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 implements MouseListener,
77 MouseMotionListener, MouseWheelListener, SequenceListener,
82 public SeqCanvas seqCanvas;
85 public AlignmentPanel ap;
87 protected int lastres;
89 protected int startseq;
91 protected AlignViewport av;
93 ScrollThread scrollThread = null;
95 boolean mouseDragging = false;
97 boolean editingSeqs = false;
99 boolean groupEditing = false;
101 // ////////////////////////////////////////
102 // ///Everything below this is for defining the boundary of the rubberband
103 // ////////////////////////////////////////
106 boolean changeEndSeq = false;
108 boolean changeStartSeq = false;
110 boolean changeEndRes = false;
112 boolean changeStartRes = false;
114 SequenceGroup stretchGroup = null;
116 boolean remove = false;
118 Point lastMousePress;
120 boolean mouseWheelPressed = false;
122 StringBuffer keyboardNo1;
124 StringBuffer keyboardNo2;
126 java.net.URL linkImageURL;
128 private final SequenceAnnotationReport seqARep;
130 StringBuilder tooltipText = new StringBuilder();
134 EditCommand editCommand;
136 StructureSelectionManager ssm;
138 SearchResultsI lastSearchResults;
141 * Creates a new SeqPanel object.
148 public SeqPanel(AlignViewport av, AlignmentPanel ap)
150 linkImageURL = getClass().getResource("/images/link.gif");
151 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
152 ToolTipManager.sharedInstance().registerComponent(this);
153 ToolTipManager.sharedInstance().setInitialDelay(0);
154 ToolTipManager.sharedInstance().setDismissDelay(10000);
156 setBackground(Color.white);
158 seqCanvas = new SeqCanvas(ap);
159 setLayout(new BorderLayout());
160 add(seqCanvas, BorderLayout.CENTER);
166 addMouseMotionListener(this);
167 addMouseListener(this);
168 addMouseWheelListener(this);
169 ssm = av.getStructureSelectionManager();
170 ssm.addStructureViewerListener(this);
171 ssm.addSelectionListener(this);
175 int startWrapBlock = -1;
177 int wrappedBlock = -1;
180 * Returns the aligned sequence position (base 0) at the mouse position, or
181 * the closest visible one
186 int findColumn(MouseEvent evt)
191 if (av.getWrapAlignment())
194 int hgap = av.getCharHeight();
195 if (av.getScaleAboveWrapped())
197 hgap += av.getCharHeight();
200 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
201 + hgap + seqCanvas.getAnnotationHeight();
205 x -= seqCanvas.LABEL_WEST;
207 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
213 wrappedBlock = y / cHeight;
214 wrappedBlock += av.getRanges().getStartRes() / cwidth;
216 res = wrappedBlock * cwidth + x / av.getCharWidth();
221 if (x > seqCanvas.getX() + seqCanvas.getWidth())
223 // make sure we calculate relative to visible alignment, rather than
225 x = seqCanvas.getX() + seqCanvas.getWidth();
227 res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
228 if (res > av.getRanges().getEndRes())
231 res = av.getRanges().getEndRes();
235 if (av.hasHiddenColumns())
237 res = av.getAlignment().getHiddenColumns()
238 .adjustForHiddenColumns(res);
245 int findSeq(MouseEvent evt)
250 if (av.getWrapAlignment())
252 int hgap = av.getCharHeight();
253 if (av.getScaleAboveWrapped())
255 hgap += av.getCharHeight();
258 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
259 + hgap + seqCanvas.getAnnotationHeight();
263 seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
268 seq = Math.min((y / av.getCharHeight())
269 + av.getRanges().getStartSeq(),
271 .getAlignment().getHeight() - 1);
278 * When all of a sequence of edits are complete, put the resulting edit list
279 * on the history stack (undo list), and reset flags for editing in progress.
285 if (editCommand != null && editCommand.getSize() > 0)
287 ap.alignFrame.addHistoryItem(editCommand);
288 av.firePropertyChange("alignment", null, av.getAlignment()
294 * Tidy up come what may...
