X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=3b1757bf18ad52cfe2269c0e6413f16f1e1d7a32;hb=e93bc0a7b2def06392a2f6b0f563c1e07fb917a1;hp=c1e174191dc4f52cf408138e2aed7add9867cb61;hpb=beff7ac7ab7be2c24ccb179be16b8816d2c18610;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index c1e1741..3b1757b 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -36,151 +36,137 @@ package jalview.datamodel;
  * @author JimP
  * 
  */
+import java.util.Locale;
+
 public class DBRefSource
 {
-  
-  
-  
+
   public static final String UNIPROT = "UNIPROT";
-  public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
+
+  public static final String UP_NAME = "UNIPROT_NAME"
+          .toUpperCase(Locale.ROOT);
+
   /**
    * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
    */
-  public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL"
+          .toUpperCase(Locale.ROOT);
+
+  public static final String ENSEMBL = "ENSEMBL";
 
-  public static final String ENSEMBL        = "ENSEMBL";
   public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
-  
-  public static final String EMBL           = "EMBL";
-  public static final String EMBLCDS        = "EMBLCDS";
-  public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
 
-  public static final String PDB    = "PDB";
-  public static final String PFAM   = "PFAM";
-  public static final String RFAM   = "RFAM";
-  public static final String GENEDB = "GeneDB".toUpperCase();
+  public static final String EMBL = "EMBL";
+
+  public static final String EMBLCDS = "EMBLCDS";
+
+  public static final String EMBLCDSProduct = "EMBLCDSProtein"
+          .toUpperCase(Locale.ROOT);
+
+  public static final String PDB = "PDB";
+
+  public static final String PFAM = "PFAM";
+
+  public static final String RFAM = "RFAM";
+
+  public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT);
 
   public static final String PDB_CANONICAL_NAME = PDB;
 
+  public static final String[] allSources = new String[] { UNIPROT, UP_NAME,
+      UNIPROTKB, ENSEMBL, ENSEMBLGENOMES, EMBL, EMBLCDS, EMBLCDSProduct,
+      PDB, PFAM, RFAM, GENEDB };
+
+  public static final int UNIPROT_MASK = 1 << 0;
+
+  public static final int UP_NAME_MASK = 1 << 1;
+
+  public static final int UNIPROT_KB_MASK = 1 << 2;
+
+  public static final int ENSEMBL_MASK = 1 << 3;
+
+  public static final int ENSEMBL_GENOMES_MASK = 1 << 4;
+
+  public static final int EMBL_MASK = 1 << 5;
+
+  public static final int EMBL_CDS_MASK = 1 << 6;
+
+  public static final int EMBL_CDS_PRODUCT_MASK = 1 << 7;
+
+  public static final int PDB_MASK = 1 << 8;
+
+  public static final int PFAM_MASK = 1 << 9;
+
+  public static final int RFAM_MASK = 1 << 10;
 
