2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.api.AlignViewportI;
24 import jalview.bin.Cache;
25 import jalview.commands.EditCommand;
26 import jalview.commands.EditCommand.Action;
27 import jalview.commands.EditCommand.Edit;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.HiddenColumns;
31 import jalview.datamodel.SearchResultMatchI;
32 import jalview.datamodel.SearchResults;
33 import jalview.datamodel.SearchResultsI;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.io.SequenceAnnotationReport;
39 import jalview.renderer.ResidueShaderI;
40 import jalview.schemes.ResidueProperties;
41 import jalview.structure.SelectionListener;
42 import jalview.structure.SelectionSource;
43 import jalview.structure.SequenceListener;
44 import jalview.structure.StructureSelectionManager;
45 import jalview.structure.VamsasSource;
46 import jalview.util.Comparison;
47 import jalview.util.MappingUtils;
48 import jalview.util.MessageManager;
49 import jalview.util.Platform;
50 import jalview.viewmodel.AlignmentViewport;
52 import java.awt.BorderLayout;
53 import java.awt.Color;
55 import java.awt.FontMetrics;
56 import java.awt.Point;
57 import java.awt.event.MouseEvent;
58 import java.awt.event.MouseListener;
59 import java.awt.event.MouseMotionListener;
60 import java.awt.event.MouseWheelEvent;
61 import java.awt.event.MouseWheelListener;
62 import java.util.ArrayList;
63 import java.util.Collections;
64 import java.util.List;
66 import javax.swing.JPanel;
67 import javax.swing.SwingUtilities;
68 import javax.swing.ToolTipManager;
74 * @version $Revision: 1.130 $
76 public class SeqPanel extends JPanel
77 implements MouseListener, MouseMotionListener, MouseWheelListener,
78 SequenceListener, SelectionListener
82 public SeqCanvas seqCanvas;
85 public AlignmentPanel ap;
88 * last column position for mouseMoved event
90 private int lastMouseColumn;
93 * last sequence offset for mouseMoved event
95 private int lastMouseSeq;
97 protected int lastres;
99 protected int startseq;
101 protected AlignViewport av;
103 ScrollThread scrollThread = null;
105 boolean mouseDragging = false;
107 boolean editingSeqs = false;
109 boolean groupEditing = false;
111 // ////////////////////////////////////////
112 // ///Everything below this is for defining the boundary of the rubberband
113 // ////////////////////////////////////////
116 boolean changeEndSeq = false;
118 boolean changeStartSeq = false;
120 boolean changeEndRes = false;
122 boolean changeStartRes = false;
124 SequenceGroup stretchGroup = null;
126 boolean remove = false;
128 Point lastMousePress;
130 boolean mouseWheelPressed = false;
132 StringBuffer keyboardNo1;
134 StringBuffer keyboardNo2;
136 java.net.URL linkImageURL;
138 private final SequenceAnnotationReport seqARep;
140 StringBuilder tooltipText = new StringBuilder();
144 EditCommand editCommand;
146 StructureSelectionManager ssm;
148 SearchResultsI lastSearchResults;
151 * Creates a new SeqPanel object.
158 public SeqPanel(AlignViewport av, AlignmentPanel ap)
160 linkImageURL = getClass().getResource("/images/link.gif");
161 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
162 ToolTipManager.sharedInstance().registerComponent(this);
163 ToolTipManager.sharedInstance().setInitialDelay(0);
164 ToolTipManager.sharedInstance().setDismissDelay(10000);
166 setBackground(Color.white);
168 seqCanvas = new SeqCanvas(ap);
169 setLayout(new BorderLayout());
170 add(seqCanvas, BorderLayout.CENTER);
176 addMouseMotionListener(this);
177 addMouseListener(this);
178 addMouseWheelListener(this);
179 ssm = av.getStructureSelectionManager();
180 ssm.addStructureViewerListener(this);
181 ssm.addSelectionListener(this);
184 lastMouseColumn = -1;
188 int startWrapBlock = -1;
190 int wrappedBlock = -1;
193 * Returns the aligned sequence position (base 0) at the mouse position, or
194 * the closest visible one
199 int findColumn(MouseEvent evt)
204 int startRes = av.getRanges().getStartRes();
205 if (av.getWrapAlignment())
208 int hgap = av.getCharHeight();
209 if (av.getScaleAboveWrapped())
211 hgap += av.getCharHeight();
214 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
215 + hgap + seqCanvas.getAnnotationHeight();
218 y = Math.max(0, y - hgap);
219 x = Math.max(0, x - seqCanvas.getLabelWidthWest());
221 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
227 wrappedBlock = y / cHeight;
228 wrappedBlock += startRes / cwidth;
229 // allow for wrapped view scrolled right (possible from Overview)
230 int startOffset = startRes % cwidth;
231 res = wrappedBlock * cwidth + startOffset
232 + +Math.min(cwidth - 1, x / av.getCharWidth());
236 if (x > seqCanvas.getX() + seqCanvas.getWidth())
238 // make sure we calculate relative to visible alignment, rather than
240 x = seqCanvas.getX() + seqCanvas.getWidth();
242 res = (x / av.getCharWidth()) + startRes;
243 if (res > av.getRanges().getEndRes())
246 res = av.getRanges().getEndRes();
250 if (av.hasHiddenColumns())
252 res = av.getAlignment().getHiddenColumns()
253 .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;
323 scrollToVisible(true);
326 void setCursorColumn()
328 seqCanvas.cursorX = getKeyboardNo1() - 1;
329 scrollToVisible(true);
332 void setCursorRowAndColumn()
334 if (keyboardNo2 == null)
336 keyboardNo2 = new StringBuffer();
340 seqCanvas.cursorX = getKeyboardNo1() - 1;
341 seqCanvas.cursorY = getKeyboardNo2() - 1;
342 scrollToVisible(true);
346 void setCursorPosition()
348 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
350 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
351 scrollToVisible(true);
354 void moveCursor(int dx, int dy)
356 seqCanvas.cursorX += dx;
357 seqCanvas.cursorY += dy;
359 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
361 if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
363 int original = seqCanvas.cursorX - dx;
364 int maxWidth = av.getAlignment().getWidth();
366 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;
379 scrollToVisible(false);
383 * Scroll to make the cursor visible in the viewport.
