JAL-2089 Merge branch releases/Release_2_10_Branch to master

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

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index cf15ff8..58c63ad 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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,10 @@
  */
 package jalview.datamodel;
 
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Defines internal constants for unambiguous annotation of DbRefEntry source
  * strings and describing the data retrieved from external database sources (see
@@ -36,12 +40,12 @@ public class DBRefSource
   /**
    * UNIPROT Accession Number
    */
-  public static String UNIPROT = "UNIPROT";
+  public static final String UNIPROT = "UNIPROT";
 
   /**
    * UNIPROT Entry Name
    */
-  public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
+  public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
 
   /**
    * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
@@ -54,32 +58,27 @@ public class DBRefSource
   /**
    * PDB Entry Code
    */
-  public static String PDB = "PDB";
-
-  /**
-   * mmCIF Entry Code
-   */
-  public static String MMCIF = "mmCIF";
+  public static final String PDB = "PDB";
 
   /**
    * EMBL ID
    */
-  public static String EMBL = "EMBL";
+  public static final String EMBL = "EMBL";
 
   /**
    * EMBLCDS ID
    */
-  public static String EMBLCDS = "EMBLCDS";
+  public static final String EMBLCDS = "EMBLCDS";
 
   /**
    * PFAM ID
    */
-  public static String PFAM = "PFAM";
+  public static final String PFAM = "PFAM";
 
   /**
    * RFAM ID
    */
-  public static String RFAM = "RFAM";
+  public static final String RFAM = "RFAM";
 
   /**
    * GeneDB ID
@@ -101,6 +100,25 @@ public class DBRefSource
 
   public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
-  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+  public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
       EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+
+  public static String[] allSources()
+  {
+    List<String> src = new ArrayList<String>();
+    for (Field f : DBRefSource.class.getFields())
+    {
+      if (String.class.equals(f.getType()))
+      {
+        try
+        {
+          src.add((String) f.get(null));
+        } catch (Exception x)
+        {
+          x.printStackTrace();
+        }
+      }
+    }
+    return src.toArray(new String[0]);
+  }
 }