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.
21 package jalview.appletgui;
23 import jalview.api.AlignViewportI;
24 import jalview.commands.EditCommand;
25 import jalview.commands.EditCommand.Action;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.ColumnSelection;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.SearchResultMatchI;
30 import jalview.datamodel.SearchResults;
31 import jalview.datamodel.SearchResultsI;
32 import jalview.datamodel.Sequence;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceGroup;
35 import jalview.datamodel.SequenceI;
36 import jalview.schemes.ResidueProperties;
37 import jalview.structure.SelectionListener;
38 import jalview.structure.SelectionSource;
39 import jalview.structure.SequenceListener;
40 import jalview.structure.StructureSelectionManager;
41 import jalview.structure.VamsasSource;
42 import jalview.util.Comparison;
43 import jalview.util.MappingUtils;
44 import jalview.util.MessageManager;
45 import jalview.viewmodel.AlignmentViewport;
46 import jalview.viewmodel.ViewportRanges;
48 import java.awt.BorderLayout;
50 import java.awt.FontMetrics;
51 import java.awt.Panel;
52 import java.awt.Point;
53 import java.awt.event.InputEvent;
54 import java.awt.event.MouseEvent;
55 import java.awt.event.MouseListener;
56 import java.awt.event.MouseMotionListener;
57 import java.util.Vector;
59 public class SeqPanel extends Panel implements MouseMotionListener,
60 MouseListener, SequenceListener, SelectionListener
63 public SeqCanvas seqCanvas;
65 public AlignmentPanel ap;
67 protected int lastres;
69 protected int startseq;
71 protected AlignViewport av;
73 // if character is inserted or deleted, we will need to recalculate the
75 boolean seqEditOccurred = false;
77 ScrollThread scrollThread = null;
79 boolean mouseDragging = false;
81 boolean editingSeqs = false;
83 boolean groupEditing = false;
87 boolean changeEndSeq = false;
89 boolean changeStartSeq = false;
91 boolean changeEndRes = false;
93 boolean changeStartRes = false;
95 SequenceGroup stretchGroup = null;
97 StringBuffer keyboardNo1;
99 StringBuffer keyboardNo2;
101 boolean mouseWheelPressed = false;
103 Point lastMousePress;
105 EditCommand editCommand;
107 StructureSelectionManager ssm;
109 public SeqPanel(AlignViewport avp, AlignmentPanel p)
113 seqCanvas = new SeqCanvas(avp);
114 setLayout(new BorderLayout());
119 seqCanvas.addMouseMotionListener(this);
120 seqCanvas.addMouseListener(this);
121 ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
122 ssm.addStructureViewerListener(this);
123 ssm.addSelectionListener(this);
130 if (editCommand != null && editCommand.getSize() > 0)
132 ap.alignFrame.addHistoryItem(editCommand);
133 av.firePropertyChange("alignment", null, av.getAlignment()
140 groupEditing = false;
148 seqCanvas.cursorY = getKeyboardNo1() - 1;
152 void setCursorColumn()
154 seqCanvas.cursorX = getKeyboardNo1() - 1;
158 void setCursorRowAndColumn()
160 if (keyboardNo2 == null)
162 keyboardNo2 = new StringBuffer();
166 seqCanvas.cursorX = getKeyboardNo1() - 1;
167 seqCanvas.cursorY = getKeyboardNo2() - 1;
172 void setCursorPosition()
174 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
176 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
180 void moveCursor(int dx, int dy)
182 seqCanvas.cursorX += dx;
183 seqCanvas.cursorY += dy;
184 if (av.hasHiddenColumns()
185 && !av.getAlignment().getHiddenColumns()
186 .isVisible(seqCanvas.cursorX))
188 int original = seqCanvas.cursorX - dx;
189 int maxWidth = av.getAlignment().getWidth();
191 while (!av.getAlignment().getHiddenColumns()
192 .isVisible(seqCanvas.cursorX)
193 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
