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 av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
235 ViewportRanges ranges = av.getRanges();
236 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
237 while (seqCanvas.cursorY < ranges.getStartSeq())
239 ranges.scrollUp(true);
241 while (seqCanvas.cursorY > ranges.getEndSeq())
243 ranges.scrollUp(false);
245 while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(ranges
249 if (!ranges.scrollRight(false))
254 while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(ranges
257 if (!ranges.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 column in sequence or -1 if at gap
422 void setStatusMessage(SequenceI sequence, int column, 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(column));
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(column);
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 boolean didDrag = mouseDragging; // did we come here after a drag
590 mouseDragging = false;
591 mouseWheelPressed = false;
595 doMouseReleasedDefineMode(evt, didDrag);
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 // don't allow highlight of protein/cDNA to also scroll a complementary
751 // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
752 // over residue to change abruptly, causing highlighted residue in panel 2
753 // to change, causing a scroll in panel 1 etc)
754 ap.setToScrollComplementPanel(false);
755 if (ap.scrollToPosition(results, true))
757 ap.alignFrame.repaint();
759 ap.setToScrollComplementPanel(true);
761 setStatusMessage(results);
762 seqCanvas.highlightSearchResults(results);
767 public VamsasSource getVamsasSource()
769 return this.ap == null ? null : this.ap.av;
773 public void updateColours(SequenceI seq, int index)
775 System.out.println("update the seqPanel colours");
780 public void mouseMoved(MouseEvent evt)
782 final int column = findRes(evt);
783 int seq = findSeq(evt);
785 if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
794 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
795 if (column > sequence.getLength())
804 final char ch = sequence.getCharAt(column);
805 int respos = Comparison.isGap(ch) ? -1 : sequence.findPosition(column);
807 if (ssm != null && respos != -1)
809 mouseOverSequence(sequence, column, respos);
812 StringBuilder text = new StringBuilder();
813 text.append("Sequence ").append(Integer.toString(seq + 1))
814 .append(" ID: ").append(sequence.getName());
819 if (av.getAlignment().isNucleotide())
821 obj = ResidueProperties.nucleotideName.get(ch);
824 text.append(" Nucleotide: ").append(obj);
829 obj = (ch == 'x' || ch == 'X') ? "X" : ResidueProperties.aa2Triplet
830 .get(String.valueOf(ch));
833 text.append(" Residue: ").append(obj);
838 text.append(" (").append(Integer.toString(respos)).append(")");
842 ap.alignFrame.statusBar.setText(text.toString());
844 StringBuilder tooltipText = new StringBuilder();
845 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
848 for (int g = 0; g < groups.length; g++)
850 if (groups[g].getStartRes() <= column && groups[g].getEndRes() >= column)
852 if (!groups[g].getName().startsWith("JTreeGroup")
853 && !groups[g].getName().startsWith("JGroup"))
855 tooltipText.append(groups[g].getName()).append(" ");
857 if (groups[g].getDescription() != null)
859 tooltipText.append(groups[g].getDescription());
861 tooltipText.append("\n");
867 * add feature details to tooltip if over one or more features
871 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
872 sequence.findPosition(column));
875 while (index < allFeatures.length)
877 SequenceFeature sf = allFeatures[index];
879 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
881 if (sf.getDescription() != null)
883 tooltipText.append(" " + sf.getDescription());
886 if (sf.getValue("status") != null)
888 String status = sf.getValue("status").toString();
889 if (status.length() > 0)
891 tooltipText.append(" (" + sf.getValue("status") + ")");
894 tooltipText.append("\n");
902 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
906 tooltip.setTip(tooltipText.toString());
910 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
912 Vector tmp = new Vector();
913 SequenceFeature[] features = sequence.getSequenceFeatures();
914 if (features != null)
916 for (int i = 0; i < features.length; i++)
918 if (av.getFeaturesDisplayed() == null
919 || !av.getFeaturesDisplayed().isVisible(
920 features[i].getType()))
925 if (features[i].featureGroup != null
926 && !seqCanvas.fr.checkGroupVisibility(
927 features[i].featureGroup, false))
932 if ((features[i].getBegin() <= res)
933 && (features[i].getEnd() >= res))
935 tmp.addElement(features[i]);
940 features = new SequenceFeature[tmp.size()];
941 tmp.copyInto(features);
949 * set when the current UI interaction has resulted in a change that requires
950 * overview shading to be recalculated. this could be changed to something
951 * more expressive that indicates what actually has changed, so selective
952 * redraws can be applied
954 private boolean needOverviewUpdate; // TODO: refactor to avcontroller
957 public void mouseDragged(MouseEvent evt)
959 if (mouseWheelPressed)
961 int oldWidth = av.getCharWidth();
963 // Which is bigger, left-right or up-down?