386 * just jump to the location rather than scrolling
388 void scrollToVisible(boolean jump)
390 if (seqCanvas.cursorX < 0)
392 seqCanvas.cursorX = 0;
394 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
396 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
399 if (seqCanvas.cursorY < 0)
401 seqCanvas.cursorY = 0;
403 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
405 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
410 boolean repaintNeeded = true;
413 // only need to repaint if the viewport did not move, as otherwise it will
415 repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
420 if (av.getWrapAlignment())
422 av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
426 av.getRanges().scrollToVisible(seqCanvas.cursorX,
431 if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
433 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
434 seqCanvas.cursorX, seqCanvas.cursorY);
444 void setSelectionAreaAtCursor(boolean topLeft)
446 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
448 if (av.getSelectionGroup() != null)
450 SequenceGroup sg = av.getSelectionGroup();
451 // Find the top and bottom of this group
452 int min = av.getAlignment().getHeight(), max = 0;
453 for (int i = 0; i < sg.getSize(); i++)
455 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
470 sg.setStartRes(seqCanvas.cursorX);
471 if (sg.getEndRes() < seqCanvas.cursorX)
473 sg.setEndRes(seqCanvas.cursorX);
476 min = seqCanvas.cursorY;
480 sg.setEndRes(seqCanvas.cursorX);
481 if (sg.getStartRes() > seqCanvas.cursorX)
483 sg.setStartRes(seqCanvas.cursorX);
486 max = seqCanvas.cursorY + 1;
491 // Only the user can do this
492 av.setSelectionGroup(null);
496 // Now add any sequences between min and max
497 sg.getSequences(null).clear();
498 for (int i = min; i < max; i++)
500 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
505 if (av.getSelectionGroup() == null)
507 SequenceGroup sg = new SequenceGroup();
508 sg.setStartRes(seqCanvas.cursorX);
509 sg.setEndRes(seqCanvas.cursorX);
510 sg.addSequence(sequence, false);
511 av.setSelectionGroup(sg);
514 ap.paintAlignment(false, false);
518 void insertGapAtCursor(boolean group)
520 groupEditing = group;
521 startseq = seqCanvas.cursorY;
522 lastres = seqCanvas.cursorX;
523 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
527 void deleteGapAtCursor(boolean group)
529 groupEditing = group;
530 startseq = seqCanvas.cursorY;
531 lastres = seqCanvas.cursorX + getKeyboardNo1();
532 editSequence(false, false, seqCanvas.cursorX);
536 void insertNucAtCursor(boolean group, String nuc)
538 // TODO not called - delete?
539 groupEditing = group;
540 startseq = seqCanvas.cursorY;
541 lastres = seqCanvas.cursorX;
542 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
546 void numberPressed(char value)
548 if (keyboardNo1 == null)
550 keyboardNo1 = new StringBuffer();
553 if (keyboardNo2 != null)
555 keyboardNo2.append(value);
559 keyboardNo1.append(value);
567 if (keyboardNo1 != null)
569 int value = Integer.parseInt(keyboardNo1.toString());
573 } catch (Exception x)
584 if (keyboardNo2 != null)
586 int value = Integer.parseInt(keyboardNo2.toString());
590 } catch (Exception x)
604 public void mouseReleased(MouseEvent evt)
606 boolean didDrag = mouseDragging; // did we come here after a drag
607 mouseDragging = false;
608 mouseWheelPressed = false;
610 if (evt.isPopupTrigger()) // Windows: mouseReleased
619 doMouseReleasedDefineMode(evt, didDrag);
633 public void mousePressed(MouseEvent evt)
635 lastMousePress = evt.getPoint();
637 if (SwingUtilities.isMiddleMouseButton(evt))
639 mouseWheelPressed = true;
643 boolean isControlDown = Platform.isControlDown(evt);
644 if (evt.isShiftDown() || isControlDown)
654 doMousePressedDefineMode(evt);
658 int seq = findSeq(evt);
659 int res = findColumn(evt);
661 if (seq < 0 || res < 0)
666 if ((seq < av.getAlignment().getHeight())
667 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
684 public void mouseOverSequence(SequenceI sequence, int index, int pos)
686 String tmp = sequence.hashCode() + " " + index + " " + pos;
688 if (lastMessage == null || !lastMessage.equals(tmp))
690 // System.err.println("mouseOver Sequence: "+tmp);
691 ssm.mouseOverSequence(sequence, index, pos, av);
697 * Highlight the mapped region described by the search results object (unless
698 * unchanged). This supports highlight of protein while mousing over linked
699 * cDNA and vice versa. The status bar is also updated to show the location of
700 * the start of the highlighted region.
