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.SearchResults;
31 import jalview.datamodel.SearchResults.Match;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceGroup;
35 import jalview.datamodel.SequenceI;
36 import jalview.io.SequenceAnnotationReport;
37 import jalview.schemes.ResidueProperties;
38 import jalview.structure.SelectionListener;
39 import jalview.structure.SelectionSource;
40 import jalview.structure.SequenceListener;
41 import jalview.structure.StructureSelectionManager;
42 import jalview.structure.VamsasSource;
43 import jalview.util.Comparison;
44 import jalview.util.MappingUtils;
45 import jalview.util.MessageManager;
46 import jalview.viewmodel.AlignmentViewport;
48 import java.awt.BorderLayout;
49 import java.awt.Color;
51 import java.awt.FontMetrics;
52 import java.awt.Point;
53 import java.awt.event.MouseEvent;
54 import java.awt.event.MouseListener;
55 import java.awt.event.MouseMotionListener;
56 import java.awt.event.MouseWheelEvent;
57 import java.awt.event.MouseWheelListener;
58 import java.util.ArrayList;
59 import java.util.List;
61 import javax.swing.JOptionPane;
62 import javax.swing.JPanel;
63 import javax.swing.SwingUtilities;
64 import javax.swing.ToolTipManager;
70 * @version $Revision: 1.130 $
72 public class SeqPanel extends JPanel implements MouseListener,
73 MouseMotionListener, MouseWheelListener, SequenceListener,
78 public SeqCanvas seqCanvas;
81 public AlignmentPanel ap;
83 protected int lastres;
85 protected int startseq;
87 protected AlignViewport av;
89 ScrollThread scrollThread = null;
91 boolean mouseDragging = false;
93 boolean editingSeqs = false;
95 boolean groupEditing = false;
97 // ////////////////////////////////////////
98 // ///Everything below this is for defining the boundary of the rubberband
99 // ////////////////////////////////////////
102 boolean changeEndSeq = false;
104 boolean changeStartSeq = false;
106 boolean changeEndRes = false;
108 boolean changeStartRes = false;
110 SequenceGroup stretchGroup = null;
112 boolean remove = false;
114 Point lastMousePress;
116 boolean mouseWheelPressed = false;
118 StringBuffer keyboardNo1;
120 StringBuffer keyboardNo2;
122 java.net.URL linkImageURL;
124 private final SequenceAnnotationReport seqARep;
126 StringBuffer tooltipText = new StringBuffer();
130 EditCommand editCommand;
132 StructureSelectionManager ssm;
134 SearchResults lastSearchResults;
137 * Creates a new SeqPanel object.
144 public SeqPanel(AlignViewport av, AlignmentPanel ap)
146 linkImageURL = getClass().getResource("/images/link.gif");
147 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
148 ToolTipManager.sharedInstance().registerComponent(this);
149 ToolTipManager.sharedInstance().setInitialDelay(0);
150 ToolTipManager.sharedInstance().setDismissDelay(10000);
152 setBackground(Color.white);
154 seqCanvas = new SeqCanvas(ap);
155 setLayout(new BorderLayout());
156 add(seqCanvas, BorderLayout.CENTER);
162 addMouseMotionListener(this);
163 addMouseListener(this);
164 addMouseWheelListener(this);
165 ssm = av.getStructureSelectionManager();
166 ssm.addStructureViewerListener(this);
167 ssm.addSelectionListener(this);
171 int startWrapBlock = -1;
173 int wrappedBlock = -1;
176 * Returns the aligned sequence position (base 0) at the mouse position, or
177 * the closest visible one
182 int findRes(MouseEvent evt)
187 if (av.getWrapAlignment())
190 int hgap = av.getCharHeight();
191 if (av.getScaleAboveWrapped())
193 hgap += av.getCharHeight();
196 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
197 + hgap + seqCanvas.getAnnotationHeight();
201 x -= seqCanvas.LABEL_WEST;
203 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
209 wrappedBlock = y / cHeight;
210 wrappedBlock += av.getStartRes() / cwidth;
212 res = wrappedBlock * cwidth + x / av.getCharWidth();
217 if (x > seqCanvas.getX() + seqCanvas.getWidth())
219 // make sure we calculate relative to visible alignment, rather than
221 x = seqCanvas.getX() + seqCanvas.getWidth();
223 res = (x / av.getCharWidth()) + av.getStartRes();
224 if (res > av.getEndRes())
227 res = av.getEndRes();
231 if (av.hasHiddenColumns())
233 res = av.getColumnSelection().adjustForHiddenColumns(res);
240 int findSeq(MouseEvent evt)
245 if (av.getWrapAlignment())
247 int hgap = av.getCharHeight();
248 if (av.getScaleAboveWrapped())
250 hgap += av.getCharHeight();
253 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
254 + hgap + seqCanvas.getAnnotationHeight();
258 seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
263 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
264 .getAlignment().getHeight() - 1);
271 * When all of a sequence of edits are complete, put the resulting edit list
272 * on the history stack (undo list), and reset flags for editing in progress.