964 if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
967 int fontSize = av.font.getSize();
969 if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
973 else if (evt.getY() > lastMousePress.y)
984 new Font(av.font.getName(), av.font.getStyle(), fontSize),
986 av.setCharWidth(oldWidth);
990 if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
992 av.setCharWidth(av.getCharWidth() - 1);
994 else if (evt.getX() > lastMousePress.x)
996 av.setCharWidth(av.getCharWidth() + 1);
999 if (av.getCharWidth() < 1)
1007 FontMetrics fm = getFontMetrics(av.getFont());
1008 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
1010 lastMousePress = evt.getPoint();
1012 ap.paintAlignment(false);
1013 ap.annotationPanel.image = null;
1019 doMouseDraggedDefineMode(evt);
1023 int res = findRes(evt);
1030 if ((lastres == -1) || (lastres == res))
1035 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1037 // dragLeft, delete gap
1038 editSequence(false, res);
1042 editSequence(true, res);
1045 mouseDragging = true;
1046 if (scrollThread != null)
1048 scrollThread.setEvent(evt);
1053 synchronized void editSequence(boolean insertGap, int startres)
1056 int fixedRight = -1;
1057 boolean fixedColumns = false;
1058 SequenceGroup sg = av.getSelectionGroup();
1060 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1062 if (!groupEditing && av.hasHiddenRows())
1064 if (av.isHiddenRepSequence(seq))
1066 sg = av.getRepresentedSequences(seq);
1067 groupEditing = true;
1071 StringBuffer message = new StringBuffer();
1074 message.append(MessageManager.getString("action.edit_group")).append(
1076 if (editCommand == null)
1078 editCommand = new EditCommand(
1079 MessageManager.getString("action.edit_group"));
1084 message.append(MessageManager.getString("label.edit_sequence"))
1085 .append(" " + seq.getName());
1086 String label = seq.getName();
1087 if (label.length() > 10)
1089 label = label.substring(0, 10);
1091 if (editCommand == null)
1093 editCommand = new EditCommand(MessageManager.formatMessage(
1094 "label.edit_params", new String[] { label }));
1100 message.append(" insert ");
1104 message.append(" delete ");
1107 message.append(Math.abs(startres - lastres) + " gaps.");
1108 ap.alignFrame.statusBar.setText(message.toString());
1110 // Are we editing within a selection group?
1112 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1115 fixedColumns = true;
1117 // sg might be null as the user may only see 1 sequence,
1118 // but the sequence represents a group
1121 if (!av.isHiddenRepSequence(seq))
1127 sg = av.getRepresentedSequences(seq);
1130 fixedLeft = sg.getStartRes();
1131 fixedRight = sg.getEndRes();
1133 if ((startres < fixedLeft && lastres >= fixedLeft)
1134 || (startres >= fixedLeft && lastres < fixedLeft)
1135 || (startres > fixedRight && lastres <= fixedRight)
1136 || (startres <= fixedRight && lastres > fixedRight))
1142 if (fixedLeft > startres)
1144 fixedRight = fixedLeft - 1;
1147 else if (fixedRight < startres)
1149 fixedLeft = fixedRight;
1154 if (av.hasHiddenColumns())
1156 fixedColumns = true;
1157 int y1 = av.getAlignment().getHiddenColumns()
1158 .getHiddenBoundaryLeft(startres);
1159 int y2 = av.getAlignment().getHiddenColumns()
1160 .getHiddenBoundaryRight(startres);
1162 if ((insertGap && startres > y1 && lastres < y1)
1163 || (!insertGap && startres < y2 && lastres > y2))
1169 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1170 // Selection spans a hidden region
1171 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1179 fixedRight = y2 - 1;
1186 SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
1187 .toArray(new SequenceI[0]);
1192 // If the user has selected the whole sequence, and is dragging to
1193 // the right, we can still extend the alignment and selectionGroup
1194 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1195 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1197 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1198 fixedRight = sg.getEndRes();
1201 // Is it valid with fixed columns??