195 seqCanvas.cursorX += dx;
198 if (seqCanvas.cursorX >= maxWidth
199 || !av.getAlignment().getHiddenColumns()
200 .isVisible(seqCanvas.cursorX))
202 seqCanvas.cursorX = original;
208 void scrollToVisible()
210 if (seqCanvas.cursorX < 0)
212 seqCanvas.cursorX = 0;
214 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
216 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
219 if (seqCanvas.cursorY < 0)
221 seqCanvas.cursorY = 0;
223 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
225 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
229 if (av.getWrapAlignment())
231 ap.scrollToWrappedVisible(seqCanvas.cursorX);
235 ViewportRanges ranges = av.getRanges();
236 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
237 while (seqCanvas.cursorY < ranges.getStartSeq())
241 while (seqCanvas.cursorY > ranges.getEndSeq())
245 while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges
249 if (!ap.scrollRight(false))
254 while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges
257 if (!ap.scrollRight(true))
263 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
264 seqCanvas.cursorX, seqCanvas.cursorY);
269 void setSelectionAreaAtCursor(boolean topLeft)
271 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
273 if (av.getSelectionGroup() != null)
275 SequenceGroup sg = av.getSelectionGroup();
276 // Find the top and bottom of this group
277 int min = av.getAlignment().getHeight(), max = 0;
278 for (int i = 0; i < sg.getSize(); i++)
280 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
295 sg.setStartRes(seqCanvas.cursorX);
296 if (sg.getEndRes() < seqCanvas.cursorX)
298 sg.setEndRes(seqCanvas.cursorX);
301 min = seqCanvas.cursorY;
305 sg.setEndRes(seqCanvas.cursorX);
306 if (sg.getStartRes() > seqCanvas.cursorX)
308 sg.setStartRes(seqCanvas.cursorX);
311 max = seqCanvas.cursorY + 1;
316 // Only the user can do this
317 av.setSelectionGroup(null);
321 // Now add any sequences between min and max
323 for (int i = min; i < max; i++)
325 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
330 if (av.getSelectionGroup() == null)
332 SequenceGroup sg = new SequenceGroup();
333 sg.setStartRes(seqCanvas.cursorX);
334 sg.setEndRes(seqCanvas.cursorX);
335 sg.addSequence(sequence, false);
336 av.setSelectionGroup(sg);
338 ap.paintAlignment(false);
342 void insertGapAtCursor(boolean group)
344 groupEditing = group;
345 startseq = seqCanvas.cursorY;
346 lastres = seqCanvas.cursorX;
347 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
351 void deleteGapAtCursor(boolean group)
353 groupEditing = group;
354 startseq = seqCanvas.cursorY;
355 lastres = seqCanvas.cursorX + getKeyboardNo1();
356 editSequence(false, seqCanvas.cursorX);
360 void numberPressed(char value)
362 if (keyboardNo1 == null)
364 keyboardNo1 = new StringBuffer();
367 if (keyboardNo2 != null)
369 keyboardNo2.append(value);
373 keyboardNo1.append(value);
381 if (keyboardNo1 != null)
383 int value = Integer.parseInt(keyboardNo1.toString());
387 } catch (Exception x)
398 if (keyboardNo2 != null)
400 int value = Integer.parseInt(keyboardNo2.toString());
404 } catch (Exception x)
412 * Set status message in alignment panel
415 * aligned sequence object
419 * index of sequence in alignment
420 * @return position of res in sequence
422 void setStatusMessage(SequenceI sequence, int res, int seq)
424 // TODO remove duplication of identical gui method
425 StringBuilder text = new StringBuilder(32);
426 String seqno = seq == -1 ? "" : " " + (seq + 1);
427 text.append("Sequence" + seqno + " ID: " + sequence.getName());
429 String residue = null;
431 * Try to translate the display character to residue name (null for gap).
