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
28 import java.util.Vector;
\r
30 public class SeqPanel
\r
31 extends Panel implements MouseMotionListener, MouseListener
\r
34 public SeqCanvas seqCanvas;
\r
35 public AlignmentPanel ap;
\r
37 protected int lastres;
\r
38 protected int startseq;
\r
40 protected AlignViewport av;
\r
42 // if character is inserted or deleted, we will need to recalculate the conservation
\r
43 boolean seqEditOccurred = false;
\r
45 ScrollThread scrollThread = null;
\r
46 boolean mouseDragging = false;
\r
47 boolean editingSeqs = false;
\r
48 boolean groupEditing = false;
\r
51 boolean changeEndSeq = false;
\r
52 boolean changeStartSeq = false;
\r
53 boolean changeEndRes = false;
\r
54 boolean changeStartRes = false;
\r
55 SequenceGroup stretchGroup = null;
\r
57 StringBuffer keyboardNo1;
\r
58 StringBuffer keyboardNo2;
\r
60 boolean mouseWheelPressed = false;
\r
61 Point lastMousePress;
\r
63 public SeqPanel(AlignViewport avp, AlignmentPanel p)
\r
67 seqCanvas = new SeqCanvas(avp);
\r
68 setLayout(new BorderLayout());
\r
73 seqCanvas.addMouseMotionListener(this);
\r
74 seqCanvas.addMouseListener(this);
\r
76 seqCanvas.repaint();
\r
83 seqEditOccurred = false;
\r
84 editingSeqs = false;
\r
85 groupEditing = false;
\r
92 seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
\r
96 void setCursorColumn()
\r
98 seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
\r
102 void setCursorRowAndColumn()
\r
104 if(keyboardNo2==null)
\r
106 keyboardNo2 = new StringBuffer();
\r
110 seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
\r
111 seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
\r
116 void setCursorPosition()
\r
118 SequenceI sequence =
\r
119 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
\r
121 seqCanvas.cursorX = sequence.findIndex(
\r
122 getKeyboardNo(keyboardNo1)-1
\r
127 void moveCursor(int dx, int dy)
\r
129 seqCanvas.cursorX += dx;
\r
130 seqCanvas.cursorY += dy;
\r
134 void scrollToVisible()
\r
136 if (seqCanvas.cursorX < 0)
\r
137 seqCanvas.cursorX = 0;
\r
138 else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
\r
139 seqCanvas.cursorX = av.alignment.getWidth() - 1;
\r
141 if (seqCanvas.cursorY < 0)
\r
142 seqCanvas.cursorY = 0;
\r
143 else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
\r
144 seqCanvas.cursorY = av.alignment.getHeight() - 1;
\r
148 if (av.wrapAlignment)
\r
150 ap.scrollToWrappedVisible(seqCanvas.cursorX);
\r
154 while (seqCanvas.cursorY < av.startSeq)
\r
158 while (seqCanvas.cursorY + 1 > av.endSeq)
\r
160 ap.scrollUp(false);
\r
162 while (seqCanvas.cursorX < av.startRes)
\r
165 if (!ap.scrollRight(false))
\r
168 while (seqCanvas.cursorX > av.endRes)
\r
170 if (!ap.scrollRight(true))
\r
174 setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
\r
175 seqCanvas.cursorX, seqCanvas.cursorY);
\r
177 seqCanvas.repaint();
\r
180 void setSelectionAreaAtCursor(boolean topLeft)
\r
182 SequenceI sequence =
\r
183 (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
\r
185 if(av.getSelectionGroup()!=null)
\r
187 SequenceGroup sg = av.selectionGroup;
\r
188 //Find the top and bottom of this group
\r
189 int min = av.alignment.getHeight(), max = 0;
\r
190 for(int i=0; i<sg.getSize(false); i++)
\r
192 int index = av.alignment.findIndex( sg.getSequenceAt(i) );
\r
203 sg.setStartRes(seqCanvas.cursorX);
\r
204 if(sg.getEndRes()<seqCanvas.cursorX)
\r
205 sg.setEndRes(seqCanvas.cursorX);
\r
207 min = seqCanvas.cursorY;
\r
211 sg.setEndRes(seqCanvas.cursorX);
\r
212 if(sg.getStartRes()>seqCanvas.cursorX)
\r
213 sg.setStartRes(seqCanvas.cursorX);
\r
