JAL-1620 version bump and release notes

[jalview.git] / src / jalview / datamodel / DBRefSource.java

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 06e3b6f..4d3d680 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,29 +1,141 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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 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)
+ * 
+ * @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";
-    }
+  /**
+   * 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";
+
+  /**
+   * RFAM ID
+   */
+  public static String RFAM = "RFAM";
+
+  /**
+   * GeneDB ID
+   */
+  public static final String GENEDB = "GeneDB";
+
+  /**
+   * 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, RFAM };
+
+  /**
+   * 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/nucleotide 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";
+
+  /**
+   * DB query returns an alignment for each accession provided.
+   */
+  public static final Object ALIGNMENTDB = "ALIGNMENTS";
+}