{\r
\r
public SeqCanvas seqCanvas;\r
- public AlignmentPanel parent;\r
+ public AlignmentPanel ap;\r
\r
protected int startres;\r
protected int lastres;\r
protected int startseq;\r
protected int padseq;\r
\r
- public boolean editFlag;\r
protected AlignViewport av;\r
\r
- public SeqPanel(AlignViewport av, AlignmentPanel p) {\r
- this.av = av;\r
+ // if character is inserted or deleted, we will need to recalculate the conservation\r
+ int seqEditOccurred = -1;\r
\r
- seqCanvas = new SeqCanvas(av);\r
+ public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
+ this.av = avp;\r
+\r
+ seqCanvas = new SeqCanvas(avp);\r
setLayout(new BorderLayout());\r
add(seqCanvas, BorderLayout.CENTER);\r
\r
- parent = p;\r
+ ap = p;\r
\r
addMouseMotionListener( new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
- { doMouseMoved(evt); }\r
+ {\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ doMouseMoved(evt); }\r
+\r
public void mouseDragged(MouseEvent evt)\r
- { doMouseDragged(evt); }\r
+ {\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ doMouseDragged(evt);\r
+ else\r
+ doMouseDraggedDefineMode(evt);\r
+ }\r
});\r
\r
addMouseListener( new MouseAdapter()\r
{\r
public void mouseReleased(MouseEvent evt)\r
- { doMouseReleased(evt); }\r
+ {\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ doMouseReleased(evt);\r
+ else\r
+ doMouseReleasedDefineMode(evt);\r
+ }\r
public void mousePressed(MouseEvent evt)\r
- { doMousePressed(evt); }\r
+ {\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ doMousePressed(evt);\r
+ else\r
+ doMousePressedDefineMode(evt);\r
+ }\r
\r
});\r
repaint();\r
public void doMouseReleased(MouseEvent evt) {\r
\r
int x = evt.getX();\r
- int res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
+ int res = x/av.getCharWidth() + av.getStartRes();\r
\r
- endres = res;\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
+ startseq = -1;\r
+ startres = -1;\r
+ lastres = -1;\r
+ if(seqEditOccurred>-1)\r
+ updateConservation(seqEditOccurred);\r
+\r
+ seqEditOccurred = -1;\r
\r
- parent.RefreshPanels();\r
+ ap.RefreshPanels();\r
repaint();\r
\r
}\r
\r
public void doMousePressed(MouseEvent evt) {\r
- parent.alignFrame.addHistoryItem("sequence edit");\r
+ ap.alignFrame.addHistoryItem("sequence edit");\r
int seq;\r
int res;\r
\r
int x = evt.getX();\r
int y = evt.getY();\r
\r
- res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
- seq = (y)/av.getCharHeight() + av.getStartSeq();\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
int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;\r
\r
\r
- res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + (int)(x/av.getCharWidth()) + av.getStartRes();\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
else\r
{\r
- res = (int) (x / av.getCharWidth()) + av.getStartRes();\r
+ res = x / av.getCharWidth() + av.getStartRes();\r
seq = y / av.getCharHeight() + av.getStartSeq();\r
}\r
\r
if(aa!="")\r
text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
\r
- parent.alignFrame.statusBar.setText(text.toString());\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
\r
}\r
\r
public void doMouseDragged(MouseEvent evt) {\r
// If we're dragging we're editing\r
- editFlag = true;\r
- int x = evt.getX();\r
\r
- int res = (int)(x/av.getCharWidth()) + av.getStartRes();\r
- if (res < 0) {res = 0;}\r
+ int x = evt.getX();\r
\r
- if (res != lastres) {\r
- if (startseq != -1) {\r
+ int res = x/av.getCharWidth() + av.getStartRes();\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().substring(j,j+1).equals(av.getAlignment().getGapCharacter()) &&\r
- !s.getSequence().substring(j,j+1).equals(" "))\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().charAt(0));\r
- updateConservation(seq);\r
+ av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
+ seqEditOccurred=seq;\r
}\r
\r
- public void deleteChar(int j, int res, int sno)\r
+ public void deleteChar(int j, int seq)\r
{\r
\r
- if (av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||\r
- av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||\r
- av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )\r
- {\r
- av.getAlignment().getSequenceAt(sno).deleteCharAt(j);\r
- }\r
- updateConservation(sno);\r
- av.getAlignment().getWidth();\r
+ if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
+ av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+\r
+ av.alignment.getWidth();\r
repaint();\r
+ seqEditOccurred=seq;\r
}\r
\r
\r
void updateConservation(int i)\r
{\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
- public void setColourScheme(ColourSchemeI cs, boolean showConservation)\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
- if (av.getSelection().size() == 0)\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
+ {\r
+ stretchGroup = av.alignment.findGroup( (Sequence) av.getAlignment().\r
+ getSequenceAt(seq));\r
+ av.setRubberbandGroup( stretchGroup );\r
+ }\r
+\r
+ else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))\r
+ || stretchGroup.getStartRes()>res\r
+ || stretchGroup.getEndRes()<res)\r
+ {\r
+ stretchGroup = null;\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
- seqCanvas.cs = cs;\r
- for (int i = 0; i < av.alignment.getGroups().size();i++)\r
+ // define a new group here\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setStartRes(res);\r
+ sg.setEndRes(res);\r
+ sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );\r
+ av.setRubberbandGroup( sg );\r
+ stretchGroup = sg;\r
+\r