1202 // Find the next gap before the end
1203 // of the visible region boundary
1204 boolean blank = false;
1205 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1209 for (SequenceI gs : groupSeqs)
1211 for (int j = 0; j < startres - lastres; j++)
1213 if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
1229 if (sg.getSize() == av.getAlignment().getHeight())
1231 if ((av.hasHiddenColumns() && startres < av.getAlignment()
1232 .getHiddenColumns().getHiddenBoundaryRight(startres)))
1238 int alWidth = av.getAlignment().getWidth();
1239 if (av.hasHiddenRows())
1241 int hwidth = av.getAlignment().getHiddenSequences()
1243 if (hwidth > alWidth)
1248 // We can still insert gaps if the selectionGroup
1249 // contains all the sequences
1250 sg.setEndRes(sg.getEndRes() + startres - lastres);
1251 fixedRight = alWidth + startres - lastres;
1262 else if (!insertGap)
1264 // / Are we able to delete?
1265 // ie are all columns blank?
1267 for (SequenceI gs : groupSeqs)
1269 for (int j = startres; j < lastres; j++)
1271 if (gs.getLength() <= j)
1276 if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
1278 // Not a gap, block edit not valid
1288 // dragging to the right
1289 if (fixedColumns && fixedRight != -1)
1291 for (int j = lastres; j < startres; j++)
1293 insertChar(j, groupSeqs, fixedRight);
1298 editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1299 startres - lastres, av.getAlignment(), true);
1304 // dragging to the left
1305 if (fixedColumns && fixedRight != -1)
1307 for (int j = lastres; j > startres; j--)
1309 deleteChar(startres, groupSeqs, fixedRight);
1314 editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1315 lastres - startres, av.getAlignment(), true);
1321 // ///Editing a single sequence///////////
1325 // dragging to the right
1326 if (fixedColumns && fixedRight != -1)
1328 for (int j = lastres; j < startres; j++)
1330 insertChar(j, new SequenceI[] { seq }, fixedRight);
1335 editCommand.appendEdit(Action.INSERT_GAP,
1336 new SequenceI[] { seq }, lastres, startres - lastres,
1337 av.getAlignment(), true);
1342 // dragging to the left
1343 if (fixedColumns && fixedRight != -1)
1345 for (int j = lastres; j > startres; j--)
1347 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1352 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1357 // could be a keyboard edit trying to delete none gaps
1359 for (int m = startres; m < lastres; m++)
1361 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1370 editCommand.appendEdit(Action.DELETE_GAP,
1371 new SequenceI[] { seq }, startres, max,
1372 av.getAlignment(), true);
1379 seqCanvas.repaint();
1382 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1384 int blankColumn = fixedColumn;
1385 for (int s = 0; s < seq.length; s++)
1387 // Find the next gap before the end of the visible region boundary
1388 // If lastCol > j, theres a boundary after the gap insertion
1390 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1392 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1394 // Theres a space, so break and insert the gap
1399 if (blankColumn <= j)
1401 blankColumn = fixedColumn;
1407 editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
1408 av.getAlignment(), true);
1410 editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
1415 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1418 editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
1421 editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
1422 av.getAlignment(), true);
1425 // ////////////////////////////////////////
1426 // ///Everything below this is for defining the boundary of the rubberband
1427 // ////////////////////////////////////////
1428 public void doMousePressedDefineMode(MouseEvent evt)
1430 if (scrollThread != null)
1432 scrollThread.running = false;
1433 scrollThread = null;
1436 int res = findRes(evt);
1437 int seq = findSeq(evt);
1439 startWrapBlock = wrappedBlock;
1446 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1448 if (sequence == null || res > sequence.getLength())
1453 stretchGroup = av.getSelectionGroup();
1455 if (stretchGroup == null || !stretchGroup.contains(sequence, res))
1457 stretchGroup = av.getAlignment().findGroup(sequence, res);
1458 if (stretchGroup != null)
1460 // only update the current selection if the popup menu has a group to
1462 av.setSelectionGroup(stretchGroup);
1466 // DETECT RIGHT MOUSE BUTTON IN AWT
1467 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
1469 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
1470 sequence.findPosition(res));
1472 Vector<String> links = null;
1473 if (allFeatures != null)
1475 for (int i = 0; i < allFeatures.length; i++)
1477 if (allFeatures[i].links != null)
1481 links = new Vector<>();
1483 for (int j = 0; j < allFeatures[i].links.size(); j++)
1485 links.addElement(allFeatures[i].links.elementAt(j));
1490 APopupMenu popup = new APopupMenu(ap, null, links);