299 groupEditing = false;
308 seqCanvas.cursorY = getKeyboardNo1() - 1;
312 void setCursorColumn()
314 seqCanvas.cursorX = getKeyboardNo1() - 1;
318 void setCursorRowAndColumn()
320 if (keyboardNo2 == null)
322 keyboardNo2 = new StringBuffer();
326 seqCanvas.cursorX = getKeyboardNo1() - 1;
327 seqCanvas.cursorY = getKeyboardNo2() - 1;
332 void setCursorPosition()
334 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
336 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
340 void moveCursor(int dx, int dy)
342 seqCanvas.cursorX += dx;
343 seqCanvas.cursorY += dy;
345 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
347 if (av.hasHiddenColumns()
348 && !hidden.isVisible(seqCanvas.cursorX))
350 int original = seqCanvas.cursorX - dx;
351 int maxWidth = av.getAlignment().getWidth();
353 while (!hidden.isVisible(seqCanvas.cursorX)
354 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
356 seqCanvas.cursorX += dx;
359 if (seqCanvas.cursorX >= maxWidth
360 || !hidden.isVisible(seqCanvas.cursorX))
362 seqCanvas.cursorX = original;
369 void scrollToVisible()
371 if (seqCanvas.cursorX < 0)
373 seqCanvas.cursorX = 0;
375 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
377 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
380 if (seqCanvas.cursorY < 0)
382 seqCanvas.cursorY = 0;
384 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
386 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
390 if (av.getWrapAlignment())
392 av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
396 av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY,
399 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
400 seqCanvas.cursorX, seqCanvas.cursorY);
405 void setSelectionAreaAtCursor(boolean topLeft)
407 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
409 if (av.getSelectionGroup() != null)
411 SequenceGroup sg = av.getSelectionGroup();
412 // Find the top and bottom of this group
413 int min = av.getAlignment().getHeight(), max = 0;
414 for (int i = 0; i < sg.getSize(); i++)
416 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
431 sg.setStartRes(seqCanvas.cursorX);
432 if (sg.getEndRes() < seqCanvas.cursorX)
434 sg.setEndRes(seqCanvas.cursorX);
437 min = seqCanvas.cursorY;
441 sg.setEndRes(seqCanvas.cursorX);
442 if (sg.getStartRes() > seqCanvas.cursorX)
444 sg.setStartRes(seqCanvas.cursorX);
447 max = seqCanvas.cursorY + 1;
452 // Only the user can do this
453 av.setSelectionGroup(null);
457 // Now add any sequences between min and max
458 sg.getSequences(null).clear();
459 for (int i = min; i < max; i++)
461 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
466 if (av.getSelectionGroup() == null)
468 SequenceGroup sg = new SequenceGroup();
469 sg.setStartRes(seqCanvas.cursorX);
470 sg.setEndRes(seqCanvas.cursorX);
471 sg.addSequence(sequence, false);
472 av.setSelectionGroup(sg);
475 ap.paintAlignment(false);
479 void insertGapAtCursor(boolean group)
481 groupEditing = group;
482 startseq = seqCanvas.cursorY;
483 lastres = seqCanvas.cursorX;
484 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
488 void deleteGapAtCursor(boolean group)
490 groupEditing = group;
491 startseq = seqCanvas.cursorY;
492 lastres = seqCanvas.cursorX + getKeyboardNo1();
493 editSequence(false, false, seqCanvas.cursorX);
497 void insertNucAtCursor(boolean group, String nuc)
499 // TODO not called - delete?
500 groupEditing = group;
501 startseq = seqCanvas.cursorY;
502 lastres = seqCanvas.cursorX;
503 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
507 void numberPressed(char value)
509 if (keyboardNo1 == null)
511 keyboardNo1 = new StringBuffer();
514 if (keyboardNo2 != null)
516 keyboardNo2.append(value);
520 keyboardNo1.append(value);
528 if (keyboardNo1 != null)
530 int value = Integer.parseInt(keyboardNo1.toString());
534 } catch (Exception x)
545 if (keyboardNo2 != null)
547 int value = Integer.parseInt(keyboardNo2.toString());
551 } catch (Exception x)
565 public void mouseReleased(MouseEvent evt)
567 boolean didDrag = mouseDragging; // did we come here after a drag
568 mouseDragging = false;
569 mouseWheelPressed = false;
571 if (evt.isPopupTrigger()) // Windows: mouseReleased
580 doMouseReleasedDefineMode(evt, didDrag);
594 public void mousePressed(MouseEvent evt)
596 lastMousePress = evt.getPoint();
598 if (SwingUtilities.isMiddleMouseButton(evt))
600 mouseWheelPressed = true;
604 boolean isControlDown = Platform.isControlDown(evt);
605 if (evt.isShiftDown() || isControlDown)
615 doMousePressedDefineMode(evt);
619 int seq = findSeq(evt);
620 int res = findColumn(evt);
622 if (seq < 0 || res < 0)
627 if ((seq < av.getAlignment().getHeight())
628 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
645 public void mouseOverSequence(SequenceI sequence, int index, int pos)
647 String tmp = sequence.hashCode() + " " + index + " " + pos;
649 if (lastMessage == null || !lastMessage.equals(tmp))
651 // System.err.println("mouseOver Sequence: "+tmp);
652 ssm.mouseOverSequence(sequence, index, pos, av);
658 * Highlight the mapped region described by the search results object (unless
659 * unchanged). This supports highlight of protein while mousing over linked
660 * cDNA and vice versa. The status bar is also updated to show the location of
661 * the start of the highlighted region.