433 final String displayChar = String.valueOf(sequence.getCharAt(res));
434 if (av.getAlignment().isNucleotide())
436 residue = ResidueProperties.nucleotideName.get(displayChar);
439 text.append(" Nucleotide: ").append(residue);
444 residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
445 .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
449 text.append(" Residue: ").append(residue);
456 pos = sequence.findPosition(res);
457 text.append(" (").append(Integer.toString(pos)).append(")");
460 ap.alignFrame.statusBar.setText(text.toString());
464 * Set the status bar message to highlight the first matched position in
468 * @return true if results were matched, false if not
470 private boolean setStatusMessage(SearchResultsI results)
472 AlignmentI al = this.av.getAlignment();
473 int sequenceIndex = al.findIndex(results);
474 if (sequenceIndex == -1)
478 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
479 for (SearchResultMatchI m : results.getResults())
481 SequenceI seq = m.getSequence();
482 if (seq.getDatasetSequence() != null)
484 seq = seq.getDatasetSequence();
490 * Convert position in sequence (base 1) to sequence character array
493 int start = m.getStart() - m.getSequence().getStart();
494 setStatusMessage(seq, start, sequenceIndex);
502 public void mousePressed(MouseEvent evt)
504 lastMousePress = evt.getPoint();
506 // For now, ignore the mouseWheel font resizing on Macs
507 // As the Button2_mask always seems to be true
508 if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
511 mouseWheelPressed = true;
515 if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
517 if (evt.isControlDown() || evt.isAltDown())
525 doMousePressedDefineMode(evt);
529 int seq = findSeq(evt);
530 int res = findRes(evt);
532 if (seq < 0 || res < 0)
537 if ((seq < av.getAlignment().getHeight())
538 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
553 public void mouseClicked(MouseEvent evt)
555 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
556 if (evt.getClickCount() > 1)
558 if (av.getSelectionGroup() != null
559 && av.getSelectionGroup().getSize() == 1
560 && av.getSelectionGroup().getEndRes()
561 - av.getSelectionGroup().getStartRes() < 2)
563 av.setSelectionGroup(null);
566 SequenceFeature[] features = findFeaturesAtRes(sequence,
567 sequence.findPosition(findRes(evt)));
569 if (features != null && features.length > 0)
571 SearchResultsI highlight = new SearchResults();
572 highlight.addResult(sequence, features[0].getBegin(),
573 features[0].getEnd());
574 seqCanvas.highlightSearchResults(highlight);
576 if (features != null && features.length > 0)
578 seqCanvas.getFeatureRenderer().amendFeatures(
579 new SequenceI[] { sequence }, features, false, ap);
581 seqCanvas.highlightSearchResults(null);
587 public void mouseReleased(MouseEvent evt)
589 mouseDragging = false;
590 mouseWheelPressed = false;
591 ap.paintAlignment(true);
595 doMouseReleasedDefineMode(evt);
603 int startWrapBlock = -1;
605 int wrappedBlock = -1;
607 int findRes(MouseEvent evt)
612 if (av.getWrapAlignment())
615 int hgap = av.getCharHeight();
616 if (av.getScaleAboveWrapped())
618 hgap += av.getCharHeight();
621 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
622 + hgap + seqCanvas.getAnnotationHeight();
626 x -= seqCanvas.LABEL_WEST;
628 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
634 wrappedBlock = y / cHeight;
635 wrappedBlock += av.getRanges().getStartRes() / cwidth;
637 res = wrappedBlock * cwidth + x / av.getCharWidth();
642 res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
645 if (av.hasHiddenColumns())
647 res = av.getAlignment().getHiddenColumns()
648 .adjustForHiddenColumns(res);
655 int findSeq(MouseEvent evt)
657 final int sqnum = findAlRow(evt);
658 return (sqnum < 0) ? 0 : sqnum;
664 * @return row in alignment that was selected (or -1 for column selection)
666 private int findAlRow(MouseEvent evt)
671 if (av.getWrapAlignment())
673 int hgap = av.getCharHeight();
674 if (av.getScaleAboveWrapped())
676 hgap += av.getCharHeight();
679 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
680 + hgap + seqCanvas.getAnnotationHeight();
684 seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
693 seq = Math.min((y / av.getCharHeight())
694 + av.getRanges().getStartSeq(),
696 .getAlignment().getHeight() - 1);
706 public void doMousePressed(MouseEvent evt)