703 public void highlightSequence(SearchResultsI results)
705 if (results == null || results.equals(lastSearchResults))
709 lastSearchResults = results;
711 boolean wasScrolled = false;
713 if (av.isFollowHighlight())
715 // don't allow highlight of protein/cDNA to also scroll a complementary
716 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
717 // over residue to change abruptly, causing highlighted residue in panel 2
718 // to change, causing a scroll in panel 1 etc)
719 ap.setToScrollComplementPanel(false);
720 wasScrolled = ap.scrollToPosition(results, false);
723 seqCanvas.revalidate();
725 ap.setToScrollComplementPanel(true);
728 boolean noFastPaint = wasScrolled && av.getWrapAlignment();
729 if (seqCanvas.highlightSearchResults(results, noFastPaint))
731 setStatusMessage(results);
736 public VamsasSource getVamsasSource()
738 return this.ap == null ? null : this.ap.av;
742 public void updateColours(SequenceI seq, int index)
744 System.out.println("update the seqPanel colours");
749 * Action on mouse movement is to update the status bar to show the current
750 * sequence position, and (if features are shown) to show any features at the
751 * position in a tooltip. Does nothing if the mouse move does not change
757 public void mouseMoved(MouseEvent evt)
761 // This is because MacOSX creates a mouseMoved
762 // If control is down, other platforms will not.
766 final int column = findColumn(evt);
767 final int seq = findSeq(evt);
769 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
774 if (column == lastMouseColumn && seq == lastMouseSeq)
777 * just a pixel move without change of residue
781 lastMouseColumn = column;
784 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
786 if (column >= sequence.getLength())
792 * set status bar message, returning residue position in sequence
794 boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
795 final int pos = setStatusMessage(sequence, column, seq);
796 if (ssm != null && !isGapped)
798 mouseOverSequence(sequence, column, pos);
801 tooltipText.setLength(6); // Cuts the buffer back to <html>
803 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
806 for (int g = 0; g < groups.length; g++)
808 if (groups[g].getStartRes() <= column
809 && groups[g].getEndRes() >= column)
811 if (!groups[g].getName().startsWith("JTreeGroup")
812 && !groups[g].getName().startsWith("JGroup"))
814 tooltipText.append(groups[g].getName());
817 if (groups[g].getDescription() != null)
819 tooltipText.append(": " + groups[g].getDescription());
826 * add any features at the position to the tooltip; if over a gap, only
827 * add features that straddle the gap (pos may be the residue before or
830 if (av.isShowSequenceFeatures())
832 List<SequenceFeature> features = ap.getFeatureRenderer()
833 .findFeaturesAtColumn(sequence, column + 1);
834 seqARep.appendFeatures(tooltipText, pos, features,
835 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
837 if (tooltipText.length() == 6) // <html>
839 setToolTipText(null);
844 String textString = tooltipText.toString();
845 if (lastTooltip == null || !lastTooltip.equals(textString))
847 String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
849 setToolTipText(formattedTooltipText);
850 lastTooltip = textString;
855 private Point lastp = null;
860 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
863 public Point getToolTipLocation(MouseEvent event)
865 int x = event.getX(), w = getWidth();
866 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
869 if (!event.isShiftDown() || p == null)
871 p = (tooltipText != null && tooltipText.length() > 6)
872 ? new Point(event.getX() + wdth, event.getY() - 20)
876 * TODO: try to modify position region is not obcured by tooltip
884 * set when the current UI interaction has resulted in a change that requires
885 * shading in overviews and structures to be recalculated. this could be
886 * changed to a something more expressive that indicates what actually has
887 * changed, so selective redraws can be applied (ie. only structures, only
890 private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
893 * set if av.getSelectionGroup() refers to a group that is defined on the
894 * alignment view, rather than a transient selection
896 // private boolean editingDefinedGroup = false; // TODO: refactor to
897 // avcontroller or viewModel
900 * Sets the status message in alignment panel, showing the sequence number
901 * (index) and id, and residue and residue position if not at a gap, for the
902 * given sequence and column position. Returns the residue position returned
903 * by Sequence.findPosition. Note this may be for the nearest adjacent residue
904 * if at a gapped position.
