// if character is inserted or deleted, we will need to recalculate the conservation\r
int seqEditOccurred = -1;\r
\r
+ ScrollThread scrollThread = null;\r
+ boolean mouseDragging = false;\r
+\r
+\r
public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
this.av = avp;\r
\r
else\r
doMousePressedDefineMode(evt);\r
}\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
+ evt.isControlDown())\r
+ return;\r
+ doMouseExitedDefineMode(evt);\r
+\r
+ }\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
+ evt.isControlDown())\r
+ return;\r
+ doMouseEnteredDefineMode(evt);\r
+ }\r
\r
});\r
repaint();\r
y %= chunkHeight;\r
seq = y / av.getCharHeight() + av.getStartSeq();\r
\r
- // chunkHeight = (da.getHeight() + 2)*charHeight;\r
- // startx += chunkWidth;\r
}\r
else\r
{\r
return;\r
\r
SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
+ if(res>sequence.getLength())\r
+ return;\r
+\r
Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
String aa = "";\r
if(obj!=null)\r
\r
ap.alignFrame.statusBar.setText(text.toString());\r
\r
- if(av.showSequenceFeatures)\r
+ // use aa to see if the mouse pointer is on a\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
+\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
+ if(sbuffer.length()>0)\r
+ sbuffer.append("; ");\r
sbuffer.append(sf.getType() + " " + sf.getDescription());\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- this.setToolTipText(sbuffer.toString());\r
+ if(sf.getStatus().length()>0)\r
+ sbuffer.append(" ("+sf.getStatus()+")");\r
}\r
\r
}\r
+\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
+ this.setToolTipText(sbuffer.toString());\r
}\r
\r
\r
public void doMouseDragged(MouseEvent evt) {\r
// If we're dragging we're editing\r
\r
+ if(lastres==-1)\r
+ return;\r
+\r
int x = evt.getX();\r
\r
int res = x/av.getCharWidth() + av.getStartRes();\r
// Group editing\r
if (evt.isAltDown() || evt.isControlDown())\r
{\r
- SequenceGroup sg = av.getAlignment().findGroup(startseq);\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if(sg==null)\r
+ av.getAlignment().findGroup(startseq);\r
if (sg != null)\r
{\r
boolean deleteAllowed = false;\r
\r
void updateConservation(int i)\r
{\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
-\r
- Conservation c = sg.getConservation();\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
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- ccs.conserve = c;*/\r
+ av.updateConservation();\r
+ av.updateConsensus();\r
}\r
\r
//////////////////////////////////////////\r
int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
oldSeq = seq;\r
\r
- stretchGroup = av.getRubberbandGroup();\r
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
+\r
+ if(sequence==null || res>sequence.getLength())\r
+ return;\r
+\r
+ stretchGroup = av.getSelectionGroup();\r
\r
if(stretchGroup == null)\r
{\r
- stretchGroup = av.alignment.findGroup( (Sequence) av.getAlignment().\r
- getSequenceAt(seq));\r
- av.setRubberbandGroup( stretchGroup );\r
+ stretchGroup = av.alignment.findGroup( sequence );\r
+ if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
+ av.setSelectionGroup(stretchGroup);\r
+ else\r
+ stretchGroup = null;\r
}\r
\r
- else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))\r
+ else if(!stretchGroup.sequences.contains(sequence)\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
+ SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );\r
\r
if (allGroups != null)\r
for (int i = 0; i < allGroups.length; i++)\r
allGroups[i].getEndRes() >= res)\r
{\r
stretchGroup = allGroups[i];\r
- av.setRubberbandGroup(stretchGroup);\r
+ av.setSelectionGroup(stretchGroup);\r
break;\r
}\r
}\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
+ sg.addSequence( sequence );\r
+ av.setSelectionGroup( 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
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
+ if(av.getAbovePIDThreshold())\r
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
\r
}\r
else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
changeStartRes = true;\r
\r
\r
- seqCanvas.paintFlag = true;\r
repaint();\r
\r
}\r
\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
+ mouseDragging = false;\r
+\r
+ if(stretchGroup==null)\r
+ return;\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
+ ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
stretchGroup.cs = ccs;\r
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
\r
-\r
- Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
-\r
- seqCanvas.paintFlag = true;\r
repaint();\r
}\r
else\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
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
}\r
\r
}\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
+ ap.idPanel.repaint();\r
}\r
\r
\r
int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
\r
+ if(stretchGroup==null)\r
+ return;\r
+\r
+ if(res>av.alignment.getWidth()-2)\r
+ res = av.alignment.getWidth()-2;\r
+\r
\r
if(stretchGroup.getEndRes()==res)\r
// Edit end res position of selected group\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
+ while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())\r
{\r
// This routine ensures we don't skip any sequences, as the\r
// selection is quite slow.\r
}\r
else\r
{\r
+ if(seq!=null)\r
stretchGroup.addSequence(seq);\r
stretchGroup.addSequence(nextSeq);\r
}\r
}\r
oldSeq = y;\r
+ mouseDragging = true;\r
+ if(scrollThread!=null)\r
+ scrollThread.setEvent(evt);\r
\r
- seqCanvas.paintFlag = true;\r
repaint();\r
}\r
\r
+ public void doMouseEnteredDefineMode(MouseEvent e)\r
+ {\r
+ if (scrollThread != null)\r
+ scrollThread.running = false;\r
+ }\r
+\r
+ public void doMouseExitedDefineMode(MouseEvent e)\r
+ {\r
+ if (av.getWrapAlignment())\r
+ return;\r
+\r
+ if(mouseDragging)\r
+ scrollThread = new ScrollThread();\r
+\r
+ }\r
+ // this class allows scrolling off the bottom of the visible alignment\r
+ class ScrollThread extends Thread\r
+ {\r
+ MouseEvent evt;\r
+ boolean running = false;\r
+ public ScrollThread()\r
+ {\r
+ start();\r
+ }\r
+\r
+ public void setEvent(MouseEvent e)\r
+ {\r
+ evt = e;\r
+ }\r
+\r
+ public void stopScrolling()\r
+ {\r
+ running = false;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ running = true;\r
+ while (running)\r
+ {\r
+ if(evt!=null)\r
+ {\r
+\r
+ if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
+ running = ap.scrollUp(true);\r
+\r
+ if (mouseDragging && evt.getY() >= getHeight() &&\r
+ av.alignment.getHeight() > av.getEndSeq())\r
+ running = ap.scrollUp(false);\r
+\r
+ if (mouseDragging && evt.getX() < 0)\r
+ running = ap.scrollRight(true);\r
+\r
+ else if (mouseDragging && evt.getX() >= getWidth())\r
+ running = ap.scrollRight(false);\r
+ }\r
+\r
+ try\r
+ {\r
+ Thread.sleep(75);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+ }\r
+}\r
+\r
+\r
\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff