import java.awt.event.*;\r
import jalview.datamodel.*;\r
import javax.swing.*;\r
+import java.util.*;\r
import jalview.schemes.*;\r
import jalview.analysis.*;\r
\r
{\r
\r
public SeqCanvas seqCanvas;\r
- public AlignmentPanel parent;\r
+ public AlignmentPanel ap;\r
\r
protected int startres;\r
protected int lastres;\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
{\r
- if(evt.isShiftDown() || evt.isAltDown())\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
doMouseDragged(evt);\r
else\r
doMouseDraggedDefineMode(evt);\r
{\r
public void mouseReleased(MouseEvent evt)\r
{\r
- if(evt.isShiftDown() || evt.isAltDown())\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
{\r
- if(evt.isShiftDown() || evt.isAltDown())\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
doMousePressed(evt);\r
else\r
doMousePressedDefineMode(evt);\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
if(seq>=av.getAlignment().getHeight())\r
return;\r
\r
- Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;\r
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+ Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
String aa = "";\r
if(obj!=null)\r
aa = obj.toString();\r
\r
- StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());\r
+ StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());\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
+ if(av.showSequenceFeatures)\r
+ {\r
+ Vector features = sequence.getSequenceFeatures();\r
+ Enumeration e = features.elements();\r
+ StringBuffer sbuffer = new StringBuffer();\r
+\r
+ this.setToolTipText(null);\r
+ while (e.hasMoreElements())\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ if (sf.getStart() <= sequence.findPosition(res) &&\r
+ sf.getEnd() >= sequence.findPosition(res))\r
+ {\r
+ sbuffer.append(sf.getType() + " " + sf.getDescription());\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
+ this.setToolTipText(sbuffer.toString());\r
+ }\r
+\r
+ }\r
+ }\r
+\r
\r
}\r
\r
if (res != lastres)\r
{\r
// Group editing\r
- if (evt.isAltDown())\r
+ if (evt.isAltDown() || evt.isControlDown())\r
{\r
SequenceGroup sg = av.getAlignment().findGroup(startseq);\r
if (sg != null)\r
\r
if(!deleteAllowed && allGaps)\r
deleteAllowed = true;\r
-\r
}\r
}\r
\r
+ // drag to right\r
+ if (res < av.getAlignment().getWidth() && res > lastres)\r
+ sg.setEndRes(sg.getEndRes() + 1);\r
+\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
for (int i = 0; i < sg.getSize(); i++)\r
{\r
stretchGroup = av.getRubberbandGroup();\r
\r
if(stretchGroup == null)\r
- stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));\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
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
+ 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 if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
{\r
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( parent , null);\r
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);\r
pop.show(this, evt.getX(), evt.getY());\r
\r
// edit the properties of existing group\r
seqCanvas.paintFlag = true;\r
repaint();\r
\r
-\r
}\r
\r
boolean changeEndSeq = false;\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
+\r
+ else if(stretchGroup.cs instanceof ConservationColourScheme)\r
+ {\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
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
changeEndRes = true;\r
\r
else if(stretchGroup.getStartRes()==res)\r
- // Edit end res position of selected group\r
+ // Edit start res position of selected group\r
changeStartRes = true;\r
\r
\r
git://source.jalview.org / jalview.git / blobdiff