{\r
EBIFetchClient ebi = new EBIFetchClient();\r
File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
+ // File file = new File("H:/jalview/classes/fer1.xml");\r
SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
Vector entries = sff.getUniprotEntries(file);\r
\r
while (en.hasMoreElements())\r
{\r
UniprotEntry entry = (UniprotEntry) en.nextElement();\r
- StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");\r
+\r
+ StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
Enumeration en2 = entry.getAccession().elements();\r
while (en2.hasMoreElements())\r
{\r
name.append(en2.nextElement());\r
}\r
\r
- if (entry.getProteinName() != null)\r
- name.append(" " + entry.getProteinName().elementAt(0));\r
+ if (entry.getProtein() != null)\r
+ {\r
+ name.append(" " + entry.getProtein().getName().elementAt(0));\r
+ }\r
\r
result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
"\n");\r
}\r
\r
sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
- e = entry.getFeature().elements();\r
- while(e.hasMoreElements())\r
+ if (entry.getFeature() != null)\r
{\r
- sequence[i].getDatasetSequence().addSequenceFeature((SequenceFeature)e.nextElement());\r
+ e = entry.getFeature().elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ sf.setFeatureGroup("Uniprot");\r
+ sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
+ }\r
}\r
}\r
}\r