709 int seq = findSeq(evt);
710 int res = findRes(evt);
712 if (seq < av.getAlignment().getHeight()
713 && res < av.getAlignment().getSequenceAt(seq).getLength())
715 // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
716 // Find the residue's position in the sequence (res is the position
734 public void mouseOverSequence(SequenceI sequence, int index, int pos)
736 String tmp = sequence.hashCode() + index + "";
737 if (lastMessage == null || !lastMessage.equals(tmp))
739 ssm.mouseOverSequence(sequence, index, pos, av);
746 public void highlightSequence(SearchResultsI results)
748 if (av.isFollowHighlight())
750 if (ap.scrollToPosition(results, true))
752 ap.alignFrame.repaint();
755 setStatusMessage(results);
756 seqCanvas.highlightSearchResults(results);
761 public VamsasSource getVamsasSource()
763 return this.ap == null ? null : this.ap.av;
767 public void updateColours(SequenceI seq, int index)
769 System.out.println("update the seqPanel colours");
774 public void mouseMoved(MouseEvent evt)
776 final int column = findRes(evt);
777 int seq = findSeq(evt);
779 if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
788 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
789 if (column > sequence.getLength())
798 final char ch = sequence.getCharAt(column);
799 int respos = Comparison.isGap(ch) ? -1 : sequence.findPosition(column);
801 if (ssm != null && respos != -1)
803 mouseOverSequence(sequence, column, respos);
806 StringBuilder text = new StringBuilder();
807 text.append("Sequence ").append(Integer.toString(seq + 1))
808 .append(" ID: ").append(sequence.getName());
813 if (av.getAlignment().isNucleotide())
815 obj = ResidueProperties.nucleotideName.get(ch);
818 text.append(" Nucleotide: ").append(obj);
823 obj = (ch == 'x' || ch == 'X') ? "X" : ResidueProperties.aa2Triplet
824 .get(String.valueOf(ch));
827 text.append(" Residue: ").append(obj);
832 text.append(" (").append(Integer.toString(respos)).append(")");
836 ap.alignFrame.statusBar.setText(text.toString());
838 StringBuilder tooltipText = new StringBuilder();
839 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
842 for (int g = 0; g < groups.length; g++)
844 if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column)
846 if (!groups[g].getName().startsWith("JTreeGroup")
847 && !groups[g].getName().startsWith("JGroup"))
849 tooltipText.append(groups[g].getName()).append(" ");
851 if (groups[g].getDescription() != null)
853 tooltipText.append(groups[g].getDescription());
855 tooltipText.append("\n");
861 * add feature details to tooltip if over one or more features
865 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
866 sequence.findPosition(column));
869 while (index < allFeatures.length)
871 SequenceFeature sf = allFeatures[index];
873 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
875 if (sf.getDescription() != null)
877 tooltipText.append(" " + sf.getDescription());
880 if (sf.getValue("status") != null)
882 String status = sf.getValue("status").toString();
883 if (status.length() > 0)
885 tooltipText.append(" (" + sf.getValue("status") + ")");
888 tooltipText.append("\n");
896 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
900 tooltip.setTip(tooltipText.toString());
904 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
906 Vector tmp = new Vector();
907 SequenceFeature[] features = sequence.getSequenceFeatures();
908 if (features != null)
910 for (int i = 0; i < features.length; i++)
912 if (av.getFeaturesDisplayed() == null
913 || !av.getFeaturesDisplayed().isVisible(
914 features[i].getType()))
919 if (features[i].featureGroup != null
920 && !seqCanvas.fr.checkGroupVisibility(
921 features[i].featureGroup, false))
926 if ((features[i].getBegin() <= res)
927 && (features[i].getEnd() >= res))
929 tmp.addElement(features[i]);
934 features = new SequenceFeature[tmp.size()];
935 tmp.copyInto(features);
943 * set when the current UI interaction has resulted in a change that requires
944 * overview shading to be recalculated. this could be changed to something
945 * more expressive that indicates what actually has changed, so selective
946 * redraws can be applied
948 private boolean needOverviewUpdate; // TODO: refactor to avcontroller
951 public void mouseDragged(MouseEvent evt)
953 if (mouseWheelPressed)
955 int oldWidth = av.getCharWidth();
957 // Which is bigger, left-right or up-down?
