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.SearchResults;
29 import jalview.datamodel.SearchResults.Match;
30 import jalview.datamodel.Sequence;
31 import jalview.datamodel.SequenceFeature;
32 import jalview.datamodel.SequenceGroup;
33 import jalview.datamodel.SequenceI;
34 import jalview.schemes.ResidueProperties;
35 import jalview.structure.SelectionListener;
36 import jalview.structure.SelectionSource;
37 import jalview.structure.SequenceListener;
38 import jalview.structure.StructureSelectionManager;
39 import jalview.structure.VamsasSource;
40 import jalview.util.MappingUtils;
41 import jalview.util.MessageManager;
42 import jalview.viewmodel.AlignmentViewport;
44 import java.awt.BorderLayout;
46 import java.awt.FontMetrics;
47 import java.awt.Panel;
48 import java.awt.Point;
49 import java.awt.event.InputEvent;
50 import java.awt.event.MouseEvent;
51 import java.awt.event.MouseListener;
52 import java.awt.event.MouseMotionListener;
53 import java.util.Vector;
55 public class SeqPanel extends Panel implements MouseMotionListener,
56 MouseListener, SequenceListener, SelectionListener
59 public SeqCanvas seqCanvas;
61 public AlignmentPanel ap;
63 protected int lastres;
65 protected int startseq;
67 protected AlignViewport av;
69 // if character is inserted or deleted, we will need to recalculate the
71 boolean seqEditOccurred = false;
73 ScrollThread scrollThread = null;
75 boolean mouseDragging = false;
77 boolean editingSeqs = false;
79 boolean groupEditing = false;
83 boolean changeEndSeq = false;
85 boolean changeStartSeq = false;
87 boolean changeEndRes = false;
89 boolean changeStartRes = false;
91 SequenceGroup stretchGroup = null;
93 StringBuffer keyboardNo1;
95 StringBuffer keyboardNo2;
97 boolean mouseWheelPressed = false;
101 EditCommand editCommand;
103 StructureSelectionManager ssm;
105 public SeqPanel(AlignViewport avp, AlignmentPanel p)
109 seqCanvas = new SeqCanvas(avp);
110 setLayout(new BorderLayout());
115 seqCanvas.addMouseMotionListener(this);
116 seqCanvas.addMouseListener(this);
117 ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
118 ssm.addStructureViewerListener(this);
119 ssm.addSelectionListener(this);
126 if (editCommand != null && editCommand.getSize() > 0)
128 ap.alignFrame.addHistoryItem(editCommand);
129 av.firePropertyChange("alignment", null, av.getAlignment()
136 groupEditing = false;
144 seqCanvas.cursorY = getKeyboardNo1() - 1;
148 void setCursorColumn()
150 seqCanvas.cursorX = getKeyboardNo1() - 1;
154 void setCursorRowAndColumn()
156 if (keyboardNo2 == null)
158 keyboardNo2 = new StringBuffer();
162 seqCanvas.cursorX = getKeyboardNo1() - 1;
163 seqCanvas.cursorY = getKeyboardNo2() - 1;
168 void setCursorPosition()
170 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
172 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
176 void moveCursor(int dx, int dy)
178 seqCanvas.cursorX += dx;
179 seqCanvas.cursorY += dy;
180 if (av.hasHiddenColumns()
181 && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
183 int original = seqCanvas.cursorX - dx;
184 int maxWidth = av.getAlignment().getWidth();
186 while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
187 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
189 seqCanvas.cursorX += dx;
192 if (seqCanvas.cursorX >= maxWidth
193 || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
195 seqCanvas.cursorX = original;
201 void scrollToVisible()