907 * aligned sequence object
911 * index of sequence in alignment
912 * @return sequence position of residue at column, or adjacent residue if at a
915 int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
917 char sequenceChar = sequence.getCharAt(column);
918 int pos = sequence.findPosition(column);
919 setStatusMessage(sequence, seqIndex, sequenceChar, pos);
925 * Builds the status message for the current cursor location and writes it to
926 * the status bar, for example
929 * Sequence 3 ID: FER1_SOLLC
930 * Sequence 5 ID: FER1_PEA Residue: THR (4)
931 * Sequence 5 ID: FER1_PEA Residue: B (3)
932 * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
937 * sequence position in the alignment (1..)
938 * @param sequenceChar
939 * the character under the cursor
941 * the sequence residue position (if not over a gap)
943 protected void setStatusMessage(SequenceI sequence, int seqIndex,
944 char sequenceChar, int residuePos)
946 StringBuilder text = new StringBuilder(32);
949 * Sequence number (if known), and sequence name.
951 String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
952 text.append("Sequence").append(seqno).append(" ID: ")
953 .append(sequence.getName());
955 String residue = null;
958 * Try to translate the display character to residue name (null for gap).
960 boolean isGapped = Comparison.isGap(sequenceChar);
964 boolean nucleotide = av.getAlignment().isNucleotide();
965 String displayChar = String.valueOf(sequenceChar);
968 residue = ResidueProperties.nucleotideName.get(displayChar);
972 residue = "X".equalsIgnoreCase(displayChar) ? "X"
973 : ("*".equals(displayChar) ? "STOP"
974 : ResidueProperties.aa2Triplet.get(displayChar));
976 text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
977 .append(": ").append(residue == null ? displayChar : residue);
979 text.append(" (").append(Integer.toString(residuePos)).append(")");
981 ap.alignFrame.statusBar.setText(text.toString());
985 * Set the status bar message to highlight the first matched position in
990 private void setStatusMessage(SearchResultsI results)
992 AlignmentI al = this.av.getAlignment();
993 int sequenceIndex = al.findIndex(results);
994 if (sequenceIndex == -1)
998 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
999 for (SearchResultMatchI m : results.getResults())
1001 SequenceI seq = m.getSequence();
1002 if (seq.getDatasetSequence() != null)
1004 seq = seq.getDatasetSequence();
1009 int start = m.getStart();
1010 setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
1021 public void mouseDragged(MouseEvent evt)
1023 if (mouseWheelPressed)
1025 boolean inSplitFrame = ap.av.getCodingComplement() != null;
1026 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
1028 int oldWidth = av.getCharWidth();
1030 // Which is bigger, left-right or up-down?
1031 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
1032 .abs(evt.getX() - lastMousePress.getX()))
1035 * on drag up or down, decrement or increment font size
1037 int fontSize = av.font.getSize();
1038 boolean fontChanged = false;
1040 if (evt.getY() < lastMousePress.getY())
1045 else if (evt.getY() > lastMousePress.getY())
1058 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
1060 av.setFont(newFont, true);
1061 av.setCharWidth(oldWidth);
1065 ap.av.getCodingComplement().setFont(newFont, true);
1066 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1067 .getSplitViewContainer();
1068 splitFrame.adjustLayout();
1069 splitFrame.repaint();
1076 * on drag left or right, decrement or increment character width
1079 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
1081 newWidth = av.getCharWidth() - 1;
1082 av.setCharWidth(newWidth);
1084 else if (evt.getX() > lastMousePress.getX())
1086 newWidth = av.getCharWidth() + 1;
1087 av.setCharWidth(newWidth);
1091 ap.paintAlignment(false, false);
1095 * need to ensure newWidth is set on cdna, regardless of which
1096 * panel the mouse drag happened in; protein will compute its
1097 * character width as 1:1 or 3:1
1099 av.getCodingComplement().setCharWidth(newWidth);
1100 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1101 .getSplitViewContainer();
1102 splitFrame.adjustLayout();
1103 splitFrame.repaint();
1108 FontMetrics fm = getFontMetrics(av.getFont());
1109 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1111 lastMousePress = evt.getPoint();
1118 doMouseDraggedDefineMode(evt);
1122 int res = findColumn(evt);
1129 if ((lastres == -1) || (lastres == res))
1134 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1136 // dragLeft, delete gap
1137 editSequence(false, false, res);
1141 editSequence(true, false, res);
1144 mouseDragging = true;
1145 if ((scrollThread != null) && (scrollThread.isRunning()))
1147 scrollThread.setEvent(evt);
1151 // TODO: Make it more clever than many booleans
1152 synchronized void editSequence(boolean insertGap, boolean editSeq,
1156 int fixedRight = -1;
1157 boolean fixedColumns = false;
1158 SequenceGroup sg = av.getSelectionGroup();
1160 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1162 // No group, but the sequence may represent a group
1163 if (!groupEditing && av.hasHiddenRows())
1165 if (av.isHiddenRepSequence(seq))
1167 sg = av.getRepresentedSequences(seq);
1168 groupEditing = true;
1172 StringBuilder message = new StringBuilder(64);
1175 message.append("Edit group:");
1176 if (editCommand == null)
1178 editCommand = new EditCommand(
1179 MessageManager.getString("action.edit_group"));
1184 message.append("Edit sequence: " + seq.getName());
1185 String label = seq.getName();
1186 if (label.length() > 10)
1188 label = label.substring(0, 10);
1190 if (editCommand == null)
1192 editCommand = new EditCommand(MessageManager
1193 .formatMessage("label.edit_params", new String[]
1200 message.append(" insert ");
1204 message.append(" delete ");
1207 message.append(Math.abs(startres - lastres) + " gaps.");
1208 ap.alignFrame.statusBar.setText(message.toString());
1210 // Are we editing within a selection group?
