt.getPoint();
1088 doMouseDraggedDefineMode(evt);
1092 int res = findColumn(evt);
1099 if ((lastres == -1) || (lastres == res))
1104 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1106 // dragLeft, delete gap
1107 editSequence(false, false, res);
1111 editSequence(true, false, res);
1114 mouseDragging = true;
1115 if ((scrollThread != null) && (scrollThread.isRunning()))
1117 scrollThread.setEvent(evt);
1121 // TODO: Make it more clever than many booleans
1122 synchronized void editSequence(boolean insertGap, boolean editSeq,
1126 int fixedRight = -1;
1127 boolean fixedColumns = false;
1128 SequenceGroup sg = av.getSelectionGroup();
1130 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1132 // No group, but the sequence may represent a group
1133 if (!groupEditing && av.hasHiddenRows())
1135 if (av.isHiddenRepSequence(seq))
1137 sg = av.getRepresentedSequences(seq);
1138 groupEditing = true;
1142 StringBuilder message = new StringBuilder(64);
1145 message.append("Edit group:");
1146 if (editCommand == null)
1148 editCommand = new EditCommand(
1149 MessageManager.getString("action.edit_group"));
1154 message.append("Edit sequence: " + seq.getName());
1155 String label = seq.getName();
1156 if (label.length() > 10)
1158 label = label.substring(0, 10);
1160 if (editCommand == null)
1162 editCommand = new EditCommand(MessageManager
1163 .formatMessage("label.edit_params", new String[]
1170 message.append(" insert ");
1174 message.append(" delete ");
1177 message.append(Math.abs(startres - lastres) + " gaps.");
1178 ap.alignFrame.statusBar.setText(message.toString());
1180 // Are we editing within a selection group?
1181 if (groupEditing || (sg != null
1182 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1184 fixedColumns = true;
1186 // sg might be null as the user may only see 1 sequence,
1187 // but the sequence represents a group
1190 if (!av.isHiddenRepSequence(seq))
1195 sg = av.getRepresentedSequences(seq);
1198 fixedLeft = sg.getStartRes();
1199 fixedRight = sg.getEndRes();
1201 if ((startres < fixedLeft && lastres >= fixedLeft)
1202 || (startres >= fixedLeft && lastres < fixedLeft)
1203 || (startres > fixedRight && lastres <= fixedRight)
1204 || (startres <= fixedRight && lastres > fixedRight))
1210 if (fixedLeft > startres)
1212 fixedRight = fixedLeft - 1;
1215 else if (fixedRight < startres)
1217 fixedLeft = fixedRight;
1222 if (av.hasHiddenColumns())
1224 fixedColumns = true;
1225 int y1 = av.getAlignment().getHiddenColumns()
1226 .getHiddenBoundaryLeft(startres);
1227 int y2 = av.getAlignment().getHiddenColumns()
1228 .getHiddenBoundaryRight(startres);
1230 if ((insertGap && startres > y1 && lastres < y1)
1231 || (!insertGap && startres < y2 && lastres > y2))
1237 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1238 // Selection spans a hidden region
1239 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1247 fixedRight = y2 - 1;
1254 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1255 int g, groupSize = vseqs.size();
1256 SequenceI[] groupSeqs = new SequenceI[groupSize];
1257 for (g = 0; g < groupSeqs.length; g++)
1259 groupSeqs[g] = vseqs.get(g);
1265 // If the user has selected the whole sequence, and is dragging to
1266 // the right, we can still extend the alignment and selectionGroup
1267 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1268 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1270 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1271 fixedRight = sg.getEndRes();
1274 // Is it valid with fixed columns??
1275 // Find the next gap before the end
1276 // of the visible region boundary
1277 boolean blank = false;
1278 for (; fixedRight > lastres; fixedRight--)
1282 for (g = 0; g < groupSize; g++)
1284 for (int j = 0; j < startres - lastres; j++)
1286 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1301 if (sg.getSize() == av.getAlignment().getHeight())
1303 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1304 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1310 int alWidth = av.getAlignment().getWidth();
1311 if (av.hasHiddenRows())
1313 int hwidth = av.getAlignment().getHiddenSequences()
1315 if (hwidth > alWidth)
1320 // We can still insert gaps if the selectionGroup
1321 // contains all the sequences
1322 sg.setEndRes(sg.getEndRes() + startres - lastres);
1323 fixedRight = alWidth + startres - lastres;
1334 else if (!insertGap)
1336 // / Are we able to delete?
