refactored invertColumnSelection as an object method

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

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 4830bc6..7344c9e 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
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -17,31 +17,81 @@
  * 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";
-    /**
-     * 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";
-    }
+  /**
+   * 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";
+  /**
+   * List of databases whose sequences might have coding regions annotated
+   */
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS};
+  public static final String[] CODINGDBS = { EMBLCDS};
+  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.
+   */
+  public static final Object MULTIACC = "MULTIACC";
+}