1211 if (groupEditing || (sg != null
1212 && sg.getSequences(av.getHiddenRepSequences()).contains(seq)))
1214 fixedColumns = true;
1216 // sg might be null as the user may only see 1 sequence,
1217 // but the sequence represents a group
1220 if (!av.isHiddenRepSequence(seq))
1225 sg = av.getRepresentedSequences(seq);
1228 fixedLeft = sg.getStartRes();
1229 fixedRight = sg.getEndRes();
1231 if ((startres < fixedLeft && lastres >= fixedLeft)
1232 || (startres >= fixedLeft && lastres < fixedLeft)
1233 || (startres > fixedRight && lastres <= fixedRight)
1234 || (startres <= fixedRight && lastres > fixedRight))
1240 if (fixedLeft > startres)
1242 fixedRight = fixedLeft - 1;
1245 else if (fixedRight < startres)
1247 fixedLeft = fixedRight;
1252 if (av.hasHiddenColumns())
1254 fixedColumns = true;
1255 int y1 = av.getAlignment().getHiddenColumns()
1256 .getHiddenBoundaryLeft(startres);
1257 int y2 = av.getAlignment().getHiddenColumns()
1258 .getHiddenBoundaryRight(startres);
1260 if ((insertGap && startres > y1 && lastres < y1)
1261 || (!insertGap && startres < y2 && lastres > y2))
1267 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1268 // Selection spans a hidden region
1269 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1277 fixedRight = y2 - 1;
1284 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1285 int g, groupSize = vseqs.size();
1286 SequenceI[] groupSeqs = new SequenceI[groupSize];
1287 for (g = 0; g < groupSeqs.length; g++)
1289 groupSeqs[g] = vseqs.get(g);
1295 // If the user has selected the whole sequence, and is dragging to
1296 // the right, we can still extend the alignment and selectionGroup
1297 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1298 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1300 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1301 fixedRight = sg.getEndRes();
1304 // Is it valid with fixed columns??
1305 // Find the next gap before the end
1306 // of the visible region boundary
1307 boolean blank = false;
1308 for (; fixedRight > lastres; fixedRight--)
1312 for (g = 0; g < groupSize; g++)
1314 for (int j = 0; j < startres - lastres; j++)
1316 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1331 if (sg.getSize() == av.getAlignment().getHeight())
1333 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1334 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1340 int alWidth = av.getAlignment().getWidth();
1341 if (av.hasHiddenRows())
1343 int hwidth = av.getAlignment().getHiddenSequences()
1345 if (hwidth > alWidth)
1350 // We can still insert gaps if the selectionGroup
1351 // contains all the sequences
1352 sg.setEndRes(sg.getEndRes() + startres - lastres);
1353 fixedRight = alWidth + startres - lastres;
1364 else if (!insertGap)
1366 // / Are we able to delete?
1367 // ie are all columns blank?