278 if (editCommand != null && editCommand.getSize() > 0)
280 ap.alignFrame.addHistoryItem(editCommand);
281 av.firePropertyChange("alignment", null, av.getAlignment()
287 * Tidy up come what may...
292 groupEditing = false;
301 seqCanvas.cursorY = getKeyboardNo1() - 1;
305 void setCursorColumn()
307 seqCanvas.cursorX = getKeyboardNo1() - 1;
311 void setCursorRowAndColumn()
313 if (keyboardNo2 == null)
315 keyboardNo2 = new StringBuffer();
319 seqCanvas.cursorX = getKeyboardNo1() - 1;
320 seqCanvas.cursorY = getKeyboardNo2() - 1;
325 void setCursorPosition()
327 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
329 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
333 void moveCursor(int dx, int dy)
335 seqCanvas.cursorX += dx;
336 seqCanvas.cursorY += dy;
337 if (av.hasHiddenColumns()
338 && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
340 int original = seqCanvas.cursorX - dx;
341 int maxWidth = av.getAlignment().getWidth();
343 while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
344 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
346 seqCanvas.cursorX += dx;
349 if (seqCanvas.cursorX >= maxWidth
350 || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
352 seqCanvas.cursorX = original;
359 void scrollToVisible()
361 if (seqCanvas.cursorX < 0)
363 seqCanvas.cursorX = 0;
365 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
367 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
370 if (seqCanvas.cursorY < 0)
372 seqCanvas.cursorY = 0;
374 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
376 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
380 if (av.getWrapAlignment())
382 ap.scrollToWrappedVisible(seqCanvas.cursorX);
386 while (seqCanvas.cursorY < av.startSeq)
390 while (seqCanvas.cursorY + 1 > av.endSeq)
394 if (!av.getWrapAlignment())
396 while (seqCanvas.cursorX < av.getColumnSelection()
397 .adjustForHiddenColumns(av.startRes))
399 if (!ap.scrollRight(false))
404 while (seqCanvas.cursorX > av.getColumnSelection()
405 .adjustForHiddenColumns(av.endRes))
407 if (!ap.scrollRight(true))
414 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
415 seqCanvas.cursorX, seqCanvas.cursorY);
420 void setSelectionAreaAtCursor(boolean topLeft)
422 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
424 if (av.getSelectionGroup() != null)
426 SequenceGroup sg = av.getSelectionGroup();
427 // Find the top and bottom of this group
428 int min = av.getAlignment().getHeight(), max = 0;
429 for (int i = 0; i < sg.getSize(); i++)
431 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
446 sg.setStartRes(seqCanvas.cursorX);
447 if (sg.getEndRes() < seqCanvas.cursorX)
449 sg.setEndRes(seqCanvas.cursorX);
452 min = seqCanvas.cursorY;
456 sg.setEndRes(seqCanvas.cursorX);
457 if (sg.getStartRes() > seqCanvas.cursorX)
459 sg.setStartRes(seqCanvas.cursorX);
462 max = seqCanvas.cursorY + 1;
467 // Only the user can do this
468 av.setSelectionGroup(null);
472 // Now add any sequences between min and max
473 sg.getSequences(null).clear();
474 for (int i = min; i < max; i++)
476 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
481 if (av.getSelectionGroup() == null)
483 SequenceGroup sg = new SequenceGroup();
484 sg.setStartRes(seqCanvas.cursorX);
485 sg.setEndRes(seqCanvas.cursorX);
486 sg.addSequence(sequence, false);
487 av.setSelectionGroup(sg);
490 ap.paintAlignment(false);
494 void insertGapAtCursor(boolean group)
496 groupEditing = group;
497 startseq = seqCanvas.cursorY;
498 lastres = seqCanvas.cursorX;
499 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
503 void deleteGapAtCursor(boolean group)
505 groupEditing = group;
506 startseq = seqCanvas.cursorY;
507 lastres = seqCanvas.cursorX + getKeyboardNo1();
508 editSequence(false, false, seqCanvas.cursorX);
512 void insertNucAtCursor(boolean group, String nuc)
514 // TODO not called - delete?
