+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) {\r
+ wsInfo = setWebService(sh);\r
+ startJPredClient(title, seq);\r
+ }\r
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa) {\r
+ wsInfo = setWebService(sh);\r
+ startJPredClient(title, msa);\r
+ }\r
+\r
+ public JPredClient(String title, SequenceI[] msf) {\r
+ startJPredClient(title, msf);\r
+ }\r
+\r
+ public JPredClient(String title, SequenceI seq) {\r
+ startJPredClient(title, seq);\r
+ }\r
+\r
+ private void startJPredClient(String title, SequenceI[] msf)\r
+ {\r
+ if (wsInfo==null)\r
+ wsInfo = setWebService();\r
+\r
+ SequenceI seq = msf[0];\r
+\r
+ altitle = "JNet prediction on " + seq.getName() +\r
+ " using alignment from " + title;\r
+\r
+ wsInfo.setProgressText("Job details for MSA based prediction (" +\r
+ title + ") on sequence :\n>" + seq.getName() + "\n" +\r
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
+ "\n");\r
+ SequenceI aln[] = new SequenceI[msf.length];\r
+ for (int i=0,j=msf.length; i<j;i++) {\r
+ aln[i] = new jalview.datamodel.Sequence(msf[i]);\r
+ }\r
+\r
+ SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);\r
+\r
+ if (!locateWebService())\r
+ {\r
+ return;\r
+ }\r
+\r
+ JPredThread jthread = new JPredThread(aln);\r
+ jthread.start();\r
+ }\r
+\r
+ public void startJPredClient(String title, SequenceI seq)\r
+ {\r
+ if (wsInfo==null)\r
+ wsInfo = setWebService();\r
+ wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
+ seq.getName() + "\n" +\r
+ AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
+ "\n");\r
+ altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
+ title;\r
+\r
+ SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+\r
+ if (!locateWebService())\r
+ {\r
+ return;\r
+ }\r
+\r
+ JPredThread jthread = new JPredThread(seq);\r
+ jthread.start();\r
+ }\r
+\r