import javax.swing.*;\r
import java.util.*;\r
import jalview.schemes.*;\r
-import jalview.analysis.*;\r
-\r
\r
public class SeqPanel extends JPanel\r
{\r
public SeqCanvas seqCanvas;\r
public AlignmentPanel ap;\r
\r
- protected int startres;\r
protected int lastres;\r
- protected int endres;\r
-\r
protected int startseq;\r
- protected int padseq;\r
\r
protected AlignViewport av;\r
\r
\r
public void doMouseReleased(MouseEvent evt) {\r
\r
- int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
-\r
- endres = res;\r
-\r
startseq = -1;\r
- startres = -1;\r
lastres = -1;\r
if(seqEditOccurred>-1)\r
updateConservation(seqEditOccurred);\r
\r
seqEditOccurred = -1;\r
\r
- ap.RefreshPanels();\r
- repaint();\r
-\r
+ ap.repaint();\r
}\r
\r
public void doMousePressed(MouseEvent evt) {\r
\r
startseq = seq;\r
\r
- if (startseq == (av.getAlignment().getHeight() - 1))\r
- padseq = 1;\r
- else\r
- padseq = 1;\r
-\r
- startres = res;\r
lastres = res;\r
\r
}\r
else\r
{\r
startseq = -1;\r
- startres = -1;\r
lastres = -1;\r
}\r
\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
}\r
\r
public void doMouseDragged(MouseEvent evt) {\r
+\r
// If we're dragging we're editing\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ if (res < 0)\r
+ res = 0;\r
\r
- if(lastres==-1)\r
+ if (lastres == -1 || lastres == res)\r
return;\r
\r
- int x = evt.getX();\r
+ boolean dragRight = true;\r
+ if (res < av.getAlignment().getWidth() && res < lastres)\r
+ dragRight = false;\r
\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 (evt.isAltDown() || evt.isControlDown())\r
{\r
- SequenceGroup sg = av.getAlignment().findGroup(startseq);\r
- if (sg != null)\r
+ SequenceGroup sg = av.getSelectionGroup();\r
+ if(sg==null)\r
{\r
- boolean deleteAllowed = false;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
+ lastres=-1;\r
+ return;\r
+ }\r
+\r
+ // drag to right\r
+ if(dragRight)\r
+ sg.setEndRes(sg.getEndRes() + (res-lastres));\r
+\r
+ // drag to left\r
+ else\r
{\r
- /// Are we able to delete?\r
- boolean allGaps = true;\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ /// Are we able to delete?\r
+ // ie are all columns blank?\r
+ boolean deleteAllowed = false;\r
+ for (int s = 0; s < sg.getSize(); s++)\r
{\r
- SequenceI s = sg.getSequenceAt(i);\r
- for (int j = lastres-1; j >= res && allGaps; j--)\r
+ SequenceI seq = sg.getSequenceAt(s);\r
+ for (int j=res; j<lastres; j++)\r
{\r
- if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))\r
- {\r
- res = j + 1;\r
- allGaps = false;\r
- }\r
- }\r
-\r
- if(!deleteAllowed && allGaps)\r
+ if(seq.getSequence().length()<=j)\r
+ continue;\r
+\r
+ if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
+ {\r
+ // Not a gap, block edit not valid\r
+ res=j+1;\r
+ deleteAllowed = false;\r
+ continue;\r
+ }\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
+ if(!deleteAllowed)\r
+ {\r
+ lastres = -1;\r
+ return;\r
+ }\r
\r
+ sg.setEndRes(sg.getEndRes() - (lastres-res));\r
+ }\r
\r
\r
for (int i = 0; i < sg.getSize(); i++)\r
int k = av.alignment.findIndex(s);\r
\r
// drag to right\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
+ if (dragRight)\r
for (int j = lastres; j < res; j++)\r
insertChar(j, k);\r
\r
// drag to left\r
- else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)\r
+ else\r
{\r
for (int j = res; j < lastres; j++)\r
{\r
- deleteChar(j, k);\r
- startres = res;\r
+ if(s.getLength()>j)\r
+ deleteChar(res, k);\r
}\r
}\r
}\r
- }\r
}\r
else /////Editing a single sequence///////////\r
{\r
else if (res < av.getAlignment().getWidth() && res < lastres)\r
{\r
// dragging to the left\r
- for (int j = res; j < lastres; j++)\r
+ for (int j = lastres; j > res; j--)\r
{\r
- deleteChar(j, startseq);\r
- startres = res;\r
+ deleteChar(res, startseq);\r
}\r
}\r
\r
}\r
-\r
}\r
\r
lastres = res;\r
{\r
\r
if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
+ { av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
\r
+ }\r
+ else System.out.println("err "+seq+" "+j);\r
av.alignment.getWidth();\r
repaint();\r
seqEditOccurred=seq;\r
+\r
}\r
\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
+ av.updateConservation();\r
+ av.updateConsensus();\r
+\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme)\r
+ cs = ( (ConservationColourScheme) cs).cs;\r
+\r
+ if(cs instanceof ClustalxColourScheme)\r
+ cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());\r
\r
- Conservation c = sg.getConservation();\r
+ ap.alignFrame.changeColour(cs);\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
}\r
\r
//////////////////////////////////////////\r
if(stretchGroup == null)\r
{\r
stretchGroup = av.alignment.findGroup( sequence );\r
- if(res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
+ if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
av.setSelectionGroup(stretchGroup);\r
else\r
stretchGroup = null;\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
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
+ 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
if(stretchGroup==null)\r
return;\r
\r
+ if(res>av.alignment.getWidth())\r
+ res = av.alignment.getWidth()-1;\r
+\r
+\r
if(stretchGroup.getEndRes()==res)\r
// Edit end res position of selected group\r
changeEndRes = true;\r
else if (y < oldSeq)\r
dragDirection = -1;\r
\r
- while (y != oldSeq && oldSeq>0)\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
if(scrollThread!=null)\r
scrollThread.setEvent(evt);\r
\r
- seqCanvas.paintFlag = true;\r
repaint();\r
}\r
\r
running = ap.scrollRight(false);\r
}\r
\r
- ap.repaint();\r
try\r
{\r
Thread.sleep(75);\r
git://source.jalview.org / jalview.git / blobdiff