515 groupEditing = group;
516 startseq = seqCanvas.cursorY;
517 lastres = seqCanvas.cursorX;
518 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
522 void numberPressed(char value)
524 if (keyboardNo1 == null)
526 keyboardNo1 = new StringBuffer();
529 if (keyboardNo2 != null)
531 keyboardNo2.append(value);
535 keyboardNo1.append(value);
543 if (keyboardNo1 != null)
545 int value = Integer.parseInt(keyboardNo1.toString());
549 } catch (Exception x)
560 if (keyboardNo2 != null)
562 int value = Integer.parseInt(keyboardNo2.toString());
566 } catch (Exception x)
580 public void mouseReleased(MouseEvent evt)
582 mouseDragging = false;
583 mouseWheelPressed = false;
587 doMouseReleasedDefineMode(evt);
601 public void mousePressed(MouseEvent evt)
603 lastMousePress = evt.getPoint();
605 if (SwingUtilities.isMiddleMouseButton(evt))
607 mouseWheelPressed = true;
611 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
613 if (evt.isAltDown() || evt.isControlDown())
621 doMousePressedDefineMode(evt);
625 int seq = findSeq(evt);
626 int res = findRes(evt);
628 if (seq < 0 || res < 0)
633 if ((seq < av.getAlignment().getHeight())
634 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
651 public void mouseOverSequence(SequenceI sequence, int index, int pos)
653 String tmp = sequence.hashCode() + " " + index + " " + pos;
655 if (lastMessage == null || !lastMessage.equals(tmp))
657 // System.err.println("mouseOver Sequence: "+tmp);
658 ssm.mouseOverSequence(sequence, index, pos, av);
664 * Highlight the mapped region described by the search results object (unless
665 * unchanged). This supports highlight of protein while mousing over linked
666 * cDNA and vice versa. The status bar is also updated to show the location of
667 * the start of the highlighted region.
670 public void highlightSequence(SearchResults results)
672 if (results == null || results.equals(lastSearchResults))
676 lastSearchResults = results;
678 if (av.isFollowHighlight())
681 * if scrollToPosition requires a scroll adjustment, this flag prevents
682 * another scroll event being propagated back to the originator
684 * @see AlignmentPanel#adjustmentValueChanged
686 ap.setDontScrollComplement(true);
687 if (ap.scrollToPosition(results, false))
689 seqCanvas.revalidate();
692 setStatusMessage(results);
693 seqCanvas.highlightSearchResults(results);
697 public VamsasSource getVamsasSource()
699 return this.ap == null ? null : this.ap.av;
703 public void updateColours(SequenceI seq, int index)
705 System.out.println("update the seqPanel colours");
716 public void mouseMoved(MouseEvent evt)
720 // This is because MacOSX creates a mouseMoved
721 // If control is down, other platforms will not.
725 int res = findRes(evt);
726 int seq = findSeq(evt);
728 if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
733 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
735 if (res >= sequence.getLength())
740 pos = setStatusMessage(sequence, res, seq);
741 if (ssm != null && pos > -1)
743 mouseOverSequence(sequence, res, pos);
746 tooltipText.setLength(6); // Cuts the buffer back to <html>
748 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
751 for (int g = 0; g < groups.length; g++)
753 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
755 if (!groups[g].getName().startsWith("JTreeGroup")
756 && !groups[g].getName().startsWith("JGroup"))
758 tooltipText.append(groups[g].getName());
761 if (groups[g].getDescription() != null)
763 tooltipText.append(": " + groups[g].getDescription());
769 // use aa to see if the mouse pointer is on a
770 if (av.isShowSequenceFeatures())
773 List<SequenceFeature> features = ap.getFeatureRenderer()
774 .findFeaturesAtRes(sequence.getDatasetSequence(),
775 rpos = sequence.findPosition(res));
776 seqARep.appendFeatures(tooltipText, rpos, features,
777 this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
779 if (tooltipText.length() == 6) // <html></html>
781 setToolTipText(null);
786 if (lastTooltip == null
787 || !lastTooltip.equals(tooltipText.toString()))
789 String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
790 tooltipText.toString());
791 // String formatedTooltipText = tooltipText.toString();
792 setToolTipText(formatedTooltipText);
793 lastTooltip = tooltipText.toString();
800 private Point lastp = null;
805 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
808 public Point getToolTipLocation(MouseEvent event)
810 int x = event.getX(), w = getWidth();
811 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
814 if (!event.isShiftDown() || p == null)
816 p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
817 event.getX() + wdth, event.getY() - 20) : null;
820 * TODO: try to modify position region is not obcured by tooltip
828 * set when the current UI interaction has resulted in a change that requires
829 * overview shading to be recalculated. this could be changed to something
830 * more expressive that indicates what actually has changed, so selective
831 * redraws can be applied
833 private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller
836 * set if av.getSelectionGroup() refers to a group that is defined on the
837 * alignment view, rather than a transient selection
839 private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller or viewModel
842 * Set status message in alignment panel
845 * aligned sequence object
849 * index of sequence in alignment
850 * @return position of res in sequence
852 int setStatusMessage(SequenceI sequence, int res, int seq)
854 StringBuilder text = new StringBuilder(32);
857 * Sequence number (if known), and sequence name.