664 public void highlightSequence(SearchResultsI results)
666 if (results == null || results.equals(lastSearchResults))
670 lastSearchResults = results;
672 if (av.isFollowHighlight())
674 // don't allow highlight of protein/cDNA to also scroll a complementary
675 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
676 // over residue to change abruptly, causing highlighted residue in panel 2
677 // to change, causing a scroll in panel 1 etc)
678 ap.setToScrollComplementPanel(false);
679 if (ap.scrollToPosition(results, false))
681 seqCanvas.revalidate();
683 ap.setToScrollComplementPanel(true);
685 setStatusMessage(results);
686 seqCanvas.highlightSearchResults(results);
690 public VamsasSource getVamsasSource()
692 return this.ap == null ? null : this.ap.av;
696 public void updateColours(SequenceI seq, int index)
698 System.out.println("update the seqPanel colours");
709 public void mouseMoved(MouseEvent evt)
713 // This is because MacOSX creates a mouseMoved
714 // If control is down, other platforms will not.
718 final int column = findColumn(evt);
719 int seq = findSeq(evt);
720 if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
725 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
727 if (column >= sequence.getLength())
733 * set status bar message, returning residue position in sequence
735 final int pos = setStatusMessage(sequence, column, seq);
736 if (ssm != null && pos > -1)
738 mouseOverSequence(sequence, column, pos);
741 tooltipText.setLength(6); // Cuts the buffer back to <html>
743 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
746 for (int g = 0; g < groups.length; g++)
748 if (groups[g].getStartRes() <= column
749 && groups[g].getEndRes() >= column)
751 if (!groups[g].getName().startsWith("JTreeGroup")
752 && !groups[g].getName().startsWith("JGroup"))
754 tooltipText.append(groups[g].getName());
757 if (groups[g].getDescription() != null)
759 tooltipText.append(": " + groups[g].getDescription());
765 if (av.isShowSequenceFeatures() && pos != -1)
767 List<SequenceFeature> features = ap.getFeatureRenderer()
768 .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
769 seqARep.appendFeatures(tooltipText, pos, features,
770 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
772 if (tooltipText.length() == 6) // <html>
774 setToolTipText(null);
779 if (lastTooltip == null
780 || !lastTooltip.equals(tooltipText.toString()))
782 String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
783 tooltipText.toString());
784 // String formatedTooltipText = tooltipText.toString();
785 setToolTipText(formatedTooltipText);
786 lastTooltip = tooltipText.toString();
793 private Point lastp = null;
798 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
801 public Point getToolTipLocation(MouseEvent event)
803 int x = event.getX(), w = getWidth();
804 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
807 if (!event.isShiftDown() || p == null)
809 p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
810 event.getX() + wdth, event.getY() - 20) : null;
813 * TODO: try to modify position region is not obcured by tooltip
821 * set when the current UI interaction has resulted in a change that requires
822 * overview shading to be recalculated. this could be changed to something
823 * more expressive that indicates what actually has changed, so selective
824 * redraws can be applied
826 private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller
829 * set if av.getSelectionGroup() refers to a group that is defined on the
830 * alignment view, rather than a transient selection
832 // private boolean editingDefinedGroup = false; // TODO: refactor to
833 // avcontroller or viewModel
836 * Sets the status message in alignment panel, showing the sequence number
837 * (index) and id, residue and residue position for the given sequence and
838 * column position. Returns the calculated residue position in the sequence,
839 * or -1 for a gapped column position.
842 * aligned sequence object
846 * index of sequence in alignment
847 * @return position of column in sequence or -1 if at a gap
849 int setStatusMessage(SequenceI sequence, final int column, int seq)
851 StringBuilder text = new StringBuilder(32);
854 * Sequence number (if known), and sequence name.
856 String seqno = seq == -1 ? "" : " " + (seq + 1);
857 text.append("Sequence").append(seqno).append(" ID: ")
858 .append(sequence.getName());
860 String residue = null;
862 * Try to translate the display character to residue name (null for gap).
