2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
20 package jalview.appletgui;
\r
23 import java.awt.event.*;
\r
25 import jalview.datamodel.*;
\r
26 import jalview.schemes.*;
\r
27 import jalview.commands.*;
\r
29 import java.util.Vector;
\r
31 public class SeqPanel
\r
32 extends Panel implements MouseMotionListener, MouseListener
\r
35 public SeqCanvas seqCanvas;
\r
36 public AlignmentPanel ap;
\r
38 protected int lastres;
\r
39 protected int startseq;
\r
41 protected AlignViewport av;
\r
43 // if character is inserted or deleted, we will need to recalculate the conservation
\r
44 boolean seqEditOccurred = false;
\r
46 ScrollThread scrollThread = null;
\r
47 boolean mouseDragging = false;
\r
48 boolean editingSeqs = false;
\r
49 boolean groupEditing = false;
\r
52 boolean changeEndSeq = false;
\r
53 boolean changeStartSeq = false;
\r
54 boolean changeEndRes = false;
\r
55 boolean changeStartRes = false;
\r
56 SequenceGroup stretchGroup = null;
\r
58 StringBuffer keyboardNo1;
\r
59 StringBuffer keyboardNo2;
\r
61 boolean mouseWheelPressed = false;
\r
62 Point lastMousePress;
\r
64 EditCommand editCommand;
\r
66 public SeqPanel(AlignViewport avp, AlignmentPanel p)
\r
70 seqCanvas = new SeqCanvas(avp);
\r
71 setLayout(new BorderLayout());
\r
76 seqCanvas.addMouseMotionListener(this);
\r
77 seqCanvas.addMouseListener(this);
\r
79 seqCanvas.repaint();
\r
84 if (editCommand!=null && editCommand.getSize() > 0)
\r
86 ap.alignFrame.addHistoryItem(editCommand);
\r
87 av.firePropertyChange("alignment", null,
\r
88 av.getAlignment().getSequences());
\r
93 editingSeqs = false;
\r
94 groupEditing = false;
\r
100 void setCursorRow()
\r
102 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
\r
106 void setCursorColumn()
\r
108 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
\r
112 void setCursorRowAndColumn()
\r
114 if(keyboardNo2==null)
\r
116 keyboardNo2 = new StringBuffer();
\r
120 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
\r
121 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
\r
126 void setCursorPosition()
\r
128 SequenceI sequence =
\r
129 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
\r
131 seqCanvas.cursorX = sequence.findIndex(
\r
132 getKeyboardNo(keyboardNo1)-1
\r
137 void moveCursor(int dx, int dy)
\r
139 seqCanvas.cursorX += dx;
\r
140 seqCanvas.cursorY += dy;
\r
141 if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
\r
143 int original = seqCanvas.cursorX - dx;
\r
144 int maxWidth = av.alignment.getWidth();
\r
146 while(!av.colSel.isVisible(seqCanvas.cursorX)
\r
147 && seqCanvas.cursorX<maxWidth
\r
148 && seqCanvas.cursorX>0)
\r
150 seqCanvas.cursorX += dx;
\r
153 if(seqCanvas.cursorX>=maxWidth
\r
154 || !av.colSel.isVisible(seqCanvas.cursorX) )
\r
156 seqCanvas.cursorX = original;
\r
162 void scrollToVisible()
\r
164 if (seqCanvas.cursorX < 0)
\r
165 seqCanvas.cursorX = 0;
\r
166 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
\r
167 seqCanvas.cursorX = av.alignment.getWidth() - 1;
\r
169 if (seqCanvas.cursorY < 0)
\r
170 seqCanvas.cursorY = 0;
\r
171 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
\r
172 seqCanvas.cursorY = av.alignment.getHeight() - 1;
\r
176 if (av.wrapAlignment)
\r
178 ap.scrollToWrappedVisible(seqCanvas.cursorX);
\r
182 while (seqCanvas.cursorY < av.startSeq)
\r
186 while (seqCanvas.cursorY + 1 > av.endSeq)
\r
188 ap.scrollUp(false);
\r
190 while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
\r
193 if (!ap.scrollRight(false))
\r
196 while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
\r
198 if (!ap.scrollRight(true))
\r
202 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
\r
203 seqCanvas.cursorX, seqCanvas.cursorY);
\r
205 seqCanvas.repaint();
\r
208 void setSelectionAreaAtCursor(boolean topLeft)
\r
210 SequenceI sequence =
\r
211 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
\r
213 if(av.getSelectionGroup()!=null)
