{\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
public void mouseReleased(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
if (editingSeqs)\r
{\r
doMouseReleased(evt);\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
public void mouseExited(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || editingSeqs)\r
+ if (editingSeqs)\r
{\r
return;\r
}\r
\r
public void mouseEntered(MouseEvent evt)\r
{\r
- if (av.getWrapAlignment() || editingSeqs)\r
+ if (editingSeqs)\r
{\r
return;\r
}\r
ap.repaint();\r
}\r
\r
+ int findRes(MouseEvent evt)\r
+ {\r
+ int res = 0;\r
+ int x = evt.getX();\r
+\r
+ if (av.wrapAlignment)\r
+ {\r
+ int y = evt.getY();\r
+ y -= (2 * av.charHeight);\r
+ x -= seqCanvas.LABEL_WEST;\r
+\r
+ int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ int cwidth = seqCanvas.getWrappedCanvasWidth(this.getSize().width);\r
+ int block = y/chunkHeight;\r
+ block += av.getStartRes()/cwidth;\r
+\r
+ res = block*cwidth + x / av.getCharWidth();\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
+ int seq = 0;\r
+ int y = evt.getY();\r
+\r
+ if (av.wrapAlignment)\r
+ {\r
+ y -= (2 * av.charHeight);\r
+ int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;\r
+ seq = ( (y % chunkHeight) / 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
\r
public void doMouseMoved(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
-\r
- }\r
- else\r
- {\r
- res = x / av.getCharWidth() + av.getStartRes();\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
- }\r
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
\r
if (seq >= av.getAlignment().getHeight())\r
{\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
if (endEdit == startEdit)\r
{\r
- ap.alignFrame.historyList.pop();\r
- ap.alignFrame.updateEditMenuBar();\r
+ ap.alignFrame.historyList.pop();\r
+ ap.alignFrame.updateEditMenuBar();\r
}\r
\r
av.updateConservation();\r
av.updateConsensus();\r
\r
- // Y O Y CLUSTALX\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
- if (cs.conservationApplied())\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
- if (cs instanceof ClustalxColourScheme)\r
+ groupsToUpdate.addElement(av.getSelectionGroup());\r
+ int sSize = sg.getSize();\r
+ for (s = 0; s < sSize; s++)\r
{\r
- jalview.analysis.Conservation c = new jalview.analysis.Conservation\r
- ("All",\r
- ResidueProperties.propHash, 3,\r
- av.alignment.getSequences(), 0,\r
- av.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
+ SequenceI seq = sg.getSequenceAt(s);\r
\r
- ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());\r
- cs.setConservation(c);\r
- av.setGlobalColourScheme(cs);\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
- if (cs instanceof ClustalxColourScheme)\r
+ gSize = groupsToUpdate.size();\r
+ for (g = 0; g < gSize; g++)\r
{\r
- ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- av.setGlobalColourScheme(cs);\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
}\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
+ int res = findRes(evt);\r
+ int seq = findSeq(evt);\r
oldSeq = seq;\r
\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\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
{\r
res = av.getStartRes();\r
}\r
- else if (res > av.getEndRes())\r
+ else if (res > av.getEndRes() && !av.getWrapAlignment())\r
{\r
res = av.getEndRes();\r
}\r
\r
public void doMouseExitedDefineMode(MouseEvent e)\r
{\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
-\r
if (mouseDragging)\r
{\r
scrollThread = new ScrollThread();\r
git://source.jalview.org / jalview.git / blobdiff