{\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
+ 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
- if (cs instanceof ClustalxColourScheme)\r
+\r
+ // Y O Y CLUSTALX\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+\r
+ if (av.getSelectionGroup() != null)\r
{\r
- ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- av.setGlobalColourScheme(cs);\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
*/\r
void editOccurred(int i)\r
{\r
- if (endEdit == startEdit)\r
+ if (endEdit == startEdit)\r
+ {\r
+ ap.alignFrame.historyList.pop();\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\r
+\r
+ av.updateConservation();\r
+ av.updateConsensus();\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
- ap.alignFrame.historyList.pop();\r
- ap.alignFrame.updateEditMenuBar();\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
- av.updateConservation();\r
- av.updateConsensus();\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
// 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.conservationApplied())\r
+ if(cs!=null)\r
{\r
+ if (cs.conservationApplied())\r
+ {\r
Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, av.alignment.getSequences(),\r
- 0, av.alignment.getWidth() - 1);\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
+ 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
+ cs.setConservation(c);\r
+ av.setGlobalColourScheme(cs);\r
}\r
- }\r
\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ((ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\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