203 if (seqCanvas.cursorX < 0)
205 seqCanvas.cursorX = 0;
207 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
209 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
212 if (seqCanvas.cursorY < 0)
214 seqCanvas.cursorY = 0;
216 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
218 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
222 if (av.getWrapAlignment())
224 ap.scrollToWrappedVisible(seqCanvas.cursorX);
228 while (seqCanvas.cursorY < av.startSeq)
232 while (seqCanvas.cursorY + 1 > av.endSeq)
236 while (seqCanvas.cursorX < av.getColumnSelection()
237 .adjustForHiddenColumns(av.startRes))
240 if (!ap.scrollRight(false))
245 while (seqCanvas.cursorX > av.getColumnSelection()
246 .adjustForHiddenColumns(av.endRes))
248 if (!ap.scrollRight(true))
254 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
255 seqCanvas.cursorX, seqCanvas.cursorY);
260 void setSelectionAreaAtCursor(boolean topLeft)
262 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
264 if (av.getSelectionGroup() != null)
266 SequenceGroup sg = av.getSelectionGroup();
267 // Find the top and bottom of this group
268 int min = av.getAlignment().getHeight(), max = 0;
269 for (int i = 0; i < sg.getSize(); i++)
271 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
286 sg.setStartRes(seqCanvas.cursorX);
287 if (sg.getEndRes() < seqCanvas.cursorX)
289 sg.setEndRes(seqCanvas.cursorX);
292 min = seqCanvas.cursorY;
296 sg.setEndRes(seqCanvas.cursorX);
297 if (sg.getStartRes() > seqCanvas.cursorX)
299 sg.setStartRes(seqCanvas.cursorX);
302 max = seqCanvas.cursorY + 1;
307 // Only the user can do this
308 av.setSelectionGroup(null);
312 // Now add any sequences between min and max
314 for (int i = min; i < max; i++)
316 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
321 if (av.getSelectionGroup() == null)
323 SequenceGroup sg = new SequenceGroup();
324 sg.setStartRes(seqCanvas.cursorX);
325 sg.setEndRes(seqCanvas.cursorX);
326 sg.addSequence(sequence, false);
327 av.setSelectionGroup(sg);
329 ap.paintAlignment(false);
333 void insertGapAtCursor(boolean group)
335 groupEditing = group;
336 startseq = seqCanvas.cursorY;
337 lastres = seqCanvas.cursorX;
338 editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
342 void deleteGapAtCursor(boolean group)
344 groupEditing = group;
345 startseq = seqCanvas.cursorY;
346 lastres = seqCanvas.cursorX + getKeyboardNo1();
347 editSequence(false, seqCanvas.cursorX);
351 void numberPressed(char value)
353 if (keyboardNo1 == null)
355 keyboardNo1 = new StringBuffer();
358 if (keyboardNo2 != null)
360 keyboardNo2.append(value);
364 keyboardNo1.append(value);
372 if (keyboardNo1 != null)
374 int value = Integer.parseInt(keyboardNo1.toString());
378 } catch (Exception x)
389 if (keyboardNo2 != null)
391 int value = Integer.parseInt(keyboardNo2.toString());
395 } catch (Exception x)
403 * Set status message in alignment panel
406 * aligned sequence object
410 * index of sequence in alignment
411 * @return position of res in sequence
413 void setStatusMessage(SequenceI sequence, int res, int seq)
415 // TODO remove duplication of identical gui method
416 StringBuilder text = new StringBuilder(32);
417 String seqno = seq == -1 ? "" : " " + (seq + 1);
418 text.append("Sequence" + seqno + " ID: " + sequence.getName());
420 String residue = null;
422 * Try to translate the display character to residue name (null for gap).
