develop merge

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

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 4d3d680..91b49eb 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -38,12 +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
@@ -51,6 +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";
@@ -73,69 +81,21 @@ public class DBRefSource
   /**
    * 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";
+  public static final String GENEDB = "GeneDB".toUpperCase();
 
   /**
-   * database of amino acid sequences
+   * Ensembl
    */
-  public static final Object PROTSEQDB = "PROTSQ";
+  public static final String ENSEMBL = "ENSEMBL";
 
   /**
-   * 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
 }