import jalview.schemes.*;\r
\r
public class SeqPanel\r
- extends Panel\r
+ extends Panel implements MouseMotionListener, MouseListener\r
{\r
\r
public SeqCanvas seqCanvas;\r
\r
ap = p;\r
\r
- seqCanvas.addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
- doMouseMoved(evt);\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
- if (editingSeqs)\r
- {\r
- doMouseDragged(evt);\r
- }\r
- else\r
- {\r
- doMouseDraggedDefineMode(evt);\r
- }\r
- }\r
- });\r
-\r
- seqCanvas.addMouseListener(new MouseAdapter()\r
- {\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
- if (editingSeqs)\r
- {\r
- doMouseReleased(evt);\r
- }\r
- else\r
- {\r
- doMouseReleasedDefineMode(evt);\r
- }\r
-\r
- }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
- if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
- {\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- groupEditing = true;\r
- }\r
+ seqCanvas.addMouseMotionListener(this);\r
+ seqCanvas.addMouseListener(this);\r
\r
- editingSeqs = true;\r
- doMousePressed(evt);\r
- }\r
- else\r
- {\r
- doMousePressedDefineMode(evt);\r
- }\r
- }\r
+ seqCanvas.repaint();\r
+ }\r
\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || editingSeqs)\r
- {\r
- return;\r
- }\r
- doMouseExitedDefineMode(evt);\r
\r
- }\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ groupEditing = true;\r
+ }\r
+\r
+ editingSeqs = true;\r
+ doMousePressed(evt);\r
+ }\r
+ else\r
+ {\r
+ doMousePressedDefineMode(evt);\r
+ }\r
+ }\r
\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || editingSeqs)\r
- {\r
- return;\r
- }\r
- doMouseEnteredDefineMode(evt);\r
- }\r
+ public void mouseClicked(MouseEvent evt){}\r
\r
- });\r
- seqCanvas.repaint();\r
- }\r
\r
- public void doMouseReleased(MouseEvent evt)\r
+ public void mouseReleased(MouseEvent evt)\r
{\r
+ if (!editingSeqs)\r
+ {\r
+ doMouseReleasedDefineMode(evt);\r
+ return;\r
+ }\r
+\r
\r
if (seqEditOccurred > -1)\r
{\r
ap.repaint();\r
}\r
\r
+ int startWrapBlock=-1;\r
+ int wrappedBlock=-1;\r
+ int findRes(MouseEvent evt)\r
+ {\r
+ int res = 0;\r
+ int x = evt.getX();\r
+\r
+ if (av.wrapAlignment)\r
+ {\r
+\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
+\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap + seqCanvas.getAnnotationHeight();\r
+\r
+ int y = evt.getY();\r
+ y -= hgap;\r
+ x -= seqCanvas.LABEL_WEST;\r
+\r
+\r
+ int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);\r
+\r
+ wrappedBlock = y / cHeight;\r
+ wrappedBlock += av.getStartRes() / cwidth;\r
+\r
+ res = wrappedBlock * cwidth + x / av.getCharWidth();\r
+\r
+ }\r
+ else\r
+ {\r
+ res = (x / av.getCharWidth()) + av.getStartRes();\r
+ }\r
+\r
+ return res;\r
+\r
+ }\r
+\r
+ int findSeq(MouseEvent evt)\r
+ {\r
+\r
+ int seq = 0;\r
+ int y = evt.getY();\r
+\r
+ if (av.wrapAlignment)\r
+ {\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
+\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap + seqCanvas.getAnnotationHeight();\r
+\r
+ y -= hgap;\r
+\r
+ seq = ( (y % cHeight) / av.getCharHeight());\r
+ }\r
+ else\r
+ {\r
+ seq = (y / av.getCharHeight()) + av.getStartSeq();\r
+ }\r
+\r
+ return seq;\r
+ }\r
+\r
+\r
public void doMousePressed(MouseEvent evt)\r
{\r
ap.alignFrame.addHistoryItem(new HistoryItem(\r
"Edit Sequence", av.alignment, HistoryItem.EDIT));\r
- int seq;\r
- int res;\r
-\r
- int x = evt.getX();\r
- int y = evt.getY();\r
\r
- res = x / av.getCharWidth() + av.getStartRes();\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
+ int seq = findSeq(evt);\r
+ int res = findRes(evt);\r
\r
if (seq < av.getAlignment().getHeight() &&\r
res < av.getAlignment().getSequenceAt(seq).getLength())\r
return;\r
}\r
\r
- public void doMouseMoved(MouseEvent evt)\r
+ public void mouseMoved(MouseEvent evt)\r
{\r
- int res = 0, seq = 0;\r
- int x = evt.getX();\r
- int y = evt.getY();\r
- if (av.wrapAlignment)\r
- {\r
