2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.commands.EditCommand;
24 import jalview.commands.EditCommand.Action;
25 import jalview.datamodel.ColumnSelection;
26 import jalview.datamodel.SearchResults;
27 import jalview.datamodel.Sequence;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceGroup;
30 import jalview.datamodel.SequenceI;
31 import jalview.io.SequenceAnnotationReport;
32 import jalview.schemes.ResidueProperties;
33 import jalview.structure.SelectionListener;
34 import jalview.structure.SelectionSource;
35 import jalview.structure.SequenceListener;
36 import jalview.structure.StructureSelectionManager;
37 import jalview.util.MessageManager;
39 import java.awt.BorderLayout;
40 import java.awt.Color;
42 import java.awt.FontMetrics;
43 import java.awt.Point;
44 import java.awt.event.MouseEvent;
45 import java.awt.event.MouseListener;
46 import java.awt.event.MouseMotionListener;
47 import java.awt.event.MouseWheelEvent;
48 import java.awt.event.MouseWheelListener;
49 import java.util.List;
50 import java.util.Vector;
52 import javax.swing.JOptionPane;
53 import javax.swing.JPanel;
54 import javax.swing.ToolTipManager;
60 * @version $Revision: 1.130 $
62 public class SeqPanel extends JPanel implements MouseListener,
63 MouseMotionListener, MouseWheelListener, SequenceListener,
68 public SeqCanvas seqCanvas;
71 public AlignmentPanel ap;
73 protected int lastres;
75 protected int startseq;
77 protected AlignViewport av;
79 ScrollThread scrollThread = null;
81 boolean mouseDragging = false;
83 boolean editingSeqs = false;
85 boolean groupEditing = false;
87 // ////////////////////////////////////////
88 // ///Everything below this is for defining the boundary of the rubberband
89 // ////////////////////////////////////////
92 boolean changeEndSeq = false;
94 boolean changeStartSeq = false;
96 boolean changeEndRes = false;
98 boolean changeStartRes = false;
100 SequenceGroup stretchGroup = null;
102 boolean remove = false;
104 Point lastMousePress;
106 boolean mouseWheelPressed = false;
108 StringBuffer keyboardNo1;
110 StringBuffer keyboardNo2;
112 java.net.URL linkImageURL;
114 private final SequenceAnnotationReport seqARep;
116 StringBuffer tooltipText = new StringBuffer();
120 EditCommand editCommand;
122 StructureSelectionManager ssm;
125 * Creates a new SeqPanel object.
132 public SeqPanel(AlignViewport av, AlignmentPanel ap)
134 linkImageURL = getClass().getResource("/images/link.gif");
135 seqARep = new SequenceAnnotationReport(linkImageURL.toString());
136 ToolTipManager.sharedInstance().registerComponent(this);
137 ToolTipManager.sharedInstance().setInitialDelay(0);
138 ToolTipManager.sharedInstance().setDismissDelay(10000);
140 setBackground(Color.white);
142 seqCanvas = new SeqCanvas(ap);
143 setLayout(new BorderLayout());
144 add(seqCanvas, BorderLayout.CENTER);
150 addMouseMotionListener(this);
151 addMouseListener(this);
152 addMouseWheelListener(this);
153 ssm = av.getStructureSelectionManager();
154 ssm.addStructureViewerListener(this);
155 ssm.addSelectionListener(this);
159 int startWrapBlock = -1;
161 int wrappedBlock = -1;
163 int findRes(MouseEvent evt)
168 if (av.wrapAlignment)
171 int hgap = av.charHeight;
172 if (av.scaleAboveWrapped)
174 hgap += av.charHeight;
177 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
178 + seqCanvas.getAnnotationHeight();
182 x -= seqCanvas.LABEL_WEST;
184 int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
190 wrappedBlock = y / cHeight;
191 wrappedBlock += av.getStartRes() / cwidth;
193 res = wrappedBlock * cwidth + x / av.getCharWidth();
198 if (x > seqCanvas.getWidth() + seqCanvas.getWidth())