424 final String displayChar = String.valueOf(sequence.getCharAt(res));
425 if (av.getAlignment().isNucleotide())
427 residue = ResidueProperties.nucleotideName.get(displayChar);
430 text.append(" Nucleotide: ").append(residue);
435 residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*"
436 .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet
440 text.append(" Residue: ").append(residue);
447 pos = sequence.findPosition(res);
448 text.append(" (").append(Integer.toString(pos)).append(")");
451 ap.alignFrame.statusBar.setText(text.toString());
455 * Set the status bar message to highlight the first matched position in
459 * @return true if results were matched, false if not
461 private boolean setStatusMessage(SearchResults results)
463 AlignmentI al = this.av.getAlignment();
464 int sequenceIndex = al.findIndex(results);
465 if (sequenceIndex == -1)
469 SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
470 for (Match m : results.getResults())
472 SequenceI seq = m.getSequence();
473 if (seq.getDatasetSequence() != null)
475 seq = seq.getDatasetSequence();
481 * Convert position in sequence (base 1) to sequence character array
484 int start = m.getStart() - m.getSequence().getStart();
485 setStatusMessage(seq, start, sequenceIndex);
493 public void mousePressed(MouseEvent evt)
495 lastMousePress = evt.getPoint();
497 // For now, ignore the mouseWheel font resizing on Macs
498 // As the Button2_mask always seems to be true
499 if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
502 mouseWheelPressed = true;
506 if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
508 if (evt.isControlDown() || evt.isAltDown())
516 doMousePressedDefineMode(evt);
520 int seq = findSeq(evt);
521 int res = findRes(evt);
523 if (seq < 0 || res < 0)
528 if ((seq < av.getAlignment().getHeight())
529 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
544 public void mouseClicked(MouseEvent evt)
546 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
547 if (evt.getClickCount() > 1)
549 if (av.getSelectionGroup() != null
550 && av.getSelectionGroup().getSize() == 1
551 && av.getSelectionGroup().getEndRes()
552 - av.getSelectionGroup().getStartRes() < 2)
554 av.setSelectionGroup(null);
557 SequenceFeature[] features = findFeaturesAtRes(sequence,
558 sequence.findPosition(findRes(evt)));
560 if (features != null && features.length > 0)
562 SearchResults highlight = new SearchResults();
563 highlight.addResult(sequence, features[0].getBegin(),
564 features[0].getEnd());
565 seqCanvas.highlightSearchResults(highlight);
567 if (features != null && features.length > 0)
569 seqCanvas.getFeatureRenderer().amendFeatures(
570 new SequenceI[] { sequence }, features, false, ap);
572 seqCanvas.highlightSearchResults(null);
578 public void mouseReleased(MouseEvent evt)
580 mouseDragging = false;
581 mouseWheelPressed = false;
582 ap.paintAlignment(true);
586 doMouseReleasedDefineMode(evt);
594 int startWrapBlock = -1;
596 int wrappedBlock = -1;
598 int findRes(MouseEvent evt)
603 if (av.getWrapAlignment())
606 int hgap = av.getCharHeight();
607 if (av.getScaleAboveWrapped())
609 hgap += av.getCharHeight();
612 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
613 + hgap + seqCanvas.getAnnotationHeight();
617 x -= seqCanvas.LABEL_WEST;
619 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
625 wrappedBlock = y / cHeight;
626 wrappedBlock += av.getStartRes() / cwidth;
628 res = wrappedBlock * cwidth + x / av.getCharWidth();
633 res = (x / av.getCharWidth()) + av.getStartRes();
636 if (av.hasHiddenColumns())
638 res = av.getColumnSelection().adjustForHiddenColumns(res);
645 int findSeq(MouseEvent evt)
647 final int sqnum = findAlRow(evt);
648 return (sqnum < 0) ? 0 : sqnum;
654 * @return row in alignment that was selected (or -1 for column selection)
656 private int findAlRow(MouseEvent evt)
661 if (av.getWrapAlignment())
663 int hgap = av.getCharHeight();
664 if (av.getScaleAboveWrapped())
666 hgap += av.getCharHeight();
669 int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
670 + hgap + seqCanvas.getAnnotationHeight();
674 seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
683 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
684 .getAlignment().getHeight() - 1);
694 public void doMousePressed(MouseEvent evt)
697 int seq = findSeq(evt);
698 int res = findRes(evt);