864 final String displayChar = String.valueOf(sequence.getCharAt(column));
865 if (av.getAlignment().isNucleotide())
867 residue = ResidueProperties.nucleotideName.get(displayChar);
870 text.append(" Nucleotide: ").append(residue);
875 residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
876 .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
880 text.append(" Residue: ").append(residue);
887 pos = sequence.findPosition(column);
888 text.append(" (").append(Integer.toString(pos)).append(")");
890 ap.alignFrame.statusBar.setText(text.toString());
895 * Set the status bar message to highlight the first matched position in
900 private void setStatusMessage(SearchResultsI results)
902 AlignmentI al = this.av.getAlignment();
903 int sequenceIndex = al.findIndex(results);
904 if (sequenceIndex == -1)
908 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
909 for (SearchResultMatchI m : results.getResults())
911 SequenceI seq = m.getSequence();
912 if (seq.getDatasetSequence() != null)
914 seq = seq.getDatasetSequence();
920 * Convert position in sequence (base 1) to sequence character array
923 int start = m.getStart() - m.getSequence().getStart();
924 setStatusMessage(seq, start, sequenceIndex);
934 public void mouseDragged(MouseEvent evt)
936 if (mouseWheelPressed)
938 boolean inSplitFrame = ap.av.getCodingComplement() != null;
939 boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
941 int oldWidth = av.getCharWidth();
943 // Which is bigger, left-right or up-down?
944 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
945 .getX() - lastMousePress.getX()))
948 * on drag up or down, decrement or increment font size
950 int fontSize = av.font.getSize();
951 boolean fontChanged = false;
953 if (evt.getY() < lastMousePress.getY())
958 else if (evt.getY() > lastMousePress.getY())
971 Font newFont = new Font(av.font.getName(), av.font.getStyle(),
973 av.setFont(newFont, true);
974 av.setCharWidth(oldWidth);
978 ap.av.getCodingComplement().setFont(newFont, true);
979 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
980 .getSplitViewContainer();
981 splitFrame.adjustLayout();
982 splitFrame.repaint();
989 * on drag left or right, decrement or increment character width
992 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
994 newWidth = av.getCharWidth() - 1;
995 av.setCharWidth(newWidth);
997 else if (evt.getX() > lastMousePress.getX())
999 newWidth = av.getCharWidth() + 1;
1000 av.setCharWidth(newWidth);
1004 ap.paintAlignment(false);
1008 * need to ensure newWidth is set on cdna, regardless of which
1009 * panel the mouse drag happened in; protein will compute its
1010 * character width as 1:1 or 3:1
1012 av.getCodingComplement().setCharWidth(newWidth);
1013 SplitFrame splitFrame = (SplitFrame) ap.alignFrame
1014 .getSplitViewContainer();
1015 splitFrame.adjustLayout();
1016 splitFrame.repaint();
1021 FontMetrics fm = getFontMetrics(av.getFont());
1022 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1024 lastMousePress = evt.getPoint();
1031 doMouseDraggedDefineMode(evt);
1035 int res = findColumn(evt);
1042 if ((lastres == -1) || (lastres == res))
1047 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1049 // dragLeft, delete gap
1050 editSequence(false, false, res);
1054 editSequence(true, false, res);
1057 mouseDragging = true;
1058 if (scrollThread != null)
1060 scrollThread.setEvent(evt);
1064 // TODO: Make it more clever than many booleans
1065 synchronized void editSequence(boolean insertGap, boolean editSeq,
1069 int fixedRight = -1;
1070 boolean fixedColumns = false;
1071 SequenceGroup sg = av.getSelectionGroup();
1073 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1075 // No group, but the sequence may represent a group
1076 if (!groupEditing && av.hasHiddenRows())
1078 if (av.isHiddenRepSequence(seq))
1080 sg = av.getRepresentedSequences(seq);
1081 groupEditing = true;
1085 StringBuilder message = new StringBuilder(64);
1088 message.append("Edit group:");
1089 if (editCommand == null)
1091 editCommand = new EditCommand(
1092 MessageManager.getString("action.edit_group"));
1097 message.append("Edit sequence: " + seq.getName());
1098 String label = seq.getName();
1099 if (label.length() > 10)
1101 label = label.substring(0, 10);
1103 if (editCommand == null)
1105 editCommand = new EditCommand(MessageManager.formatMessage(
1106 "label.edit_params", new String[] { label }));
1112 message.append(" insert ");
1116 message.append(" delete ");
1119 message.append(Math.abs(startres - lastres) + " gaps.");
1120 ap.alignFrame.statusBar.setText(message.toString());
1122 // Are we editing within a selection group?