215 max = seqCanvas.cursorY+1;
\r
220 // Only the user can do this
\r
221 av.setSelectionGroup(null);
\r
225 // Now add any sequences between min and max
\r
226 sg.getSequences(false).removeAllElements();
\r
227 for (int i = min; i < max; i++)
\r
229 sg.addSequence(av.alignment.getSequenceAt(i), false);
\r
234 if (av.getSelectionGroup() == null)
\r
236 SequenceGroup sg = new SequenceGroup();
\r
237 sg.setStartRes(seqCanvas.cursorX);
\r
238 sg.setEndRes(seqCanvas.cursorX);
\r
239 sg.addSequence(sequence, false);
\r
240 av.setSelectionGroup(sg);
\r
247 void insertGapAtCursor(boolean group)
\r
249 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
\r
250 av.alignment, HistoryItem.EDIT));
\r
251 groupEditing = group;
\r
252 startseq = seqCanvas.cursorY;
\r
253 lastres = seqCanvas.cursorX;
\r
254 editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
\r
258 void deleteGapAtCursor(boolean group)
\r
260 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
\r
261 av.alignment, HistoryItem.EDIT));
\r
262 groupEditing = group;
\r
263 startseq = seqCanvas.cursorY;
\r
264 lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
\r
265 editSequence(false, seqCanvas.cursorX);
\r
269 void numberPressed(char value)
\r
271 if(keyboardNo1==null)
\r
272 keyboardNo1 = new StringBuffer();
\r
274 if(keyboardNo2!=null)
\r
275 keyboardNo2.append(value);
\r
277 keyboardNo1.append(value);
\r
280 int getKeyboardNo(StringBuffer kb)
\r
285 return Integer.parseInt(kb.toString());
\r
288 void setStatusMessage(SequenceI sequence, int res, int seq)
\r
290 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
\r
291 sequence.getName());
\r
294 if (av.alignment.isNucleotide())
\r
296 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
\r
299 text.append(" Nucleotide: ");
\r
303 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
\r
305 text.append(" Residue: ");
\r
313 text.append(obj + " (" + sequence.findPosition(res) +
\r
318 ap.alignFrame.statusBar.setText(text.toString());
\r
321 public void mousePressed(MouseEvent evt)
\r
323 lastMousePress = evt.getPoint();
\r
325 //For now, ignore the mouseWheel font resizing on Macs
\r
326 //As the Button2_mask always seems to be true
\r
327 if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
\r
328 InputEvent.BUTTON2_MASK && !av.MAC)
\r
330 mouseWheelPressed = true;
\r
334 if (evt.isShiftDown()
\r
335 || evt.isControlDown()
\r
336 || evt.isAltDown())
\r
338 if (evt.isControlDown() || evt.isAltDown())
\r
340 groupEditing = true;
\r
342 editingSeqs = true;
\r
346 doMousePressedDefineMode(evt);
\r
351 int seq = findSeq(evt);
\r
352 int res = findRes(evt);
\r
357 ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
\r
358 av.alignment, HistoryItem.EDIT));
\r
360 if ((seq < av.getAlignment().getHeight()) &&
\r
361 (res < av.getAlignment().getSequenceAt(seq).getLength()))
\r
375 public void mouseClicked(MouseEvent evt){}
\r
378 public void mouseReleased(MouseEvent evt)
\r
380 mouseDragging = false;
\r
381 mouseWheelPressed = false;
\r
385 doMouseReleasedDefineMode(evt);
\r
395 int startWrapBlock=-1;
\r
396 int wrappedBlock=-1;
\r
397 int findRes(MouseEvent evt)
\r
400 int x = evt.getX();
\r
402 if (av.wrapAlignment)
\r
405 int hgap = av.charHeight;
\r
406 if (av.scaleAboveWrapped)
\r
407 hgap += av.charHeight;
\r
409 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
410 + hgap + seqCanvas.getAnnotationHeight();
\r
412 int y = evt.getY();
\r
414 x -= seqCanvas.LABEL_WEST;
\r
417 int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
\r
421 wrappedBlock = y / cHeight;
\r
422 wrappedBlock += av.getStartRes() / cwidth;