\r
215 SequenceGroup sg = av.selectionGroup;
\r
216 //Find the top and bottom of this group
\r
217 int min = av.alignment.getHeight(), max = 0;
\r
218 for(int i=0; i<sg.getSize(); i++)
\r
220 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
\r
231 sg.setStartRes(seqCanvas.cursorX);
\r
232 if(sg.getEndRes()<seqCanvas.cursorX)
\r
233 sg.setEndRes(seqCanvas.cursorX);
\r
235 min = seqCanvas.cursorY;
\r
239 sg.setEndRes(seqCanvas.cursorX);
\r
240 if(sg.getStartRes()>seqCanvas.cursorX)
\r
241 sg.setStartRes(seqCanvas.cursorX);
\r
243 max = seqCanvas.cursorY+1;
\r
248 // Only the user can do this
\r
249 av.setSelectionGroup(null);
\r
253 // Now add any sequences between min and max
\r
254 sg.getSequences(null).removeAllElements();
\r
255 for (int i = min; i < max; i++)
\r
257 sg.addSequence(av.alignment.getSequenceAt(i), false);
\r
262 if (av.getSelectionGroup() == null)
\r
264 SequenceGroup sg = new SequenceGroup();
\r
265 sg.setStartRes(seqCanvas.cursorX);
\r
266 sg.setEndRes(seqCanvas.cursorX);
\r
267 sg.addSequence(sequence, false);
\r
268 av.setSelectionGroup(sg);
\r
275 void insertGapAtCursor(boolean group)
\r
277 groupEditing = group;
\r
278 startseq = seqCanvas.cursorY;
\r
279 lastres = seqCanvas.cursorX;
\r
280 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
\r
284 void deleteGapAtCursor(boolean group)
\r
286 groupEditing = group;
\r
287 startseq = seqCanvas.cursorY;
\r
288 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
\r
289 editSequence(false, seqCanvas.cursorX);
\r
293 void numberPressed(char value)
\r
295 if(keyboardNo1==null)
\r
296 keyboardNo1 = new StringBuffer();
\r
298 if(keyboardNo2!=null)
\r
299 keyboardNo2.append(value);
\r
301 keyboardNo1.append(value);
\r
304 int getKeyboardNo(StringBuffer kb)
\r
309 return Integer.parseInt(kb.toString());
\r
312 void setStatusMessage(SequenceI sequence, int res, int seq)
\r
314 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
\r
315 sequence.getName());
\r
318 if (av.alignment.isNucleotide())
\r
320 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
\r
323 text.append(" Nucleotide: ");
\r
327 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
\r
329 text.append(" Residue: ");
\r
337 text.append(obj + " (" + sequence.findPosition(res) +
\r
342 ap.alignFrame.statusBar.setText(text.toString());
\r
345 public void mousePressed(MouseEvent evt)
\r
347 lastMousePress = evt.getPoint();
\r
349 //For now, ignore the mouseWheel font resizing on Macs
\r
350 //As the Button2_mask always seems to be true
\r
351 if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
\r
352 InputEvent.BUTTON2_MASK && !av.MAC)
\r
354 mouseWheelPressed = true;
\r
358 if (evt.isShiftDown()
\r
359 || evt.isControlDown()
\r
360 || evt.isAltDown())
\r
362 if (evt.isControlDown() || evt.isAltDown())
\r
364 groupEditing = true;
\r
366 editingSeqs = true;
\r
370 doMousePressedDefineMode(evt);
\r
375 int seq = findSeq(evt);
\r
376 int res = findRes(evt);
\r
382 if ((seq < av.getAlignment().getHeight()) &&
\r
383 (res < av.getAlignment().getSequenceAt(seq).getLength()))
\r
397 public void mouseClicked(MouseEvent evt){}
\r
400 public void mouseReleased(MouseEvent evt)
\r
402 mouseDragging = false;
\r
403 mouseWheelPressed = false;
\r
407 doMouseReleasedDefineMode(evt);
\r
415 int startWrapBlock=-1;
\r
416 int wrappedBlock=-1;
\r
417 int findRes(MouseEvent evt)
\r
420 int x = evt.getX();
\r
422 if (av.wrapAlignment)
\r
425 int hgap = av.charHeight;
\r
426 if (av.scaleAboveWrapped)
\r
427 hgap += av.charHeight;
\r
429 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
430 + hgap + seqCanvas.getAnnotationHeight();
\r
432 int y = evt.getY();
\r
434 x -= seqCanvas.LABEL_WEST;
\r
437 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
\r
441 wrappedBlock = y / cHeight;
\r
442 wrappedBlock += av.getStartRes() / cwidth;
\r
444 res = wrappedBlock * cwidth + x / av.getCharWidth();