200 // make sure we calculate relative to visible alignment, rather than
202 x = seqCanvas.getX() + seqCanvas.getWidth();
204 res = (x / av.getCharWidth()) + av.getStartRes();
207 if (av.hasHiddenColumns())
209 res = av.getColumnSelection().adjustForHiddenColumns(res);
216 int findSeq(MouseEvent evt)
221 if (av.wrapAlignment)
223 int hgap = av.charHeight;
224 if (av.scaleAboveWrapped)
226 hgap += av.charHeight;
229 int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
230 + seqCanvas.getAnnotationHeight();
234 seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
239 seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
240 .getAlignment().getHeight() - 1);
246 SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
248 Vector tmp = new Vector();
249 SequenceFeature[] features = sequence.getSequenceFeatures();
250 if (features != null)
252 for (int i = 0; i < features.length; i++)
254 if (av.featuresDisplayed == null
255 || !av.featuresDisplayed.containsKey(features[i].getType()))
260 if (features[i].featureGroup != null
261 && seqCanvas.fr.featureGroups != null
262 && seqCanvas.fr.featureGroups
263 .containsKey(features[i].featureGroup)
264 && !((Boolean) seqCanvas.fr.featureGroups
265 .get(features[i].featureGroup)).booleanValue())
270 if ((features[i].getBegin() <= res)
271 && (features[i].getEnd() >= res))
273 tmp.addElement(features[i]);
278 features = new SequenceFeature[tmp.size()];
279 tmp.copyInto(features);
286 if (editCommand != null && editCommand.getSize() > 0)
288 ap.alignFrame.addHistoryItem(editCommand);
289 av.firePropertyChange("alignment", null, av.getAlignment()
296 groupEditing = false;
304 seqCanvas.cursorY = getKeyboardNo1() - 1;
308 void setCursorColumn()
310 seqCanvas.cursorX = getKeyboardNo1() - 1;
314 void setCursorRowAndColumn()
316 if (keyboardNo2 == null)
318 keyboardNo2 = new StringBuffer();
322 seqCanvas.cursorX = getKeyboardNo1() - 1;
323 seqCanvas.cursorY = getKeyboardNo2() - 1;
328 void setCursorPosition()
330 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
332 seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
336 void moveCursor(int dx, int dy)
338 seqCanvas.cursorX += dx;
339 seqCanvas.cursorY += dy;
340 if (av.hasHiddenColumns()
341 && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
343 int original = seqCanvas.cursorX - dx;
344 int maxWidth = av.getAlignment().getWidth();
346 while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
347 && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
349 seqCanvas.cursorX += dx;
352 if (seqCanvas.cursorX >= maxWidth
353 || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
355 seqCanvas.cursorX = original;
362 void scrollToVisible()
364 if (seqCanvas.cursorX < 0)
366 seqCanvas.cursorX = 0;
368 else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
370 seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
373 if (seqCanvas.cursorY < 0)
375 seqCanvas.cursorY = 0;
377 else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
379 seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
383 if (av.wrapAlignment)
385 ap.scrollToWrappedVisible(seqCanvas.cursorX);
389 while (seqCanvas.cursorY < av.startSeq)
393 while (seqCanvas.cursorY + 1 > av.endSeq)
397 if (!av.wrapAlignment)
399 while (seqCanvas.cursorX < av.getColumnSelection()
400 .adjustForHiddenColumns(av.startRes))
402 if (!ap.scrollRight(false))
407 while (seqCanvas.cursorX > av.getColumnSelection()
408 .adjustForHiddenColumns(av.endRes))
410 if (!ap.scrollRight(true))
417 setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
418 seqCanvas.cursorX, seqCanvas.cursorY);