958 if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
961 int fontSize = av.font.getSize();
963 if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
967 else if (evt.getY() > lastMousePress.y)
978 new Font(av.font.getName(), av.font.getStyle(), fontSize),
980 av.setCharWidth(oldWidth);
984 if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
986 av.setCharWidth(av.getCharWidth() - 1);
988 else if (evt.getX() > lastMousePress.x)
990 av.setCharWidth(av.getCharWidth() + 1);
993 if (av.getCharWidth() < 1)
1001 FontMetrics fm = getFontMetrics(av.getFont());
1002 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1004 lastMousePress = evt.getPoint();
1006 ap.paintAlignment(false);
1007 ap.annotationPanel.image = null;
1013 doMouseDraggedDefineMode(evt);
1017 int res = findRes(evt);
1024 if ((lastres == -1) || (lastres == res))
1029 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1031 // dragLeft, delete gap
1032 editSequence(false, res);
1036 editSequence(true, res);
1039 mouseDragging = true;
1040 if (scrollThread != null)
1042 scrollThread.setEvent(evt);
1047 synchronized void editSequence(boolean insertGap, int startres)
1050 int fixedRight = -1;
1051 boolean fixedColumns = false;
1052 SequenceGroup sg = av.getSelectionGroup();
1054 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1056 if (!groupEditing && av.hasHiddenRows())
1058 if (av.isHiddenRepSequence(seq))
1060 sg = av.getRepresentedSequences(seq);
1061 groupEditing = true;
1065 StringBuffer message = new StringBuffer();
1068 message.append(MessageManager.getString("action.edit_group")).append(
1070 if (editCommand == null)
1072 editCommand = new EditCommand(
1073 MessageManager.getString("action.edit_group"));
1078 message.append(MessageManager.getString("label.edit_sequence"))
1079 .append(" " + seq.getName());
1080 String label = seq.getName();
1081 if (label.length() > 10)
1083 label = label.substring(0, 10);
1085 if (editCommand == null)
1087 editCommand = new EditCommand(MessageManager.formatMessage(
1088 "label.edit_params", new String[] { label }));
1094 message.append(" insert ");
1098 message.append(" delete ");
1101 message.append(Math.abs(startres - lastres) + " gaps.");
1102 ap.alignFrame.statusBar.setText(message.toString());
1104 // Are we editing within a selection group?
1106 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1109 fixedColumns = true;
1111 // sg might be null as the user may only see 1 sequence,
1112 // but the sequence represents a group
1115 if (!av.isHiddenRepSequence(seq))
1121 sg = av.getRepresentedSequences(seq);
1124 fixedLeft = sg.getStartRes();
1125 fixedRight = sg.getEndRes();
1127 if ((startres < fixedLeft && lastres >= fixedLeft)
1128 || (startres >= fixedLeft && lastres < fixedLeft)
1129 || (startres > fixedRight && lastres <= fixedRight)
1130 || (startres <= fixedRight && lastres > fixedRight))
1136 if (fixedLeft > startres)
1138 fixedRight = fixedLeft - 1;
1141 else if (fixedRight < startres)
1143 fixedLeft = fixedRight;
1148 if (av.hasHiddenColumns())
1150 fixedColumns = true;
1151 int y1 = av.getAlignment().getHiddenColumns()
1152 .getHiddenBoundaryLeft(startres);
1153 int y2 = av.getAlignment().getHiddenColumns()
1154 .getHiddenBoundaryRight(startres);
1156 if ((insertGap && startres > y1 && lastres < y1)
1157 || (!insertGap && startres < y2 && lastres > y2))
1163 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1164 // Selection spans a hidden region
1165 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1173 fixedRight = y2 - 1;
1180 SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
1181 .toArray(new SequenceI[0]);
1186 // If the user has selected the whole sequence, and is dragging to
1187 // the right, we can still extend the alignment and selectionGroup
1188 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1189 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1191 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1192 fixedRight = sg.getEndRes();
1195 // Is it valid with fixed columns??
1196 // Find the next gap before the end
1197 // of the visible region boundary
1198 boolean blank = false;
1199 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1203 for (SequenceI gs : groupSeqs)
1205 for (int j = 0; j < startres - lastres; j++)
1207 if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
1223 if (sg.getSize() == av.getAlignment().getHeight())
1225 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1226 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1232 int alWidth = av.getAlignment().getWidth();
1233 if (av.hasHiddenRows())
1235 int hwidth = av.getAlignment().getHiddenSequences()
1237 if (hwidth > alWidth)
1242 // We can still insert gaps if the selectionGroup
1243 // contains all the sequences
1244 sg.setEndRes(sg.getEndRes() + startres - lastres);
1245 fixedRight = alWidth + startres - lastres;
1256 else if (!insertGap)
1258 // / Are we able to delete?
1259 // ie are all columns blank?
