if (this.msa!=null && result.getAligfile()!=null) {\r
// we ignore the returned alignment if we only predicted on a single sequence\r
String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste");\r
- if (jalview.io.FormatProperties.contains(format))\r
+ if (jalview.io.FormatAdapter.formats.contains(format))\r
{\r
- al = new Alignment(jalview.io.FormatAdapter.read(result.getAligfile(),"Paste",format));\r
+ al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format));\r
noMsa = false;\r
FirstSeq = 0;\r
}\r