1492 popup.show(this, evt.getX(), evt.getY());
1498 seqCanvas.cursorX = findRes(evt);
1499 seqCanvas.cursorY = findSeq(evt);
1500 seqCanvas.repaint();
1504 // Only if left mouse button do we want to change group sizes
1506 if (stretchGroup == null)
1508 // define a new group here
1509 SequenceGroup sg = new SequenceGroup();
1510 sg.setStartRes(res);
1512 sg.addSequence(sequence, false);
1513 av.setSelectionGroup(sg);
1516 if (av.getConservationSelected())
1518 SliderPanel.setConservationSlider(ap, av.getResidueShading(),
1521 if (av.getAbovePIDThreshold())
1523 SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
1530 public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
1532 if (stretchGroup == null)
1536 // always do this - annotation has own state
1537 // but defer colourscheme update until hidden sequences are passed in
1538 boolean vischange = stretchGroup.recalcConservation(true);
1539 // here we rely on stretchGroup == av.getSelection()
1540 needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
1542 if (stretchGroup.cs != null)
1544 stretchGroup.cs.alignmentChanged(stretchGroup,
1545 av.getHiddenRepSequences());
1547 if (stretchGroup.cs.conservationApplied())
1549 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1550 stretchGroup.getName());
1552 if (stretchGroup.cs.getThreshold() > 0)
1554 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1555 stretchGroup.getName());
1558 PaintRefresher.Refresh(ap, av.getSequenceSetId());
1559 ap.paintAlignment(needOverviewUpdate);
1560 needOverviewUpdate = false;
1561 changeEndRes = false;
1562 changeStartRes = false;
1563 stretchGroup = null;
1567 public void doMouseDraggedDefineMode(MouseEvent evt)
1569 int res = findRes(evt);
1570 int y = findSeq(evt);
1572 if (wrappedBlock != startWrapBlock)
1577 if (stretchGroup == null)
1582 mouseDragging = true;
1584 if (y > av.getAlignment().getHeight())
1586 y = av.getAlignment().getHeight() - 1;
1589 if (res >= av.getAlignment().getWidth())
1591 res = av.getAlignment().getWidth() - 1;
1594 if (stretchGroup.getEndRes() == res)
1596 // Edit end res position of selected group
1597 changeEndRes = true;
1599 else if (stretchGroup.getStartRes() == res)
1601 // Edit start res position of selected group
1602 changeStartRes = true;
1612 if (res > (stretchGroup.getStartRes() - 1))
1614 stretchGroup.setEndRes(res);
1615 needOverviewUpdate |= av.isSelectionDefinedGroup();
1618 else if (changeStartRes)
1620 if (res < (stretchGroup.getEndRes() + 1))
1622 stretchGroup.setStartRes(res);
1623 needOverviewUpdate |= av.isSelectionDefinedGroup();
1627 int dragDirection = 0;
1633 else if (y < oldSeq)
1638 while ((y != oldSeq) && (oldSeq > -1)
1639 && (y < av.getAlignment().getHeight()))
1641 // This routine ensures we don't skip any sequences, as the
1642 // selection is quite slow.
1643 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1645 oldSeq += dragDirection;
1652 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1654 if (stretchGroup.getSequences(null).contains(nextSeq))
1656 stretchGroup.deleteSequence(seq, false);
1657 needOverviewUpdate |= av.isSelectionDefinedGroup();
1663 stretchGroup.addSequence(seq, false);
1666 stretchGroup.addSequence(nextSeq, false);
1667 needOverviewUpdate |= av.isSelectionDefinedGroup();
1676 if (res > av.getRanges().getEndRes()
1677 || res < av.getRanges().getStartRes()
1678 || y < av.getRanges().getStartSeq()
1679 || y > av.getRanges().getEndSeq())
1684 if (scrollThread != null)
1686 scrollThread.setEvent(evt);
1689 seqCanvas.repaint();
1693 public void mouseEntered(MouseEvent e)
1700 if (scrollThread != null)
1702 scrollThread.running = false;
1703 scrollThread = null;
1708 public void mouseExited(MouseEvent e)
1710 if (av.getWrapAlignment())
1715 if (mouseDragging && scrollThread == null)
1717 scrollThread = new ScrollThread();
1721 void scrollCanvas(MouseEvent evt)
1725 if (scrollThread != null)
1727 scrollThread.running = false;
1728 scrollThread = null;
1730 mouseDragging = false;
1734 if (scrollThread == null)
1736 scrollThread = new ScrollThread();
1739 mouseDragging = true;
1740 scrollThread.setEvent(evt);
1745 // this class allows scrolling off the bottom of the visible alignment
1746 class ScrollThread extends Thread
1750 boolean running = false;
1752 public ScrollThread()
1757 public void setEvent(MouseEvent e)
1762 public void stopScrolling()
1777 if (mouseDragging && evt.getY() < 0
1778 && av.getRanges().getStartSeq() > 0)
1780 running = av.getRanges().scrollUp(true);
1783 if (mouseDragging && evt.getY() >= getSize().height
1784 && av.getAlignment().getHeight() > av.getRanges()
1787 running = av.getRanges().scrollUp(false);
1790 if (mouseDragging && evt.getX() < 0)
1792 running = av.getRanges().scrollRight(false);
1795 else if (mouseDragging && evt.getX() >= getSize().width)
1797 running = av.getRanges().scrollRight(true);
1804 } catch (Exception ex)
1812 * modify current selection according to a received message.