- y -= 2 * av.charHeight;\r
- int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
-\r
- res = (int) ( (y / chunkHeight) * (getSize().width / av.charWidth)) +\r
- x / av.getCharWidth() + av.getStartRes();\r
-\r
- y %= chunkHeight;\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
\r
- }\r
- else\r
- {\r
- res = x / av.getCharWidth() + av.getStartRes();\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
- }\r
-\r
- if (seq >= av.getAlignment().getHeight())\r
+ if (seq >= av.getAlignment().getHeight() || seq<0 || res<0)\r
{\r
return;\r
}\r
return;\r
}\r
\r
- Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
- String aa = "";\r
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
+ sequence.getName());\r
+\r
+ Object obj = null;\r
+ if (av.alignment.isNucleotide())\r
+ {\r
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
+ "");\r
+ if(obj!=null)\r
+ text.append(" Nucleotide: ");\r
+ }\r
+ else\r
+ {\r
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
+ if(obj!=null)\r
+ text.append(" Residue: ");\r
+ }\r
+\r
if (obj != null)\r
{\r
- aa = obj.toString();\r
+\r
+ if (obj != "")\r
+ {\r
+ text.append(obj + " (" +\r
+ av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+ }\r
}\r
\r
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
- sequence.getName());\r
- if (aa != "")\r
+ if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
{\r
- text.append(" Residue: " + aa + " (" +\r
- av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");\r
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
}\r
\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
- while (e.hasMoreElements())\r
+ if (av.showSequenceFeatures\r
+ && sequence.getSequenceFeatures()!=null\r
+ && av.featuresDisplayed!=null)\r
+ {\r
+ int index = 0;\r
+ sequence.getSequenceFeatures();\r
+ boolean first = true;\r
+ while (index < sequence.getSequenceFeatures().length)\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getStart() <= sequence.findPosition(res) &&\r
+ SequenceFeature sf = sequence.getSequenceFeatures()[index];\r
+ if (sf.getBegin() <= sequence.findPosition(res) &&\r
sf.getEnd() >= sequence.findPosition(res))\r
{\r
- if (sbuffer.length() > 0)\r
+ if(!av.featuresDisplayed.containsKey(sf.getType()))\r
+ {\r
+ index++;\r
+ continue;\r
+ }\r
+\r
+ if(first)\r
{\r
- sbuffer.append("; ");\r
+ text.append(" Sequence Feature:");\r
+ first = false;\r
}\r
- sbuffer.append(sf.getType() + " " + sf.getDescription());\r
- if (sf.getStatus().length() > 0)\r
+\r
+ text.append(" "+sf.getType());\r
+\r
+ if(sf.getDescription()!=null)\r
+ text.append(" "+sf.getDescription());\r
+\r
+ if (sf.getStatus()!=null && sf.getStatus().length() > 0)\r
{\r
- sbuffer.append(" (" + sf.getStatus() + ")");\r
+ text.append(" (" + sf.getStatus() + ")");\r
}\r
+ text.append("; ");\r
}\r
\r
+ index++;\r
+\r
}\r
}\r
\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
}\r
\r
- public void doMouseDragged(MouseEvent evt)\r
+ public void mouseDragged(MouseEvent evt)\r
{\r
+ if (!editingSeqs)\r
+ {\r
+ doMouseDraggedDefineMode(evt);\r
+ return;\r
+ }\r
\r
// If we're dragging we're editing\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ int res = findRes(evt);\r
if (res < 0)\r
{\r
res = 0;\r
}\r
else\r
{\r
-\r
+ if(scrollThread!=null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
break;\r
}\r
}\r
}\r
}\r
\r
+ mouseDragging = true;\r
+ if (res > av.endRes || res < av.startRes)\r
+ {\r
+ mouseExited(evt);\r
+ }\r
+\r
+ if (scrollThread != null)\r
+ scrollThread.setEvent(evt);\r
+\r
+\r
endEdit = res;\r
lastres = res;\r
seqCanvas.repaint();\r
}\r
\r
- public void drawChars(int seqstart, int seqend, int start)\r
- {\r
- seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, seqend,\r
- av.getStartRes(), av.getStartSeq(), 0);\r
- seqCanvas.repaint();\r
- }\r
-\r
public void insertChar(int j, int seq)\r
{\r
