+ return null;\r
+ }\r
+ Alignment al = null;\r
+ int FirstSeq = -1; // the position of the query sequence in Alignment al\r
+ boolean noMsa = true; // set if no MSA has been returned by JPred\r
+\r
+ JpredResult result = (JpredResult)this.result;\r
+\r
+ jalview.bin.Cache.log.debug("Parsing output from JNet job.");\r
+ // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
+ jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
+ getPredfile(),\r
+ "Paste");\r
+ SequenceI[] preds = prediction.getSeqsAsArray();\r
+ jalview.bin.Cache.log.debug("Got prediction profile.");\r
+\r
+ if ( (this.msa != null) && (result.getAligfile() != null))\r
+ {\r
+ jalview.bin.Cache.log.debug("Getting associated alignment.");\r
+ // we ignore the returned alignment if we only predicted on a single sequence\r
+ String format = new jalview.io.IdentifyFile().Identify(result.\r
+ getAligfile(),\r
+ "Paste");\r
+\r
+ if (jalview.io.FormatAdapter.isValidFormat(format))\r
+ {\r
+ al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),\r
+ "Paste", format));\r
+ SequenceI sqs[] = new SequenceI[al.getHeight()];\r
+ for (int i = 0, j = al.getHeight(); i < j; i++)\r
+ {\r
+ sqs[i] = al.getSequenceAt(i);\r
+ }\r
+ if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)\r
+ SequenceInfo, sqs))\r
+ {\r
+ throw (new Exception(\r
+ "Couldn't recover sequence properties for alignment."));\r
+ }\r
+\r
+ noMsa = false;\r
+ FirstSeq = 0;\r
+ }\r
+ else\r