859 String seqno = seq == -1 ? "" : " " + (seq + 1);
860 text.append("Sequence" + seqno + " ID: " + sequence.getName());
862 String residue = null;
864 * Try to translate the display character to residue name (null for gap).
866 final String displayChar = String.valueOf(sequence.getCharAt(res));
867 if (av.getAlignment().isNucleotide())
869 residue = ResidueProperties.nucleotideName.get(displayChar);
872 text.append(" Nucleotide: ").append(residue);
877 residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
878 .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
882 text.append(" Residue: ").append(residue);
889 pos = sequence.findPosition(res);
890 text.append(" (").append(Integer.toString(pos)).append(")");
892 ap.alignFrame.statusBar.setText(text.toString());
897 * Set the status bar message to highlight the first matched position in
902 private void setStatusMessage(SearchResults results)
904 AlignmentI al = this.av.getAlignment();
905 int sequenceIndex = al.findIndex(results);
906 if (sequenceIndex == -1)
910 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
911 for (Match m : results.getResults())
913 SequenceI seq = m.getSequence();
914 if (seq.getDatasetSequence() != null)
916 seq = seq.getDatasetSequence();
922 * Convert position in sequence (base 1) to sequence character array
925 int start = m.getStart() - m.getSequence().getStart();
926 setStatusMessage(seq, start, sequenceIndex);
939 public void mouseDragged(MouseEvent evt)
941 if (mouseWheelPressed)
943 int oldWidth = av.getCharWidth();
945 // Which is bigger, left-right or up-down?
946 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
947 .getX() - lastMousePress.getX()))
949 int fontSize = av.font.getSize();
951 if (evt.getY() < lastMousePress.getY())
955 else if (evt.getY() > lastMousePress.getY())
966 new Font(av.font.getName(), av.font.getStyle(), fontSize),
968 av.setCharWidth(oldWidth);
973 if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
975 av.setCharWidth(av.getCharWidth() - 1);
977 else if (evt.getX() > lastMousePress.getX())
979 av.setCharWidth(av.getCharWidth() + 1);
982 ap.paintAlignment(false);
985 FontMetrics fm = getFontMetrics(av.getFont());
986 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
988 lastMousePress = evt.getPoint();
995 doMouseDraggedDefineMode(evt);
999 int res = findRes(evt);
1006 if ((lastres == -1) || (lastres == res))
1011 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1013 // dragLeft, delete gap
1014 editSequence(false, false, res);
1018 editSequence(true, false, res);
1021 mouseDragging = true;
1022 if (scrollThread != null)
1024 scrollThread.setEvent(evt);
1028 // TODO: Make it more clever than many booleans
1029 synchronized void editSequence(boolean insertGap, boolean editSeq,
1033 int fixedRight = -1;
1034 boolean fixedColumns = false;
1035 SequenceGroup sg = av.getSelectionGroup();
1037 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1039 // No group, but the sequence may represent a group
1040 if (!groupEditing && av.hasHiddenRows())
1042 if (av.isHiddenRepSequence(seq))
1044 sg = av.getRepresentedSequences(seq);
1045 groupEditing = true;
1049 StringBuilder message = new StringBuilder(64);
1052 message.append("Edit group:");
1053 if (editCommand == null)
1055 editCommand = new EditCommand(
1056 MessageManager.getString("action.edit_group"));
1061 message.append("Edit sequence: " + seq.getName());
1062 String label = seq.getName();
1063 if (label.length() > 10)
1065 label = label.substring(0, 10);
1067 if (editCommand == null)
1069 editCommand = new EditCommand(MessageManager.formatMessage(
1070 "label.edit_params", new String[] { label }));
1076 message.append(" insert ");
1080 message.append(" delete ");
1083 message.append(Math.abs(startres - lastres) + " gaps.");
1084 ap.alignFrame.statusBar.setText(message.toString());
1086 // Are we editing within a selection group?