av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
ap.alignFrame.updateEditMenuBar();\r
}\r
\r
- av.updateConservation();\r
- av.updateConsensus();\r
-\r
-\r
- //Does the edit affect any groups?\r
- //////////////////////////////\r
- Vector groupsToUpdate = new Vector();\r
- SequenceGroup sg = av.getSelectionGroup();\r
-\r
- int s, g, gSize = av.alignment.getGroups().size();\r
- if (sg != null)\r
- {\r
- groupsToUpdate.addElement(av.getSelectionGroup());\r
- int sSize = sg.getSize();\r
- for (s = 0; s < sSize; s++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(s);\r
-\r
- for (g = 0; g < gSize; g++)\r
- {\r
- SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().\r
- elementAt(\r
- g);\r
- if (sg2.sequences.contains(seq))\r
- {\r
- if (!groupsToUpdate.contains(sg2))\r
- groupsToUpdate.addElement(sg2);\r
- continue;\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- SequenceI seq = av.alignment.getSequenceAt(startseq);\r
- for (g = 0; g < gSize; g++)\r
- {\r
- SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(\r
- g);\r
- if (sg2.sequences.contains(seq))\r
- {\r
- if (!groupsToUpdate.contains(sg2))\r
- groupsToUpdate.addElement(sg2);\r
- continue;\r
- }\r
- }\r
- }\r
-\r
- gSize = groupsToUpdate.size();\r
- for (g = 0; g < gSize; g++)\r
- {\r
- ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();\r
- }\r
- ////End of updating groups\r
- //////////////////////////////////////////\r
-\r
-\r
- // Y O Y CLUSTALX\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
-\r
- if (av.getSelectionGroup() != null)\r
- {\r
- av.getSelectionGroup().recalcConservation();\r
- }\r
-\r
- if(cs!=null)\r
- {\r
- if (cs.conservationApplied())\r
- {\r
- jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- av.alignment.getSequences(),\r
- 0, av.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ClustalxColourScheme cxs = (ClustalxColourScheme) cs;\r
- cxs.resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- cs.setConservation(c);\r
- av.setGlobalColourScheme(cs);\r
- }\r
- else\r
- {\r
- cs.setConservation(c);\r
- av.setGlobalColourScheme(cs);\r
- }\r
-\r
- }\r
-\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- av.setGlobalColourScheme(cs);\r
- }\r
- }\r
+ av.firePropertyChange("alignment", null,av.getAlignment().getSequences());\r
}\r
\r
//////////////////////////////////////////\r
int oldSeq = -1;\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
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
+\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
oldSeq = seq;\r
+ startWrapBlock=wrappedBlock;\r
+\r
+ if(seq==-1)\r
+ return;\r
\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
\r
\r
public void doMouseReleasedDefineMode(MouseEvent evt)\r
{\r
- if(mouseDragging)\r
- {\r
- stretchGroup.recalcConservation();\r
- mouseDragging = false;\r
- }\r
-\r
if (stretchGroup == null)\r
{\r
- return;\r
+ return;\r
}\r
\r
if(stretchGroup.cs!=null)\r
{\r
+ if (stretchGroup.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.\r
+ sequences,\r
+ stretchGroup.getWidth());\r
+ }\r
+\r
if (stretchGroup.cs.conservationApplied())\r
{\r
SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
stretchGroup.getName());\r
+ stretchGroup.recalcConservation();\r
}\r
else\r
{\r
changeEndRes = false;\r
changeStartRes = false;\r
stretchGroup = null;\r
- seqCanvas.repaint();\r
+ PaintRefresher.Refresh(av.alignment);\r
ap.repaint();\r
}\r
\r
- boolean remove = false;\r
public void doMouseDraggedDefineMode(MouseEvent evt)\r
{\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- int y = evt.getY() / av.getCharHeight() + av.getStartSeq();\r
+ int res = findRes(evt);\r
+ int y = findSeq(evt);\r
\r
- if (stretchGroup == null)\r
- {\r
+ if(wrappedBlock!=startWrapBlock)\r
return;\r
- }\r
\r
- if (res > av.alignment.getWidth())\r
- {\r
- res = av.alignment.getWidth() - 1;\r
- }\r