1369 for (g = 0; g < groupSize; g++)
1371 for (int j = startres; j < lastres; j++)
1373 if (groupSeqs[g].getLength() <= j)
1378 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1380 // Not a gap, block edit not valid
1390 // dragging to the right
1391 if (fixedColumns && fixedRight != -1)
1393 for (int j = lastres; j < startres; j++)
1395 insertChar(j, groupSeqs, fixedRight);
1400 appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1401 startres - lastres);
1406 // dragging to the left
1407 if (fixedColumns && fixedRight != -1)
1409 for (int j = lastres; j > startres; j--)
1411 deleteChar(startres, groupSeqs, fixedRight);
1416 appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1417 lastres - startres);
1423 // ///Editing a single sequence///////////
1427 // dragging to the right
1428 if (fixedColumns && fixedRight != -1)
1430 for (int j = lastres; j < startres; j++)
1432 insertChar(j, new SequenceI[] { seq }, fixedRight);
1437 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1438 startres - lastres);
1445 // dragging to the left
1446 if (fixedColumns && fixedRight != -1)
1448 for (int j = lastres; j > startres; j--)
1450 if (!Comparison.isGap(seq.getCharAt(startres)))
1455 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1460 // could be a keyboard edit trying to delete none gaps
1462 for (int m = startres; m < lastres; m++)
1464 if (!Comparison.isGap(seq.getCharAt(m)))
1473 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1479 {// insertGap==false AND editSeq==TRUE;
1480 if (fixedColumns && fixedRight != -1)
1482 for (int j = lastres; j < startres; j++)
1484 insertChar(j, new SequenceI[] { seq }, fixedRight);
1489 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1490 startres - lastres);
1497 seqCanvas.repaint();
1500 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1502 int blankColumn = fixedColumn;
1503 for (int s = 0; s < seq.length; s++)
1505 // Find the next gap before the end of the visible region boundary
1506 // If lastCol > j, theres a boundary after the gap insertion
1508 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1510 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1512 // Theres a space, so break and insert the gap
1517 if (blankColumn <= j)
1519 blankColumn = fixedColumn;
1525 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1527 appendEdit(Action.INSERT_GAP, seq, j, 1);
1532 * Helper method to add and perform one edit action.
1539 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1543 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1544 av.getAlignment().getGapCharacter());
1546 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1549 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1552 appendEdit(Action.DELETE_GAP, seq, j, 1);
1554 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1564 public void mouseEntered(MouseEvent e)
1571 if ((scrollThread != null) && (scrollThread.isRunning()))
1573 scrollThread.stopScrolling();
1574 scrollThread = null;
1585 public void mouseExited(MouseEvent e)
1587 if (av.getWrapAlignment())
1592 if (mouseDragging && scrollThread == null)
1594 scrollThread = new ScrollThread();
1599 * Handler for double-click on a position with one or more sequence features.
1600 * Opens the Amend Features dialog to allow feature details to be amended, or
1601 * the feature deleted.
1604 public void mouseClicked(MouseEvent evt)
1606 SequenceGroup sg = null;
1607 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1608 if (evt.getClickCount() > 1)
1610 sg = av.getSelectionGroup();
1611 if (sg != null && sg.getSize() == 1
1612 && sg.getEndRes() - sg.getStartRes() < 2)
1614 av.setSelectionGroup(null);
1617 int column = findColumn(evt);
1620 * find features at the position (if not gapped), or straddling
1621 * the position (if at a gap)
1623 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1624 .findFeaturesAtColumn(sequence, column + 1);
1626 if (!features.isEmpty())
1629 * highlight the first feature at the position on the alignment
1631 SearchResultsI highlight = new SearchResults();
1632 highlight.addResult(sequence, features.get(0).getBegin(), features
1634 seqCanvas.highlightSearchResults(highlight, false);
1637 * open the Amend Features dialog; clear highlighting afterwards,
1638 * whether changes were made or not
1640 List<SequenceI> seqs = Collections.singletonList(sequence);
1641 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1643 av.setSearchResults(null); // clear highlighting
1644 seqCanvas.repaint(); // draw new/amended features
1650 public void mouseWheelMoved(MouseWheelEvent e)
1653 if (e.getWheelRotation() > 0)
1655 if (e.isShiftDown())
1657 av.getRanges().scrollRight(true);
1662 av.getRanges().scrollUp(false);
1667 if (e.isShiftDown())
1669 av.getRanges().scrollRight(false);
1673 av.getRanges().scrollUp(true);
1678 * update status bar and tooltip for new position
1679 * (need to synthesize a mouse movement to refresh tooltip)
1682 ToolTipManager.sharedInstance().mouseMoved(e);
1691 public void doMousePressedDefineMode(MouseEvent evt)
1693 final int res = findColumn(evt);
1694 final int seq = findSeq(evt);
1696 updateOverviewAndStructs = false;
1698 startWrapBlock = wrappedBlock;
1700 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1702 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1703 MessageManager.getString(
1704 "label.cannot_edit_annotations_in_wrapped_view"),
1705 MessageManager.getString("label.wrapped_view_no_edit"),
1706 JvOptionPane.WARNING_MESSAGE);
1710 if (seq < 0 || res < 0)
1715 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1717 if ((sequence == null) || (res > sequence.getLength()))
1722 stretchGroup = av.getSelectionGroup();
1724 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1726 stretchGroup = av.getAlignment().findGroup(sequence, res);
1727 if (stretchGroup != null)
1729 // only update the current selection if the popup menu has a group to
1731 av.setSelectionGroup(stretchGroup);
1735 if (evt.isPopupTrigger()) // Mac: mousePressed
1742 * defer right-mouse click handling to mouseReleased on Windows
1743 * (where isPopupTrigger() will answer true)
1744 * NB isRightMouseButton is also true for Cmd-click on Mac
1746 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1753 seqCanvas.cursorX = findColumn(evt);
1754 seqCanvas.cursorY = findSeq(evt);
1755 seqCanvas.repaint();
1759 if (stretchGroup == null)
1761 createStretchGroup(res, sequence);
1764 if (stretchGroup != null)
1766 stretchGroup.addPropertyChangeListener(seqCanvas);
1769 seqCanvas.repaint();
1772 private void createStretchGroup(int res, SequenceI sequence)
1774 // Only if left mouse button do we want to change group sizes
1775 // define a new group here
1776 SequenceGroup sg = new SequenceGroup();
1777 sg.setStartRes(res);
1779 sg.addSequence(sequence, false);
1780 av.setSelectionGroup(sg);
1783 if (av.getConservationSelected())
1785 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1789 if (av.getAbovePIDThreshold())
1791 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1794 // TODO: stretchGroup will always be not null. Is this a merge error ?