1088 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1091 fixedColumns = true;
1093 // sg might be null as the user may only see 1 sequence,
1094 // but the sequence represents a group
1097 if (!av.isHiddenRepSequence(seq))
1102 sg = av.getRepresentedSequences(seq);
1105 fixedLeft = sg.getStartRes();
1106 fixedRight = sg.getEndRes();
1108 if ((startres < fixedLeft && lastres >= fixedLeft)
1109 || (startres >= fixedLeft && lastres < fixedLeft)
1110 || (startres > fixedRight && lastres <= fixedRight)
1111 || (startres <= fixedRight && lastres > fixedRight))
1117 if (fixedLeft > startres)
1119 fixedRight = fixedLeft - 1;
1122 else if (fixedRight < startres)
1124 fixedLeft = fixedRight;
1129 if (av.hasHiddenColumns())
1131 fixedColumns = true;
1132 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1133 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1135 if ((insertGap && startres > y1 && lastres < y1)
1136 || (!insertGap && startres < y2 && lastres > y2))
1142 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1143 // Selection spans a hidden region
1144 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1152 fixedRight = y2 - 1;
1159 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1160 int g, groupSize = vseqs.size();
1161 SequenceI[] groupSeqs = new SequenceI[groupSize];
1162 for (g = 0; g < groupSeqs.length; g++)
1164 groupSeqs[g] = vseqs.get(g);
1170 // If the user has selected the whole sequence, and is dragging to
1171 // the right, we can still extend the alignment and selectionGroup
1172 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1173 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1175 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1176 fixedRight = sg.getEndRes();
1179 // Is it valid with fixed columns??
1180 // Find the next gap before the end
1181 // of the visible region boundary
1182 boolean blank = false;
1183 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1187 for (g = 0; g < groupSize; g++)
1189 for (int j = 0; j < startres - lastres; j++)
1191 if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
1206 if (sg.getSize() == av.getAlignment().getHeight())
1208 if ((av.hasHiddenColumns() && startres < av
1209 .getColumnSelection().getHiddenBoundaryRight(startres)))
1215 int alWidth = av.getAlignment().getWidth();
1216 if (av.hasHiddenRows())
1218 int hwidth = av.getAlignment().getHiddenSequences()
1220 if (hwidth > alWidth)
1225 // We can still insert gaps if the selectionGroup
1226 // contains all the sequences
1227 sg.setEndRes(sg.getEndRes() + startres - lastres);
1228 fixedRight = alWidth + startres - lastres;
1239 else if (!insertGap)
1241 // / Are we able to delete?
1242 // ie are all columns blank?
