public class DBRefSource
{
-
-
-
+
public static final String UNIPROT = "UNIPROT";
- public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(Locale.ROOT);
+
+ public static final String UP_NAME = "UNIPROT_NAME"
+ .toUpperCase(Locale.ROOT);
+
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
- public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase(Locale.ROOT);
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL"
+ .toUpperCase(Locale.ROOT);
+
+ public static final String ENSEMBL = "ENSEMBL";
- public static final String ENSEMBL = "ENSEMBL";
public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
-
- 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 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 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)
+ 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++)
{
- return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
+ 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 boolean isPrimaryCandidate(String ucversion) {
+ 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);
+ }
+
+ 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.
for (int i = allSources.length; --i >= 0;)
{
- if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase(Locale.ROOT) unnecessary here for allSources
+ if (ucversion.startsWith(allSources[i])) // BH 2019.01.25
+ // .toUpperCase(Locale.ROOT)
+ // unnecessary here for
+ // allSources
{
// by convention, many secondary references inherit the primary
// reference's
}
}
return true;
-}
-
-
+ }
-
}