- /**
- * List of databases whose sequences might have coding regions annotated
- */
- public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
- ENSEMBL, ENSEMBLGENOMES };
-
- public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
-
- public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
- EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+ 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
+ };
+
+ 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)
+ {
+ return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
+ }