700 if (seq < av.getAlignment().getHeight()
701 && res < av.getAlignment().getSequenceAt(seq).getLength())
703 // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
704 // Find the residue's position in the sequence (res is the position
722 public void mouseOverSequence(SequenceI sequence, int index, int pos)
724 String tmp = sequence.hashCode() + index + "";
725 if (lastMessage == null || !lastMessage.equals(tmp))
727 ssm.mouseOverSequence(sequence, index, pos, av);
734 public void highlightSequence(SearchResults results)
736 if (av.isFollowHighlight())
738 if (ap.scrollToPosition(results, true))
740 ap.alignFrame.repaint();
743 setStatusMessage(results);
744 seqCanvas.highlightSearchResults(results);
749 public VamsasSource getVamsasSource()
751 return this.ap == null ? null : this.ap.av;
755 public void updateColours(SequenceI seq, int index)
757 System.out.println("update the seqPanel colours");
762 public void mouseMoved(MouseEvent evt)
764 int res = findRes(evt);
765 int seq = findSeq(evt);
767 if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
776 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
777 if (res > sequence.getLength())
786 int respos = sequence.findPosition(res);
789 mouseOverSequence(sequence, res, respos);
792 StringBuilder text = new StringBuilder();
793 text.append("Sequence ").append(Integer.toString(seq + 1))
794 .append(" ID: ").append(sequence.getName());
797 final String ch = String.valueOf(sequence.getCharAt(res));
798 if (av.getAlignment().isNucleotide())
800 obj = ResidueProperties.nucleotideName.get(ch);
803 text.append(" Nucleotide: ").append(obj);
808 obj = "X".equalsIgnoreCase(ch) ? "X" : ResidueProperties.aa2Triplet
812 text.append(" Residue: ").append(obj);
818 text.append(" (").append(Integer.toString(respos)).append(")");
821 ap.alignFrame.statusBar.setText(text.toString());
823 StringBuilder tooltipText = new StringBuilder();
824 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
827 for (int g = 0; g < groups.length; g++)
829 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
831 if (!groups[g].getName().startsWith("JTreeGroup")
832 && !groups[g].getName().startsWith("JGroup"))
834 tooltipText.append(groups[g].getName()).append(" ");
836 if (groups[g].getDescription() != null)
838 tooltipText.append(groups[g].getDescription());
840 tooltipText.append("\n");
845 // use aa to see if the mouse pointer is on a
846 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
847 sequence.findPosition(res));
850 while (index < allFeatures.length)
852 SequenceFeature sf = allFeatures[index];
854 tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
856 if (sf.getDescription() != null)
858 tooltipText.append(" " + sf.getDescription());
861 if (sf.getValue("status") != null)
863 String status = sf.getValue("status").toString();
864 if (status.length() > 0)
866 tooltipText.append(" (" + sf.getValue("status") + ")");
869 tooltipText.append("\n");
876 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
880 tooltip.setTip(tooltipText.toString());
884 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
886 Vector tmp = new Vector();
887 SequenceFeature[] features = sequence.getSequenceFeatures();
888 if (features != null)
890 for (int i = 0; i < features.length; i++)
892 if (av.getFeaturesDisplayed() == null
893 || !av.getFeaturesDisplayed().isVisible(
894 features[i].getType()))
899 if (features[i].featureGroup != null
900 && !seqCanvas.fr.checkGroupVisibility(
901 features[i].featureGroup, false))
906 if ((features[i].getBegin() <= res)
907 && (features[i].getEnd() >= res))
909 tmp.addElement(features[i]);
914 features = new SequenceFeature[tmp.size()];
915 tmp.copyInto(features);
923 * set when the current UI interaction has resulted in a change that requires
924 * overview shading to be recalculated. this could be changed to something
925 * more expressive that indicates what actually has changed, so selective
926 * redraws can be applied
928 private boolean needOverviewUpdate; // TODO: refactor to avcontroller
931 * set if av.getSelectionGroup() refers to a group that is defined on the
932 * alignment view, rather than a transient selection
934 private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller
938 public void mouseDragged(MouseEvent evt)
940 if (mouseWheelPressed)
942 int oldWidth = av.getCharWidth();
944 // Which is bigger, left-right or up-down?
