git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
implemented embl validation properly
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Uniprot.java
diff --git
a/src/jalview/ws/dbsources/Uniprot.java
b/src/jalview/ws/dbsources/Uniprot.java
index
1140a1b
..
ab0b10c
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-51,11
+51,12
@@
import jalview.ws.seqfetcher.DbSourceProxyImpl;
*/
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
{
*/
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
{
- public Uniprot() {
+ public Uniprot()
+ {
super();
addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
addDbSourceProperty(DBRefSource.PROTSEQDB);
super();
addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
addDbSourceProperty(DBRefSource.PROTSEQDB);
-// addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
+ // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
}
/*
}
/*
@@
-106,7
+107,8
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
try
{
// 1. Load the mapping information from the file
try
{
// 1. Load the mapping information from the file
- org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());
+ org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(
+ uni.getClass().getClassLoader());
java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
map.loadMapping(url);
java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
map.loadMapping(url);
@@
-116,8
+118,7
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
unmar.setMapping(map);
uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
unmar.setMapping(map);
uni = (UniprotFile) unmar.unmarshal(new FileReader(file));
- }
- catch (Exception e)
+ } catch (Exception e)
{
System.out.println("Error getUniprotEntries() " + e);
}
{
System.out.println("Error getUniprotEntries() " + e);
}
@@
-135,11
+136,12
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
startQuery();
try
{
startQuery();
try
{
- Alignment al=null;
+ Alignment al = null;
ebi = new EBIFetchClient();
ebi = new EBIFetchClient();
- StringBuffer result=new StringBuffer();
+ StringBuffer result = new StringBuffer();
// uniprotxml parameter required since december 2007
// uniprotxml parameter required since december 2007
- File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml", null);
+ File file = ebi.fetchDataAsFile("uniprot:" + queries, "uniprotxml",
+ null);
Vector entries = getUniprotEntries(file);
if (entries != null)
Vector entries = getUniprotEntries(file);
if (entries != null)
@@
-164,12
+166,13
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
name.append(en2.nextElement());
}
name.append(en2.nextElement());
}
- if (entry.getProtein()!=null && entry.getProtein().getName()!=null)
+ if (entry.getProtein() != null
+ && entry.getProtein().getName() != null)
{
{
- for (int nm=0,nmSize=entry.getProtein().getName().size(); nm<nmSize;nm++)
- {
- name.append(" " + entry.getProtein().getName().elementAt(nm));
- }
+ for (int nm = 0, nmSize = entry.getProtein().getName().size(); nm < nmSize; nm++)
+ {
+ name.append(" " + entry.getProtein().getName().elementAt(nm));
+ }
}
result.append(name + "\n"
}
result.append(name + "\n"
@@
-179,11
+182,13
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
// Then read in the features and apply them to the dataset
al = parseResult(result.toString());
// Then read in the features and apply them to the dataset
al = parseResult(result.toString());
- if (al!=null)
+ if (al != null)
{
// Decorate the alignment with database entries.
addUniprotXrefs(al, entries);
{
// Decorate the alignment with database entries.
addUniprotXrefs(al, entries);
- } else {
+ }
+ else
+ {
results = result;
}
}
results = result;
}
}
@@
-192,7
+197,7
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
} catch (Exception e)
{
stopQuery();
} catch (Exception e)
{
stopQuery();
- throw(e);
+ throw (e);
}
}
}
}
@@
-200,9
+205,9
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
* add an ordered set of UniprotEntry objects to an ordered set of seuqences.
*
* @param al -
* add an ordered set of UniprotEntry objects to an ordered set of seuqences.
*
* @param al -
- * a sequence of n sequences
+ * a sequence of n sequences
* @param entries
* @param entries
- * a seuqence of n uniprot entries to be analysed.
+ * a seuqence of n uniprot entries to be analysed.
*/
public void addUniprotXrefs(Alignment al, Vector entries)
{
*/
public void addUniprotXrefs(Alignment al, Vector entries)
{
@@
-218,17
+223,17
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
DBRefEntry dbr = new DBRefEntry();
dbr.setSource(pdb.getType());
dbr.setAccessionId(pdb.getId());
DBRefEntry dbr = new DBRefEntry();
dbr.setSource(pdb.getType());
dbr.setAccessionId(pdb.getId());
- dbr.setVersion(DBRefSource.UNIPROT+":"+getDbVersion());
+ dbr.setVersion(DBRefSource.UNIPROT + ":" + getDbVersion());
dbxrefs.addElement(dbr);
if (!pdb.getType().equals("PDB"))
{
continue;
}
dbxrefs.addElement(dbr);
if (!pdb.getType().equals("PDB"))
{
continue;
}
-
+
onlyPdbEntries.addElement(pdb);
}
SequenceI sq = al.getSequenceAt(i);
onlyPdbEntries.addElement(pdb);
}
SequenceI sq = al.getSequenceAt(i);
- while (sq.getDatasetSequence()!=null)
+ while (sq.getDatasetSequence() != null)
{
sq = sq.getDatasetSequence();
}
{
sq = sq.getDatasetSequence();
}
@@
-237,16
+242,15
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
while (en2.hasMoreElements())
{
// we always add as uniprot if we retrieved from uniprot or uniprot name
while (en2.hasMoreElements())
{
// we always add as uniprot if we retrieved from uniprot or uniprot name
- sq.addDBRef(
- new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()
- .toString()));
+ sq.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2
+ .nextElement().toString()));
}
en2 = dbxrefs.elements();
while (en2.hasMoreElements())
{
}
en2 = dbxrefs.elements();
while (en2.hasMoreElements())
{
- // we always add as uniprot if we retrieved from uniprot or uniprot name
+ // we always add as uniprot if we retrieved from uniprot or uniprot name
sq.addDBRef((DBRefEntry) en2.nextElement());
sq.addDBRef((DBRefEntry) en2.nextElement());
-
+
}
sq.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
}
sq.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
@@
-271,6
+275,7
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
{
return true;
}
{
return true;
}
+
/**
* return LDHA_CHICK uniprot entry
*/
/**
* return LDHA_CHICK uniprot entry
*/
@@
-278,6
+283,7
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
{
return "P00340";
}
{
return "P00340";
}
+
public String getDbName()
{
return "Uniprot"; // getDbSource();
public String getDbName()
{
return "Uniprot"; // getDbSource();