+\r
+ void displayResults(boolean newFrame)\r
+ {\r
+ SequenceI [] seqs = getVamsasAlignment(result.getMsa());\r
+\r
+ if (seqs != null)\r
+ {\r
+ AlignmentOrder msaorder = new AlignmentOrder(seqs);\r
+\r
+ if (preserveOrder)\r
+ {\r
+ jalview.analysis.AlignmentSorter.recoverOrder(seqs);\r
+ }\r
+\r
+ jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);\r
+\r
+ Alignment al = new Alignment(seqs);\r
+ if (dataset!=null)\r
+ {\r
+ al.setDataset(dataset);\r
+ }\r
+\r
+ if(newFrame)\r
+ {\r
+ // TODO: JBPNote Should also rename the query sequence sometime...\r
+ AlignFrame af = new AlignFrame(al);\r
+\r
+ //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+ af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());\r
+\r
+ af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
+ msaorder);\r
+\r
+ Desktop.addInternalFrame(af, alTitle,\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+\r
+ }\r
+ else\r
+ {\r
+ System.out.println("MERGE WITH OLD FRAME");\r
+\r
+ }\r
+ }\r
+ }\r