public static final String UNIPROT = "UNIPROT";
- public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
+
+ public static final String UP_NAME = "UNIPROT_NAME";
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
public static final String PDB = "PDB";
- public static final String PFAM = "PFAM";
+
+ public static final String PFAM = "PFAM";
+
public static final String RFAM = "RFAM";
public static final String GENEDB = "GeneDB".toUpperCase();
+ public static final String PFAM_FULL = "PFAM (Full)";
+
+ public static final String PFAM_SEED = "PFAM (Seed)";
+
+ public static final String RFAM_SEED = "RFAM (Seed)";
+
public static final String PDB_CANONICAL_NAME = PDB;
public static int getSourceKey(String name) {
for (int i = 0; i < MASK_COUNT; i++) {
if (name.equals(allSources[i]))
- return 1<<i;
+ {
+ return 1<<i;
+ }
}
return 0;
}
// CODINGDBS, DNACODINGDBS, PROTEINDBS };
//
public static final int PRIMARY_SOURCES_MASK = CODING_MASK | DNA_CODING_MASK | PROTEIN_MASK;
-
+
public static boolean isPrimarySource(String source)
{
return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
}
-
-// public static String[] allSourcesFromReflection;
-//
-// public static String[] allSources()
-//
-// {
-// /**
-// * @j2sNative
-// *
-// * return C$.allTypes;
-// *
-// */
-//
-// {
-// if (allSourcesFromReflection == null)
-// {
-// List<String> 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();
-// }
-// }
-// }
-// allSourcesFromReflection = src.toArray(new String[0]);
-// }
-// return allSourcesFromReflection;
-// }
-// }
-
public static boolean isPrimaryCandidate(String ucversion) {
// tricky - this test really needs to search the sequence's set of dbrefs to
// see if there is a primary reference that derived this reference.