\r
424 res = wrappedBlock * cwidth + x / av.getCharWidth();
\r
429 res = (x / av.getCharWidth()) + av.getStartRes();
\r
432 if(av.hasHiddenColumns)
\r
433 res = av.getColumnSelection().adjustForHiddenColumns(res);
\r
439 int findSeq(MouseEvent evt)
\r
443 int y = evt.getY();
\r
445 if (av.wrapAlignment)
\r
447 int hgap = av.charHeight;
\r
448 if (av.scaleAboveWrapped)
\r
449 hgap += av.charHeight;
\r
451 int cHeight = av.getAlignment().getHeight() * av.charHeight
\r
452 + hgap + seqCanvas.getAnnotationHeight();
\r
456 seq = Math.min( (y % cHeight) / av.getCharHeight(),
\r
457 av.alignment.getHeight() -1);
\r
463 seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
\r
464 av.alignment.getHeight() -1);
\r
473 public void doMousePressed(MouseEvent evt)
\r
475 ap.alignFrame.addHistoryItem(new HistoryItem(
\r
476 "Edit Sequence", av.alignment, HistoryItem.EDIT));
\r
478 int seq = findSeq(evt);
\r
479 int res = findRes(evt);
\r
481 if (seq < av.getAlignment().getHeight() &&
\r
482 res < av.getAlignment().getSequenceAt(seq).getLength())
\r
484 //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
\r
485 // Find the residue's position in the sequence (res is the position
\r
486 // in the alignment
\r
500 public void mouseMoved(MouseEvent evt)
\r
502 int res = findRes(evt);
\r
503 int seq = findSeq(evt);
\r
505 if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)
\r
510 SequenceI sequence = av.getAlignment().getSequenceAt(seq);
\r
511 if (res > sequence.getLength())
\r
516 StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
\r
517 sequence.getName());
\r
520 if (av.alignment.isNucleotide())
\r
522 obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
\r
525 text.append(" Nucleotide: ");
\r
529 obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
\r
531 text.append(" Residue: ");
\r
538 text.append(obj + " (" + sequence.findPosition(res) + ")");
\r
542 if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
\r
544 seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
\r
547 ap.alignFrame.statusBar.setText(text.toString());
\r
550 // use aa to see if the mouse pointer is on a
\r
551 if (av.showSequenceFeatures
\r
552 && sequence.getSequenceFeatures()!=null
\r
553 && av.featuresDisplayed!=null)
\r
555 StringBuffer featureText = new StringBuffer();
\r
556 Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
\r
559 while (index < allFeatures.size())
\r
561 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
\r
563 featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);
\r
565 if (sf.getDescription() != null)
\r
566 featureText.append(" " + sf.getDescription());
\r
568 if (sf.getValue("status") != null )
\r
570 String status = sf.getValue("status").toString();
\r
571 if(status.length()>0)
\r
572 featureText.append(" (" + sf.getValue("status") + ")");
\r
574 featureText.append("\n");
\r
580 if (tooltip == null)
\r
581 tooltip = new Tooltip(featureText.toString(), seqCanvas);
\r
583 tooltip.setTip(featureText.toString());
\r
590 Vector getAllFeaturesAtRes(SequenceI seq, int res)
\r
592 Vector allFeatures = new Vector();
\r
594 if(seq.getSequenceFeatures()!=null)
\r
596 while (index < seq.getSequenceFeatures().length)
\r
598 SequenceFeature sf = seq.getSequenceFeatures()[index];
\r
599 if (sf.getBegin() <= res &&
\r
600 sf.getEnd() >= res)
\r
602 if (av.featuresDisplayed.containsKey(sf.getType()))
\r
604 allFeatures.addElement(sf);
\r
610 return allFeatures;
\r
615 public void mouseDragged(MouseEvent evt)
\r
617 if (mouseWheelPressed)
\r
619 int oldWidth = av.charWidth;
\r
621 //Which is bigger, left-right or up-down?
