redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
HistoryItem.HIDE));\r
restoreHistoryItem(hi);\r
+ resetAllColourSchemes();\r
}\r
\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\r
restoreHistoryItem(hi);\r
updateEditMenuBar();\r
viewport.updateConsensus();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
alignPanel.repaint();\r
}\r
\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
- resetAllClustalSchemes();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
\r
}\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
- resetAllClustalSchemes();\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
\r
- void resetAllClustalSchemes()\r
+ void resetAllColourSchemes()\r
{\r
+ ColourSchemeI cs = viewport.globalColourScheme;\r
+ if(cs!=null)\r
+ {\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if(cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\r
+\r
if(viewport.getGlobalColourScheme()!=null\r
&& viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
{\r
for(s=0; s<sSize; s++)\r
{\r
SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
- if(sg.cs instanceof ClustalxColourScheme)\r
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
{\r
((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
}\r
+\r
+ sg.recalcConservation();\r
+\r
}\r
}\r
\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
HistoryItem.HIDE));\r
restoreHistoryItem(hi);\r
+ resetAllColourSchemes();\r
}\r
\r
/**\r
restoreHistoryItem(hi);\r
updateEditMenuBar();\r
viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
\r
- resetAllClustalSchemes();\r
+ resetAllColourSchemes();\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
alignPanel.repaint();\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
\r
- resetAllClustalSchemes();\r
\r
viewport.updateConservation();\r
viewport.updateConsensus();\r
+ resetAllColourSchemes();\r
alignPanel.repaint();\r
}\r
\r
- void resetAllClustalSchemes()\r
+\r
+ void resetAllColourSchemes()\r
{\r
+ ColourSchemeI cs = viewport.globalColourScheme;\r
+ if(cs!=null)\r
+ {\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if(cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\r
+\r
if(viewport.getGlobalColourScheme()!=null\r
&& viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
{\r
for(s=0; s<sSize; s++)\r
{\r
SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
- if(sg.cs instanceof ClustalxColourScheme)\r
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
{\r
((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
}\r
+\r
+ sg.recalcConservation();\r
+\r
}\r
}\r
\r