1337 // ie are all columns blank?
1339 for (g = 0; g < groupSize; g++)
1341 for (int j = startres; j < lastres; j++)
1343 if (groupSeqs[g].getLength() <= j)
1348 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1350 // Not a gap, block edit not valid
1360 // dragging to the right
1361 if (fixedColumns && fixedRight != -1)
1363 for (int j = lastres; j < startres; j++)
1365 insertChar(j, groupSeqs, fixedRight);
1370 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1371 startres - lastres);
1376 // dragging to the left
1377 if (fixedColumns && fixedRight != -1)
1379 for (int j = lastres; j > startres; j--)
1381 deleteChar(startres, groupSeqs, fixedRight);
1386 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1387 lastres - startres);
1393 // ///Editing a single sequence///////////
1397 // dragging to the right
1398 if (fixedColumns && fixedRight != -1)
1400 for (int j = lastres; j < startres; j++)
1402 insertChar(j, new SequenceI[] { seq }, fixedRight);
1407 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1408 startres - lastres);
1415 // dragging to the left
1416 if (fixedColumns && fixedRight != -1)
1418 for (int j = lastres; j > startres; j--)
1420 if (!Comparison.isGap(seq.getCharAt(startres)))
1425 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1430 // could be a keyboard edit trying to delete none gaps
1432 for (int m = startres; m < lastres; m++)
1434 if (!Comparison.isGap(seq.getCharAt(m)))
1443 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1449 {// insertGap==false AND editSeq==TRUE;
1450 if (fixedColumns && fixedRight != -1)
1452 for (int j = lastres; j < startres; j++)
1454 insertChar(j, new SequenceI[] { seq }, fixedRight);
1459 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1460 startres - lastres);
1467 seqCanvas.repaint();
1470 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1472 int blankColumn = fixedColumn;
1473 for (int s = 0; s < seq.length; s++)
1475 // Find the next gap before the end of the visible region boundary
1476 // If lastCol > j, theres a boundary after the gap insertion
1478 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1480 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1482 // Theres a space, so break and insert the gap
1487 if (blankColumn <= j)
1489 blankColumn = fixedColumn;
1495 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1497 appendEdit(Action.INSERT_GAP, seq, j, 1);
1502 * Helper method to add and perform one edit action.
1509 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1513 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1514 av.getAlignment().getGapCharacter());
1516 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1519 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1522 appendEdit(Action.DELETE_GAP, seq, j, 1);
1524 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1534 public void mouseEntered(MouseEvent e)
1541 if ((scrollThread != null) && (scrollThread.isRunning()))
1543 scrollThread.stopScrolling();
1544 scrollThread = null;
1555 public void mouseExited(MouseEvent e)
1557 if (av.getWrapAlignment())
1562 if (mouseDragging && scrollThread == null)
1564 scrollThread = new ScrollThread();
1569 * Handler for double-click on a position with one or more sequence features.
1570 * Opens the Amend Features dialog to allow feature details to be amended, or
1571 * the feature deleted.