\r
449 res = (x / av.getCharWidth()) + av.getStartRes();
\r
452 if(av.hasHiddenColumns)
\r
453 res = av.getColumnSelection().adjustForHiddenColumns(res);
\r
459 int findSeq(MouseEvent evt)
\r
463 int y = evt.getY();
\r
465 if (av.wrapAlignment)
\r
467 int hgap = av.charHeight;
\r
468 if (av.scaleAboveWrapped)
\r
469 hgap += av.charHeight;
\r
471 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
472 + hgap + seqCanvas.getAnnotationHeight();
\r
476 seq = Math.min( (y % cHeight) / av.getCharHeight(),
\r
477 av.alignment.getHeight() -1);
\r
483 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
\r
484 av.alignment.getHeight() -1);
\r
493 public void doMousePressed(MouseEvent evt)
\r
496 int seq = findSeq(evt);
\r
497 int res = findRes(evt);
\r
499 if (seq < av.getAlignment().getHeight() &&
\r
500 res < av.getAlignment().getSequenceAt(seq).getLength())
\r
502 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
\r
503 // Find the residue's position in the sequence (res is the position
\r
504 // in the alignment
\r
518 public void mouseMoved(MouseEvent evt)
\r
520 int res = findRes(evt);
\r
521 int seq = findSeq(evt);
\r
523 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
\r
528 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
\r
529 if (res > sequence.getLength())
\r
534 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
\r
535 sequence.getName());
\r
538 if (av.alignment.isNucleotide())
\r
540 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
\r
543 text.append(" Nucleotide: ");
\r
547 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
\r
549 text.append(" Residue: ");
\r
556 text.append(obj + " (" + sequence.findPosition(res) + ")");
\r
560 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
\r
562 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
\r
565 ap.alignFrame.statusBar.setText(text.toString());
\r
567 StringBuffer tooltipText = new StringBuffer();
\r
568 SequenceGroup [] groups = av.alignment.findAllGroups(sequence);
\r
571 for(int g=0; g<groups.length; g++)
\r
573 if(groups[g].getStartRes()<=res && groups[g].getEndRes()>=res)
\r
575 if (!groups[g].getName().startsWith("JTreeGroup") &&
\r
576 !groups[g].getName().startsWith("JGroup"))
\r
577 tooltipText.append(groups[g].getName() + " ");
\r
578 if(groups[g].getDescription()!=null)
\r
579 tooltipText.append(groups[g].getDescription());
\r
580 tooltipText.append("\n");
\r
585 // use aa to see if the mouse pointer is on a
\r
586 if (av.showSequenceFeatures
\r
587 && sequence.getSequenceFeatures()!=null
\r
588 && av.featuresDisplayed!=null)
\r
591 Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
\r
594 while (index < allFeatures.size())
\r
596 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
\r
598 tooltipText.append(sf.getType()+" "+sf.begin+":"+sf.end);
\r
600 if (sf.getDescription() != null)
\r
601 tooltipText.append(" " + sf.getDescription());
\r
603 if (sf.getValue("status") != null )
\r
605 String status = sf.getValue("status").toString();
\r
606 if(status.length()>0)
\r
607 tooltipText.append(" (" + sf.getValue("status") + ")");
\r
609 tooltipText.append("\n");
\r
615 if (tooltip == null)
\r
616 tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
\r
618 tooltip.setTip(tooltipText.toString());
\r
624 Vector getAllFeaturesAtRes(SequenceI seq, int res)
\r
626 Vector allFeatures = new Vector();
\r
628 if(seq.getSequenceFeatures()!=null)
\r
630 while (index < seq.getSequenceFeatures().length)
\r
632 SequenceFeature sf = seq.getSequenceFeatures()[index];
\r
633 if (sf.getBegin() <= res &&
\r
634 sf.getEnd() >= res)
\r
636 if (av.featuresDisplayed.containsKey(sf.getType()))
\r
638 allFeatures.addElement(sf);
\r
644 return allFeatures;
\r
649 public void mouseDragged(MouseEvent evt)
\r
651 if (mouseWheelPressed)
\r
653 int oldWidth = av.charWidth;
\r
655 //Which is bigger, left-right or up-down?