945 if (Math.abs(evt.getY() - lastMousePress.y) > Math.abs(evt.getX()
948 int fontSize = av.font.getSize();
950 if (evt.getY() < lastMousePress.y && av.getCharHeight() > 1)
954 else if (evt.getY() > lastMousePress.y)
964 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
965 av.setCharWidth(oldWidth);
969 if (evt.getX() < lastMousePress.x && av.getCharWidth() > 1)
971 av.setCharWidth(av.getCharWidth() - 1);
973 else if (evt.getX() > lastMousePress.x)
975 av.setCharWidth(av.getCharWidth() + 1);
978 if (av.getCharWidth() < 1)
986 FontMetrics fm = getFontMetrics(av.getFont());
987 av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
989 lastMousePress = evt.getPoint();
991 ap.paintAlignment(false);
992 ap.annotationPanel.image = null;
998 doMouseDraggedDefineMode(evt);
1002 int res = findRes(evt);
1009 if ((lastres == -1) || (lastres == res))
1014 if ((res < av.getAlignment().getWidth()) && (res < lastres))
1016 // dragLeft, delete gap
1017 editSequence(false, res);
1021 editSequence(true, res);
1024 mouseDragging = true;
1025 if (scrollThread != null)
1027 scrollThread.setEvent(evt);
1032 synchronized void editSequence(boolean insertGap, int startres)
1035 int fixedRight = -1;
1036 boolean fixedColumns = false;
1037 SequenceGroup sg = av.getSelectionGroup();
1039 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
1041 if (!groupEditing && av.hasHiddenRows())
1043 if (av.isHiddenRepSequence(seq))
1045 sg = av.getRepresentedSequences(seq);
1046 groupEditing = true;
1050 StringBuffer message = new StringBuffer();
1053 message.append(MessageManager.getString("action.edit_group")).append(
1055 if (editCommand == null)
1057 editCommand = new EditCommand(
1058 MessageManager.getString("action.edit_group"));
1063 message.append(MessageManager.getString("label.edit_sequence"))
1064 .append(" " + seq.getName());
1065 String label = seq.getName();
1066 if (label.length() > 10)
1068 label = label.substring(0, 10);
1070 if (editCommand == null)
1072 editCommand = new EditCommand(MessageManager.formatMessage(
1073 "label.edit_params", new String[] { label }));
1079 message.append(" insert ");
1083 message.append(" delete ");
1086 message.append(Math.abs(startres - lastres) + " gaps.");
1087 ap.alignFrame.statusBar.setText(message.toString());
1089 // Are we editing within a selection group?
1091 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1094 fixedColumns = true;
1096 // sg might be null as the user may only see 1 sequence,
1097 // but the sequence represents a group
1100 if (!av.isHiddenRepSequence(seq))
1106 sg = av.getRepresentedSequences(seq);
1109 fixedLeft = sg.getStartRes();
1110 fixedRight = sg.getEndRes();
1112 if ((startres < fixedLeft && lastres >= fixedLeft)
1113 || (startres >= fixedLeft && lastres < fixedLeft)
1114 || (startres > fixedRight && lastres <= fixedRight)
1115 || (startres <= fixedRight && lastres > fixedRight))
1121 if (fixedLeft > startres)
1123 fixedRight = fixedLeft - 1;
1126 else if (fixedRight < startres)
1128 fixedLeft = fixedRight;
1133 if (av.hasHiddenColumns())
1135 fixedColumns = true;
1136 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1137 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1139 if ((insertGap && startres > y1 && lastres < y1)
1140 || (!insertGap && startres < y2 && lastres > y2))
1146 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1147 // Selection spans a hidden region
1148 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1156 fixedRight = y2 - 1;
1163 SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
1164 .toArray(new SequenceI[0]);
1169 // If the user has selected the whole sequence, and is dragging to
1170 // the right, we can still extend the alignment and selectionGroup
1171 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1172 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1174 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1175 fixedRight = sg.getEndRes();
1178 // Is it valid with fixed columns??