\r
622 if (Math.abs(evt.getY() - lastMousePress.y)
\r
623 > Math.abs(evt.getX() - lastMousePress.x))
\r
625 int fontSize = av.font.getSize();
\r
627 if (evt.getY() < lastMousePress.y && av.charHeight > 1)
\r
631 else if (evt.getY() > lastMousePress.y)
\r
640 av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
\r
641 av.charWidth = oldWidth;
\r
645 if (evt.getX() < lastMousePress.x && av.charWidth > 1)
\r
649 else if (evt.getX() > lastMousePress.x)
\r
662 FontMetrics fm = getFontMetrics(av.getFont());
\r
663 av.validCharWidth = fm.charWidth('M') <= av.charWidth;
\r
665 lastMousePress = evt.getPoint();
\r
668 ap.annotationPanel.image = null;
\r
674 doMouseDraggedDefineMode(evt);
\r
678 int res = findRes(evt);
\r
685 if ((lastres == -1) || (lastres == res))
\r
690 if ( (res < av.getAlignment().getWidth()) && (res < lastres))
\r
692 // dragLeft, delete gap
\r
693 editSequence(false, res);
\r
696 editSequence(true, res);
\r
698 mouseDragging = true;
\r
699 if(scrollThread!=null)
\r
700 scrollThread.setEvent(evt);
\r
704 synchronized void editSequence(boolean insertGap, int startres)
\r
706 int fixedLeft = -1;
\r
707 int fixedRight = -1;
\r
708 boolean fixedColumns = false;
\r
709 SequenceGroup sg = av.getSelectionGroup();
\r
712 if (!groupEditing && av.hasHiddenRows)
\r
714 if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
\r
716 groupEditing = true;
\r
720 //No group, but the sequence may represent a group
\r
723 && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
\r
725 groupEditing = false;
\r
728 SequenceI seq = av.alignment.getSequenceAt(startseq);
\r
729 StringBuffer message = new StringBuffer();
\r
731 message.append("Edit group:");
\r
733 message.append("Edit sequence: "+seq.getName());
\r
736 message.append(" insert ");
\r
738 message.append(" delete ");
\r
740 message.append(Math.abs(startres-lastres)+" gaps.");
\r
741 ap.alignFrame.statusBar.setText(message.toString());
\r
744 //Are we editing within a selection group?
\r
746 || (sg != null && sg.getSequences(true).contains(seq)))
\r
748 fixedColumns = true;
\r
750 //sg might be null as the user may only see 1 sequence,
\r
751 //but the sequence represents a group
\r
754 sg = new SequenceGroup(null, null, false, false, false, 0,
\r
755 av.alignment.getWidth()-1);
\r
756 sg.addSequence(av.alignment.getSequenceAt(startseq), false);
\r
759 fixedLeft = sg.getStartRes();
\r
760 fixedRight = sg.getEndRes();
\r
762 if ( (startres < fixedLeft && lastres >= fixedLeft)
\r
763 || (startres >= fixedLeft && lastres < fixedLeft)
\r
764 || (startres > fixedRight && lastres <=fixedRight)
\r
765 || (startres <= fixedRight && lastres > fixedRight))
\r
771 if (fixedLeft > startres)
\r
773 fixedRight = fixedLeft - 1;
\r
776 else if (fixedRight < startres)
\r
778 fixedLeft = fixedRight;
\r
784 if(av.hasHiddenColumns )
\r
786 fixedColumns = true;
\r
787 int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
\r
788 int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
\r
790 if ( (insertGap && startres > y1 && lastres < y1)
\r
791 || (!insertGap && startres < y2 && lastres > y2))
\r
797 //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
\r
798 //Selection spans a hidden region
\r
799 if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
\r
807 fixedRight = y2 - 1;
\r
818 //If the user has selected the whole sequence, and is dragging to
\r
819 // the right, we can still extend the alignment and selectionGroup
\r
820 if( sg.getStartRes() == 0
\r
821 && sg.getEndRes() == fixedRight
\r
822 && sg.getEndRes() == av.alignment.getWidth()-1
\r
825 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
\r
826 fixedRight = sg.getEndRes();
\r
829 // Is it valid with fixed columns??