+ if (stretchGroup == null)\r
+ {\r
+ return;\r
+ }\r
\r
- if (stretchGroup.getEndRes() == res)\r
- {\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
- }\r
+ mouseDragging = true;\r
\r
- else if (stretchGroup.getStartRes() == res)\r
- {\r
- // Edit start res position of selected group\r
- changeStartRes = true;\r
- }\r
\r
- if (res < av.getStartRes())\r
- {\r
- res = av.getStartRes();\r
- }\r
- else if (res > av.getEndRes())\r
- {\r
- res = av.getEndRes();\r
- }\r
+ if(y > av.alignment.getHeight())\r
+ {\r
+ y = av.alignment.getHeight() -1;\r
+ }\r
\r
- if (changeEndRes)\r
- {\r
- if (res > stretchGroup.getStartRes() - 1)\r
+ if(res>av.alignment.getWidth())\r
+ res = av.alignment.getWidth()-1;\r
+\r
+ if (stretchGroup.getEndRes() == res)\r
{\r
- stretchGroup.setEndRes(res);\r
+ // Edit end res position of selected group\r
+ changeEndRes = true;\r
}\r
- }\r
- else if (changeStartRes)\r
- {\r
- if (res < stretchGroup.getEndRes() + 1)\r
+ else if (stretchGroup.getStartRes() == res)\r
{\r
- stretchGroup.setStartRes(res);\r
+ // Edit start res position of selected group\r
+ changeStartRes = true;\r
}\r
- }\r
\r
- int dragDirection = 0;\r
- if (y > oldSeq)\r
- {\r
- dragDirection = 1;\r
- }\r
- else if (y < oldSeq)\r
- {\r
- dragDirection = -1;\r
- }\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
\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
- Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+ if (changeEndRes)\r
+ {\r
+ if (res > (stretchGroup.getStartRes() - 1))\r
+ {\r
+ stretchGroup.setEndRes(res);\r
+ }\r
+ }\r
+ else if (changeStartRes)\r
+ {\r
+ if (res < (stretchGroup.getEndRes() + 1))\r
+ {\r
+ stretchGroup.setStartRes(res);\r
+ }\r
+ }\r
\r
- oldSeq += dragDirection;\r
- Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+ int dragDirection = 0;\r
\r
- if (stretchGroup.sequences.contains(nextSeq))\r
+ if (y > oldSeq)\r
{\r
- stretchGroup.deleteSequence(seq, false);\r
+ dragDirection = 1;\r
}\r
- else\r
+ else if (y < oldSeq)\r
{\r
- if (seq != null)\r
- {\r
- stretchGroup.addSequence(seq, false);\r
- }\r
- stretchGroup.addSequence(nextSeq, false);\r
+ dragDirection = -1;\r
}\r
- }\r
- oldSeq = y;\r
- mouseDragging = true;\r
- if (scrollThread != null)\r
- {\r
- scrollThread.setEvent(evt);\r
- }\r
\r
- seqCanvas.repaint();\r
- }\r
\r
- public void doMouseEnteredDefineMode(MouseEvent e)\r
- {\r
- if (scrollThread != null)\r
+ while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\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
+\r
+ if(oldSeq<0)\r
+ break;\r
+\r
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
+\r
+ if (stretchGroup.sequences.contains(nextSeq))\r
+ {\r
+ stretchGroup.deleteSequence(seq, false);\r
+ }\r
+ else\r
+ {\r
+ if (seq != null)\r
+ {\r
+ stretchGroup.addSequence(seq, false);\r
+ }\r
+\r
+ stretchGroup.addSequence(nextSeq, false);\r
+ }\r
+ }\r
+\r
+ if(oldSeq < 0)\r
+ oldSeq = -1;\r
+\r
+\r
+ if(res>av.endRes || res<av.startRes\r
+ || y<av.startSeq || y>av.endSeq)\r
+ {\r
+ mouseExited(evt);\r
+ }\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.setEvent(evt);\r
+ }\r
+\r
+ seqCanvas.repaint();\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent e)\r
{\r
- scrollThread.running = false;\r
+ if (oldSeq < 0)\r
+ oldSeq = 0;\r
+\r
+ if (scrollThread != null)\r
+ {\r
+ scrollThread.running = false;\r
+ scrollThread = null;\r
+ }\r
}\r
- }\r
\r
- public void doMouseExitedDefineMode(MouseEvent e)\r
+ public void mouseExited(MouseEvent e)\r
{\r
if (av.getWrapAlignment())\r
{\r
return;\r
}\r
\r
- if (mouseDragging)\r
+ if (mouseDragging && scrollThread==null)\r
{\r
scrollThread = new ScrollThread();\r
}\r
-\r
}\r
\r
// this class allows scrolling off the bottom of the visible alignment\r
running = true;\r
while (running)\r
{\r
+\r
if (evt != null)\r
{\r
\r
git://source.jalview.org / jalview.git / blobdiff