423 void setSelectionAreaAtCursor(boolean topLeft)
425 SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
427 if (av.getSelectionGroup() != null)
429 SequenceGroup sg = av.getSelectionGroup();
430 // Find the top and bottom of this group
431 int min = av.getAlignment().getHeight(), max = 0;
432 for (int i = 0; i < sg.getSize(); i++)
434 int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
449 sg.setStartRes(seqCanvas.cursorX);
450 if (sg.getEndRes() < seqCanvas.cursorX)
452 sg.setEndRes(seqCanvas.cursorX);
455 min = seqCanvas.cursorY;
459 sg.setEndRes(seqCanvas.cursorX);
460 if (sg.getStartRes() > seqCanvas.cursorX)
462 sg.setStartRes(seqCanvas.cursorX);
465 max = seqCanvas.cursorY + 1;
470 // Only the user can do this
471 av.setSelectionGroup(null);
475 // Now add any sequences between min and max
476 sg.getSequences(null).clear();
477 for (int i = min; i < max; i++)
479 sg.addSequence(av.getAlignment().getSequenceAt(i), false);
484 if (av.getSelectionGroup() == null)
486 SequenceGroup sg = new SequenceGroup();
487 sg.setStartRes(seqCanvas.cursorX);
488 sg.setEndRes(seqCanvas.cursorX);
489 sg.addSequence(sequence, false);
490 av.setSelectionGroup(sg);
493 ap.paintAlignment(false);
497 void insertGapAtCursor(boolean group)
499 groupEditing = group;
500 startseq = seqCanvas.cursorY;
501 lastres = seqCanvas.cursorX;
502 editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
506 void deleteGapAtCursor(boolean group)
508 groupEditing = group;
509 startseq = seqCanvas.cursorY;
510 lastres = seqCanvas.cursorX + getKeyboardNo1();
511 editSequence(false, false, seqCanvas.cursorX);
515 void insertNucAtCursor(boolean group, String nuc)
517 groupEditing = group;
518 startseq = seqCanvas.cursorY;
519 lastres = seqCanvas.cursorX;
520 editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
524 void numberPressed(char value)
526 if (keyboardNo1 == null)
528 keyboardNo1 = new StringBuffer();
531 if (keyboardNo2 != null)
533 keyboardNo2.append(value);
537 keyboardNo1.append(value);
545 if (keyboardNo1 != null)
547 int value = Integer.parseInt(keyboardNo1.toString());
551 } catch (Exception x)
562 if (keyboardNo2 != null)
564 int value = Integer.parseInt(keyboardNo2.toString());
568 } catch (Exception x)
582 public void mouseReleased(MouseEvent evt)
584 mouseDragging = false;
585 mouseWheelPressed = false;
589 doMouseReleasedDefineMode(evt);
603 public void mousePressed(MouseEvent evt)
605 lastMousePress = evt.getPoint();
607 if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
609 mouseWheelPressed = true;
613 if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
615 if (evt.isAltDown() || evt.isControlDown())
623 doMousePressedDefineMode(evt);
627 int seq = findSeq(evt);
628 int res = findRes(evt);
630 if (seq < 0 || res < 0)
635 if ((seq < av.getAlignment().getHeight())
636 && (res < av.getAlignment().getSequenceAt(seq).getLength()))
653 public void mouseOverSequence(SequenceI sequence, int index, int pos)
655 String tmp = sequence.hashCode() + " " + index + " " + pos;
657 if (lastMessage == null || !lastMessage.equals(tmp))
659 // System.err.println("mouseOver Sequence: "+tmp);
660 ssm.mouseOverSequence(sequence, index, pos, av);
666 public void highlightSequence(SearchResults results)
668 if (av.followHighlight)
670 if (ap.scrollToPosition(results, false))
672 seqCanvas.revalidate();
675 seqCanvas.highlightSearchResults(results);
679 public void updateColours(SequenceI seq, int index)
681 System.out.println("update the seqPanel colours");
692 public void mouseMoved(MouseEvent evt)
696 // This is because MacOSX creates a mouseMoved
697 // If control is down, other platforms will not.