1179 // Find the next gap before the end
1180 // of the visible region boundary
1181 boolean blank = false;
1182 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1186 for (SequenceI gs : groupSeqs)
1188 for (int j = 0; j < startres - lastres; j++)
1190 if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
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 (SequenceI gs : groupSeqs)
1246 for (int j = startres; j < lastres; j++)
1248 if (gs.getLength() <= j)
1253 if (!jalview.util.Comparison.isGap(gs.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 editCommand.appendEdit(Action.INSERT_GAP, groupSeqs, startres,
1276 startres - lastres, av.getAlignment(), true);
1281 // dragging to the left
1282 if (fixedColumns && fixedRight != -1)
1284 for (int j = lastres; j > startres; j--)
1286 deleteChar(startres, groupSeqs, fixedRight);
1291 editCommand.appendEdit(Action.DELETE_GAP, groupSeqs, startres,
1292 lastres - startres, av.getAlignment(), true);
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 editCommand.appendEdit(Action.INSERT_GAP,
1313 new SequenceI[] { seq }, lastres, startres - lastres,
1314 av.getAlignment(), true);
1319 // dragging to the left
1320 if (fixedColumns && fixedRight != -1)
1322 for (int j = lastres; j > startres; j--)
1324 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1329 deleteChar(startres, new SequenceI[] { seq }, fixedRight);
1334 // could be a keyboard edit trying to delete none gaps
1336 for (int m = startres; m < lastres; m++)
1338 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1347 editCommand.appendEdit(Action.DELETE_GAP,
1348 new SequenceI[] { seq }, startres, max,
1349 av.getAlignment(), true);
1356 seqCanvas.repaint();
1359 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1361 int blankColumn = fixedColumn;
1362 for (int s = 0; s < seq.length; s++)
1364 // Find the next gap before the end of the visible region boundary
1365 // If lastCol > j, theres a boundary after the gap insertion
1367 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1369 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1371 // Theres a space, so break and insert the gap
1376 if (blankColumn <= j)
1378 blankColumn = fixedColumn;
1384 editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
1385 av.getAlignment(), true);
1387 editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1, av.getAlignment(),
1392 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1395 editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1, av.getAlignment(),
1398 editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
1399 av.getAlignment(), true);
1402 // ////////////////////////////////////////
1403 // ///Everything below this is for defining the boundary of the rubberband
1404 // ////////////////////////////////////////
1405 public void doMousePressedDefineMode(MouseEvent evt)
1407 if (scrollThread != null)
1409 scrollThread.running = false;
1410 scrollThread = null;
1413 int res = findRes(evt);
1414 int seq = findSeq(evt);
1416 startWrapBlock = wrappedBlock;
1423 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1425 if (sequence == null || res > sequence.getLength())
1430 stretchGroup = av.getSelectionGroup();
1432 if (stretchGroup == null)
1434 stretchGroup = av.getAlignment().findGroup(sequence);
1435 if (stretchGroup != null && res > stretchGroup.getStartRes()
1436 && res < stretchGroup.getEndRes())
1438 av.setSelectionGroup(stretchGroup);
1439 editingDefinedGroup = true;
1443 stretchGroup = null;
1444 editingDefinedGroup = false;
1448 else if (!stretchGroup.getSequences(null).contains(sequence)
1449 || stretchGroup.getStartRes() > res
1450 || stretchGroup.getEndRes() < res)
1452 stretchGroup = null;
1454 SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
1456 if (allGroups != null)
1458 for (int i = 0; i < allGroups.length; i++)
1460 if (allGroups[i].getStartRes() <= res
1461 && allGroups[i].getEndRes() >= res)
1463 stretchGroup = allGroups[i];
1464 editingDefinedGroup = true;
1469 av.setSelectionGroup(stretchGroup);
1472 // DETECT RIGHT MOUSE BUTTON IN AWT
1473 if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
1475 SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
1476 sequence.findPosition(res));
1478 Vector<String> links = null;
1479 if (allFeatures != null)
1481 for (int i = 0; i < allFeatures.length; i++)
1483 if (allFeatures[i].links != null)
1487 links = new Vector<String>();
1489 for (int j = 0; j < allFeatures[i].links.size(); j++)
1491 links.addElement(allFeatures[i].links.elementAt(j));
1496 APopupMenu popup = new APopupMenu(ap, null, links);
1498 popup.show(this, evt.getX(), evt.getY());