\r
830 // Find the next gap before the end
\r
831 // of the visible region boundary
\r
832 boolean blank = false;
\r
833 for (fixedRight = fixedRight;
\r
834 fixedRight > lastres;
\r
838 for (int s = 0; s < sg.getSize(true); s++)
\r
840 seq = (SequenceI)sg.getSequences(true).elementAt(s);
\r
841 for (int j = 0; j < startres - lastres; j++)
\r
843 if (!jalview.util.Comparison.isGap(
\r
844 seq.getCharAt(fixedRight - j)))
\r
857 if(sg.getSize(false) == av.alignment.getHeight() )
\r
859 if((av.hasHiddenColumns
\r
860 && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
\r
866 int alWidth = av.alignment.getWidth();
\r
867 if(av.hasHiddenRows)
\r
869 int hwidth = av.alignment.getHiddenSequences().getWidth();
\r
873 //We can still insert gaps if the selectionGroup
\r
874 //contains all the sequences
\r
875 sg.setEndRes(sg.getEndRes()+startres-lastres);
\r
876 fixedRight = alWidth+startres-lastres;
\r
888 else if(!insertGap)
\r
890 /// Are we able to delete?
\r
891 // ie are all columns blank?
\r
893 for (int s = 0; s < sg.getSize(true); s++)
\r
895 seq = (SequenceI)sg.getSequences(true).elementAt(s);
\r
897 for (int j = startres; j < lastres; j++)
\r
899 if (seq.getSequence().length() <= j)
\r
904 if (!jalview.util.Comparison.isGap(
\r
905 seq.getSequence().charAt(j)))
\r
907 // Not a gap, block edit not valid
\r
916 for (int i = 0; i < sg.getSize(true); i++)
\r
918 seq = (SequenceI) sg.getSequences(true).elementAt(i);
\r
922 // dragging to the right
\r
923 for (int j = lastres; j < startres; j++)
\r
925 if (fixedColumns && fixedRight != -1)
\r
927 insertChar(j, seq, fixedRight);
\r
930 insertChar(j, seq);
\r
935 // dragging to the left
\r
936 for (int j = lastres; j > startres; j--)
\r
938 if (fixedColumns && fixedRight != -1)
\r
940 deleteChar(startres, seq, fixedRight);
\r
944 deleteChar(startres, seq);
\r
950 else /////Editing a single sequence///////////
\r
954 // dragging to the right
\r
955 for (int j = lastres; j < startres; j++)
\r
957 if (fixedColumns && fixedRight != -1)
\r
959 insertChar(j, seq, fixedRight);
\r
962 insertChar(j, seq);
\r
967 // dragging to the left
\r
968 for (int j = lastres; j > startres; j--)
\r
970 if (fixedColumns && fixedRight != -1)
\r
972 deleteChar(startres, seq, fixedRight);
\r
976 deleteChar(startres, seq);
\r
982 lastres = startres;
\r
983 seqCanvas.repaint();
\r
990 * @param j DOCUMENT ME!
\r
991 * @param seq DOCUMENT ME!
\r
993 void insertChar(int j, SequenceI seq)
\r
995 seq.insertCharAt(j, av.getGapCharacter());
\r
996 seqEditOccurred = true;
\r
999 void insertChar(int j, SequenceI seq, int fixedColumn)
\r
1001 //Find the next gap before the end of the visible region boundary
\r
1002 //If lastCol > j, theres a boundary after the gap insertion
\r
1003 int blankColumn = fixedColumn;
\r
1004 for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
\r
1006 if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
\r
1008 //Theres a space, so break and insert the gap
\r
1013 if (blankColumn <= j)
\r
1019 if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
\r
1022 System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
\r
1026 seq.deleteCharAt(blankColumn);
\r
1027 seq.insertCharAt(j, av.getGapCharacter());
\r
1028 seqEditOccurred = true;
\r
1031 void deleteChar(int j, SequenceI seq, int fixedColumn)
\r
1033 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1035 ap.alignFrame.statusBar.setText(
\r
1036 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1039 seq.deleteCharAt(j);
\r
1040 seq.insertCharAt(fixedColumn, av.getGapCharacter());
\r
1041 seqEditOccurred = true;
\r
1047 * @param j DOCUMENT ME!
\r
1048 * @param seq DOCUMENT ME!