1261 for (SequenceI gs : groupSeqs)
1263 for (int j = startres; j < lastres; j++)
1265 if (gs.getLength() <= j)
1270 if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
1272 // Not a gap, block edit not valid
1282 // dragging to the right
1283 if (fixedColumns && fixedRight != -1)
1285 for (int j = lastres; j < startres; j++)
1287 insertChar(j, groupSeqs, fixedRight);
1292 editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1293 startres - lastres, av.getAlignment(), true);
1298 // dragging to the left
1299 if (fixedColumns && fixedRight != -1)
1301 for (int j = lastres; j > startres; j--)
1303 deleteChar(startres, groupSeqs, fixedRight);
1308 editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1309 lastres - startres, av.getAlignment(), true);
1315 // ///Editing a single sequence///////////
1319 // dragging to the right
1320 if (fixedColumns && fixedRight != -1)
1322 for (int j = lastres; j < startres; j++)
1324 insertChar(j, new SequenceI[] { seq }, fixedRight);
1329 editCommand.appendEdit(Action.INSERT_GAP,
1330 new SequenceI[] { seq }, lastres, startres - lastres,
1331 av.getAlignment(), true);
1336 // dragging to the left
1337 if (fixedColumns && fixedRight != -1)
1339 for (int j = lastres; j > startres; j--)
1341 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1346 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1351 // could be a keyboard edit trying to delete none gaps
1353 for (int m = startres; m < lastres; m++)
1355 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1364 editCommand.appendEdit(Action.DELETE_GAP,
1365 new SequenceI[] { seq }, startres, max,
1366 av.getAlignment(), true);
1373 seqCanvas.repaint();
1376 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1378 int blankColumn = fixedColumn;
1379 for (int s = 0; s < seq.length; s++)
1381 // Find the next gap before the end of the visible region boundary
1382 // If lastCol > j, theres a boundary after the gap insertion
1384 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1386 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1388 // Theres a space, so break and insert the gap
1393 if (blankColumn <= j)
1395 blankColumn = fixedColumn;
1401 editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
1402 av.getAlignment(), true);
1404 editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
1409 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1412 editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
1415 editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
1416 av.getAlignment(), true);
1419 // ////////////////////////////////////////
1420 // ///Everything below this is for defining the boundary of the rubberband
1421 // ////////////////////////////////////////
1422 public void doMousePressedDefineMode(MouseEvent evt)
1424 if (scrollThread != null)
1426 scrollThread.running = false;
1427 scrollThread = null;
1430 int res = findRes(evt);
1431 int seq = findSeq(evt);
1433 startWrapBlock = wrappedBlock;
1440 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1442 if (sequence == null || res > sequence.getLength())
1447 stretchGroup = av.getSelectionGroup();
1449 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1451 stretchGroup = av.getAlignment().findGroup(sequence, res);
1452 if (stretchGroup != null)
1454 // only update the current selection if the popup menu has a group to
1456 av.setSelectionGroup(stretchGroup);
1460 // DETECT RIGHT MOUSE BUTTON IN AWT
1461 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
1463 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
1464 sequence.findPosition(res));
1466 Vector<String> links = null;
1467 if (allFeatures != null)
1469 for (int i = 0; i < allFeatures.length; i++)
1471 if (allFeatures[i].links != null)
1475 links = new Vector<String>();
1477 for (int j = 0; j < allFeatures[i].links.size(); j++)
1479 links.addElement(allFeatures[i].links.elementAt(j));
1484 APopupMenu popup = new APopupMenu(ap, null, links);
1486 popup.show(this, evt.getX(), evt.getY());
1492 seqCanvas.cursorX = findRes(evt);
1493 seqCanvas.cursorY = findSeq(evt);
1494 seqCanvas.repaint();
1498 // Only if left mouse button do we want to change group sizes
1500 if (stretchGroup == null)
1502 // define a new group here
1503 SequenceGroup sg = new SequenceGroup();
1504 sg.setStartRes(res);
1506 sg.addSequence(sequence, false);
1507 av.setSelectionGroup(sg);
1510 if (av.getConservationSelected())