1574 public void mouseClicked(MouseEvent evt)
1576 SequenceGroup sg = null;
1577 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1578 if (evt.getClickCount() > 1)
1580 sg = av.getSelectionGroup();
1581 if (sg != null && sg.getSize() == 1
1582 && sg.getEndRes() - sg.getStartRes() < 2)
1584 av.setSelectionGroup(null);
1587 int column = findColumn(evt);
1590 * find features at the position (if not gapped), or straddling
1591 * the position (if at a gap)
1593 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1594 .findFeaturesAtColumn(sequence, column + 1);
1596 if (!features.isEmpty())
1599 * highlight the first feature at the position on the alignment
1601 SearchResultsI highlight = new SearchResults();
1602 highlight.addResult(sequence, features.get(0).getBegin(), features
1604 seqCanvas.highlightSearchResults(highlight, false);
1607 * open the Amend Features dialog; clear highlighting afterwards,
1608 * whether changes were made or not
1610 List<SequenceI> seqs = Collections.singletonList(sequence);
1611 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1613 av.setSearchResults(null); // clear highlighting
1614 seqCanvas.repaint(); // draw new/amended features
1620 public void mouseWheelMoved(MouseWheelEvent e)
1623 if (e.getWheelRotation() > 0)
1625 if (e.isShiftDown())
1627 av.getRanges().scrollRight(true);
1630 else if (!av.getWrapAlignment())
1632 av.getRanges().scrollUp(false);
1637 if (e.isShiftDown())
1639 av.getRanges().scrollRight(false);
1641 else if (!av.getWrapAlignment())
1643 av.getRanges().scrollUp(true);
1646 // TODO Update tooltip for new position.
1655 public void doMousePressedDefineMode(MouseEvent evt)
1657 final int res = findColumn(evt);
1658 final int seq = findSeq(evt);
1660 updateOverviewAndStructs = false;
1662 startWrapBlock = wrappedBlock;
1664 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1666 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1667 MessageManager.getString(
1668 "label.cannot_edit_annotations_in_wrapped_view"),
1669 MessageManager.getString("label.wrapped_view_no_edit"),
1670 JvOptionPane.WARNING_MESSAGE);
1674 if (seq < 0 || res < 0)
1679 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1681 if ((sequence == null) || (res > sequence.getLength()))
1686 stretchGroup = av.getSelectionGroup();
1688 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1690 stretchGroup = av.getAlignment().findGroup(sequence, res);
1691 if (stretchGroup != null)
1693 // only update the current selection if the popup menu has a group to
1695 av.setSelectionGroup(stretchGroup);
1699 if (evt.isPopupTrigger()) // Mac: mousePressed
1706 * defer right-mouse click handling to mouseReleased on Windows
1707 * (where isPopupTrigger() will answer true)
1708 * NB isRightMouseButton is also true for Cmd-click on Mac
1710 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1717 seqCanvas.cursorX = findColumn(evt);
1718 seqCanvas.cursorY = findSeq(evt);
1719 seqCanvas.repaint();
1723 if (stretchGroup == null)
1725 createStretchGroup(res, sequence);
1728 if (stretchGroup != null)
1730 stretchGroup.addPropertyChangeListener(seqCanvas);
1733 seqCanvas.repaint();
1736 private void createStretchGroup(int res, SequenceI sequence)
1738 // Only if left mouse button do we want to change group sizes
1739 // define a new group here
1740 SequenceGroup sg = new SequenceGroup();
1741 sg.setStartRes(res);
1743 sg.addSequence(sequence, false);
1744 av.setSelectionGroup(sg);
1747 if (av.getConservationSelected())
1749 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1753 if (av.getAbovePIDThreshold())
1755 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1758 // TODO: stretchGroup will always be not null. Is this a merge error ?
1759 // or is there a threading issue here?