1244 for (g = 0; g < groupSize; g++)
1246 for (int j = startres; j < lastres; j++)
1248 if (groupSeqs[g].getLength() <= j)
1253 if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
1255 // Not a gap, block edit not valid
1265 // dragging to the right
1266 if (fixedColumns && fixedRight != -1)
1268 for (int j = lastres; j < startres; j++)
1270 insertChar(j, groupSeqs, fixedRight);
1275 appendEdit(Action.INSERT_GAP, groupSeqs, startres, startres
1281 // dragging to the left
1282 if (fixedColumns && fixedRight != -1)
1284 for (int j = lastres; j > startres; j--)
1286 deleteChar(startres, groupSeqs, fixedRight);
1291 appendEdit(Action.DELETE_GAP, groupSeqs, startres, lastres
1298 // ///Editing a single sequence///////////
1302 // dragging to the right
1303 if (fixedColumns && fixedRight != -1)
1305 for (int j = lastres; j < startres; j++)
1307 insertChar(j, new SequenceI[] { seq }, fixedRight);
1312 appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
1313 startres - lastres);
1320 // dragging to the left
1321 if (fixedColumns && fixedRight != -1)
1323 for (int j = lastres; j > startres; j--)
1325 if (!Comparison.isGap(seq.getCharAt(startres)))
1330 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1335 // could be a keyboard edit trying to delete none gaps
1337 for (int m = startres; m < lastres; m++)
1339 if (!Comparison.isGap(seq.getCharAt(m)))
1348 appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
1354 {// insertGap==false AND editSeq==TRUE;
1355 if (fixedColumns && fixedRight != -1)
1357 for (int j = lastres; j < startres; j++)
1359 insertChar(j, new SequenceI[] { seq }, fixedRight);
1364 appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
1365 startres - lastres);
1372 seqCanvas.repaint();
1375 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1377 int blankColumn = fixedColumn;
1378 for (int s = 0; s < seq.length; s++)
1380 // Find the next gap before the end of the visible region boundary
1381 // If lastCol > j, theres a boundary after the gap insertion
1383 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1385 if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
1387 // Theres a space, so break and insert the gap
1392 if (blankColumn <= j)
1394 blankColumn = fixedColumn;
1400 appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
1402 appendEdit(Action.INSERT_GAP, seq, j, 1);
1407 * Helper method to add and perform one edit action.
1414 protected void appendEdit(Action action, SequenceI[] seq, int pos,
1418 final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
1419 av.getAlignment().getGapCharacter());
1421 editCommand.appendEdit(edit, av.getAlignment(), true, null);
1424 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1427 appendEdit(Action.DELETE_GAP, seq, j, 1);
1429 appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
1439 public void mouseEntered(MouseEvent e)
1446 if (scrollThread != null)
1448 scrollThread.running = false;
1449 scrollThread = null;
1460 public void mouseExited(MouseEvent e)
1462 if (av.getWrapAlignment())
1469 scrollThread = new ScrollThread();
1474 public void mouseClicked(MouseEvent evt)
1476 SequenceGroup sg = null;
1477 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1478 if (evt.getClickCount() > 1)
1480 sg = av.getSelectionGroup();
1481 if (sg != null && sg.getSize() == 1
1482 && sg.getEndRes() - sg.getStartRes() < 2)
1484 av.setSelectionGroup(null);
1487 List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
1488 .findFeaturesAtRes(sequence.getDatasetSequence(),
1489 sequence.findPosition(findRes(evt)));
1491 if (features != null && features.size() > 0)
1493 SearchResults highlight = new SearchResults();
1494 highlight.addResult(sequence, features.get(0).getBegin(), features
1496 seqCanvas.highlightSearchResults(highlight);
1498 if (features != null && features.size() > 0)
1500 seqCanvas.getFeatureRenderer().amendFeatures(
1501 new SequenceI[] { sequence },
1502 features.toArray(new SequenceFeature[features.size()]),
1505 seqCanvas.highlightSearchResults(null);
1511 public void mouseWheelMoved(MouseWheelEvent e)
1514 if (e.getWheelRotation() > 0)
1516 if (e.isShiftDown())
1518 ap.scrollRight(true);
1528 if (e.isShiftDown())
1530 ap.scrollRight(false);
1537 // TODO Update tooltip for new position.
