apply gpl development license

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

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 06e3b6f..575ba68 100755 (executable)
--- 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";
-    }
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
+package jalview.datamodel;\r
+\r
+/**\r
+ * Defines internal constants for unambiguous annotation of DbRefEntry source\r
+ * strings and describing the data retrieved from external database sources (see\r
+ * jalview.ws.DbSourcProxy)\r
+ * \r
+ * @author JimP\r
+ * \r
+ */\r
+public class DBRefSource\r
+{\r
+  /**\r
+   * UNIPROT Accession Number\r
+   */\r
+  public static String UNIPROT = "UNIPROT";\r
+\r
+  /**\r
+   * UNIPROT Entry Name\r
+   */\r
+  public static String UP_NAME = "UNIPROT_NAME";\r
+\r
+  /**\r
+   * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.\r
+   */\r
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL";\r
+\r
+  /**\r
+   * PDB Entry Code\r
+   */\r
+  public static String PDB = "PDB";\r
+\r
+  /**\r
+   * EMBL ID\r
+   */\r
+  public static String EMBL = "EMBL";\r
+\r
+  /**\r
+   * EMBLCDS ID\r
+   */\r
+  public static String EMBLCDS = "EMBLCDS";\r
+\r
+  /**\r
+   * PFAM ID\r
+   */\r
+  public static String PFAM = "PFAM";\r
+\r
+  /**\r
+   * GeneDB ID\r
+   */\r
+  public static final String GENEDB = "GeneDB";\r
+\r
+  /**\r
+   * List of databases whose sequences might have coding regions annotated\r
+   */\r
+  public static final String[] DNACODINGDBS =\r
+  { EMBL, EMBLCDS, GENEDB };\r
+\r
+  public static final String[] CODINGDBS =\r
+  { EMBLCDS, GENEDB };\r
+\r
+  public static final String[] PROTEINDBS =\r
+  { UNIPROT, PDB, UNIPROTKB };\r
+\r
+  public static final String[] PROTEINSEQ =\r
+  { UNIPROT, UNIPROTKB };\r
+\r
+  public static final String[] PROTEINSTR =\r
+  { PDB };\r
+\r
+  public static final String[] DOMAINDBS =\r
+  { PFAM };\r
+\r
+  /**\r
+   * set of unique DBRefSource property constants. These could be used to\r
+   * reconstruct the above groupings\r
+   */\r
+  public static final Object SEQDB = "SQ";\r
+\r
+  /**\r
+   * database of nucleic acid sequences\r
+   */\r
+  public static final Object DNASEQDB = "NASQ";\r
+\r
+  /**\r
+   * database of amino acid sequences\r
+   */\r
+  public static final Object PROTSEQDB = "PROTSQ";\r
+\r
+  /**\r
+   * database of cDNA sequences\r
+   */\r
+  public static final Object CODINGSEQDB = "CODING";\r
+\r
+  /**\r
+   * database of na sequences with exon annotation\r
+   */\r
+  public static final Object DNACODINGSEQDB = "XONCODING";\r
+\r
+  /**\r
+   * DB returns several sequences associated with a protein domain\r
+   */\r
+  public static final Object DOMAINDB = "DOMAIN";\r
+\r
+  /**\r
+   * DB query can take multiple accession codes concatenated by a separator.\r
+   * Value of property indicates maximum number of accession codes to send at a\r
+   * time.\r
+   */\r
+  public static final Object MULTIACC = "MULTIACC";\r
+}\r