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Fixed protein desc bug
[jalview.git]
/
src
/
jalview
/
gui
/
SequenceFetcher.java
diff --git
a/src/jalview/gui/SequenceFetcher.java
b/src/jalview/gui/SequenceFetcher.java
index
2e2456b
..
fc8f042
100755
(executable)
--- a/
src/jalview/gui/SequenceFetcher.java
+++ b/
src/jalview/gui/SequenceFetcher.java
@@
-239,6
+239,7
@@
public class SequenceFetcher
{
\r
EBIFetchClient ebi = new EBIFetchClient();
\r
File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
\r
{
\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
SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
\r
Vector entries = sff.getUniprotEntries(file);
\r
\r
@@
-249,7
+250,8
@@
public class SequenceFetcher
while (en.hasMoreElements())
\r
{
\r
UniprotEntry entry = (UniprotEntry) en.nextElement();
\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
Enumeration en2 = entry.getAccession().elements();
\r
while (en2.hasMoreElements())
\r
{
\r
@@
-263,8
+265,10
@@
public class SequenceFetcher
name.append(en2.nextElement());
\r
}
\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
result.append(name + "\n" + entry.getUniprotSequence().getContent() +
\r
"\n");
\r
@@
-288,10
+292,15
@@
public class SequenceFetcher
}
\r
\r
sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
\r
}
\r
\r
sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
\r
- e = entry.getFeature().elements();
\r
- while(e.hasMoreElements())
\r
+ if (entry.getFeature() != null)
\r
{
\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
}
\r
}
\r
}
\r