X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=575ba68166edef3efc12ef6d41a57ea75f493d79;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=06e3b6f356c67b2978d648a2f9b01a55f01ccf9c;hpb=1f8a874a302e0d56d73e6ce9a43ceaa722bcbe09;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 06e3b6f..575ba68 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,29 +1,129 @@
-package jalview.datamodel;
-
-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";
-    }
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
+ * 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.
+ * 
+ * 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
+ */
+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";
+
+  /**
+   * 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
+   */
+  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 };
+
+  /**
+   * 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";
+}