1760 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1762 // Edit end res position of selected group
1763 changeEndRes = true;
1765 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1767 // Edit end res position of selected group
1768 changeStartRes = true;
1770 stretchGroup.getWidth();
1775 * Build and show a pop-up menu at the right-click mouse position
1781 void showPopupMenu(MouseEvent evt)
1783 final int column = findColumn(evt);
1784 final int seq = findSeq(evt);
1785 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1786 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1787 .findFeaturesAtColumn(sequence, column + 1);
1788 List<String> links = new ArrayList<>();
1789 for (SequenceFeature sf : allFeatures)
1791 if (sf.links != null)
1793 for (String link : sf.links)
1800 PopupMenu pop = new PopupMenu(ap, null, links);
1801 pop.show(this, evt.getX(), evt.getY());
1805 * Update the display after mouse up on a selection or group
1808 * mouse released event details
1810 * true if this event is happening after a mouse drag (rather than a
1813 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1815 if (stretchGroup == null)
1820 stretchGroup.removePropertyChangeListener(seqCanvas);
1822 // always do this - annotation has own state
1823 // but defer colourscheme update until hidden sequences are passed in
1824 boolean vischange = stretchGroup.recalcConservation(true);
1825 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1827 if (stretchGroup.cs != null)
1829 stretchGroup.cs.alignmentChanged(stretchGroup,
1830 av.getHiddenRepSequences());
1832 ResidueShaderI groupColourScheme = stretchGroup
1833 .getGroupColourScheme();
1834 String name = stretchGroup.getName();
1835 if (stretchGroup.cs.conservationApplied())
1837 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1839 if (stretchGroup.cs.getThreshold() > 0)
1841 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1844 PaintRefresher.Refresh(this, av.getSequenceSetId());
1845 // TODO: structure colours only need updating if stretchGroup used to or now
1846 // does contain sequences with structure views
1847 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1848 updateOverviewAndStructs = false;
1849 changeEndRes = false;
1850 changeStartRes = false;
1851 stretchGroup = null;
1861 public void doMouseDraggedDefineMode(MouseEvent evt)
1863 int res = findColumn(evt);
1864 int y = findSeq(evt);
1866 if (wrappedBlock != startWrapBlock)
1871 if (stretchGroup == null)
1876 if (res >= av.getAlignment().getWidth())
1878 res = av.getAlignment().getWidth() - 1;
1881 if (stretchGroup.getEndRes() == res)
1883 // Edit end res position of selected group
1884 changeEndRes = true;
1886 else if (stretchGroup.getStartRes() == res)
1888 // Edit start res position of selected group
1889 changeStartRes = true;
1892 if (res < av.getRanges().getStartRes())
1894 res = av.getRanges().getStartRes();
1899 if (res > (stretchGroup.getStartRes() - 1))
1901 stretchGroup.setEndRes(res);
1902 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1905 else if (changeStartRes)
1907 if (res < (stretchGroup.getEndRes() + 1))
1909 stretchGroup.setStartRes(res);
1910 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1914 int dragDirection = 0;
1920 else if (y < oldSeq)
1925 while ((y != oldSeq) && (oldSeq > -1)
1926 && (y < av.getAlignment().getHeight()))
1928 // This routine ensures we don't skip any sequences, as the
1929 // selection is quite slow.
1930 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1932 oldSeq += dragDirection;
1939 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1941 if (stretchGroup.getSequences(null).contains(nextSeq))
1943 stretchGroup.deleteSequence(seq, false);
1944 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1950 stretchGroup.addSequence(seq, false);
1953 stretchGroup.addSequence(nextSeq, false);
1954 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1963 mouseDragging = true;
1965 if ((scrollThread != null) && (scrollThread.isRunning()))
1967 scrollThread.setEvent(evt);
1971 void scrollCanvas(MouseEvent evt)
1975 if ((scrollThread != null) && (scrollThread.isRunning()))
1977 scrollThread.stopScrolling();
1978 scrollThread = null;
1980 mouseDragging = false;
1984 if (scrollThread == null)
1986 scrollThread = new ScrollThread();
1989 mouseDragging = true;
1990 scrollThread.setEvent(evt);
1995 // this class allows scrolling off the bottom of the visible alignment
1996 class ScrollThread extends Thread
2000 private volatile boolean threadRunning = true;
2002 public ScrollThread()
2007 public void setEvent(MouseEvent e)
2012 public void stopScrolling()
2014 threadRunning = false;
2017 public boolean isRunning()
2019 return threadRunning;
2025 while (threadRunning)
2029 if (mouseDragging && (evt.getY() < 0)
2030 && (av.getRanges().getStartSeq() > 0))
2032 av.getRanges().scrollUp(true);
2035 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2036 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2038 av.getRanges().scrollUp(false);
2041 if (mouseDragging && (evt.getX() < 0))
2043 av.getRanges().scrollRight(false);
2045 else if (mouseDragging && (evt.getX() >= getWidth()))
2047 av.getRanges().scrollRight(true);
2054 } catch (Exception ex)
2062 * modify current selection according to a received message.
