protected int startseq;\r
protected int padseq;\r
\r
- public boolean editFlag;\r
protected AlignViewport av;\r
\r
// if character is inserted or deleted, we will need to recalculate the conservation\r
addMouseMotionListener( new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
- { doMouseMoved(evt); }\r
+ { doMouseMoved(evt); }\r
+\r
public void mouseDragged(MouseEvent evt)\r
{\r
- if(av.groupDefiningMode)\r
- doMouseDraggedDefineMode(evt);\r
- else\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
doMouseDragged(evt);\r
+ else\r
+ doMouseDraggedDefineMode(evt);\r
}\r
});\r
\r
{\r
public void mouseReleased(MouseEvent evt)\r
{\r
- if(av.groupDefiningMode)\r
- doMouseReleasedDefineMode(evt);\r
- else\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
doMouseReleased(evt);\r
+ else\r
+ doMouseReleasedDefineMode(evt);\r
}\r
public void mousePressed(MouseEvent evt)\r
{\r
- if(av.groupDefiningMode)\r
- doMousePressedDefineMode(evt);\r
- else\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
doMousePressed(evt);\r
+ else\r
+ doMousePressedDefineMode(evt);\r
}\r
\r
});\r
\r
endres = res;\r
\r
- // This is to detect edits - we're at the end of an edit if mouse is up\r
- editFlag = false;\r
startseq = -1;\r
startres = -1;\r
lastres = -1;\r
res = x/av.getCharWidth() + av.getStartRes();\r
seq = y/av.getCharHeight() + av.getStartSeq();\r
\r
- if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())\r
+ if (seq < av.getAlignment().getHeight() &&\r
+ res < av.getAlignment().getSequenceAt(seq).getLength())\r
{\r
//char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
// Find the residue's position in the sequence (res is the position\r
\r
startseq = seq;\r
\r
- if (startseq == (av.getAlignment().getHeight()-1)) {\r
+ if (startseq == (av.getAlignment().getHeight() - 1))\r
padseq = 1;\r
- } else {\r
+ else\r
padseq = 1;\r
- }\r
\r
startres = res;\r
lastres = res;\r
\r
- } else {\r
+ }\r
+ else\r
+ {\r
startseq = -1;\r
startres = -1;\r
lastres = -1;\r
\r
res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();\r
\r
- System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) );\r
y %= chunkHeight;\r
seq = y / av.getCharHeight() + av.getStartSeq();\r
\r
\r
public void doMouseDragged(MouseEvent evt) {\r
// If we're dragging we're editing\r
- editFlag = true;\r
+\r
int x = evt.getX();\r
\r
int res = x/av.getCharWidth() + av.getStartRes();\r
- if (res < 0) {res = 0;}\r
-\r
- if (res != lastres) {\r
- if (startseq != -1) {\r
+ if (res < 0)\r
+ res = 0;\r
\r
+ if (res != lastres)\r
+ {\r
// Group editing\r
- if (av.getGroupEdit()) {\r
+ if (evt.isAltDown() || evt.isControlDown())\r
+ {\r
SequenceGroup sg = av.getAlignment().findGroup(startseq);\r
-\r
- if(sg!=null)\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
+ if (sg != null)\r
{\r
- boolean flag = false;\r
- for (int i= 0 ; i < sg.getSize(); i++)\r
+ boolean deleteAllowed = false;\r
+ if (res < av.getAlignment().getWidth() && res < lastres)\r
{\r
- SequenceI s = (SequenceI)sg.getSequenceAt(i);\r
- for (int j=lastres-1; j >= res; j--)\r
+ /// Are we able to delete?\r
+ boolean allGaps = true;\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
- if (!flag)\r
+ SequenceI s = sg.getSequenceAt(i);\r
+ for (int j = lastres-1; j >= res && allGaps; j--)\r
{\r
- if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() &&\r
- s.getSequence().charAt(j)==' ')\r
- {\r
- res = j+1;\r
- flag = true;\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- if(sg!=null)\r
- for (int i= 0 ; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = (SequenceI)sg.getSequenceAt(i);\r
- boolean found = false;\r
- int sno = -1;\r
- for (int k = 0; k < av.getAlignment().getHeight(); k++)\r
- {\r
- if (av.getAlignment().getSequenceAt(k) == s)\r
- {\r
- found = true;\r
- sno = k;\r
- break;\r
- }\r
- }\r