1504 seqCanvas.cursorX = findRes(evt);
1505 seqCanvas.cursorY = findSeq(evt);
1506 seqCanvas.repaint();
1510 // Only if left mouse button do we want to change group sizes
1512 if (stretchGroup == null)
1514 // define a new group here
1515 SequenceGroup sg = new SequenceGroup();
1516 sg.setStartRes(res);
1518 sg.addSequence(sequence, false);
1519 av.setSelectionGroup(sg);
1520 editingDefinedGroup = false;
1523 if (av.getConservationSelected())
1525 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1528 if (av.getAbovePIDThreshold())
1530 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1537 public void doMouseReleasedDefineMode(MouseEvent evt)
1539 if (stretchGroup == null)
1543 // always do this - annotation has own state
1544 // but defer colourscheme update until hidden sequences are passed in
1545 boolean vischange = stretchGroup.recalcConservation(true);
1546 needOverviewUpdate |= vischange && editingDefinedGroup;
1547 if (stretchGroup.cs != null)
1549 stretchGroup.cs.alignmentChanged(stretchGroup,
1550 av.getHiddenRepSequences());
1552 if (stretchGroup.cs.conservationApplied())
1554 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1555 stretchGroup.getName());
1559 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1560 stretchGroup.getName());
1563 PaintRefresher.Refresh(ap, av.getSequenceSetId());
1564 ap.paintAlignment(needOverviewUpdate);
1565 needOverviewUpdate =false;
1566 editingDefinedGroup = false;
1567 changeEndRes = false;
1568 changeStartRes = false;
1569 stretchGroup = null;
1573 public void doMouseDraggedDefineMode(MouseEvent evt)
1575 int res = findRes(evt);
1576 int y = findSeq(evt);
1578 if (wrappedBlock != startWrapBlock)
1583 if (stretchGroup == null)
1588 mouseDragging = true;
1590 if (y > av.getAlignment().getHeight())
1592 y = av.getAlignment().getHeight() - 1;
1595 if (res >= av.getAlignment().getWidth())
1597 res = av.getAlignment().getWidth() - 1;
1600 if (stretchGroup.getEndRes() == res)
1602 // Edit end res position of selected group
1603 changeEndRes = true;
1605 else if (stretchGroup.getStartRes() == res)
1607 // Edit start res position of selected group
1608 changeStartRes = true;
1618 if (res > (stretchGroup.getStartRes() - 1))
1620 stretchGroup.setEndRes(res);
1621 needOverviewUpdate |= editingDefinedGroup;
1624 else if (changeStartRes)
1626 if (res < (stretchGroup.getEndRes() + 1))
1628 stretchGroup.setStartRes(res);
1629 needOverviewUpdate |= editingDefinedGroup;
1633 int dragDirection = 0;
1639 else if (y < oldSeq)
1644 while ((y != oldSeq) && (oldSeq > -1)
1645 && (y < av.getAlignment().getHeight()))
1647 // This routine ensures we don't skip any sequences, as the
1648 // selection is quite slow.
1649 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1651 oldSeq += dragDirection;
1658 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1660 if (stretchGroup.getSequences(null).contains(nextSeq))
1662 stretchGroup.deleteSequence(seq, false);
1663 needOverviewUpdate |= editingDefinedGroup;
1669 stretchGroup.addSequence(seq, false);
1672 stretchGroup.addSequence(nextSeq, false);
1673 needOverviewUpdate |= editingDefinedGroup;
1682 if (res > av.endRes || res < av.startRes || y < av.startSeq
1688 if (scrollThread != null)
1690 scrollThread.setEvent(evt);
1693 seqCanvas.repaint();
1697 public void mouseEntered(MouseEvent e)
1704 if (scrollThread != null)
1706 scrollThread.running = false;
1707 scrollThread = null;
1712 public void mouseExited(MouseEvent e)
1714 if (av.getWrapAlignment())
1719 if (mouseDragging && scrollThread == null)
1721 scrollThread = new ScrollThread();
1725 void scrollCanvas(MouseEvent evt)
1729 if (scrollThread != null)
1731 scrollThread.running = false;
1732 scrollThread = null;
1734 mouseDragging = false;
1738 if (scrollThread == null)
1740 scrollThread = new ScrollThread();
1743 mouseDragging = true;
1744 scrollThread.setEvent(evt);
1749 // this class allows scrolling off the bottom of the visible alignment
1750 class ScrollThread extends Thread
1754 boolean running = false;
1756 public ScrollThread()
1761 public void setEvent(MouseEvent e)
1766 public void stopScrolling()
1781 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
1783 running = ap.scrollUp(true);
1786 if (mouseDragging && evt.getY() >= getSize().height
1787 && av.getAlignment().getHeight() > av.getEndSeq())
1789 running = ap.scrollUp(false);
1792 if (mouseDragging && evt.getX() < 0)
1794 running = ap.scrollRight(false);
1797 else if (mouseDragging && evt.getX() >= getSize().width)
1799 running = ap.scrollRight(true);
1806 } catch (Exception ex)
1814 * modify current selection according to a received message.
