X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=cb853419154542c2a41d4df6beb24c0dcd531f71;hb=HEAD;hp=0552b2ce675b391bc9a59f958b203a10c57f2e59;hpb=3448f766a6dfe127f1d01e533c14d10aede962fa;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 0552b2c..cb85341 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,102 +1,181 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
+
 /**
- * Defines internal constants for unambiguous annotation
- * of DbRefEntry source strings and describing the data
- * retrieved from external database sources (see jalview.ws.DbSourcProxy)
+ * 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) <br/>
+ * TODO: replace with ontology to allow recognition of particular attributes
+ * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
+ * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
+ * 
+ * 
+ * 
  * @author JimP
- *
+ * 
  */
+import java.util.Locale;
+
 public class DBRefSource
 {
+
+  public static final String UNIPROT = "UNIPROT";
+
+  public static final String UP_NAME = "UNIPROT_NAME"
+          .toUpperCase(Locale.ROOT);
+
   /**
-   * UNIPROT Accession Number
-   */
-  public static String UNIPROT = "UNIPROT";
-  /**
-   * UNIPROT Entry Name
-   */
-  public static String UP_NAME = "UNIPROT_NAME";
-  /**
-   * Uniprot Knowledgebase/TrEMBL
-   * as served from EMBL protein products.
-   */
-  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
-  /**
-   * PDB Entry Code
-   */
-  public static String PDB = "PDB";
-  /**
-   * EMBL ID
-   */
-  public static String EMBL = "EMBL";
-  /**
-   * EMBLCDS ID
-   */
-  public static String EMBLCDS = "EMBLCDS";
-  /**
-   * PFAM ID
-   */
-  public static String PFAM = "PFAM";
-  /**
-   * GeneDB ID
+   * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
    */
-  public static final String GENEDB = "GeneDB";
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL"
+          .toUpperCase(Locale.ROOT);
+
+  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 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 = { EMBL, EMBLCDS, GENEDB};
-  public static final String[] CODINGDBS = { EMBLCDS, GENEDB};
-  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB};
-  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB};
-  public static final String[] PROTEINSTR = { PDB };
-  public static final String[] DOMAINDBS = { PFAM };
-  /**
-   * set of unique DBRefSource property constants.
-   * These could be used to reconstruct the above groupings
-   */
-  public static final Object SEQDB = "SQ";
-  /**
-   * database of nucleic acid sequences
-   */
-  public static final Object DNASEQDB = "NASQ";
-  /**
-   * database of amino acid sequences
-   */
-  public static final Object PROTSEQDB = "PROTSQ";
-  /**
-   * database of cDNA sequences
-   */
-  public static final Object CODINGSEQDB = "CODING";
-  /**
-   * database of na sequences with exon annotation
-   */
-  public static final Object DNACODINGSEQDB = "XONCODING";
-  /**
-   * DB returns several sequences associated with a protein domain
-   */
-  public static final Object DOMAINDB = "DOMAIN";
-  /**
-   * DB query can take multiple accession codes concatenated
-   * by a separator. Value of property indicates maximum number of accession codes to send at a time.
-   */
-  public static final Object MULTIACC = "MULTIACC";
+  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);
+  }
+
+  public static boolean isPrimaryCandidate(String ucversion)
+  {
+    if (ucversion == null)
+    {
+      // Null/empty version is not a real reference ?
+      return false;
+    }
+    // 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
+      {
+        // 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 true;
+  }
+
 }