1124 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1127 fixedColumns = true;
1129 // sg might be null as the user may only see 1 sequence,
1130 // but the sequence represents a group
1133 if (!av.isHiddenRepSequence(seq))
1138 sg = av.getRepresentedSequences(seq);
1141 fixedLeft = sg.getStartRes();
1142 fixedRight = sg.getEndRes();
1144 if ((startres < fixedLeft && lastres >= fixedLeft)
1145 || (startres >= fixedLeft && lastres < fixedLeft)
1146 || (startres > fixedRight && lastres <= fixedRight)
1147 || (startres <= fixedRight && lastres > fixedRight))
1153 if (fixedLeft > startres)
1155 fixedRight = fixedLeft - 1;
1158 else if (fixedRight < startres)
1160 fixedLeft = fixedRight;
1165 if (av.hasHiddenColumns())
1167 fixedColumns = true;
1168 int y1 = av.getAlignment().getHiddenColumns()
1169 .getHiddenBoundaryLeft(startres);
1170 int y2 = av.getAlignment().getHiddenColumns()
1171 .getHiddenBoundaryRight(startres);
1173 if ((insertGap && startres > y1 && lastres < y1)
1174 || (!insertGap && startres < y2 && lastres > y2))
1180 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1181 // Selection spans a hidden region
1182 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1190 fixedRight = y2 - 1;
1197 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1198 int g, groupSize = vseqs.size();
1199 SequenceI[] groupSeqs = new SequenceI[groupSize];
1200 for (g = 0; g < groupSeqs.length; g++)
1202 groupSeqs[g] = vseqs.get(g);
1208 // If the user has selected the whole sequence, and is dragging to
1209 // the right, we can still extend the alignment and selectionGroup
1210 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1211 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1213 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1214 fixedRight = sg.getEndRes();
1217 // Is it valid with fixed columns??
1218 // Find the next gap before the end
1219 // of the visible region boundary
1220 boolean blank = false;
1221 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1225 for (g = 0; g < groupSize; g++)
1227 for (int j = 0; j < startres - lastres; j++)
1229 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1244 if (sg.getSize() == av.getAlignment().getHeight())
1246 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1247 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1253 int alWidth = av.getAlignment().getWidth();
1254 if (av.hasHiddenRows())
1256 int hwidth = av.getAlignment().getHiddenSequences()
1258 if (hwidth > alWidth)
1263 // We can still insert gaps if the selectionGroup
1264 // contains all the sequences
1265 sg.setEndRes(sg.getEndRes() + startres - lastres);
1266 fixedRight = alWidth + startres - lastres;
1277 else if (!insertGap)
1279 // / Are we able to delete?
1280 // ie are all columns blank?
1282 for (g = 0; g < groupSize; g++)
1284 for (int j = startres; j < lastres; j++)
1286 if (groupSeqs[g].getLength() <= j)
1291 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1293 // Not a gap, block edit not valid
1303 // dragging to the right
1304 if (fixedColumns && fixedRight != -1)
1306 for (int j = lastres; j < startres; j++)
1308 insertChar(j, groupSeqs, fixedRight);
1313 appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
1319 // dragging to the left
1320 if (fixedColumns && fixedRight != -1)
1322 for (int j = lastres; j > startres; j--)
1324 deleteChar(startres, groupSeqs, fixedRight);
1329 appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
1336 // ///Editing a single sequence///////////
1340 // dragging to the right
1341 if (fixedColumns && fixedRight != -1)
1343 for (int j = lastres; j < startres; j++)
1345 insertChar(j, new SequenceI[] { seq }, fixedRight);
1350 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1351 startres - lastres);
1358 // dragging to the left
1359 if (fixedColumns && fixedRight != -1)
1361 for (int j = lastres; j > startres; j--)
1363 if (!Comparison.isGap(seq.getCharAt(startres)))
1368 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1373 // could be a keyboard edit trying to delete none gaps
1375 for (int m = startres; m < lastres; m++)
1377 if (!Comparison.isGap(seq.getCharAt(m)))
1386 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1392 {// insertGap==false AND editSeq==TRUE;
1393 if (fixedColumns && fixedRight != -1)
1395 for (int j = lastres; j < startres; j++)
1397 insertChar(j, new SequenceI[] { seq }, fixedRight);
1402 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1403 startres - lastres);
1410 seqCanvas.repaint();
1413 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1415 int blankColumn = fixedColumn;
1416 for (int s = 0; s < seq.length; s++)
1418 // Find the next gap before the end of the visible region boundary
1419 // If lastCol > j, theres a boundary after the gap insertion
1421 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1423 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1425 // Theres a space, so break and insert the gap
1430 if (blankColumn <= j)
1432 blankColumn = fixedColumn;
1438 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1440 appendEdit(Action.INSERT_GAP, seq, j, 1);
1445 * Helper method to add and perform one edit action.
