X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=2f948841e7c05cff48b8cf977b1ea420f35bdf04;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=0ac14e54e8ebc38f8f1722df64abef6782335297;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 0ac14e5..2f94884 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -20,11 +20,10 @@
*/
package jalview.datamodel;
-import java.lang.reflect.Field;
-import java.util.ArrayList;
-import java.util.List;
-
/**
+ * BH 2018 SwingJS note: If additional final static Strings are added to this
+ * file, they should be added to public static final String[] allTypes.
+ *
* Defines internal constants for unambiguous annotation of DbRefEntry source
* strings and describing the data retrieved from external database sources (see
* jalview.ws.DbSourcProxy)
@@ -32,93 +31,134 @@ import java.util.List;
* (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
* genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
*
+ *
+ *
* @author JimP
*
*/
public class DBRefSource
{
- /**
- * UNIPROT Accession Number
- */
+
+
+
public static final String UNIPROT = "UNIPROT";
-
- /**
- * UNIPROT Entry Name
- */
public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
-
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
- public static final String EMBLCDSProduct = "EMBLCDSProtein"
- .toUpperCase();
-
- /**
- * PDB Entry Code
- */
- public static final String PDB = "PDB";
-
- /**
- * EMBL ID
- */
- public static final String EMBL = "EMBL";
-
- /**
- * EMBLCDS ID
- */
- public static final String EMBLCDS = "EMBLCDS";
-
- /**
- * PFAM ID
- */
- public static final String PFAM = "PFAM";
-
- /**
- * RFAM ID
- */
- public static final String RFAM = "RFAM";
-
- /**
- * GeneDB ID
- */
- public static final String GENEDB = "GeneDB".toUpperCase();
-
- /**
- * Ensembl
- */
- 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();
+
+ 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();
- /**
- * List of databases whose sequences might have coding regions annotated
- */
- public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
- ENSEMBL };
-
- 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< src = new ArrayList();
- for (Field f : DBRefSource.class.getFields())
+ 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 (String.class.equals(f.getType()))
+ if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
{
- try
- {
- src.add((String) f.get(null));
- } catch (Exception x)
- {
- x.printStackTrace();
- }
+ // by convention, many secondary references inherit the primary
+ // reference's
+ // source string as a prefix for any version information from the
+ // secondary reference.
+ return false;
}
}
- return src.toArray(new String[0]);
- }
+ return true;
+}
+
+
+
+
}