- if (found && sno != -1) {\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- {\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j,sno);\r
+ if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))\r
+ {\r
+ res = j + 1;\r
+ allGaps = false;\r
+ }\r
+ }\r
\r
- int index = av.getAlignment().findIndex(s);\r
- if (index != -1)\r
- drawChars(index,index+1,lastres);\r
+ if(!deleteAllowed && allGaps)\r
+ deleteAllowed = true;\r
+ }\r
+ }\r
\r
+ // drag to right\r
+ if (res < av.getAlignment().getWidth() && res > lastres)\r
+ sg.setEndRes(sg.getEndRes() + 1);\r
\r
- } else if (res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- deleteChar(j,res,sno);\r
- startres = res;\r
- }\r
- int index = av.getAlignment().findIndex(s);\r
- if (index != -1)\r
- drawChars(index,index+1,res);\r
+ // drag to left\r
+ else if (deleteAllowed && res < av.getAlignment().getWidth() &&\r
+ res < lastres)\r
+ sg.setEndRes(sg.getEndRes() - 1);\r
\r
- }\r
- }\r
\r
- }\r
- lastres = res;\r
- } else {\r
\r
\r
- if (res < av.getAlignment().getWidth() && res > lastres) {\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j,startseq);\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI s = sg.getSequenceAt(i);\r
+ int k = av.alignment.findIndex(s);\r
\r
- drawChars(startseq,startseq+1,lastres);\r
+ // drag to right\r
+ if (res < av.getAlignment().getWidth() && res > lastres)\r
+ for (int j = lastres; j < res; j++)\r
+ insertChar(j, k);\r
\r
- } else if (res < av.getAlignment().getWidth() && res < lastres)\r
+ // drag to left\r
+ else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)\r
+ {\r
+ for (int j = res; j < lastres; j++)\r
+ {\r
+ deleteChar(j, k);\r
+ startres = res;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else /////Editing a single sequence///////////\r
+ {\r
+ if (res < av.getAlignment().getWidth() && res > lastres)\r
+ {\r
+ // dragging to the right\r
+ for (int j = lastres; j < res; j++)\r
+ insertChar(j, startseq);\r
+ }\r
+ else if (res < av.getAlignment().getWidth() && res < lastres)\r
{\r
-\r
// dragging to the left\r
- for (int j = res; j < lastres; j++) {\r
- deleteChar(j,res,startseq);\r
- startres = res;\r
- }\r
- drawChars(startseq,startseq+1,res);\r
+ for (int j = res; j < lastres; j++)\r
+ {\r
+ deleteChar(j, startseq);\r
+ startres = res;\r
+ }\r
}\r
+\r
}\r
- }\r
- lastres = res;\r
+\r
}\r
\r
+ lastres = res;\r
repaint();\r
- return;\r
}\r
\r
public void drawChars(int seqstart, int seqend, int start) {\r
\r
public void insertChar(int j, int seq)\r
{\r
- av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
+ av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
seqEditOccurred=seq;\r
}\r
\r
- public void deleteChar(int j, int res, int seq)\r
+ public void deleteChar(int j, int seq)\r
{\r
\r
- if (av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='.' ||\r
- av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='-' ||\r
- av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)==' ' )\r
- {\r
- av.getAlignment().getSequenceAt(seq).deleteCharAt(j);\r
- }\r
+ if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
+ av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
\r
- av.getAlignment().getWidth();\r
+ av.alignment.getWidth();\r
repaint();\r
seqEditOccurred=seq;\r
}\r
\r
void updateConservation(int i)\r
{\r
- Alignment al = (Alignment) av.getAlignment();\r
+ /* Alignment al = (Alignment) av.getAlignment();\r
SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));\r
if(sg==null || !(sg.cs instanceof ConservationColourScheme))\r
return;\r
c.verdict(false, 100);\r
sg.setConservation(c);\r
ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- ccs.conserve = c;\r
+ ccs.conserve = c;*/\r
}\r
\r
-\r
+//////////////////////////////////////////\r
+/////Everything below this is for defining the boundary of the rubberband\r
+//////////////////////////////////////////\r