\r
1050 void deleteChar(int j, SequenceI seq)
\r
1052 if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
\r
1054 ap.alignFrame.statusBar.setText(
\r
1055 "End editing: Tried removing residue " + seq.getCharAt(j));
\r
1059 seq.deleteCharAt(j);
\r
1060 seqEditOccurred = true;
\r
1061 seqCanvas.repaint();
\r
1067 * @param i DOCUMENT ME!
\r
1069 void editOccurred()
\r
1071 if (!seqEditOccurred)
\r
1073 ap.alignFrame.historyList.pop();
\r
1074 ap.alignFrame.updateEditMenuBar();
\r
1079 av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
\r
1083 //////////////////////////////////////////
\r
1084 /////Everything below this is for defining the boundary of the rubberband
\r
1085 //////////////////////////////////////////
\r
1086 public void doMousePressedDefineMode(MouseEvent evt)
\r
1090 if (scrollThread != null)
\r
1092 scrollThread.running = false;
\r
1093 scrollThread = null;
\r
1096 int res = findRes(evt);
\r
1097 int seq = findSeq(evt);
\r
1099 startWrapBlock=wrappedBlock;
\r
1104 SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
\r
1106 if (sequence == null || res > sequence.getLength())
\r
1111 stretchGroup = av.getSelectionGroup();
\r
1113 if (stretchGroup == null)
\r
1115 stretchGroup = av.alignment.findGroup(sequence);
\r
1116 if (stretchGroup != null && res > stretchGroup.getStartRes() &&
\r
1117 res < stretchGroup.getEndRes())
\r
1119 av.setSelectionGroup(stretchGroup);
\r
1123 stretchGroup = null;
\r
1127 else if (!stretchGroup.getSequences(false).contains(sequence)
\r
1128 || stretchGroup.getStartRes() > res
\r
1129 || stretchGroup.getEndRes() < res)
\r
1131 stretchGroup = null;
\r
1133 SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
\r
1135 if (allGroups != null)
\r
1137 for (int i = 0; i < allGroups.length; i++)
\r
1139 if (allGroups[i].getStartRes() <= res &&
\r
1140 allGroups[i].getEndRes() >= res)
\r
1142 stretchGroup = allGroups[i];
\r
1147 av.setSelectionGroup(stretchGroup);
\r
1151 // DETECT RIGHT MOUSE BUTTON IN AWT
\r
1152 if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
\r
1153 InputEvent.BUTTON3_MASK)
\r
1155 Vector allFeatures = getAllFeaturesAtRes(sequence,
\r
1156 sequence.findPosition(res));
\r
1158 Vector links = null;
\r
1159 if(allFeatures!=null)
\r
1161 for (int i = 0; i < allFeatures.size(); i++)
\r
1163 SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
\r
1164 if (sf.links != null)
\r
1166 links = new Vector();
\r
1167 for (int j = 0; j < sf.links.size(); j++)
\r
1169 links.addElement(sf.links.elementAt(j));
\r
1174 APopupMenu popup = new APopupMenu(ap, null, links);
\r
1176 popup.show(this, evt.getX(), evt.getY());
\r
1181 if (av.cursorMode)
\r
1183 seqCanvas.cursorX = findRes(evt);
\r
1184 seqCanvas.cursorY = findSeq(evt);
\r
1185 seqCanvas.repaint();
\r
1189 //Only if left mouse button do we want to change group sizes
\r
1191 if (stretchGroup == null)
\r
1193 // define a new group here
\r
1194 SequenceGroup sg = new SequenceGroup();
\r
1195 sg.setStartRes(res);
\r
1196 sg.setEndRes(res);
\r
1197 sg.addSequence(sequence, false);
\r
1198 av.setSelectionGroup(sg);
\r
1199 stretchGroup = sg;
\r
1201 if (av.getConservationSelected())
\r
1203 SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
\r
1206 if (av.getAbovePIDThreshold())
\r
1208 SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
\r
1215 public void doMouseReleasedDefineMode(MouseEvent evt)
\r
1217 if (stretchGroup == null)
\r
1222 if(stretchGroup.cs!=null)
\r
1224 if (stretchGroup.cs instanceof ClustalxColourScheme)
\r
1226 ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
