- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
-\r
- public void alignmentChanged()\r
- {\r
- viewport.alignment.padGaps();\r
- if(viewport.autocalculateConsensus)\r
- {\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- }\r
-\r
- resetAllColourSchemes();\r
- if(alignPanel.overviewPanel!=null)\r
- alignPanel.overviewPanel.updateOverviewImage();\r
-\r
- viewport.alignment.adjustSequenceAnnotations();\r
- alignPanel.repaint();\r
- }\r
-\r
- void resetAllColourSchemes()\r
- {\r
- ColourSchemeI cs = viewport.globalColourScheme;\r
- if(cs!=null)\r
- {\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
- }\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