1546 public void doMousePressedDefineMode(MouseEvent evt)
1548 int res = findRes(evt);
1549 int seq = findSeq(evt);
1552 startWrapBlock = wrappedBlock;
1554 if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
1556 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1557 .getString("label.cannot_edit_annotations_in_wrapped_view"),
1558 MessageManager.getString("label.wrapped_view_no_edit"),
1559 JOptionPane.WARNING_MESSAGE);
1563 if (seq < 0 || res < 0)
1568 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1570 if ((sequence == null) || (res > sequence.getLength()))
1575 stretchGroup = av.getSelectionGroup();
1577 if (stretchGroup == null)
1579 stretchGroup = av.getAlignment().findGroup(sequence);
1581 if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
1582 && (res < stretchGroup.getEndRes()))
1584 av.setSelectionGroup(stretchGroup);
1585 editingDefinedGroup = true;
1589 stretchGroup = null;
1590 editingDefinedGroup = false;
1593 else if (!stretchGroup.getSequences(null).contains(sequence)
1594 || (stretchGroup.getStartRes() > res)
1595 || (stretchGroup.getEndRes() < res))
1597 stretchGroup = null;
1599 SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
1601 if (allGroups != null)
1603 for (int i = 0; i < allGroups.length; i++)
1605 if ((allGroups[i].getStartRes() <= res)
1606 && (allGroups[i].getEndRes() >= res))
1608 stretchGroup = allGroups[i];
1609 editingDefinedGroup = true;
1615 av.setSelectionGroup(stretchGroup);
1619 if (evt.isPopupTrigger())
1621 List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
1622 .findFeaturesAtRes(sequence.getDatasetSequence(),
1623 sequence.findPosition(res));
1624 List<String> links = new ArrayList<String>();
1625 for (SequenceFeature sf : allFeatures)
1627 if (sf.links != null)
1629 for (String link : sf.links)
1636 PopupMenu pop = new PopupMenu(ap, null, links);
1637 pop.show(this, evt.getX(), evt.getY());
1643 seqCanvas.cursorX = findRes(evt);
1644 seqCanvas.cursorY = findSeq(evt);
1645 seqCanvas.repaint();
1649 if (stretchGroup == null)
1651 // Only if left mouse button do we want to change group sizes
1653 // define a new group here
1654 SequenceGroup sg = new SequenceGroup();
1655 sg.setStartRes(res);
1657 sg.addSequence(sequence, false);
1658 av.setSelectionGroup(sg);
1659 editingDefinedGroup = false;
1662 if (av.getConservationSelected())
1664 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1668 if (av.getAbovePIDThreshold())
1670 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1673 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1675 // Edit end res position of selected group
1676 changeEndRes = true;
1678 else if ((stretchGroup != null)
1679 && (stretchGroup.getStartRes() == res))
1681 // Edit end res position of selected group
1682 changeStartRes = true;
1684 stretchGroup.getWidth();
1687 seqCanvas.repaint();
1696 public void doMouseReleasedDefineMode(MouseEvent evt)
1698 if (stretchGroup == null)
1702 // always do this - annotation has own state
1703 // but defer colourscheme update until hidden sequences are passed in
1704 boolean vischange = stretchGroup.recalcConservation(true);
1705 needOverviewUpdate |= vischange && editingDefinedGroup;
1706 if (stretchGroup.cs != null)
1708 stretchGroup.cs.alignmentChanged(stretchGroup,
1709 av.getHiddenRepSequences());
1711 if (stretchGroup.cs.conservationApplied())
1713 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1714 stretchGroup.getName());
1718 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1719 stretchGroup.getName());
1722 PaintRefresher.Refresh(this, av.getSequenceSetId());
1723 ap.paintAlignment(needOverviewUpdate);
1724 needOverviewUpdate =false;
1725 editingDefinedGroup = false;
1726 changeEndRes = false;
1727 changeStartRes = false;
1728 stretchGroup = null;
1738 public void doMouseDraggedDefineMode(MouseEvent evt)
1740 int res = findRes(evt);
1741 int y = findSeq(evt);
1743 if (wrappedBlock != startWrapBlock)
1748 if (stretchGroup == null)
1753 if (res >= av.getAlignment().getWidth())
1755 res = av.getAlignment().getWidth() - 1;
1758 if (stretchGroup.getEndRes() == res)
1760 // Edit end res position of selected group
1761 changeEndRes = true;
1763 else if (stretchGroup.getStartRes() == res)
1765 // Edit start res position of selected group
1766 changeStartRes = true;
1769 if (res < av.getStartRes())
1771 res = av.getStartRes();
1776 if (res > (stretchGroup.getStartRes() - 1))
1778 stretchGroup.setEndRes(res);
1779 needOverviewUpdate |= editingDefinedGroup;
1782 else if (changeStartRes)
1784 if (res < (stretchGroup.getEndRes() + 1))
1786 stretchGroup.setStartRes(res);
1787 needOverviewUpdate |= editingDefinedGroup;
1791 int dragDirection = 0;
1797 else if (y < oldSeq)
1802 while ((y != oldSeq) && (oldSeq > -1)
1803 && (y < av.getAlignment().getHeight()))
1805 // This routine ensures we don't skip any sequences, as the
1806 // selection is quite slow.
