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
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
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
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.isControlDown())\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.isControlDown())\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.isControlDown())\r
+ if(av.getWrapAlignment())\r
+ return;\r
+ if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
doMousePressed(evt);\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
\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
\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
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
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
+ if(res>sequence.getLength())\r
+ return;\r
+\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
+ // 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
+\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
+ 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
}\r
\r
public void doMouseDragged(MouseEvent evt) {\r
// If we're dragging we're editing\r
\r
- editFlag = true;\r
+ if(lastres==-1)\r
+ return;\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 (evt.isControlDown()) {\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
+ if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))\r
+ {\r
+ res = j + 1;\r
+ allGaps = false;\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(!deleteAllowed && allGaps)\r
+ deleteAllowed = true;\r
+ }\r
+ }\r
\r
- int index = av.getAlignment().findIndex(s);\r
- if (index != -1)\r
- drawChars(index,index+1,lastres);\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
- } 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
\r
- }\r
- }\r
\r
- }\r
- lastres = res;\r
- } else {\r
\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
- 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
-\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
ccs.conserve = c;*/\r
}\r
\r
+//////////////////////////////////////////\r
+/////Everything below this is for defining the boundary of the rubberband\r
+//////////////////////////////////////////\r
int oldSeq = -1;\r
-\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
+ 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
- stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));\r
+ {\r
+ stretchGroup = av.alignment.findGroup( sequence );\r
+ if(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 );\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.setSelectionGroup(stretchGroup);\r
+ break;\r
+ }\r
}\r
\r
if(stretchGroup==null)\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
+\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
+ 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
+\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
+ 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(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
+ // Edit start res position of selected group\r
changeStartRes = true;\r
\r
\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)\r
{\r
// This routine ensures we don't skip any sequences, as the\r
// selection is quite slow.\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
+ ap.repaint();\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