+ int oldSeq = -1;\r
public void doMousePressedDefineMode(MouseEvent evt)\r
{\r
int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+ oldSeq = seq;\r
\r
stretchGroup = av.getRubberbandGroup();\r
+\r
if(stretchGroup == null)\r
stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));\r
- else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))\r
- || stretchGroup.getStartRes()<res\r
- || stretchGroup.getEndRes()>res)\r
+\r
+ else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))\r
+ || stretchGroup.getStartRes()>res\r
+ || stretchGroup.getEndRes()<res)\r
{\r
- System.out.println(stretchGroup.getStartRes()+" "+stretchGroup.getEndRes()+" "+res);\r
stretchGroup = null;\r
- }\r
-\r
\r
+ SequenceGroup[] allGroups = av.alignment.findAllGroups( (Sequence) av.\r
+ getAlignment().\r
+ getSequenceAt(seq));\r
+\r
+ if (allGroups != null)\r
+ for (int i = 0; i < allGroups.length; i++)\r
+ if (allGroups[i].getStartRes() <= res &&\r
+ allGroups[i].getEndRes() >= res)\r
+ {\r
+ stretchGroup = allGroups[i];\r
+ av.setRubberbandGroup(stretchGroup);\r
+ break;\r
+ }\r
+ }\r
\r
if(stretchGroup==null)\r
{\r
sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );\r
av.setRubberbandGroup( sg );\r
stretchGroup = sg;\r
- System.out.println("new rubberband group");\r
}\r
else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
{\r
- // edit the properties of existing group\r
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( parent , null);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+\r
+ // edit the properties of existing group\r
}\r
\r
if(stretchGroup!=null && stretchGroup.getEndRes()==res)\r
- {\r
// Edit end res position of selected group\r
changeEndRes = true;\r
- }\r
- if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
- {\r
+\r
+ else if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
// Edit end res position of selected group\r
changeStartRes = true;\r
- }\r
+\r
\r
seqCanvas.paintFlag = true;\r
repaint();\r
boolean changeStartRes = false;\r
SequenceGroup stretchGroup = null;\r
\r
-\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
changeEndRes = false;\r
stretchGroup = null;\r
}\r
\r
+\r
+ boolean remove = false;\r
public void doMouseDraggedDefineMode(MouseEvent evt)\r
{\r
int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- Sequence seq = (Sequence)av.getAlignment().getSequenceAt(\r
- evt.getY()/av.getCharHeight() + av.getStartSeq());\r
+ int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
+\r
+\r
+ if(stretchGroup.getEndRes()==res)\r
+ // Edit end res position of selected group\r
+ changeEndRes = true;\r
+\r
+ else if(stretchGroup.getStartRes()==res)\r
+ // Edit end res position of selected group\r
+ changeStartRes = true;\r
\r
- // SequenceGroup newSeqGroup = av.alignment.findGroup(seq);\r
\r
if(res<av.getStartRes())\r
res = av.getStartRes();\r
stretchGroup.setStartRes( res );\r
}\r
\r
- /* if(newSeqGroup != stretchGroup)\r
+\r
+ int dragDirection = 0;\r
+ if (y > oldSeq)\r
+ dragDirection = 1;\r
+ else if (y < oldSeq)\r
+ dragDirection = -1;\r
+\r
+ while (y != oldSeq)\r
{\r
- if(newSeqGroup !=null)\r
- av.getAlignment().removeFromGroup(newSeqGroup, seq );\r
+ // This routine ensures we don't skip any sequences, as the\r
+ // selection is quite slow.\r
+ Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
\r
- if(stretchGroup!=null)\r
- stretchGroup.addSequence( seq );\r
- }*/\r
+ oldSeq += dragDirection;\r
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+ if (stretchGroup.sequences.contains(nextSeq))\r
+ {\r
+ stretchGroup.deleteSequence(seq);\r
+ stretchGroup.deleteSequence(nextSeq);\r
+ }\r
+ else\r
+ {\r
+ stretchGroup.addSequence(seq);\r
+ stretchGroup.addSequence(nextSeq);\r
+ }\r
+ }\r
+ oldSeq = y;\r
\r
seqCanvas.paintFlag = true;\r
repaint();\r
-\r
}\r
\r
+\r
}\r
\r
\r
git://source.jalview.org / jalview.git / blobdiff