1512 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1515 if (av.getAbovePIDThreshold())
1517 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1524 public void doMouseReleasedDefineMode(MouseEvent evt)
1526 if (stretchGroup == null)
1530 // always do this - annotation has own state
1531 // but defer colourscheme update until hidden sequences are passed in
1532 boolean vischange = stretchGroup.recalcConservation(true);
1533 // here we rely on stretchGroup == av.getSelection()
1534 needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
1535 if (stretchGroup.cs != null)
1537 stretchGroup.cs.alignmentChanged(stretchGroup,
1538 av.getHiddenRepSequences());
1540 if (stretchGroup.cs.conservationApplied())
1542 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1543 stretchGroup.getName());
1545 if (stretchGroup.cs.getThreshold() > 0)
1547 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1548 stretchGroup.getName());
1551 PaintRefresher.Refresh(ap, av.getSequenceSetId());
1552 ap.paintAlignment(needOverviewUpdate);
1553 needOverviewUpdate = false;
1554 changeEndRes = false;
1555 changeStartRes = false;
1556 stretchGroup = null;
1560 public void doMouseDraggedDefineMode(MouseEvent evt)
1562 int res = findRes(evt);
1563 int y = findSeq(evt);
1565 if (wrappedBlock != startWrapBlock)
1570 if (stretchGroup == null)
1575 mouseDragging = true;
1577 if (y > av.getAlignment().getHeight())
1579 y = av.getAlignment().getHeight() - 1;
1582 if (res >= av.getAlignment().getWidth())
1584 res = av.getAlignment().getWidth() - 1;
1587 if (stretchGroup.getEndRes() == res)
1589 // Edit end res position of selected group
1590 changeEndRes = true;
1592 else if (stretchGroup.getStartRes() == res)
1594 // Edit start res position of selected group
1595 changeStartRes = true;
1605 if (res > (stretchGroup.getStartRes() - 1))
1607 stretchGroup.setEndRes(res);
1608 needOverviewUpdate |= av.isSelectionDefinedGroup();
1611 else if (changeStartRes)
1613 if (res < (stretchGroup.getEndRes() + 1))
1615 stretchGroup.setStartRes(res);
1616 needOverviewUpdate |= av.isSelectionDefinedGroup();
1620 int dragDirection = 0;
1626 else if (y < oldSeq)
1631 while ((y != oldSeq) && (oldSeq > -1)
1632 && (y < av.getAlignment().getHeight()))
1634 // This routine ensures we don't skip any sequences, as the
1635 // selection is quite slow.
1636 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1638 oldSeq += dragDirection;
1645 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1647 if (stretchGroup.getSequences(null).contains(nextSeq))
1649 stretchGroup.deleteSequence(seq, false);
1650 needOverviewUpdate |= av.isSelectionDefinedGroup();
1656 stretchGroup.addSequence(seq, false);
1659 stretchGroup.addSequence(nextSeq, false);
1660 needOverviewUpdate |= av.isSelectionDefinedGroup();
1669 if (res > av.getRanges().getEndRes()
1670 || res < av.getRanges().getStartRes()
1671 || y < av.getRanges().getStartSeq()
1672 || y > av.getRanges().getEndSeq())
1677 if (scrollThread != null)
1679 scrollThread.setEvent(evt);
1682 seqCanvas.repaint();
1686 public void mouseEntered(MouseEvent e)
1693 if (scrollThread != null)
1695 scrollThread.running = false;
1696 scrollThread = null;
1701 public void mouseExited(MouseEvent e)
1703 if (av.getWrapAlignment())
1708 if (mouseDragging && scrollThread == null)
1710 scrollThread = new ScrollThread();
1714 void scrollCanvas(MouseEvent evt)
1718 if (scrollThread != null)
1720 scrollThread.running = false;
1721 scrollThread = null;
1723 mouseDragging = false;
1727 if (scrollThread == null)
1729 scrollThread = new ScrollThread();
1732 mouseDragging = true;
1733 scrollThread.setEvent(evt);
1738 // this class allows scrolling off the bottom of the visible alignment
1739 class ScrollThread extends Thread
1743 boolean running = false;
1745 public ScrollThread()
1750 public void setEvent(MouseEvent e)
1755 public void stopScrolling()
1770 if (mouseDragging && evt.getY() < 0
1771 && av.getRanges().getStartSeq() > 0)
1773 running = ap.scrollUp(true);
1776 if (mouseDragging && evt.getY() >= getSize().height
1777 && av.getAlignment().getHeight() > av.getRanges()
1780 running = ap.scrollUp(false);
1783 if (mouseDragging && evt.getX() < 0)
1785 running = ap.scrollRight(false);
1788 else if (mouseDragging && evt.getX() >= getSize().width)
1790 running = ap.scrollRight(true);
1797 } catch (Exception ex)
1805 * modify current selection according to a received message.