1795 // or is there a threading issue here?
1796 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1798 // Edit end res position of selected group
1799 changeEndRes = true;
1801 else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
1803 // Edit end res position of selected group
1804 changeStartRes = true;
1806 stretchGroup.getWidth();
1811 * Build and show a pop-up menu at the right-click mouse position
1817 void showPopupMenu(MouseEvent evt)
1819 final int column = findColumn(evt);
1820 final int seq = findSeq(evt);
1821 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1822 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1823 .findFeaturesAtColumn(sequence, column + 1);
1824 List<String> links = new ArrayList<>();
1825 for (SequenceFeature sf : allFeatures)
1827 if (sf.links != null)
1829 for (String link : sf.links)
1836 PopupMenu pop = new PopupMenu(ap, null, links);
1837 pop.show(this, evt.getX(), evt.getY());
1841 * Update the display after mouse up on a selection or group
1844 * mouse released event details
1846 * true if this event is happening after a mouse drag (rather than a
1849 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1851 if (stretchGroup == null)
1856 stretchGroup.removePropertyChangeListener(seqCanvas);
1858 // always do this - annotation has own state
1859 // but defer colourscheme update until hidden sequences are passed in
1860 boolean vischange = stretchGroup.recalcConservation(true);
1861 updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
1863 if (stretchGroup.cs != null)
1865 stretchGroup.cs.alignmentChanged(stretchGroup,
1866 av.getHiddenRepSequences());
1868 ResidueShaderI groupColourScheme = stretchGroup
1869 .getGroupColourScheme();
1870 String name = stretchGroup.getName();
1871 if (stretchGroup.cs.conservationApplied())
1873 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1875 if (stretchGroup.cs.getThreshold() > 0)
1877 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1880 PaintRefresher.Refresh(this, av.getSequenceSetId());
1881 // TODO: structure colours only need updating if stretchGroup used to or now
1882 // does contain sequences with structure views
1883 ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
1884 updateOverviewAndStructs = false;
1885 changeEndRes = false;
1886 changeStartRes = false;
1887 stretchGroup = null;
1897 public void doMouseDraggedDefineMode(MouseEvent evt)
1899 int res = findColumn(evt);
1900 int y = findSeq(evt);
1902 if (wrappedBlock != startWrapBlock)
1907 if (stretchGroup == null)
1912 if (res >= av.getAlignment().getWidth())
1914 res = av.getAlignment().getWidth() - 1;
1917 if (stretchGroup.getEndRes() == res)
1919 // Edit end res position of selected group
1920 changeEndRes = true;
1922 else if (stretchGroup.getStartRes() == res)
1924 // Edit start res position of selected group
1925 changeStartRes = true;
1928 if (res < av.getRanges().getStartRes())
1930 res = av.getRanges().getStartRes();
1935 if (res > (stretchGroup.getStartRes() - 1))
1937 stretchGroup.setEndRes(res);
1938 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1941 else if (changeStartRes)
1943 if (res < (stretchGroup.getEndRes() + 1))
1945 stretchGroup.setStartRes(res);
1946 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1950 int dragDirection = 0;
1956 else if (y < oldSeq)
1961 while ((y != oldSeq) && (oldSeq > -1)
1962 && (y < av.getAlignment().getHeight()))
1964 // This routine ensures we don't skip any sequences, as the
1965 // selection is quite slow.