+ if(av.getConservationSelected())\r
+ Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
+ else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold())\r
{\r
- SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);\r
- sg.cs = cs;\r
- if(!showConservation\r
- && !(sg.cs instanceof Blosum62ColourScheme)\r
- && sg.cs instanceof ConservationColourScheme)\r
- {\r
- // remove ConservationColouring from existing Conservation group\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
- }\r
- else if(showConservation && !(sg.cs instanceof ConservationColourScheme))\r
- {\r
- // add ConservationColouring to new group\r
- Conservation c = sg.getConservation();\r
- Alignment al = (Alignment) av.getAlignment();\r
- c = new Conservation("All", al.cons,\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- al.getWidth() );\r
- c.calculate();\r
- c.verdict(false, 100);\r
- sg.setConservation(c);\r
- sg.cs = new ConservationColourScheme(sg);\r
- }\r
+ ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme();\r
+ int threshold = rcs.getThreshold();\r
+ if (threshold > 0)\r
+ Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
}\r
+\r
}\r
- else\r
+ else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
{\r
- SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));\r
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);\r
+ pop.show(this, evt.getX(), evt.getY());\r
\r
- if( isNewSelection(sg) )\r
- {\r
- sg = av.getAlignment().addGroup();\r
- for (int i=0; i < av.getSelection().size(); i++)\r
- {\r
- av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.\r
- sel.sequenceAt(i)),\r
- (Sequence) av.sel.sequenceAt(i));\r
- av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));\r
- }\r
- }\r
+ // edit the properties of existing group\r
+ }\r
\r
+ if(stretchGroup!=null && stretchGroup.getEndRes()==res)\r
+ // Edit end res position of selected group\r
+ changeEndRes = true;\r
\r
- sg.cs = cs;\r
+ else if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
+ // Edit end res position of selected group\r
+ changeStartRes = true;\r
\r
- // Selection is made, we only want to change the conservationColour for selected group\r
- if( showConservation\r
- && !(sg.cs instanceof ConservationColourScheme)\r
- && !(sg.cs instanceof Blosum62ColourScheme))\r
- {\r
- Conservation c = sg.getConservation();\r
- Alignment al = (Alignment) av.getAlignment();\r
-\r
- c = new Conservation("All", al.cons,\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- al.getWidth() );\r
- c.calculate();\r
- c.verdict(false, 100);\r
- sg.setConservation(c);\r
- sg.cs = new ConservationColourScheme(sg);\r
+\r
+ seqCanvas.paintFlag = true;\r
+ repaint();\r
+\r
+ }\r
+\r
+ boolean changeEndSeq = false;\r
+ boolean changeStartSeq = false;\r
+ boolean changeEndRes = false;\r
+ boolean changeStartRes = false;\r
+ SequenceGroup stretchGroup = null;\r
+\r
+ public void doMouseReleasedDefineMode(MouseEvent evt)\r
+ {\r
+\r
+ if(stretchGroup.cs instanceof ClustalxColourScheme)\r
+ {\r
+ stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
+ seqCanvas.paintFlag = true;\r
+ repaint();\r
}\r
- else if( !showConservation && sg.cs instanceof ConservationColourScheme)\r
+\r
+ else if(stretchGroup.cs instanceof ConservationColourScheme)\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
+ ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
+\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3, stretchGroup.sequences, 0,\r
+ av.alignment.getWidth() );\r
+\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+ ccs = new ConservationColourScheme(c, ccs.cs);\r
+\r
+ stretchGroup.cs = ccs;\r
+\r
+\r
+ Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
+\r
+ seqCanvas.paintFlag = true;\r
+ repaint();\r
}\r
+ else\r
+ {\r
+ if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())\r
+ {\r
+ ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;\r
+ int threshold = rcs.getThreshold();\r
+ if(threshold>0)\r
+ Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
+ }\r
\r
+ }\r
\r
\r
- }\r
- seqCanvas.paintFlag = true;\r
- repaint();\r
+ changeEndRes = false;\r
+ changeStartRes = false;\r
+ stretchGroup = null;\r
}\r
\r
- boolean isNewSelection(SequenceGroup sg)\r
+\r
+ boolean remove = false;\r
+ public void doMouseDraggedDefineMode(MouseEvent evt)\r
{\r
- if(sg.getSize()!=av.getSelection().size())\r
- return true;\r
+ int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
+ int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
\r
- for(int i=0; i<sg.getSize(); i++)\r
- if( !av.getSelection().contains( sg.getSequenceAt(i) ))\r
- return true;\r
\r
- return false;\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 start res position of selected group\r
+ changeStartRes = true;\r
\r
- public ColourSchemeI getColourScheme()\r
- {\r
- if(av.getSelection().size()>0)\r
- return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;\r
- else\r
- return seqCanvas.cs;\r
+\r
+ if(res<av.getStartRes())\r
+ res = av.getStartRes();\r
+ else if(res>av.getEndRes())\r
+ res = av.getEndRes();\r
+\r
+ if(changeEndRes)\r
+ {\r
+ if(res>stretchGroup.getStartRes()-1)\r
+ stretchGroup.setEndRes( res );\r
+ }\r
+ else if(changeStartRes)\r
+ {\r
+ if(res<stretchGroup.getEndRes()+1)\r
+ stretchGroup.setStartRes( res );\r
+ }\r
+\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
+ // 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
+ 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
git://source.jalview.org / jalview.git / blobdiff