1452 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1456 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1457 av.getAlignment().getGapCharacter());
1459 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1462 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1465 appendEdit(Action.DELETE_GAP, seq, j, 1);
1467 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1477 public void mouseEntered(MouseEvent e)
1484 if (scrollThread != null)
1486 scrollThread.running = false;
1487 scrollThread = null;
1498 public void mouseExited(MouseEvent e)
1500 if (av.getWrapAlignment())
1507 scrollThread = new ScrollThread();
1512 * Handler for double-click on a position with one or more sequence features.
1513 * Opens the Amend Features dialog to allow feature details to be amended, or
1514 * the feature deleted.
1517 public void mouseClicked(MouseEvent evt)
1519 SequenceGroup sg = null;
1520 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1521 if (evt.getClickCount() > 1)
1523 sg = av.getSelectionGroup();
1524 if (sg != null && sg.getSize() == 1
1525 && sg.getEndRes() - sg.getStartRes() < 2)
1527 av.setSelectionGroup(null);
1530 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1531 .findFeaturesAtRes(sequence.getDatasetSequence(),
1532 sequence.findPosition(findColumn(evt)));
1534 if (!features.isEmpty())
1537 * highlight the first feature at the position on the alignment
1539 SearchResultsI highlight = new SearchResults();
1540 highlight.addResult(sequence, features.get(0).getBegin(), features
1542 seqCanvas.highlightSearchResults(highlight);
1545 * open the Amend Features dialog; clear highlighting afterwards,
1546 * whether changes were made or not
1548 List<SequenceI> seqs = Collections.singletonList(sequence);
1549 seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
1551 seqCanvas.highlightSearchResults(null);
1557 public void mouseWheelMoved(MouseWheelEvent e)
1560 if (e.getWheelRotation() > 0)
1562 if (e.isShiftDown())
1564 av.getRanges().scrollRight(true);
1569 av.getRanges().scrollUp(false);
1574 if (e.isShiftDown())
1576 av.getRanges().scrollRight(false);
1580 av.getRanges().scrollUp(true);
1583 // TODO Update tooltip for new position.
1592 public void doMousePressedDefineMode(MouseEvent evt)
1594 final int res = findColumn(evt);
1595 final int seq = findSeq(evt);
1597 needOverviewUpdate = false;
1599 startWrapBlock = wrappedBlock;
1601 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1603 JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1604 .getString("label.cannot_edit_annotations_in_wrapped_view"),
1605 MessageManager.getString("label.wrapped_view_no_edit"),
1606 JvOptionPane.WARNING_MESSAGE);
1610 if (seq < 0 || res < 0)
1615 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1617 if ((sequence == null) || (res > sequence.getLength()))
1622 stretchGroup = av.getSelectionGroup();
1624 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1626 stretchGroup = av.getAlignment().findGroup(sequence, res);
1627 if (stretchGroup != null)
1629 // only update the current selection if the popup menu has a group to
1631 av.setSelectionGroup(stretchGroup);
1635 if (evt.isPopupTrigger()) // Mac: mousePressed
1642 * defer right-mouse click handling to mouseReleased on Windows
1643 * (where isPopupTrigger() will answer true)
1644 * NB isRightMouseButton is also true for Cmd-click on Mac
1646 if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
1653 seqCanvas.cursorX = findColumn(evt);
1654 seqCanvas.cursorY = findSeq(evt);
1655 seqCanvas.repaint();
1659 if (stretchGroup == null)
1661 // Only if left mouse button do we want to change group sizes
1663 // define a new group here
1664 SequenceGroup sg = new SequenceGroup();
1665 sg.setStartRes(res);
1667 sg.addSequence(sequence, false);
1668 av.setSelectionGroup(sg);
1671 if (av.getConservationSelected())
1673 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1677 if (av.getAbovePIDThreshold())
1679 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1682 // TODO: stretchGroup will always be not null. Is this a merge error ?
