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Merge branch 'develop' into feature/JAL-2759
[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
c868576
..
73775cf
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-31,13
+31,13
@@
import jalview.datamodel.SequenceI;
import jalview.datamodel.xdb.uniprot.UniprotEntry;
import jalview.datamodel.xdb.uniprot.UniprotFeature;
import jalview.datamodel.xdb.uniprot.UniprotFile;
import jalview.datamodel.xdb.uniprot.UniprotEntry;
import jalview.datamodel.xdb.uniprot.UniprotFeature;
import jalview.datamodel.xdb.uniprot.UniprotFile;
-import jalview.ws.ebi.EBIFetchClient;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import java.io.File;
-import java.io.FileReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
import java.io.Reader;
import java.net.URL;
import java.io.Reader;
import java.net.URL;
+import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Vector;
import java.util.ArrayList;
import java.util.Vector;
@@
-162,17
+162,21
@@
public class Uniprot extends DbSourceProxyImpl
queries = queries.toUpperCase().replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
queries = queries.toUpperCase().replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
- EBIFetchClient ebi = new EBIFetchClient();
- // uniprotxml parameter required since december 2007
- // uniprotkb dbname changed introduced december 2008
- File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
- "xml");
+
+ String downloadstring = "http://www.uniprot.org/uniprot/" + queries
+ + ".xml";
+ URL url = null;
+ URLConnection urlconn = null;
+
+ url = new URL(downloadstring);
+ urlconn = url.openConnection();
+ InputStream istr = urlconn.getInputStream();
Vector<UniprotEntry> entries = getUniprotEntries(
Vector<UniprotEntry> entries = getUniprotEntries(
- new FileReader(file));
+ new InputStreamReader(istr, "UTF-8"));
if (entries != null)
{
if (entries != null)
{
- ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ ArrayList<SequenceI> seqs = new ArrayList<>();
for (UniprotEntry entry : entries)
{
seqs.add(uniprotEntryToSequenceI(entry));
for (UniprotEntry entry : entries)
{
seqs.add(uniprotEntryToSequenceI(entry));
@@
-184,8
+188,10
@@
public class Uniprot extends DbSourceProxyImpl
return al;
} catch (Exception e)
{
return al;
} catch (Exception e)
{
- stopQuery();
throw (e);
throw (e);
+ } finally
+ {
+ stopQuery();
}
}
}
}
@@
-203,7
+209,7
@@
public class Uniprot extends DbSourceProxyImpl
sequence.setDescription(getUniprotEntryDescription(entry));
final String dbVersion = getDbVersion();
sequence.setDescription(getUniprotEntryDescription(entry));
final String dbVersion = getDbVersion();
- ArrayList<DBRefEntry> dbRefs = new ArrayList<DBRefEntry>();
+ ArrayList<DBRefEntry> dbRefs = new ArrayList<>();
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
@@
-213,7
+219,7
@@
public class Uniprot extends DbSourceProxyImpl
dbRefs.add(dbRef);
}
dbRefs.add(dbRef);
}
- Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
+ Vector<PDBEntry> onlyPdbEntries = new Vector<>();
for (PDBEntry pdb : entry.getDbReference())
{
DBRefEntry dbr = new DBRefEntry();
for (PDBEntry pdb : entry.getDbReference())
{
DBRefEntry dbr = new DBRefEntry();
@@
-304,23
+310,18
@@
public class Uniprot extends DbSourceProxyImpl
/**
*
* @param entry
/**
*
* @param entry
- * UniportEntry
+ * UniprotEntry
* @return The accession id(s) and name(s) delimited by '|'.
*/
public static String getUniprotEntryId(UniprotEntry entry)
{
StringBuilder name = new StringBuilder(32);
* @return The accession id(s) and name(s) delimited by '|'.
*/
public static String getUniprotEntryId(UniprotEntry entry)
{
StringBuilder name = new StringBuilder(32);
- // name.append("UniProt/Swiss-Prot");
- // use 'canonicalised' name for optimal id matching
- name.append(DBRefSource.UNIPROT);
- for (String accessionId : entry.getAccession())
- {
- name.append(BAR_DELIMITER);
- name.append(accessionId);
- }
for (String n : entry.getName())
{
for (String n : entry.getName())
{
- name.append(BAR_DELIMITER);
+ if (name.length() > 0)
+ {
+ name.append(BAR_DELIMITER);
+ }
name.append(n);
}
return name.toString();
name.append(n);
}
return name.toString();