1817 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1818 SelectionSource source)
1820 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1821 // handles selection messages...
1822 // TODO: extend config options to allow user to control if selections may be
1823 // shared between viewports.
1825 && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignmentViewport) source)
1826 .getSequenceSetId().equals(av.getSequenceSetId()))))
1832 * Check for selection in a view of which this one is a dna/protein
1835 if (selectionFromTranslation(seqsel, colsel, source))
1840 // do we want to thread this ? (contention with seqsel and colsel locks, I
1842 // rules are: colsel is copied if there is a real intersection between
1843 // sequence selection
1844 boolean repaint = false, copycolsel = true;
1845 if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
1847 SequenceGroup sgroup = null;
1848 if (seqsel != null && seqsel.getSize() > 0)
1850 if (av.getAlignment() == null)
1853 .println("Selection message: alignviewport av SeqSetId="
1854 + av.getSequenceSetId() + " ViewId="
1856 + " 's alignment is NULL! returning immediatly.");
1859 sgroup = seqsel.intersect(av.getAlignment(),
1860 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1861 if ((sgroup == null || sgroup.getSize() == 0)
1862 && (colsel == null || colsel.isEmpty()))
1864 // don't copy columns if the region didn't intersect.
1868 if (sgroup != null && sgroup.getSize() > 0)
1870 av.setSelectionGroup(sgroup);
1874 av.setSelectionGroup(null);
1876 repaint = av.isSelectionGroupChanged(true);
1879 && (av.getColumnSelection() == null || !av
1880 .isColSelChanged(true)))
1882 // the current selection is unset or from a previous message
1883 // so import the new colsel.
1884 if (colsel == null || colsel.isEmpty())
1886 if (av.getColumnSelection() != null)
1888 av.getColumnSelection().clear();
1893 // TODO: shift colSel according to the intersecting sequences
1894 if (av.getColumnSelection() == null)
1896 av.setColumnSelection(new ColumnSelection(colsel));
1900 av.getColumnSelection().setElementsFrom(colsel);
1903 repaint |= av.isColSelChanged(true);
1906 && av.hasHiddenColumns()
1907 && (av.getColumnSelection() == null || av.getColumnSelection()
1908 .getHiddenColumns() == 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.startSeq : row;
1929 column = column < 0 ? ap.av.startRes : 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.startSeq : row;
1942 ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
1946 * scroll to the given column - or nearest visible location
1950 public void scrollToColumn(int column)
1953 column = column < 0 ? ap.av.startRes : column;
1954 ap.scrollTo(column, column, ap.av.startSeq, true, true);
1958 * If this panel is a cdna/protein translation view of the selection source,
1959 * tries to map the source selection to a local one, and returns true. Else
1966 protected boolean selectionFromTranslation(SequenceGroup seqsel,
1967 ColumnSelection colsel, SelectionSource source)
1969 if (!(source instanceof AlignViewportI))
1973 final AlignViewportI sourceAv = (AlignViewportI) source;
1974 if (sourceAv.getCodingComplement() != av
1975 && av.getCodingComplement() != sourceAv)
1981 * Map sequence selection
1983 SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
1984 av.setSelectionGroup(sg);
1985 av.isSelectionGroupChanged(true);
1988 * Map column selection
1990 ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
1992 av.setColumnSelection(cs);
1993 av.isColSelChanged(true);
1995 ap.scalePanelHolder.repaint();