701 int res = findRes(evt);
702 int seq = findSeq(evt);
704 if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
709 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
711 if (res >= sequence.getLength())
716 pos = setStatusMessage(sequence, res, seq);
717 if (ssm != null && pos > -1)
719 mouseOverSequence(sequence, res, pos);
722 tooltipText.setLength(6); // Cuts the buffer back to <html>
724 SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
727 for (int g = 0; g < groups.length; g++)
729 if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
731 if (!groups[g].getName().startsWith("JTreeGroup")
732 && !groups[g].getName().startsWith("JGroup"))
734 tooltipText.append(groups[g].getName());
737 if (groups[g].getDescription() != null)
739 tooltipText.append(": " + groups[g].getDescription());
745 // use aa to see if the mouse pointer is on a
746 if (av.showSequenceFeatures)
749 SequenceFeature[] features = findFeaturesAtRes(
750 sequence.getDatasetSequence(),
751 rpos = sequence.findPosition(res));
752 seqARep.appendFeatures(tooltipText, rpos, features,
753 this.ap.seqPanel.seqCanvas.fr.minmax);
755 if (tooltipText.length() == 6) // <html></html>
757 setToolTipText(null);
762 if (lastTooltip == null
763 || !lastTooltip.equals(tooltipText.toString()))
765 String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
766 tooltipText.toString());
767 // String formatedTooltipText = tooltipText.toString();
768 setToolTipText(formatedTooltipText);
769 lastTooltip = tooltipText.toString();
776 private Point lastp = null;
781 * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
783 public Point getToolTipLocation(MouseEvent event)
785 int x = event.getX(), w = getWidth();
786 int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
789 if (!event.isShiftDown() || p == null)
791 p = (tooltipText != null && tooltipText.length() > 6) ? new Point(
792 event.getX() + wdth, event.getY() - 20) : null;
795 * TODO: try to modify position region is not obcured by tooltip
803 * Set status message in alignment panel
806 * aligned sequence object
810 * index of sequence in alignment
811 * @return position of res in sequence
813 int setStatusMessage(SequenceI sequence, int res, int seq)
816 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
817 + sequence.getName());
820 if (av.getAlignment().isNucleotide())
822 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
826 text.append(" Nucleotide: ");
831 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
834 text.append(" Residue: ");
840 pos = sequence.findPosition(res);
843 text.append(obj + " (" + pos + ")");
846 ap.alignFrame.statusBar.setText(text.toString());
857 public void mouseDragged(MouseEvent evt)
859 if (mouseWheelPressed)
861 int oldWidth = av.charWidth;
863 // Which is bigger, left-right or up-down?
864 if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt
865 .getX() - lastMousePress.getX()))
867 int fontSize = av.font.getSize();
869 if (evt.getY() < lastMousePress.getY())
873 else if (evt.getY() > lastMousePress.getY())
883 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
884 av.charWidth = oldWidth;
889 if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
893 else if (evt.getX() > lastMousePress.getX())
898 ap.paintAlignment(false);
901 FontMetrics fm = getFontMetrics(av.getFont());
902 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
904 lastMousePress = evt.getPoint();
911 doMouseDraggedDefineMode(evt);
915 int res = findRes(evt);
922 if ((lastres == -1) || (lastres == res))
927 if ((res < av.getAlignment().getWidth()) && (res < lastres))
929 // dragLeft, delete gap
930 editSequence(false, false, res);
934 editSequence(true, false, res);
937 mouseDragging = true;
938 if (scrollThread != null)
940 scrollThread.setEvent(evt);
944 // TODO: Make it more clever than many booleans
945 synchronized void editSequence(boolean insertGap, boolean editSeq,
950 boolean fixedColumns = false;
951 SequenceGroup sg = av.getSelectionGroup();
953 SequenceI seq = av.getAlignment().getSequenceAt(startseq);
955 // No group, but the sequence may represent a group
956 if (!groupEditing && av.hasHiddenRows())
958 if (av.isHiddenRepSequence(seq))
960 sg = av.getRepresentedSequences(seq);
965 StringBuffer message = new StringBuffer();
968 message.append("Edit group:");
969 if (editCommand == null)
971 editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
976 message.append("Edit sequence: " + seq.getName());
977 String label = seq.getName();
978 if (label.length() > 10)
980 label = label.substring(0, 10);
982 if (editCommand == null)
984 editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
990 message.append(" insert ");
994 message.append(" delete ");
997 message.append(Math.abs(startres - lastres) + " gaps.");
998 ap.alignFrame.statusBar.setText(message.toString());
1000 // Are we editing within a selection group?
