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JAL-2758 flag and tests for omitting uniprot accession prefix from sequence names
[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
c9beb8e
..
2452aed
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-60,6
+60,11
@@
public class Uniprot extends DbSourceProxyImpl
private static Mapping map;
/**
private static Mapping map;
/**
+ * configurable parameter controlling prefixing of entry names with accessions
+ */
+ private boolean includeAllIds = false;
+
+ /**
* Constructor
*/
public Uniprot()
* Constructor
*/
public Uniprot()
@@
-203,7
+208,7
@@
public class Uniprot extends DbSourceProxyImpl
*/
public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
{
*/
public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
{
- String id = getUniprotEntryId(entry);
+ String id = getUniprotEntryId(entry, includeAllIds);
SequenceI sequence = new Sequence(id,
entry.getUniprotSequence().getContent());
sequence.setDescription(getUniprotEntryDescription(entry));
SequenceI sequence = new Sequence(id,
entry.getUniprotSequence().getContent());
sequence.setDescription(getUniprotEntryDescription(entry));
@@
-313,20
+318,27
@@
public class Uniprot extends DbSourceProxyImpl
* UniportEntry
* @return The accession id(s) and name(s) delimited by '|'.
*/
* UniportEntry
* @return The accession id(s) and name(s) delimited by '|'.
*/
- public static String getUniprotEntryId(UniprotEntry entry)
+ public static String getUniprotEntryId(UniprotEntry entry,
+ boolean includeAllIds)
{
StringBuilder name = new StringBuilder(32);
{
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())
+ if (includeAllIds)
{
{
- name.append(BAR_DELIMITER);
- name.append(accessionId);
+ // // 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();