- 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
- };
-
- public static final int DNA_CODING_MASK =
- ENSEMBL_MASK | ENSEMBL_GENOMES_MASK
- | EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;
-
-
-
- public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
-
- public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK | ENSEMBL_MASK;
-
-
-
- public static final String[] PROTEINDBS = {
- UNIPROT, UNIPROTKB,
- ENSEMBL, EMBLCDSProduct }; // Ensembl ENSP* entries are protein
-
- public static final int PROTEIN_MASK =
- UNIPROT_MASK | UNIPROT_KB_MASK
- | ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK ;
-
-
- // for SequenceAnnotationReport only
-
-// public static final String[][] PRIMARY_SOURCES = new String[][] {
-// CODINGDBS, DNACODINGDBS, PROTEINDBS };
-//
- public static final int PRIMARY_SOURCES_MASK = CODING_MASK | DNA_CODING_MASK | PROTEIN_MASK;
-
- public static boolean isPrimarySource(String source)