\r
656 if (Math.abs(evt.getY() - lastMousePress.y)
\r
657 > Math.abs(evt.getX() - lastMousePress.x))
\r
659 int fontSize = av.font.getSize();
\r
661 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
\r
665 else if (evt.getY() > lastMousePress.y)
\r
674 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
\r
675 av.charWidth = oldWidth;
\r
679 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
\r
683 else if (evt.getX() > lastMousePress.x)
\r
696 FontMetrics fm = getFontMetrics(av.getFont());
\r
697 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
\r
699 lastMousePress = evt.getPoint();
\r
702 ap.annotationPanel.image = null;
\r
708 doMouseDraggedDefineMode(evt);
\r
712 int res = findRes(evt);
\r
719 if ((lastres == -1) || (lastres == res))
\r
724 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
\r
726 // dragLeft, delete gap
\r
727 editSequence(false, res);
\r
730 editSequence(true, res);
\r
732 mouseDragging = true;
\r
733 if(scrollThread!=null)
\r
734 scrollThread.setEvent(evt);
\r
738 synchronized void editSequence(boolean insertGap, int startres)
\r
740 int fixedLeft = -1;
\r
741 int fixedRight = -1;
\r
742 boolean fixedColumns = false;
\r
743 SequenceGroup sg = av.getSelectionGroup();
\r
745 SequenceI seq = av.alignment.getSequenceAt(startseq);
\r
747 if (!groupEditing && av.hasHiddenRows)
\r
749 if (av.hiddenRepSequences!=null
\r
750 && av.hiddenRepSequences.containsKey(seq))
\r
752 sg = (SequenceGroup)av.hiddenRepSequences.get(seq);
\r
753 groupEditing = true;
\r
757 StringBuffer message = new StringBuffer();
\r
760 message.append("Edit group:");
\r
761 if (editCommand == null)
\r
762 editCommand = new EditCommand("Edit Group");
\r
766 message.append("Edit sequence: " + seq.getName());
\r
767 String label = seq.getName();
\r
768 if(label.length()>10)
\r
769 label = label.substring(0,10);
\r
770 if(editCommand==null)
\r
771 editCommand = new EditCommand("Edit "+label);
\r
775 message.append(" insert ");
\r
777 message.append(" delete ");
\r
779 message.append(Math.abs(startres-lastres)+" gaps.");
\r
780 ap.alignFrame.statusBar.setText(message.toString());
\r
783 //Are we editing within a selection group?
\r
785 || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
\r
787 fixedColumns = true;
\r
789 //sg might be null as the user may only see 1 sequence,
\r
790 //but the sequence represents a group
\r
793 sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
\r
796 fixedLeft = sg.getStartRes();
\r
797 fixedRight = sg.getEndRes();
\r
799 if ( (startres < fixedLeft && lastres >= fixedLeft)
\r
800 || (startres >= fixedLeft && lastres < fixedLeft)
\r
801 || (startres > fixedRight && lastres <=fixedRight)
\r
802 || (startres <= fixedRight && lastres > fixedRight))
\r
808 if (fixedLeft > startres)
\r
810 fixedRight = fixedLeft - 1;
\r
813 else if (fixedRight < startres)
\r
815 fixedLeft = fixedRight;
\r
821 if(av.hasHiddenColumns )
\r
823 fixedColumns = true;
\r
824 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
\r
825 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
\r
827 if ( (insertGap && startres > y1 && lastres < y1)
\r
828 || (!insertGap && startres < y2 && lastres > y2))
\r
834 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
\r
835 //Selection spans a hidden region
\r
836 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
\r
844 fixedRight = y2 - 1;
\r
852 Vector vseqs = sg.getSequences(av.hiddenRepSequences);
\r
853 int g, groupSize = vseqs.size();
\r
854 SequenceI[] groupSeqs = new SequenceI[groupSize];
\r
855 for (g = 0; g < groupSeqs.length; g++)
\r
856 groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
\r
861 //If the user has selected the whole sequence, and is dragging to
\r
862 // the right, we can still extend the alignment and selectionGroup
\r
863 if( sg.getStartRes() == 0
\r
864 && sg.getEndRes() == fixedRight
\r
865 && sg.getEndRes() == av.alignment.getWidth()-1
\r
868 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
\r
869 fixedRight = sg.getEndRes();
\r
872 // Is it valid with fixed columns??
