- public static final String[] allTypes = new String[] {
- UNIPROT, UP_NAME, UNIPROTKB,
- EMBLCDSProduct, PDB, EMBL,
- EMBLCDS, PFAM, RFAM,
- GENEDB, ENSEMBL, ENSEMBLGENOMES
- };
-
-public static final String PROTEINDBSKEYS, DNACODINGDBSKEYS;
-
-public static final String[] PROMTYPES;
-
-
-public static final int UNIPROT_MASK = 1;
-
-public static final int ENSEMBL_MASK = 2;
-
-public static final int ALL_MASKS = UNIPROT_MASK | ENSEMBL_MASK;
-
-public static final String PDB_CANONICAL_NAME = PDB;
-
-static {
- // BH 2019.01.25 trying to speed this up
- String s = ";";
- for (int i = PROTEINDBS.length; --i >= 0;)
- s += PROTEINDBS[i] + ";";
- PROTEINDBSKEYS = s;
-
- s = ";";
- for (int i = DNACODINGDBS.length; --i >= 0;)
- s += DNACODINGDBS[i] + ";";
- DNACODINGDBSKEYS = s;
+ public static final String EMBL = "EMBL";
+ public static final String EMBLCDS = "EMBLCDS";
+ public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase(Locale.ROOT);
+
+ public static final String PDB = "PDB";
+ public static final String PFAM = "PFAM";
+ public static final String RFAM = "RFAM";
+ public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT);
+
+ public static final String PDB_CANONICAL_NAME = PDB;
+
+
+ public static final String[] allSources = new String[] {
+ UNIPROT,
+ UP_NAME, UNIPROTKB,
+ ENSEMBL, ENSEMBLGENOMES,
+ EMBL, EMBLCDS, EMBLCDSProduct,
+ PDB, PFAM, RFAM, GENEDB
+ };
+
+ public static final int UNIPROT_MASK = 1<<0;
+ public static final int UP_NAME_MASK = 1<<1;
+ public static final int UNIPROT_KB_MASK = 1<<2;
+ public static final int ENSEMBL_MASK = 1<<3;
+ public static final int ENSEMBL_GENOMES_MASK = 1<<4;
+ public static final int EMBL_MASK = 1<<5;
+ public static final int EMBL_CDS_MASK = 1<<6;
+ public static final int EMBL_CDS_PRODUCT_MASK = 1<<7;
+ public static final int PDB_MASK = 1<<8;
+ public static final int PFAM_MASK = 1<<9;
+ public static final int RFAM_MASK = 1<<10;
+ public static final int GENE_DB_MASK = 1<<11;
+
+ public static final int MASK_COUNT = 12;
+
+ public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;
+
+ public static int getSourceKey(String name) {
+ for (int i = 0; i < MASK_COUNT; i++) {
+ if (name.equals(allSources[i]))
+ {
+ return 1<<i;
+ }
+ }
+ return 0;
+ }
+
+ public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;
+
+ /**
+ * List of databases whose sequences might have coding regions annotated
+ */
+ public static final String[] DNACODINGDBS = {
+ ENSEMBL, ENSEMBLGENOMES,
+ EMBL, EMBLCDS, GENEDB
+ };