1002 || (sg != null && sg.getSequences(av.getHiddenRepSequences())
1005 fixedColumns = true;
1007 // sg might be null as the user may only see 1 sequence,
1008 // but the sequence represents a group
1011 if (!av.isHiddenRepSequence(seq))
1016 sg = av.getRepresentedSequences(seq);
1019 fixedLeft = sg.getStartRes();
1020 fixedRight = sg.getEndRes();
1022 if ((startres < fixedLeft && lastres >= fixedLeft)
1023 || (startres >= fixedLeft && lastres < fixedLeft)
1024 || (startres > fixedRight && lastres <= fixedRight)
1025 || (startres <= fixedRight && lastres > fixedRight))
1031 if (fixedLeft > startres)
1033 fixedRight = fixedLeft - 1;
1036 else if (fixedRight < startres)
1038 fixedLeft = fixedRight;
1043 if (av.hasHiddenColumns())
1045 fixedColumns = true;
1046 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
1047 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
1049 if ((insertGap && startres > y1 && lastres < y1)
1050 || (!insertGap && startres < y2 && lastres > y2))
1056 // System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
1057 // Selection spans a hidden region
1058 if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
1066 fixedRight = y2 - 1;
1073 List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
1074 int g, groupSize = vseqs.size();
1075 SequenceI[] groupSeqs = new SequenceI[groupSize];
1076 for (g = 0; g < groupSeqs.length; g++)
1078 groupSeqs[g] = vseqs.get(g);
1084 // If the user has selected the whole sequence, and is dragging to
1085 // the right, we can still extend the alignment and selectionGroup
1086 if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
1087 && sg.getEndRes() == av.getAlignment().getWidth() - 1)
1089 sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
1090 fixedRight = sg.getEndRes();
1093 // Is it valid with fixed columns??
1094 // Find the next gap before the end
1095 // of the visible region boundary
1096 boolean blank = false;
1097 for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
1101 for (g = 0; g < groupSize; g++)
1103 for (int j = 0; j < startres - lastres; j++)
1105 if (!jalview.util.Comparison.isGap(groupSeqs[g]
1106 .getCharAt(fixedRight - j)))
1121 if (sg.getSize() == av.getAlignment().getHeight())
1123 if ((av.hasHiddenColumns() && startres < av
1124 .getColumnSelection().getHiddenBoundaryRight(startres)))
1130 int alWidth = av.getAlignment().getWidth();
1131 if (av.hasHiddenRows())
1133 int hwidth = av.getAlignment().getHiddenSequences()
1135 if (hwidth > alWidth)
1140 // We can still insert gaps if the selectionGroup
1141 // contains all the sequences
1142 sg.setEndRes(sg.getEndRes() + startres - lastres);
1143 fixedRight = alWidth + startres - lastres;
1154 else if (!insertGap)
1156 // / Are we able to delete?
1157 // ie are all columns blank?
