+\r
+\r
+ AlignmentI al = new Alignment(newSeq);\r
+ al.setDataset(null);\r
+\r
+\r
+ ////////////////////////////////\r
+ // Copy annotations across\r
+ jalview.datamodel.AlignmentAnnotation[] annotations\r
+ = viewport.alignment.getAlignmentAnnotation();\r
+ int a, aSize;\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+\r
+ if (annotations[i].label.equals("Quality") ||\r
+ annotations[i].label.equals("Conservation") ||\r
+ annotations[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ aSize = viewport.alignment.getWidth()/3;\r
+ jalview.datamodel.Annotation [] anots =\r
+ new jalview.datamodel.Annotation[aSize];\r
+\r
+ for(a=0; a<viewport.alignment.getWidth(); a++)\r
+ {\r
+ if( annotations[i].annotations[a]==null\r
+ || annotations[i].annotations[a]==null)\r
+ continue;\r
+\r
+ anots[a/3] = new Annotation(\r
+ annotations[i].annotations[a].displayCharacter,\r
+ annotations[i].annotations[a].description,\r
+ annotations[i].annotations[a].secondaryStructure,\r
+ annotations[i].annotations[a].value,\r
+ annotations[i].annotations[a].colour);\r
+ }\r
+\r
+ jalview.datamodel.AlignmentAnnotation aa\r
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
+ annotations[i].description, anots );\r
+ al.addAnnotation(aa);\r
+ }\r
+\r
+\r
+ // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
+ // NEW_WINDOW_WIDTH,\r
+ // NEW_WINDOW_HEIGHT);\r
+\r
+ AlignViewport newViewport = new AlignViewport(al);\r
+ AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
+ tabbedPane.add("Protein", ap);\r
+ viewports.add(newViewport);\r
+ alignPanels.add(ap);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ AlignViewport ds = new AlignViewport(al.getDataset());\r
+ ds.setDataset(true);\r
+ AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ tabbedPane.add("Dataset", dap);\r
+ viewports.add(ds);\r
+ alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
+\r
+}\r
+\r
+public void tabSelected()\r
+{\r
+ int index = tabbedPane.getSelectedIndex();\r
+ viewport = (AlignViewport)viewports.elementAt(index);\r
+ alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
+}\r
+\r