\r
1227 stretchGroup.getSequences(true),
\r
1228 stretchGroup.getWidth());
\r
1231 if (stretchGroup.cs.conservationApplied())
\r
1233 SliderPanel.setConservationSlider(ap, stretchGroup.cs,
\r
1234 stretchGroup.getName());
\r
1235 stretchGroup.recalcConservation();
\r
1239 SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
\r
1240 stretchGroup.getName());
\r
1243 changeEndRes = false;
\r
1244 changeStartRes = false;
\r
1245 stretchGroup = null;
\r
1246 PaintRefresher.Refresh(av.alignment);
\r
1250 public void doMouseDraggedDefineMode(MouseEvent evt)
\r
1252 int res = findRes(evt);
\r
1253 int y = findSeq(evt);
\r
1255 if(wrappedBlock!=startWrapBlock)
\r
1258 if (stretchGroup == null)
\r
1263 mouseDragging = true;
\r
1266 if(y > av.alignment.getHeight())
\r
1268 y = av.alignment.getHeight() -1;
\r
1271 if(res>av.alignment.getWidth())
\r
1272 res = av.alignment.getWidth()-1;
\r
1274 if (stretchGroup.getEndRes() == res)
\r
1276 // Edit end res position of selected group
\r
1277 changeEndRes = true;
\r
1279 else if (stretchGroup.getStartRes() == res)
\r
1281 // Edit start res position of selected group
\r
1282 changeStartRes = true;
\r
1292 if (res > (stretchGroup.getStartRes() - 1))
\r
1294 stretchGroup.setEndRes(res);
\r
1297 else if (changeStartRes)
\r
1299 if (res < (stretchGroup.getEndRes() + 1))
\r
1301 stretchGroup.setStartRes(res);
\r
1305 int dragDirection = 0;
\r
1309 dragDirection = 1;
\r
1311 else if (y < oldSeq)
\r
1313 dragDirection = -1;
\r
1317 while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
\r
1319 // This routine ensures we don't skip any sequences, as the
\r
1320 // selection is quite slow.
\r
1321 Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1323 oldSeq += dragDirection;
\r
1328 Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
\r
1330 if (stretchGroup.getSequences(false).contains(nextSeq))
\r
1332 stretchGroup.deleteSequence(seq, false);
\r
1338 stretchGroup.addSequence(seq, false);
\r
1341 stretchGroup.addSequence(nextSeq, false);
\r
1349 if(res>av.endRes || res<av.startRes
\r
1350 || y<av.startSeq || y>av.endSeq)
\r
1355 if (scrollThread != null)
\r
1357 scrollThread.setEvent(evt);
\r
1360 seqCanvas.repaint();
\r
1363 public void mouseEntered(MouseEvent e)
\r
1368 if (scrollThread != null)
\r
1370 scrollThread.running = false;
\r
1371 scrollThread = null;
\r
1375 public void mouseExited(MouseEvent e)
\r
1377 if (av.getWrapAlignment())
\r
1382 if (mouseDragging && scrollThread==null)
\r
1384 scrollThread = new ScrollThread();
\r
1388 void scrollCanvas(MouseEvent evt)
\r
1392 if(scrollThread!=null)
\r
1394 scrollThread.running = false;
\r
1395 scrollThread = null;
\r
1397 mouseDragging = false;
\r
1401 if (scrollThread == null)
\r
1402 scrollThread = new ScrollThread();
\r
1404 mouseDragging = true;
\r
1405 scrollThread.setEvent(evt);
\r
1410 // this class allows scrolling off the bottom of the visible alignment
\r
1411 class ScrollThread
\r
1415 boolean running = false;
\r
1416 public ScrollThread()
\r
1421 public void setEvent(MouseEvent e)
\r
1426 public void stopScrolling()
\r
1440 if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
\r
1442 running = ap.scrollUp(true);
\r
1445 if (mouseDragging && evt.getY() >= getSize().height &&
\r
1446 av.alignment.getHeight() > av.getEndSeq())
\r
1448 running = ap.scrollUp(false);
\r
1451 if (mouseDragging && evt.getX() < 0)
\r
1453 running = ap.scrollRight(false);
\r
1456 else if (mouseDragging && evt.getX() >= getSize().width)
\r
1458 running = ap.scrollRight(true);
\r
1466 catch (Exception ex)
\r