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JAL-2758 remove configurable behaviour - Uniprot sequences are only assigned IDs...
[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
94bc582
..
73775cf
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-60,11
+60,6
@@
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()
@@
-208,7
+203,7
@@
public class Uniprot extends DbSourceProxyImpl
*/
public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
{
*/
public SequenceI uniprotEntryToSequenceI(UniprotEntry entry)
{
- String id = getUniprotEntryId(entry, includeAllIds);
+ String id = getUniprotEntryId(entry);
SequenceI sequence = new Sequence(id,
entry.getUniprotSequence().getContent());
sequence.setDescription(getUniprotEntryDescription(entry));
SequenceI sequence = new Sequence(id,
entry.getUniprotSequence().getContent());
sequence.setDescription(getUniprotEntryDescription(entry));
@@
-318,21
+313,9
@@
public class Uniprot extends DbSourceProxyImpl
* UniprotEntry
* @return The accession id(s) and name(s) delimited by '|'.
*/
* UniprotEntry
* @return The accession id(s) and name(s) delimited by '|'.
*/
- public static String getUniprotEntryId(UniprotEntry entry,
- boolean includeAllIds)
+ public static String getUniprotEntryId(UniprotEntry entry)
{
StringBuilder name = new StringBuilder(32);
{
StringBuilder name = new StringBuilder(32);
- if (includeAllIds)
- {
- // // 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())
{
if (name.length() > 0)
for (String n : entry.getName())
{
if (name.length() > 0)