\r
873 // Find the next gap before the end
\r
874 // of the visible region boundary
\r
875 boolean blank = false;
\r
876 for (fixedRight = fixedRight;
\r
877 fixedRight > lastres;
\r
882 for (g = 0; g < groupSize; g++)
\r
884 for (int j = 0; j < startres - lastres; j++)
\r
886 if (!jalview.util.Comparison.isGap(
\r
887 groupSeqs[g].getCharAt(fixedRight - j)))
\r
900 if(sg.getSize() == av.alignment.getHeight() )
\r
902 if((av.hasHiddenColumns
\r
903 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
\r
909 int alWidth = av.alignment.getWidth();
\r
910 if(av.hasHiddenRows)
\r
912 int hwidth = av.alignment.getHiddenSequences().getWidth();
\r
916 //We can still insert gaps if the selectionGroup
\r
917 //contains all the sequences
\r
918 sg.setEndRes(sg.getEndRes()+startres-lastres);
\r
919 fixedRight = alWidth+startres-lastres;
\r
931 else if(!insertGap)
\r
933 /// Are we able to delete?
\r
934 // ie are all columns blank?
\r
936 for (g = 0; g < groupSize; g++)
\r
938 for (int j = startres; j < lastres; j++)
\r
940 if (groupSeqs[g].getLength() <= j)
\r
945 if (!jalview.util.Comparison.isGap(
\r
946 groupSeqs[g].getCharAt(j)))
\r
948 // Not a gap, block edit not valid
\r
958 // dragging to the right
\r
959 if (fixedColumns && fixedRight != -1)
\r
961 for (int j = lastres; j < startres; j++)
\r
963 insertChar(j, groupSeqs, fixedRight);
\r
968 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
970 startres, startres-lastres,
\r
977 // dragging to the left
\r
978 if (fixedColumns && fixedRight != -1)
\r
980 for (int j = lastres; j > startres; j--)
\r
982 deleteChar(startres, groupSeqs, fixedRight);
\r
986 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
988 startres, lastres - startres,
\r
994 else /////Editing a single sequence///////////
\r
998 // dragging to the right
\r
999 if (fixedColumns && fixedRight != -1)
\r
1001 for (int j = lastres; j < startres; j++)
\r
1003 insertChar(j, new SequenceI[]{seq}, fixedRight);
\r
1008 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1011 lastres, startres-lastres,
\r
1018 // dragging to the left
\r
1019 if (fixedColumns && fixedRight != -1)
\r
1021 for (int j = lastres; j > startres; j--)
\r
1023 if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
\r
1028 deleteChar(startres, new SequenceI[]{seq}, fixedRight);
\r
1033 //could be a keyboard edit trying to delete none gaps
\r
1035 for(int m = startres; m<lastres; m++)
\r
1037 if(!jalview.util.Comparison.isGap(seq.getCharAt(m)))
\r
1044 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1055 lastres = startres;
\r
1056 seqCanvas.repaint();
\r
1061 void insertChar(int j, SequenceI [] seq, int fixedColumn)
\r
1063 int blankColumn = fixedColumn;
\r
1064 for(int s=0; s<seq.length; s++)
\r
1066 //Find the next gap before the end of the visible region boundary
\r
1067 //If lastCol > j, theres a boundary after the gap insertion
\r
1069 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1071 if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
\r
1073 //Theres a space, so break and insert the gap
\r
1078 if (blankColumn <= j)
\r
1080 blankColumn = fixedColumn;
\r
1086 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1088 blankColumn, 1, av.alignment, true);
\r
1090 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1092 j, 1, av.alignment,
\r
1097 void deleteChar(int j, SequenceI [] seq, int fixedColumn)
\r
1100 editCommand.appendEdit(EditCommand.DELETE_GAP,
\r