1159 for (g = 0; g < groupSize; g++)
1161 for (int j = startres; j < lastres; j++)
1163 if (groupSeqs[g].getLength() <= j)
1168 if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
1170 // Not a gap, block edit not valid
1180 // dragging to the right
1181 if (fixedColumns && fixedRight != -1)
1183 for (int j = lastres; j < startres; j++)
1185 insertChar(j, groupSeqs, fixedRight);
1190 editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
1191 startres, startres - lastres, av.getAlignment(), true);
1196 // dragging to the left
1197 if (fixedColumns && fixedRight != -1)
1199 for (int j = lastres; j > startres; j--)
1201 deleteChar(startres, groupSeqs, fixedRight);
1206 editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
1207 startres, lastres - startres, av.getAlignment(), true);
1213 // ///Editing a single sequence///////////
1217 // dragging to the right
1218 if (fixedColumns && fixedRight != -1)
1220 for (int j = lastres; j < startres; j++)
1222 insertChar(j, new SequenceI[]
1223 { seq }, fixedRight);
1228 editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
1229 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1236 // dragging to the left
1237 if (fixedColumns && fixedRight != -1)
1239 for (int j = lastres; j > startres; j--)
1241 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
1246 deleteChar(startres, new SequenceI[]
1247 { seq }, fixedRight);
1252 // could be a keyboard edit trying to delete none gaps
1254 for (int m = startres; m < lastres; m++)
1256 if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
1265 editCommand.appendEdit(Action.DELETE_GAP,
1267 { seq }, startres, max, av.getAlignment(), true);
1272 {// insertGap==false AND editSeq==TRUE;
1273 if (fixedColumns && fixedRight != -1)
1275 for (int j = lastres; j < startres; j++)
1277 insertChar(j, new SequenceI[]
1278 { seq }, fixedRight);
1283 editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[]
1284 { seq }, lastres, startres - lastres, av.getAlignment(), true);
1291 seqCanvas.repaint();
1294 void insertChar(int j, SequenceI[] seq, int fixedColumn)
1296 int blankColumn = fixedColumn;
1297 for (int s = 0; s < seq.length; s++)
1299 // Find the next gap before the end of the visible region boundary
1300 // If lastCol > j, theres a boundary after the gap insertion
1302 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
1304 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
1306 // Theres a space, so break and insert the gap
1311 if (blankColumn <= j)
1313 blankColumn = fixedColumn;
1319 editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
1320 av.getAlignment(), true);
1322 editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
1323 av.getAlignment(), true);
1327 void deleteChar(int j, SequenceI[] seq, int fixedColumn)
1330 editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
1331 av.getAlignment(), true);
1333 editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
1334 av.getAlignment(), true);
1344 public void mouseEntered(MouseEvent e)
1351 if (scrollThread != null)
1353 scrollThread.running = false;
1354 scrollThread = null;
1365 public void mouseExited(MouseEvent e)
1367 if (av.getWrapAlignment())
1374 scrollThread = new ScrollThread();
1379 public void mouseClicked(MouseEvent evt)
1381 SequenceGroup sg = null;
1382 SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
1383 if (evt.getClickCount() > 1)
1385 sg = av.getSelectionGroup();
1386 if (sg != null && sg.getSize() == 1
1387 && sg.getEndRes() - sg.getStartRes() < 2)
1389 av.setSelectionGroup(null);
1392 SequenceFeature[] features = findFeaturesAtRes(
1393 sequence.getDatasetSequence(),
1394 sequence.findPosition(findRes(evt)));
1396 if (features != null && features.length > 0)
1398 SearchResults highlight = new SearchResults();
1399 highlight.addResult(sequence, features[0].getBegin(),
1400 features[0].getEnd());
1401 seqCanvas.highlightSearchResults(highlight);
1403 if (features != null && features.length > 0)
1405 seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
1406 { sequence }, features, false, ap);
1408 seqCanvas.highlightSearchResults(null);
1414 public void mouseWheelMoved(MouseWheelEvent e)
1417 if (e.getWheelRotation() > 0)
1419 if (e.isShiftDown())
1421 ap.scrollRight(true);
1431 if (e.isShiftDown())
1433 ap.scrollRight(false);
1440 // TODO Update tooltip for new position.
