X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=0ac14e54e8ebc38f8f1722df64abef6782335297;hb=567c2595554096f10feab130153f97286f3f7d80;hp=99c68ba8a54d752bfd3b42f7bfb7e3d4699d361d;hpb=409fd993c6e32e999b24082aae107a043a590f8f;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 99c68ba..0ac14e5 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -20,10 +20,17 @@
*/
package jalview.datamodel;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Defines internal constants for unambiguous annotation of DbRefEntry source
* strings and describing the data retrieved from external database sources (see
- * jalview.ws.DbSourcProxy)
+ * jalview.ws.DbSourcProxy)
+ * TODO: replace with ontology to allow recognition of particular attributes
+ * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
+ * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
*
* @author JimP
*
@@ -33,12 +40,12 @@ public class DBRefSource
/**
* UNIPROT Accession Number
*/
- public static String UNIPROT = "UNIPROT";
+ public static final String UNIPROT = "UNIPROT";
/**
* UNIPROT Entry Name
*/
- public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
+ public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
@@ -51,27 +58,27 @@ public class DBRefSource
/**
* PDB Entry Code
*/
- public static String PDB = "PDB";
+ public static final String PDB = "PDB";
/**
* EMBL ID
*/
- public static String EMBL = "EMBL";
+ public static final String EMBL = "EMBL";
/**
* EMBLCDS ID
*/
- public static String EMBLCDS = "EMBLCDS";
+ public static final String EMBLCDS = "EMBLCDS";
/**
* PFAM ID
*/
- public static String PFAM = "PFAM";
+ public static final String PFAM = "PFAM";
/**
* RFAM ID
*/
- public static String RFAM = "RFAM";
+ public static final String RFAM = "RFAM";
/**
* GeneDB ID
@@ -79,19 +86,39 @@ public class DBRefSource
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[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
- EMBLCDSProduct };
+ public static final String ENSEMBL = "ENSEMBL";
- public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
- EMBLCDSProduct };
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
- public static final String[] PROTEINSTR = { PDB };
-
- public static final String[] DOMAINDBS = { PFAM, RFAM };
+ /**
+ * List of databases whose sequences might have coding regions annotated
+ */
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+ ENSEMBL };
+
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+ public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
+ EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+
+ public static String[] allSources()
+ {
+ List src = new ArrayList();
+ for (Field f : DBRefSource.class.getFields())
+ {
+ if (String.class.equals(f.getType()))
+ {
+ try
+ {
+ src.add((String) f.get(null));
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ }
+ }
+ }
+ return src.toArray(new String[0]);
+ }
}