X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=2f948841e7c05cff48b8cf977b1ea420f35bdf04;hb=8fa69554edf6aeb278b4a4afd8e2b60264fdccd8;hp=4830bc6ab95c37e541c75d0afa0a6bd17dcd2008;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 4830bc6..2f94884 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,47 +1,164 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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;
 
+/**
+ * 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
+ * 
+ */
 public class DBRefSource
 {
-    /**
-     * UNIPROT Accession Number
-     */
-    public static String UNIPROT="UNIPROT";
-    /**
-     * UNIPROT Entry Name
-     */
-    public static String UP_NAME="UNIPROT_NAME";
-    /**
-     * 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";
+  
+  
+  
+  public static final String UNIPROT = "UNIPROT";
+  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 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();
+
+  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);
     }
+
+  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() 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;
+}
+
+
+
+  
+}