X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=f8039bb6341844f2a7a994845f913d67e45c7854;hb=7459ed95f5ad213bafb1c691b193283850889e52;hp=aaf0ada5660c8bdca325b7196da995f1019241d3;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index aaf0ada..f8039bb 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,47 +1,189 @@
 /*
- * 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;
 
+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) <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";
+  public static final String UNIPROT = "UNIPROT";
+
   /**
    * UNIPROT Entry Name
    */
-  public static String UP_NAME = "UNIPROT_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 String PDB = "PDB";
+  public static final String PDB = "PDB";
+
   /**
    * EMBL ID
    */
-  public static String EMBL = "EMBL";
+  public static final String EMBL = "EMBL";
+
   /**
    * EMBLCDS ID
    */
-  public static String EMBLCDS = "EMBLCDS";
+  public static final String EMBLCDS = "EMBLCDS";
+
+  
   /**
    * PFAM ID
    */
-  public static String PFAM = "PFAM";
+  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 ENSEMBLGENOMES = "ENSEMBLGENOMES";
+
+  
+   /**
+   * 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[] allTypes = new String[] {
+      UNIPROT, UP_NAME, UNIPROTKB, 
+      EMBLCDSProduct, PDB, EMBL, 
+      EMBLCDS, PFAM, RFAM, 
+      GENEDB, ENSEMBL, ENSEMBLGENOMES 
+      };
+
+public static final String PROTEINDBSKEYS, DNACODINGDBSKEYS;
+
+public static final String[] PROMTYPES;
+
+
+public static final int UNIPROT_MASK = 1;
+
+public static final int ENSEMBL_MASK = 2;
+
+public static final int ALL_MASKS = UNIPROT_MASK | ENSEMBL_MASK;
+
+public static final String PDB_CANONICAL_NAME = PDB;
+
+static {
+	// BH 2019.01.25 trying to speed this up
+	String s = ";";
+	for (int i = PROTEINDBS.length; --i >= 0;)
+		s += PROTEINDBS[i] + ";";
+	PROTEINDBSKEYS = s;	
+	
+	s = ";";
+	for (int i = DNACODINGDBS.length; --i >= 0;)
+		s += DNACODINGDBS[i] + ";";
+	DNACODINGDBSKEYS = s;	
+	
+	PROMTYPES = new String[] { null, ";" + UNIPROT + ";", ";" + ENSEMBL + ";" , ";" + UNIPROT + ";"  + ENSEMBL + ";" };
+}
+
+  public static String[] allSourcesFromReflection;
+
+  public static String[] allSources()
+
+  {
+    /**
+     * @j2sNative
+     * 
+     *            return C$.allTypes;
+     * 
+     */
+
+    {
+      if (allSourcesFromReflection == null)
+      {
+        List<String> src = new ArrayList<>();
+        for (Field f : DBRefSource.class.getFields())
+        {
+          if (String.class.equals(f.getType()))
+          {
+            try
+            {
+              src.add((String) f.get(null));
+            } catch (Exception x)
+            {
+              x.printStackTrace();
+            }
+          }
+        }
+        allSourcesFromReflection = src.toArray(new String[0]);
+      }
+      return allSourcesFromReflection;
+    }
+  }
+  
+  
 }