1966 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1968 oldSeq += dragDirection;
1975 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1977 if (stretchGroup.getSequences(null).contains(nextSeq))
1979 stretchGroup.deleteSequence(seq, false);
1980 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1986 stretchGroup.addSequence(seq, false);
1989 stretchGroup.addSequence(nextSeq, false);
1990 updateOverviewAndStructs |= av.isSelectionDefinedGroup();
1999 mouseDragging = true;
2001 if ((scrollThread != null) && (scrollThread.isRunning()))
2003 scrollThread.setEvent(evt);
2007 void scrollCanvas(MouseEvent evt)
2011 if ((scrollThread != null) && (scrollThread.isRunning()))
2013 scrollThread.stopScrolling();
2014 scrollThread = null;
2016 mouseDragging = false;
2020 if (scrollThread == null)
2022 scrollThread = new ScrollThread();
2025 mouseDragging = true;
2026 scrollThread.setEvent(evt);
2031 // this class allows scrolling off the bottom of the visible alignment
2032 class ScrollThread extends Thread
2036 private volatile boolean threadRunning = true;
2038 public ScrollThread()
2043 public void setEvent(MouseEvent e)
2048 public void stopScrolling()
2050 threadRunning = false;
2053 public boolean isRunning()
2055 return threadRunning;
2061 while (threadRunning)
2065 if (mouseDragging && (evt.getY() < 0)
2066 && (av.getRanges().getStartSeq() > 0))
2068 av.getRanges().scrollUp(true);
2071 if (mouseDragging && (evt.getY() >= getHeight()) && (av
2072 .getAlignment().getHeight() > av.getRanges().getEndSeq()))
2074 av.getRanges().scrollUp(false);
2077 if (mouseDragging && (evt.getX() < 0))
2079 av.getRanges().scrollRight(false);
2081 else if (mouseDragging && (evt.getX() >= getWidth()))
2083 av.getRanges().scrollRight(true);
2090 } catch (Exception ex)
2098 * modify current selection according to a received message.
2101 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
2102 HiddenColumns hidden, SelectionSource source)
2104 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
2105 // handles selection messages...
2106 // TODO: extend config options to allow user to control if selections may be
2107 // shared between viewports.
2108 boolean iSentTheSelection = (av == source
2109 || (source instanceof AlignViewport
2110 && ((AlignmentViewport) source).getSequenceSetId()
2111 .equals(av.getSequenceSetId())));
2113 if (iSentTheSelection)
2115 // respond to our own event by updating dependent dialogs
2116 if (ap.getCalculationDialog() != null)
2118 ap.getCalculationDialog().validateCalcTypes();
2124 // process further ?
2125 if (!av.followSelection)
2131 * Ignore the selection if there is one of our own pending.
2133 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2139 * Check for selection in a view of which this one is a dna/protein
2142 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2147 // do we want to thread this ? (contention with seqsel and colsel locks, I
2150 * only copy colsel if there is a real intersection between
2151 * sequence selection and this panel's alignment
2153 boolean repaint = false;
2154 boolean copycolsel = false;
2156 SequenceGroup sgroup = null;
2157 if (seqsel != null && seqsel.getSize() > 0)
2159 if (av.getAlignment() == null)
2161 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2162 + " ViewId=" + av.getViewId()
2163 + " 's alignment is NULL! returning immediately.");
2166 sgroup = seqsel.intersect(av.getAlignment(),
2167 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2168 if ((sgroup != null && sgroup.getSize() > 0))
2173 if (sgroup != null && sgroup.getSize() > 0)
2175 av.setSelectionGroup(sgroup);
2179 av.setSelectionGroup(null);
2181 av.isSelectionGroupChanged(true);
2186 // the current selection is unset or from a previous message
2187 // so import the new colsel.
2188 if (colsel == null || colsel.isEmpty())
2190 if (av.getColumnSelection() != null)
2192 av.getColumnSelection().clear();
2198 // TODO: shift colSel according to the intersecting sequences
2199 if (av.getColumnSelection() == null)
2201 av.setColumnSelection(new ColumnSelection(colsel));
2205 av.getColumnSelection().setElementsFrom(colsel,
2206 av.getAlignment().getHiddenColumns());
2209 av.isColSelChanged(true);
2213 if (copycolsel && av.hasHiddenColumns()
2214 && (av.getAlignment().getHiddenColumns() == null))
2216 System.err.println("Bad things");
2218 if (repaint) // always true!
2220 // probably finessing with multiple redraws here
2221 PaintRefresher.Refresh(this, av.getSequenceSetId());
2222 // ap.paintAlignment(false);
2225 // lastly, update dependent dialogs
2226 if (ap.getCalculationDialog() != null)
2228 ap.getCalculationDialog().validateCalcTypes();
2234 * If this panel is a cdna/protein translation view of the selection source,
2235 * tries to map the source selection to a local one, and returns true. Else
2242 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2243 ColumnSelection colsel, HiddenColumns hidden,
2244 SelectionSource source)
2246 if (!(source instanceof AlignViewportI))
2250 final AlignViewportI sourceAv = (AlignViewportI) source;
2251 if (sourceAv.getCodingComplement() != av
2252 && av.getCodingComplement() != sourceAv)
2258 * Map sequence selection
2260 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2261 av.setSelectionGroup(sg);
2262 av.isSelectionGroupChanged(true);
2265 * Map column selection
2267 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2269 ColumnSelection cs = new ColumnSelection();
2270 HiddenColumns hs = new HiddenColumns();
2271 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2272 av.setColumnSelection(cs);
2273 av.getAlignment().setHiddenColumns(hs);
2275 // lastly, update any dependent dialogs
2276 if (ap.getCalculationDialog() != null)
2278 ap.getCalculationDialog().validateCalcTypes();
2281 PaintRefresher.Refresh(this, av.getSequenceSetId());