X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=a2243be9f9389d67fccbd216056d2448b07b35aa;hb=1c6ddae580d69eb0fa5b4291ba84fd6ba9b83621;hp=313e15d02c697c9c651869094595b4c165a4ffc7;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 313e15d..a2243be 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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;
 
@@ -35,12 +38,15 @@ public class DBRefSource
   /**
    * UNIPROT Entry Name
    */
-  public static String UP_NAME = "UNIPROT_NAME";
+  public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
 
   /**
    * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
    */
-  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+
+  public static final String EMBLCDSProduct = "EMBLCDSProtein"
+          .toUpperCase();
 
   /**
    * PDB Entry Code
@@ -48,6 +54,11 @@ public class DBRefSource
   public static String PDB = "PDB";
 
   /**
+   * mmCIF Entry Code
+   */
+  public static String MMCIF = "mmCIF";
+
+  /**
    * EMBL ID
    */
   public static String EMBL = "EMBL";
@@ -70,69 +81,23 @@ public class DBRefSource
   /**
    * GeneDB ID
    */
-  public static final String GENEDB = "GeneDB";
+  public static final String GENEDB = "GeneDB".toUpperCase();
 
   /**
-   * List of databases whose sequences might have coding regions annotated
+   * Ensembl
    */
-  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 ENSEMBL = "ENSEMBL";
 
-  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";
+  public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
 
   /**
-   * 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
+   * List of databases whose sequences might have coding regions annotated
    */
-  public static final Object DOMAINDB = "DOMAIN";
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+      ENSEMBL };
 
-  /**
-   * 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";
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
-  /**
-   * DB query returns an alignment for each accession provided.
-   */
-  public static final Object ALIGNMENTDB = "ALIGNMENTS";
+  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+      EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
 }