1449 public void doMousePressedDefineMode(MouseEvent evt)
1451 int res = findRes(evt);
1452 int seq = findSeq(evt);
1455 startWrapBlock = wrappedBlock;
1457 if (av.wrapAlignment && seq > av.getAlignment().getHeight())
1459 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
1460 .getString("label.cannot_edit_annotations_in_wrapped_view"),
1461 MessageManager.getString("label.wrapped_view_no_edit"),
1462 JOptionPane.WARNING_MESSAGE);
1466 if (seq < 0 || res < 0)
1471 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
1473 if ((sequence == null) || (res > sequence.getLength()))
1478 stretchGroup = av.getSelectionGroup();
1480 if (stretchGroup == null)
1482 stretchGroup = av.getAlignment().findGroup(sequence);
1484 if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
1485 && (res < stretchGroup.getEndRes()))
1487 av.setSelectionGroup(stretchGroup);
1491 stretchGroup = null;
1494 else if (!stretchGroup.getSequences(null).contains(sequence)
1495 || (stretchGroup.getStartRes() > res)
1496 || (stretchGroup.getEndRes() < res))
1498 stretchGroup = null;
1500 SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
1502 if (allGroups != null)
1504 for (int i = 0; i < allGroups.length; i++)
1506 if ((allGroups[i].getStartRes() <= res)
1507 && (allGroups[i].getEndRes() >= res))
1509 stretchGroup = allGroups[i];
1515 av.setSelectionGroup(stretchGroup);
1519 if (javax.swing.SwingUtilities.isRightMouseButton(evt))
1521 SequenceFeature[] allFeatures = findFeaturesAtRes(
1522 sequence.getDatasetSequence(), sequence.findPosition(res));
1523 Vector links = new Vector();
1524 for (int i = 0; i < allFeatures.length; i++)
1526 if (allFeatures[i].links != null)
1528 for (int j = 0; j < allFeatures[i].links.size(); j++)
1530 links.addElement(allFeatures[i].links.elementAt(j));
1535 jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
1536 pop.show(this, evt.getX(), evt.getY());
1542 seqCanvas.cursorX = findRes(evt);
1543 seqCanvas.cursorY = findSeq(evt);
1544 seqCanvas.repaint();
1548 if (stretchGroup == null)
1550 // Only if left mouse button do we want to change group sizes
1552 // define a new group here
1553 SequenceGroup sg = new SequenceGroup();
1554 sg.setStartRes(res);
1556 sg.addSequence(sequence, false);
1557 av.setSelectionGroup(sg);
1561 if (av.getConservationSelected())
1563 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
1567 if (av.getAbovePIDThreshold())
1569 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
1572 if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
1574 // Edit end res position of selected group
1575 changeEndRes = true;
1577 else if ((stretchGroup != null)
1578 && (stretchGroup.getStartRes() == res))
1580 // Edit end res position of selected group
1581 changeStartRes = true;
1583 stretchGroup.getWidth();
1586 seqCanvas.repaint();
1595 public void doMouseReleasedDefineMode(MouseEvent evt)
1597 if (stretchGroup == null)
1602 stretchGroup.recalcConservation(); // always do this - annotation has own
1604 if (stretchGroup.cs != null)
1606 stretchGroup.cs.alignmentChanged(stretchGroup,
1607 av.getHiddenRepSequences());
1609 if (stretchGroup.cs.conservationApplied())
1611 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
1612 stretchGroup.getName());
1616 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
1617 stretchGroup.getName());
1620 PaintRefresher.Refresh(this, av.getSequenceSetId());
1621 ap.paintAlignment(true);
1623 changeEndRes = false;
1624 changeStartRes = false;
1625 stretchGroup = null;
1635 public void doMouseDraggedDefineMode(MouseEvent evt)
1637 int res = findRes(evt);
1638 int y = findSeq(evt);
1640 if (wrappedBlock != startWrapBlock)
1645 if (stretchGroup == null)
1650 if (res >= av.getAlignment().getWidth())
1652 res = av.getAlignment().getWidth() - 1;
1655 if (stretchGroup.getEndRes() == res)
1657 // Edit end res position of selected group
1658 changeEndRes = true;
1660 else if (stretchGroup.getStartRes() == res)
1662 // Edit start res position of selected group
1663 changeStartRes = true;
1666 if (res < av.getStartRes())
1668 res = av.getStartRes();
1673 if (res > (stretchGroup.getStartRes() - 1))
1675 stretchGroup.setEndRes(res);
1678 else if (changeStartRes)
1680 if (res < (stretchGroup.getEndRes() + 1))
1682 stretchGroup.setStartRes(res);
1686 int dragDirection = 0;
1692 else if (y < oldSeq)
1697 while ((y != oldSeq) && (oldSeq > -1)
1698 && (y < av.getAlignment().getHeight()))
1700 // This routine ensures we don't skip any sequences, as the
1701 // selection is quite slow.
