seqIndex++, i++)\r
{\r
Sequence sequence = (Sequence) sequences.get(seqIndex);\r
- if(sequence.getSequenceFeatures()==null)\r
+ Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] { "Uniprot"});\r
+ if (uprefs!=null)\r
{\r
+ // we know the id for this entry, so don't note its ID in the unknownSequences list\r
+ for (int j=0,k=uprefs.size(); j<k; j++)\r
+ ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());\r
+ unknownSequences.add(sequence);\r
+ } else {\r
if (!ids.contains(sequence.getName()))\r
{\r
ids.add(sequence.getName());\r
// javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);\r
javax.swing.JOptionPane.showMessageDialog(\r
Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences.",\r
- "Blast for Unidentified Sequences",\r
+ "Unidentified Sequences",\r
javax.swing.JOptionPane.WARNING_MESSAGE);\r
\r
\r
}\r
\r
sequence.setPDBId(onlyPdbEntries);\r
- sequence.setSequenceFeatures(entry.getFeature());\r
+ if (entry.getFeature()!=null) {\r
+ e = entry.getFeature().elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ sf.setFeatureGroup("Uniprot");\r
+ sequence.addSequenceFeature( sf );\r
+ }\r
+ }\r
sequence.setStart(absStart);\r
sequence.setEnd(absEnd);\r
\r