1807 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1809 oldSeq += dragDirection;
1816 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1818 if (stretchGroup.getSequences(null).contains(nextSeq))
1820 stretchGroup.deleteSequence(seq, false);
1821 needOverviewUpdate |= editingDefinedGroup;
1827 stretchGroup.addSequence(seq, false);
1830 stretchGroup.addSequence(nextSeq, false);
1831 needOverviewUpdate |= editingDefinedGroup;
1840 mouseDragging = true;
1842 if (scrollThread != null)
1844 scrollThread.setEvent(evt);
1847 seqCanvas.repaint();
1850 void scrollCanvas(MouseEvent evt)
1854 if (scrollThread != null)
1856 scrollThread.running = false;
1857 scrollThread = null;
1859 mouseDragging = false;
1863 if (scrollThread == null)
1865 scrollThread = new ScrollThread();
1868 mouseDragging = true;
1869 scrollThread.setEvent(evt);
1874 // this class allows scrolling off the bottom of the visible alignment
1875 class ScrollThread extends Thread
1879 boolean running = false;
1881 public ScrollThread()
1886 public void setEvent(MouseEvent e)
1891 public void stopScrolling()
1905 if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
1907 running = ap.scrollUp(true);
1910 if (mouseDragging && (evt.getY() >= getHeight())
1911 && (av.getAlignment().getHeight() > av.getEndSeq()))
1913 running = ap.scrollUp(false);
1916 if (mouseDragging && (evt.getX() < 0))
1918 running = ap.scrollRight(false);
1920 else if (mouseDragging && (evt.getX() >= getWidth()))
1922 running = ap.scrollRight(true);
1929 } catch (Exception ex)
1937 * modify current selection according to a received message.
1940 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1941 SelectionSource source)
1943 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1944 // handles selection messages...
1945 // TODO: extend config options to allow user to control if selections may be
1946 // shared between viewports.
1947 boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source)
1948 .getSequenceSetId().equals(av.getSequenceSetId())));
1949 if (iSentTheSelection || !av.followSelection)
1955 * Ignore the selection if there is one of our own pending.
1957 if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
1963 * Check for selection in a view of which this one is a dna/protein
1966 if (selectionFromTranslation(seqsel, colsel, source))
1971 // do we want to thread this ? (contention with seqsel and colsel locks, I
1974 * only copy colsel if there is a real intersection between
1975 * sequence selection and this panel's alignment
1977 boolean repaint = false;
1978 boolean copycolsel = false;
1980 SequenceGroup sgroup = null;
1981 if (seqsel != null && seqsel.getSize() > 0)
1983 if (av.getAlignment() == null)
1985 Cache.log.warn("alignviewport av SeqSetId="
1986 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
1987 + " 's alignment is NULL! returning immediately.");
1990 sgroup = seqsel.intersect(av.getAlignment(),
1991 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1992 if ((sgroup != null && sgroup.getSize() > 0))
1997 if (sgroup != null && sgroup.getSize() > 0)
1999 av.setSelectionGroup(sgroup);
2003 av.setSelectionGroup(null);
2005 av.isSelectionGroupChanged(true);
2010 // the current selection is unset or from a previous message
2011 // so import the new colsel.
2012 if (colsel == null || colsel.isEmpty())
2014 if (av.getColumnSelection() != null)
2016 av.getColumnSelection().clear();
2022 // TODO: shift colSel according to the intersecting sequences
2023 if (av.getColumnSelection() == null)
2025 av.setColumnSelection(new ColumnSelection(colsel));
2029 av.getColumnSelection().setElementsFrom(colsel);
2032 av.isColSelChanged(true);
2037 && av.hasHiddenColumns()
2038 && (av.getColumnSelection() == null || av.getColumnSelection()
2039 .getHiddenColumns() == null))
2041 System.err.println("Bad things");
2043 if (repaint) // always true!
2045 // probably finessing with multiple redraws here
2046 PaintRefresher.Refresh(this, av.getSequenceSetId());
2047 // ap.paintAlignment(false);
2052 * If this panel is a cdna/protein translation view of the selection source,
2053 * tries to map the source selection to a local one, and returns true. Else
2060 protected boolean selectionFromTranslation(SequenceGroup seqsel,
2061 ColumnSelection colsel, SelectionSource source)
2063 if (!(source instanceof AlignViewportI))
2067 final AlignViewportI sourceAv = (AlignViewportI) source;
2068 if (sourceAv.getCodingComplement() != av
2069 && av.getCodingComplement() != sourceAv)
2075 * Map sequence selection
2077 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
2078 av.setSelectionGroup(sg);
2079 av.isSelectionGroupChanged(true);
2082 * Map column selection
2084 ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
2086 av.setColumnSelection(cs);
2088 PaintRefresher.Refresh(this, av.getSequenceSetId());