2065 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2066 HiddenColumns hidden, SelectionSource source)
2068 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2069 // handles selection messages...
2070 // TODO: extend config options to allow user to control if selections may be
2071 // shared between viewports.
2072 boolean iSentTheSelection = (av == source
2073 || (source instanceof AlignViewport
2074 && ((AlignmentViewport) source).getSequenceSetId()
2075 .equals(av.getSequenceSetId())));
2077 if (iSentTheSelection)
2079 // respond to our own event by updating dependent dialogs
2080 if (ap.getCalculationDialog() != null)
2082 ap.getCalculationDialog().validateCalcTypes();
2088 // process further ?
2089 if (!av.followSelection)
2095 * Ignore the selection if there is one of our own pending.
2097 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2103 * Check for selection in a view of which this one is a dna/protein
2106 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2111 // do we want to thread this ? (contention with seqsel and colsel locks, I
2114 * only copy colsel if there is a real intersection between
2115 * sequence selection and this panel's alignment
2117 boolean repaint = false;
2118 boolean copycolsel = false;
2120 SequenceGroup sgroup = null;
2121 if (seqsel != null && seqsel.getSize() > 0)
2123 if (av.getAlignment() == null)
2125 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2126 + " ViewId=" + av.getViewId()
2127 + " 's alignment is NULL! returning immediately.");
2130 sgroup = seqsel.intersect(av.getAlignment(),
2131 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2132 if ((sgroup != null && sgroup.getSize() > 0))
2137 if (sgroup != null && sgroup.getSize() > 0)
2139 av.setSelectionGroup(sgroup);
2143 av.setSelectionGroup(null);
2145 av.isSelectionGroupChanged(true);
2150 // the current selection is unset or from a previous message
2151 // so import the new colsel.
2152 if (colsel == null || colsel.isEmpty())
2154 if (av.getColumnSelection() != null)
2156 av.getColumnSelection().clear();
2162 // TODO: shift colSel according to the intersecting sequences
2163 if (av.getColumnSelection() == null)
2165 av.setColumnSelection(new ColumnSelection(colsel));
2169 av.getColumnSelection().setElementsFrom(colsel,
2170 av.getAlignment().getHiddenColumns());
2173 av.isColSelChanged(true);
2177 if (copycolsel && av.hasHiddenColumns()
2178 && (av.getAlignment().getHiddenColumns() == null))
2180 System.err.println("Bad things");
2182 if (repaint) // always true!
2184 // probably finessing with multiple redraws here
2185 PaintRefresher.Refresh(this, av.getSequenceSetId());
2186 // ap.paintAlignment(false);
2189 // lastly, update dependent dialogs
2190 if (ap.getCalculationDialog() != null)
2192 ap.getCalculationDialog().validateCalcTypes();
2198 * If this panel is a cdna/protein translation view of the selection source,
2199 * tries to map the source selection to a local one, and returns true. Else
2206 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2207 ColumnSelection colsel, HiddenColumns hidden,
2208 SelectionSource source)
2210 if (!(source instanceof AlignViewportI))
2214 final AlignViewportI sourceAv = (AlignViewportI) source;
2215 if (sourceAv.getCodingComplement() != av
2216 && av.getCodingComplement() != sourceAv)
2222 * Map sequence selection
2224 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2225 av.setSelectionGroup(sg);
2226 av.isSelectionGroupChanged(true);
2229 * Map column selection
2231 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2233 ColumnSelection cs = new ColumnSelection();
2234 HiddenColumns hs = new HiddenColumns();
2235 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2236 av.setColumnSelection(cs);
2237 av.getAlignment().setHiddenColumns(hs);
2239 // lastly, update any dependent dialogs
2240 if (ap.getCalculationDialog() != null)
2242 ap.getCalculationDialog().validateCalcTypes();
2245 PaintRefresher.Refresh(this, av.getSequenceSetId());