X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=fbd11adb54d7020203208e3df5384be3d20c18dd;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=9e394bb1d277c6a32dd73c76c7d22a29037712d3;hpb=3bf07ba3afb39cea37a1e3eb32da7d498a1fd901;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 9e394bb..fbd11ad 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,51 +1,138 @@
-/*
- * 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
- * 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;
-
-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";
-  /**
-   * List of databases whose sequences might have coding regions annotated
-   */
-  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS};
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+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";
+  
+  /**
+   * 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";
+}