1683 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1685 // Edit end res position of selected group
1686 changeEndRes = true;
1688 else if ((stretchGroup != null)
1689 && (stretchGroup.getStartRes() == res))
1691 // Edit end res position of selected group
1692 changeStartRes = true;
1694 stretchGroup.getWidth();
1697 seqCanvas.repaint();
1701 * Build and show a pop-up menu at the right-click mouse position
1707 void showPopupMenu(MouseEvent evt)
1709 final int res = findColumn(evt);
1710 final int seq = findSeq(evt);
1711 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1712 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1713 .findFeaturesAtRes(sequence.getDatasetSequence(),
1714 sequence.findPosition(res));
1715 List<String> links = new ArrayList<>();
1716 for (SequenceFeature sf : allFeatures)
1718 if (sf.links != null)
1720 for (String link : sf.links)
1727 PopupMenu pop = new PopupMenu(ap, null, links);
1728 pop.show(this, evt.getX(), evt.getY());
1732 * Update the display after mouse up on a selection or group
1735 * mouse released event details
1737 * true if this event is happening after a mouse drag (rather than a
1740 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1742 if (stretchGroup == null)
1746 // always do this - annotation has own state
1747 // but defer colourscheme update until hidden sequences are passed in
1748 boolean vischange = stretchGroup.recalcConservation(true);
1749 needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
1751 if (stretchGroup.cs != null)
1753 stretchGroup.cs.alignmentChanged(stretchGroup,
1754 av.getHiddenRepSequences());
1756 ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme();
1757 String name = stretchGroup.getName();
1758 if (stretchGroup.cs.conservationApplied())
1760 SliderPanel.setConservationSlider(ap, groupColourScheme, name);
1762 if (stretchGroup.cs.getThreshold() > 0)
1764 SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
1767 PaintRefresher.Refresh(this, av.getSequenceSetId());
1768 ap.paintAlignment(needOverviewUpdate);
1769 needOverviewUpdate = false;
1770 changeEndRes = false;
1771 changeStartRes = false;
1772 stretchGroup = null;
1782 public void doMouseDraggedDefineMode(MouseEvent evt)
1784 int res = findColumn(evt);
1785 int y = findSeq(evt);
1787 if (wrappedBlock != startWrapBlock)
1792 if (stretchGroup == null)
1797 if (res >= av.getAlignment().getWidth())
1799 res = av.getAlignment().getWidth() - 1;
1802 if (stretchGroup.getEndRes() == res)
1804 // Edit end res position of selected group
1805 changeEndRes = true;
1807 else if (stretchGroup.getStartRes() == res)
1809 // Edit start res position of selected group
1810 changeStartRes = true;
1813 if (res < av.getRanges().getStartRes())
1815 res = av.getRanges().getStartRes();
1820 if (res > (stretchGroup.getStartRes() - 1))
1822 stretchGroup.setEndRes(res);
1823 needOverviewUpdate |= av.isSelectionDefinedGroup();
1826 else if (changeStartRes)
1828 if (res < (stretchGroup.getEndRes() + 1))
1830 stretchGroup.setStartRes(res);
1831 needOverviewUpdate |= av.isSelectionDefinedGroup();
1835 int dragDirection = 0;
1841 else if (y < oldSeq)
1846 while ((y != oldSeq) && (oldSeq > -1)
1847 && (y < av.getAlignment().getHeight()))
1849 // This routine ensures we don't skip any sequences, as the
1850 // selection is quite slow.
1851 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1853 oldSeq += dragDirection;
1860 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1862 if (stretchGroup.getSequences(null).contains(nextSeq))
1864 stretchGroup.deleteSequence(seq, false);
1865 needOverviewUpdate |= av.isSelectionDefinedGroup();
1871 stretchGroup.addSequence(seq, false);
1874 stretchGroup.addSequence(nextSeq, false);
1875 needOverviewUpdate |= av.isSelectionDefinedGroup();
1884 mouseDragging = true;
1886 if (scrollThread != null)
1888 scrollThread.setEvent(evt);
1891 seqCanvas.repaint();
1894 void scrollCanvas(MouseEvent evt)
1898 if (scrollThread != null)
1900 scrollThread.running = false;
1901 scrollThread = null;
1903 mouseDragging = false;
1907 if (scrollThread == null)
1909 scrollThread = new ScrollThread();
1912 mouseDragging = true;
1913 scrollThread.setEvent(evt);
1918 // this class allows scrolling off the bottom of the visible alignment
1919 class ScrollThread extends Thread
1923 boolean running = false;
1925 public ScrollThread()
1930 public void setEvent(MouseEvent e)
1935 public void stopScrolling()
1949 if (mouseDragging && (evt.getY() < 0)
1950 && (av.getRanges().getStartSeq() > 0))
1952 running = av.getRanges().scrollUp(true);
1955 if (mouseDragging && (evt.getY() >= getHeight())
1956 && (av.getAlignment().getHeight() > av.getRanges()
1959 running = av.getRanges().scrollUp(false);
1962 if (mouseDragging && (evt.getX() < 0))
1964 running = av.getRanges().scrollRight(false);
1966 else if (mouseDragging && (evt.getX() >= getWidth()))
1968 running = av.getRanges().scrollRight(true);
1975 } catch (Exception ex)
1983 * modify current selection according to a received message.
