Viewport[] views = jms.getViewport();\r
Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
\r
- AlignFrame af = new AlignFrame(al);\r
+ AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
\r
\r
// af.changeColour() );\r
af.viewport.setStartRes(view.getStartRes());\r
af.viewport.setStartSeq(view.getStartSeq());\r
af.viewport.setShowAnnotation(view.getShowAnnotation());\r
- af.viewport.showConservation = view.getShowConservation();\r
- af.viewport.showQuality = view.getShowQuality();\r
- af.viewport.showIdentity = view.getShowIdentity();\r
af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
af.abovePIDThreshold.setSelected(view.getPidSelected());\r
af.viewport.setColourText(view.getShowColourText());\r
if(cs!=null)\r
{\r
cs.setThreshold(view.getPidThreshold(), true);\r
- cs.setConsensus(af.viewport.vconsensus);\r
+ cs.setConsensus(af.viewport.hconsensus);\r
}\r
}\r
\r