1102 j, 1, av.alignment, true);
\r
1104 editCommand.appendEdit(EditCommand.INSERT_GAP,
\r
1106 fixedColumn, 1, av.alignment, true);
\r
1110 //////////////////////////////////////////
\r
1111 /////Everything below this is for defining the boundary of the rubberband
\r
1112 //////////////////////////////////////////
\r
1113 public void doMousePressedDefineMode(MouseEvent evt)
\r
1115 if (scrollThread != null)
\r
1117 scrollThread.running = false;
\r
1118 scrollThread = null;
\r
1121 int res = findRes(evt);
\r
1122 int seq = findSeq(evt);
\r
1124 startWrapBlock=wrappedBlock;
\r
1129 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1131 if (sequence == null || res > sequence.getLength())
\r
1136 stretchGroup = av.getSelectionGroup();
\r
1138 if (stretchGroup == null)
\r
1140 stretchGroup = av.alignment.findGroup(sequence);
\r
1141 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
\r
1142 res < stretchGroup.getEndRes())
\r
1144 av.setSelectionGroup(stretchGroup);
\r
1148 stretchGroup = null;
\r
1152 else if (!stretchGroup.getSequences(null).contains(sequence)
\r
1153 || stretchGroup.getStartRes() > res
\r
1154 || stretchGroup.getEndRes() < res)
\r
1156 stretchGroup = null;
\r
1158 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1160 if (allGroups != null)
\r
1162 for (int i = 0; i < allGroups.length; i++)
\r
1164 if (allGroups[i].getStartRes() <= res &&
\r
1165 allGroups[i].getEndRes() >= res)
\r
1167 stretchGroup = allGroups[i];
\r
1172 av.setSelectionGroup(stretchGroup);
\r
1176 // DETECT RIGHT MOUSE BUTTON IN AWT
\r
1177 if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
\r
1178 InputEvent.BUTTON3_MASK)
\r
1180 Vector allFeatures = getAllFeaturesAtRes(sequence,
\r
1181 sequence.findPosition(res));
\r
1183 Vector links = null;
\r
1184 if(allFeatures!=null)
\r
1186 for (int i = 0; i < allFeatures.size(); i++)
\r
1188 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1189 if (sf.links != null)
\r
1191 links = new Vector();
\r
1192 for (int j = 0; j < sf.links.size(); j++)
\r
1194 links.addElement(sf.links.elementAt(j));
\r
1199 APopupMenu popup = new APopupMenu(ap, null, links);
\r
1201 popup.show(this, evt.getX(), evt.getY());
\r
1206 if (av.cursorMode)
\r
1208 seqCanvas.cursorX = findRes(evt);
\r
1209 seqCanvas.cursorY = findSeq(evt);
\r
1210 seqCanvas.repaint();
\r
1214 //Only if left mouse button do we want to change group sizes
\r
1216 if (stretchGroup == null)
\r
1218 // define a new group here
\r
1219 SequenceGroup sg = new SequenceGroup();
\r
1220 sg.setStartRes(res);
\r
1221 sg.setEndRes(res);
\r
1222 sg.addSequence(sequence, false);
\r
1223 av.setSelectionGroup(sg);
\r
1224 stretchGroup = sg;
\r
1226 if (av.getConservationSelected())
\r
1228 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
\r
1231 if (av.getAbovePIDThreshold())
\r
1233 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1240 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1242 if (stretchGroup == null)
\r
1247 if(stretchGroup.cs!=null)
\r
1249 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1251 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1252 stretchGroup.getSequences(av.hiddenRepSequences),
\r
1253 stretchGroup.getWidth());
\r
1256 if (stretchGroup.cs instanceof Blosum62ColourScheme
\r
1257 || stretchGroup.cs instanceof PIDColourScheme
\r
1258 || stretchGroup.cs.conservationApplied()
\r
1259 || stretchGroup.cs.getThreshold() > 0)
\r
1260 stretchGroup.recalcConservation();
\r