1702 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1704 oldSeq += dragDirection;
1711 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
1713 if (stretchGroup.getSequences(null).contains(nextSeq))
1715 stretchGroup.deleteSequence(seq, false);
1721 stretchGroup.addSequence(seq, false);
1724 stretchGroup.addSequence(nextSeq, false);
1733 mouseDragging = true;
1735 if (scrollThread != null)
1737 scrollThread.setEvent(evt);
1740 seqCanvas.repaint();
1743 void scrollCanvas(MouseEvent evt)
1747 if (scrollThread != null)
1749 scrollThread.running = false;
1750 scrollThread = null;
1752 mouseDragging = false;
1756 if (scrollThread == null)
1758 scrollThread = new ScrollThread();
1761 mouseDragging = true;
1762 scrollThread.setEvent(evt);
1767 // this class allows scrolling off the bottom of the visible alignment
1768 class ScrollThread extends Thread
1772 boolean running = false;
1774 public ScrollThread()
1779 public void setEvent(MouseEvent e)
1784 public void stopScrolling()
1798 if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
1800 running = ap.scrollUp(true);
1803 if (mouseDragging && (evt.getY() >= getHeight())
1804 && (av.getAlignment().getHeight() > av.getEndSeq()))
1806 running = ap.scrollUp(false);
1809 if (mouseDragging && (evt.getX() < 0))
1811 running = ap.scrollRight(false);
1813 else if (mouseDragging && (evt.getX() >= getWidth()))
1815 running = ap.scrollRight(true);
1822 } catch (Exception ex)
1830 * modify current selection according to a received message.
1833 public void selection(SequenceGroup seqsel, ColumnSelection colsel,
1834 SelectionSource source)
1836 // TODO: fix this hack - source of messages is align viewport, but SeqPanel
1837 // handles selection messages...
1838 // TODO: extend config options to allow user to control if selections may be
1839 // shared between viewports.
1841 || !av.followSelection
1842 || (av.isSelectionGroupChanged(false) || av
1843 .isColSelChanged(false))
1844 || (source instanceof AlignViewport && ((AlignViewport) source)
1845 .getSequenceSetId().equals(av.getSequenceSetId())))
1849 // do we want to thread this ? (contention with seqsel and colsel locks, I
1851 // rules are: colsel is copied if there is a real intersection between
1852 // sequence selection
1853 boolean repaint = false, copycolsel = true;
1854 // if (!av.isSelectionGroupChanged(false))
1856 SequenceGroup sgroup = null;
1857 if (seqsel != null && seqsel.getSize() > 0)
1859 if (av.getAlignment() == null)
1861 jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
1862 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
1863 + " 's alignment is NULL! returning immediatly.");
1866 sgroup = seqsel.intersect(av.getAlignment(),
1867 (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
1868 if ((sgroup == null || sgroup.getSize() == 0)
1869 || (colsel == null || colsel.size() == 0))
1871 // don't copy columns if the region didn't intersect.
1875 if (sgroup != null && sgroup.getSize() > 0)
1877 av.setSelectionGroup(sgroup);
1881 av.setSelectionGroup(null);
1883 av.isSelectionGroupChanged(true);
1888 // the current selection is unset or from a previous message
1889 // so import the new colsel.
1890 if (colsel == null || colsel.size() == 0)
1892 if (av.getColumnSelection() != null)
1894 av.getColumnSelection().clear();
1900 // TODO: shift colSel according to the intersecting sequences
1901 if (av.getColumnSelection() == null)
1903 av.setColumnSelection(new ColumnSelection(colsel));
1907 av.getColumnSelection().setElementsFrom(colsel);
1910 av.isColSelChanged(true);
1914 && av.hasHiddenColumns()
1915 && (av.getColumnSelection() == null || av.getColumnSelection()
1916 .getHiddenColumns() == null))
1918 System.err.println("Bad things");
1922 // probably finessing with multiple redraws here
1923 PaintRefresher.Refresh(this, av.getSequenceSetId());
1924 // ap.paintAlignment(false);