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
JAL-2110 fixes and tests for adding dbrefs to EMBL sequence and products
[jalview.git]
/
src
/
jalview
/
datamodel
/
DBRefSource.java
diff --git
a/src/jalview/datamodel/DBRefSource.java
b/src/jalview/datamodel/DBRefSource.java
index
99c68ba
..
a2243be
100755
(executable)
--- a/
src/jalview/datamodel/DBRefSource.java
+++ b/
src/jalview/datamodel/DBRefSource.java
@@
-54,6
+54,11
@@
public class DBRefSource
public static String PDB = "PDB";
/**
public static String PDB = "PDB";
/**
+ * mmCIF Entry Code
+ */
+ public static String MMCIF = "mmCIF";
+
+ /**
* EMBL ID
*/
public static String EMBL = "EMBL";
* EMBL ID
*/
public static String EMBL = "EMBL";
@@
-79,19
+84,20
@@
public class DBRefSource
public static final String GENEDB = "GeneDB".toUpperCase();
/**
public static final String GENEDB = "GeneDB".toUpperCase();
/**
- * List of databases whose sequences might have coding regions annotated
+ * Ensembl
*/
*/
- public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB };
-
- public static final String[] CODINGDBS = { EMBLCDS, GENEDB };
+ public static final String ENSEMBL = "ENSEMBL";
- public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
- EMBLCDSProduct };
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
- public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
- EMBLCDSProduct };
+ /**
+ * List of databases whose sequences might have coding regions annotated
+ */
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+ ENSEMBL };
- public static final String[] PROTEINSTR = { PDB };
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
- public static final String[] DOMAINDBS = { PFAM, RFAM };
+ public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+ EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
}
}