1263 if (stretchGroup.cs.conservationApplied())
\r
1265 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1266 stretchGroup.getName());
\r
1267 stretchGroup.recalcConservation();
\r
1271 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1272 stretchGroup.getName());
\r
1275 changeEndRes = false;
\r
1276 changeStartRes = false;
\r
1277 stretchGroup = null;
\r
1278 PaintRefresher.Refresh(ap, av.getSequenceSetId());
\r
1282 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1284 int res = findRes(evt);
\r
1285 int y = findSeq(evt);
\r
1287 if(wrappedBlock!=startWrapBlock)
\r
1290 if (stretchGroup == null)
\r
1295 mouseDragging = true;
\r
1298 if(y > av.alignment.getHeight())
\r
1300 y = av.alignment.getHeight() -1;
\r
1303 if(res>=av.alignment.getWidth())
\r
1304 res = av.alignment.getWidth()-1;
\r
1306 if (stretchGroup.getEndRes() == res)
\r
1308 // Edit end res position of selected group
\r
1309 changeEndRes = true;
\r
1311 else if (stretchGroup.getStartRes() == res)
\r
1313 // Edit start res position of selected group
\r
1314 changeStartRes = true;
\r
1324 if (res > (stretchGroup.getStartRes() - 1))
\r
1326 stretchGroup.setEndRes(res);
\r
1329 else if (changeStartRes)
\r
1331 if (res < (stretchGroup.getEndRes() + 1))
\r
1333 stretchGroup.setStartRes(res);
\r
1337 int dragDirection = 0;
\r
1341 dragDirection = 1;
\r
1343 else if (y < oldSeq)
\r
1345 dragDirection = -1;
\r
1349 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1351 // This routine ensures we don't skip any sequences, as the
\r
1352 // selection is quite slow.
\r
1353 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1355 oldSeq += dragDirection;
\r
1360 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1362 if (stretchGroup.getSequences(null).contains(nextSeq))
\r
1364 stretchGroup.deleteSequence(seq, false);
\r
1370 stretchGroup.addSequence(seq, false);
\r
1373 stretchGroup.addSequence(nextSeq, false);
\r
1381 if(res>av.endRes || res<av.startRes
\r
1382 || y<av.startSeq || y>av.endSeq)
\r
1387 if (scrollThread != null)
\r
1389 scrollThread.setEvent(evt);
\r
1392 seqCanvas.repaint();
\r
1395 public void mouseEntered(MouseEvent e)
\r
1400 if (scrollThread != null)
\r
1402 scrollThread.running = false;
\r
1403 scrollThread = null;
\r
1407 public void mouseExited(MouseEvent e)
\r
1409 if (av.getWrapAlignment())
\r
1414 if (mouseDragging && scrollThread==null)
\r
1416 scrollThread = new ScrollThread();
\r
1420 void scrollCanvas(MouseEvent evt)
\r
1424 if(scrollThread!=null)
\r
1426 scrollThread.running = false;
\r
1427 scrollThread = null;
\r
1429 mouseDragging = false;
\r
1433 if (scrollThread == null)
\r
1434 scrollThread = new ScrollThread();
\r
1436 mouseDragging = true;
\r
1437 scrollThread.setEvent(evt);
\r
1442 // this class allows scrolling off the bottom of the visible alignment
\r
1443 class ScrollThread
\r
1447 boolean running = false;
\r
1448 public ScrollThread()
\r
1453 public void setEvent(MouseEvent e)
\r
1458 public void stopScrolling()
\r
1472 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1474 running = ap.scrollUp(true);
\r
1477 if (mouseDragging && evt.getY() >= getSize().height &&
\r
1478 av.alignment.getHeight() > av.getEndSeq())
\r
1480 running = ap.scrollUp(false);
\r
1483 if (mouseDragging && evt.getX() < 0)
\r
1485 running = ap.scrollRight(false);
\r
1488 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1490 running = ap.scrollRight(true);
\r
1498 catch (Exception ex)
\r