1808 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1809 HiddenColumns hidden, SelectionSource source)
1811 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1812 // handles selection messages...
1813 // TODO: extend config options to allow user to control if selections may be
1814 // shared between viewports.
1816 && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
1817 .getSequenceSetId().equals(av.getSequenceSetId()))))
1823 * Check for selection in a view of which this one is a dna/protein
1826 if (selectionFromTranslation(seqsel, colsel, hidden, source))
1831 // do we want to thread this ? (contention with seqsel and colsel locks, I
1834 * only copy colsel if there is a real intersection between
1835 * sequence selection and this panel's alignment
1837 boolean repaint = false;
1838 boolean copycolsel = false;
1839 if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
1841 SequenceGroup sgroup = null;
1842 if (seqsel != null && seqsel.getSize() > 0)
1844 if (av.getAlignment() == null)
1847 .println("Selection message: alignviewport av SeqSetId="
1848 + av.getSequenceSetId() + " ViewId="
1850 + " 's alignment is NULL! returning immediatly.");
1853 sgroup = seqsel.intersect(av.getAlignment(),
1854 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1855 if ((sgroup != null && sgroup.getSize() > 0))
1860 if (sgroup != null && sgroup.getSize() > 0)
1862 av.setSelectionGroup(sgroup);
1866 av.setSelectionGroup(null);
1868 repaint = av.isSelectionGroupChanged(true);
1871 && (av.getColumnSelection() == null || !av
1872 .isColSelChanged(true)))
1874 // the current selection is unset or from a previous message
1875 // so import the new colsel.
1876 if (colsel == null || colsel.isEmpty())
1878 if (av.getColumnSelection() != null)
1880 av.getColumnSelection().clear();
1885 // TODO: shift colSel according to the intersecting sequences
1886 if (av.getColumnSelection() == null)
1888 av.setColumnSelection(new ColumnSelection(colsel));
1892 av.getColumnSelection().setElementsFrom(colsel,
1893 av.getAlignment().getHiddenColumns());
1896 repaint |= av.isColSelChanged(true);
1899 && av.hasHiddenColumns()
1900 && (av.getColumnSelection() == null || av.getAlignment()
1901 .getHiddenColumns().getHiddenRegions() == null))
1903 System.err.println("Bad things");
1907 ap.scalePanelHolder.repaint();
1913 * scroll to the given row/column - or nearest visible location
1918 public void scrollTo(int row, int column)
1921 row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
1922 column = column < 0 ? ap.av.getRanges().getStartRes() : column;
1923 ap.scrollTo(column, column, row, true, true);
1927 * scroll to the given row - or nearest visible location
1931 public void scrollToRow(int row)
1934 row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
1935 ap.scrollTo(ap.av.getRanges().getStartRes(), ap.av.getRanges()
1936 .getStartRes(), row, true, true);
1940 * scroll to the given column - or nearest visible location
1944 public void scrollToColumn(int column)
1947 column = column < 0 ? ap.av.getRanges().getStartRes() : column;
1948 ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, true);
1952 * If this panel is a cdna/protein translation view of the selection source,
1953 * tries to map the source selection to a local one, and returns true. Else
1960 protected boolean selectionFromTranslation(SequenceGroup seqsel,
1961 ColumnSelection colsel, HiddenColumns hidden,
1962 SelectionSource source)
1964 if (!(source instanceof AlignViewportI))
1968 final AlignViewportI sourceAv = (AlignViewportI) source;
1969 if (sourceAv.getCodingComplement() != av
1970 && av.getCodingComplement() != sourceAv)
1976 * Map sequence selection
1978 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
1979 av.setSelectionGroup(sg);
1980 av.isSelectionGroupChanged(true);
1983 * Map column selection
1985 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
1987 ColumnSelection cs = new ColumnSelection();
1988 HiddenColumns hs = new HiddenColumns();
1989 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
1990 av.setColumnSelection(cs);
1991 av.getAlignment().setHiddenColumns(hs);
1993 ap.scalePanelHolder.repaint();