1986 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1987 HiddenColumns hidden, SelectionSource source)
1989 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1990 // handles selection messages...
1991 // TODO: extend config options to allow user to control if selections may be
1992 // shared between viewports.
1993 boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
1994 .getSequenceSetId().equals(av.getSequenceSetId())));
1996 if (iSentTheSelection)
1998 // respond to our own event by updating dependent dialogs
1999 if (ap.getCalculationDialog() != null)
2001 ap.getCalculationDialog().validateCalcTypes();
2007 // process further ?
2008 if (!av.followSelection)
2014 * Ignore the selection if there is one of our own pending.
2016 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
2022 * Check for selection in a view of which this one is a dna/protein
2025 if (selectionFromTranslation(seqsel, colsel, hidden, source))
2030 // do we want to thread this ? (contention with seqsel and colsel locks, I
2033 * only copy colsel if there is a real intersection between
2034 * sequence selection and this panel's alignment
2036 boolean repaint = false;
2037 boolean copycolsel = false;
2039 SequenceGroup sgroup = null;
2040 if (seqsel != null && seqsel.getSize() > 0)
2042 if (av.getAlignment() == null)
2044 Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
2045 + " ViewId=" + av.getViewId()
2046 + " 's alignment is NULL! returning immediately.");
2049 sgroup = seqsel.intersect(av.getAlignment(),
2050 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
2051 if ((sgroup != null && sgroup.getSize() > 0))
2056 if (sgroup != null && sgroup.getSize() > 0)
2058 av.setSelectionGroup(sgroup);
2062 av.setSelectionGroup(null);
2064 av.isSelectionGroupChanged(true);
2069 // the current selection is unset or from a previous message
2070 // so import the new colsel.
2071 if (colsel == null || colsel.isEmpty())
2073 if (av.getColumnSelection() != null)
2075 av.getColumnSelection().clear();
2081 // TODO: shift colSel according to the intersecting sequences
2082 if (av.getColumnSelection() == null)
2084 av.setColumnSelection(new ColumnSelection(colsel));
2088 av.getColumnSelection().setElementsFrom(colsel,
2089 av.getAlignment().getHiddenColumns());
2092 av.isColSelChanged(true);
2097 && av.hasHiddenColumns()
2098 && (av.getAlignment().getHiddenColumns() == null || av
2099 .getAlignment().getHiddenColumns().getHiddenRegions() == null))
2101 System.err.println("Bad things");
2103 if (repaint) // always true!
2105 // probably finessing with multiple redraws here
2106 PaintRefresher.Refresh(this, av.getSequenceSetId());
2107 // ap.paintAlignment(false);
2110 // lastly, update dependent dialogs
2111 if (ap.getCalculationDialog() != null)
2113 ap.getCalculationDialog().validateCalcTypes();
2119 * If this panel is a cdna/protein translation view of the selection source,
2120 * tries to map the source selection to a local one, and returns true. Else
2127 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2128 ColumnSelection colsel, HiddenColumns hidden,
2129 SelectionSource source)
2131 if (!(source instanceof AlignViewportI))
2135 final AlignViewportI sourceAv = (AlignViewportI) source;
2136 if (sourceAv.getCodingComplement() != av
2137 && av.getCodingComplement() != sourceAv)
2143 * Map sequence selection
2145 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2146 av.setSelectionGroup(sg);
2147 av.isSelectionGroupChanged(true);
2150 * Map column selection
2152 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2154 ColumnSelection cs = new ColumnSelection();
2155 HiddenColumns hs = new HiddenColumns();
2156 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
2157 av.setColumnSelection(cs);
2158 av.getAlignment().setHiddenColumns(hs);
2160 // lastly, update any dependent dialogs
2161 if (ap.getCalculationDialog() != null)
2163 ap.getCalculationDialog().validateCalcTypes();
2166 PaintRefresher.Refresh(this, av.getSequenceSetId());