1815 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1816 HiddenColumns hidden, SelectionSource source)
1818 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1819 // handles selection messages...
1820 // TODO: extend config options to allow user to control if selections may be
1821 // shared between viewports.
1823 && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
1824 .getSequenceSetId().equals(av.getSequenceSetId()))))
1830 * Check for selection in a view of which this one is a dna/protein
1833 if (selectionFromTranslation(seqsel, colsel, hidden, source))
1838 // do we want to thread this ? (contention with seqsel and colsel locks, I
1841 * only copy colsel if there is a real intersection between
1842 * sequence selection and this panel's alignment
1844 boolean repaint = false;
1845 boolean copycolsel = false;
1846 if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
1848 SequenceGroup sgroup = null;
1849 if (seqsel != null && seqsel.getSize() > 0)
1851 if (av.getAlignment() == null)
1854 .println("Selection message: alignviewport av SeqSetId="
1855 + av.getSequenceSetId() + " ViewId="
1857 + " 's alignment is NULL! returning immediatly.");
1860 sgroup = seqsel.intersect(av.getAlignment(),
1861 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1862 if ((sgroup != null && sgroup.getSize() > 0))
1867 if (sgroup != null && sgroup.getSize() > 0)
1869 av.setSelectionGroup(sgroup);
1873 av.setSelectionGroup(null);
1875 repaint = av.isSelectionGroupChanged(true);
1878 && (av.getColumnSelection() == null || !av
1879 .isColSelChanged(true)))
1881 // the current selection is unset or from a previous message
1882 // so import the new colsel.
1883 if (colsel == null || colsel.isEmpty())
1885 if (av.getColumnSelection() != null)
1887 av.getColumnSelection().clear();
1892 // TODO: shift colSel according to the intersecting sequences
1893 if (av.getColumnSelection() == null)
1895 av.setColumnSelection(new ColumnSelection(colsel));
1899 av.getColumnSelection().setElementsFrom(colsel,
1900 av.getAlignment().getHiddenColumns());
1903 repaint |= av.isColSelChanged(true);
1906 && av.hasHiddenColumns()
1907 && (av.getColumnSelection() == null || av.getAlignment()
1908 .getHiddenColumns().getHiddenRegions() == null))
1910 System.err.println("Bad things");
1914 ap.scalePanelHolder.repaint();
1920 * scroll to the given row/column - or nearest visible location
1925 public void scrollTo(int row, int column)
1928 row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
1929 column = column < 0 ? ap.av.getRanges().getStartRes() : column;
1930 ap.scrollTo(column, column, row, true, true);
1934 * scroll to the given row - or nearest visible location
1938 public void scrollToRow(int row)
1941 row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
1942 ap.scrollTo(ap.av.getRanges().getStartRes(), ap.av.getRanges()
1943 .getStartRes(), row, true, true);
1947 * scroll to the given column - or nearest visible location
1951 public void scrollToColumn(int column)
1954 column = column < 0 ? ap.av.getRanges().getStartRes() : column;
1955 ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, true);
1959 * If this panel is a cdna/protein translation view of the selection source,
1960 * tries to map the source selection to a local one, and returns true. Else
1967 protected boolean selectionFromTranslation(SequenceGroup seqsel,
1968 ColumnSelection colsel, HiddenColumns hidden,
1969 SelectionSource source)
1971 if (!(source instanceof AlignViewportI))
1975 final AlignViewportI sourceAv = (AlignViewportI) source;
1976 if (sourceAv.getCodingComplement() != av
1977 && av.getCodingComplement() != sourceAv)
1983 * Map sequence selection
1985 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
1986 av.setSelectionGroup(sg);
1987 av.isSelectionGroupChanged(true);
1990 * Map column selection
1992 // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
1994 ColumnSelection cs = new ColumnSelection();
1995 HiddenColumns hs = new HiddenColumns();
1996 MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
1997 av.setColumnSelection(cs);
1998 av.getAlignment().setHiddenColumns(hs);
2000 ap.scalePanelHolder.repaint();