-  public static final String[] allSources = new String[] {
-      UNIPROT, 
-      UP_NAME, UNIPROTKB, 
-      ENSEMBL, ENSEMBLGENOMES, 
-      EMBL, EMBLCDS, EMBLCDSProduct, 
-      PDB, PFAM, RFAM, GENEDB 
-      };  
-
-	public static final int UNIPROT_MASK          = 1<<0;
-	public static final int UP_NAME_MASK          = 1<<1;
-	public static final int UNIPROT_KB_MASK       = 1<<2;
-	public static final int ENSEMBL_MASK          = 1<<3;
-	public static final int ENSEMBL_GENOMES_MASK  = 1<<4;
-	public static final int EMBL_MASK             = 1<<5;
-	public static final int EMBL_CDS_MASK         = 1<<6;
-	public static final int EMBL_CDS_PRODUCT_MASK = 1<<7;
-	public static final int PDB_MASK              = 1<<8;
-	public static final int PFAM_MASK             = 1<<9;
-	public static final int RFAM_MASK             = 1<<10;
-	public static final int GENE_DB_MASK          = 1<<11;
-
-    public static final int MASK_COUNT = 12;
-	  
-    public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;
-
-	public static int getSourceKey(String name) {
-		  for (int i = 0; i < MASK_COUNT; i++) {
-			  if (name.equals(allSources[i]))
-				return 1<<i;
-		  }
-		  return 0;	  
-	  }
-
-	public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;
-
-	  /**
-	  * List of databases whose sequences might have coding regions annotated
-	  */
-	 public static final String[] DNACODINGDBS = { 
-		     ENSEMBL, ENSEMBLGENOMES,
-			 EMBL, EMBLCDS, GENEDB
-	     };
-	
-     public static final int DNA_CODING_MASK = 
-    		 ENSEMBL_MASK | ENSEMBL_GENOMES_MASK
-    	  | EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;
-
-    
-     
-    public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
-
-    public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK | ENSEMBL_MASK;
-  
-   
-  
-    public static final String[] PROTEINDBS = { 
-    		UNIPROT, UNIPROTKB,
-    		ENSEMBL, EMBLCDSProduct }; // Ensembl ENSP* entries are protein
-
-    public static final int PROTEIN_MASK = 
-    		  UNIPROT_MASK | UNIPROT_KB_MASK 
-    		| ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK ;
-
-
-    // for SequenceAnnotationReport only
-    
-//    public static final String[][] PRIMARY_SOURCES = new String[][] {
-//  	  CODINGDBS, DNACODINGDBS, PROTEINDBS };
-//  	  
-  	public static final int PRIMARY_SOURCES_MASK = CODING_MASK | DNA_CODING_MASK | PROTEIN_MASK;
-      	
-    public static boolean isPrimarySource(String source)
+  public static final int GENE_DB_MASK = 1 << 11;
+
+  public static final int MASK_COUNT = 12;
+
+  public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;
+
+  public static int getSourceKey(String name)
+  {
+    for (int i = 0; i < MASK_COUNT; i++)
     {
-    	return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
+      if (name.equals(allSources[i]))
+      {
+        return 1 << i;
+      }
     }
+    return 0;
+  }
+
+  public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;
+
+  /**
+   * List of databases whose sequences might have coding regions annotated
+   */
+  public static final String[] DNACODINGDBS = { ENSEMBL, ENSEMBLGENOMES,
+      EMBL, EMBLCDS, GENEDB };
+
+  public static final int DNA_CODING_MASK = ENSEMBL_MASK
+          | ENSEMBL_GENOMES_MASK | EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;
+
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
+  public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK
+          | ENSEMBL_MASK;
 
-//  public static String[] allSourcesFromReflection;
-//
-//  public static String[] allSources()
-//
-//  {
-//    /**
-//     * @j2sNative
-//     * 
-//     *            return C$.allTypes;
-//     * 
-//     */
-//
-//    {
-//      if (allSourcesFromReflection == null)
-//      {
-//        List<String> src = new ArrayList<>();
-//        for (Field f : DBRefSource.class.getFields())
-//        {
-//          if (String.class.equals(f.getType()))
-//          {
-//            try
-//            {
-//              src.add((String) f.get(null));
-//            } catch (Exception x)
-//            {
-//              x.printStackTrace();
-//            }
-//          }
-//        }
-//        allSourcesFromReflection = src.toArray(new String[0]);
-//      }
-//      return allSourcesFromReflection;
-//    }
-//  }
-
-  public static boolean isPrimaryCandidate(String ucversion) {	
+  public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB, ENSEMBL,
+      EMBLCDSProduct }; // Ensembl ENSP* entries are protein
+
+  public static final int PROTEIN_MASK = UNIPROT_MASK | UNIPROT_KB_MASK
+          | ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK;
+
+  // for SequenceAnnotationReport only
+
+  // public static final String[][] PRIMARY_SOURCES = new String[][] {
+  // CODINGDBS, DNACODINGDBS, PROTEINDBS };
+  //
+  public static final int PRIMARY_SOURCES_MASK = CODING_MASK
+          | DNA_CODING_MASK | PROTEIN_MASK;
+
+  public static boolean isPrimarySource(String source)
+  {
+    return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
+  }
+
+  public static boolean isPrimaryCandidate(String ucversion)
+  {
+    if (ucversion==null)
+    {
+      // Null/empty version is not a real reference ?
+      return false;
+    }
     // tricky - this test really needs to search the sequence's set of dbrefs to
     // see if there is a primary reference that derived this reference.
     for (int i = allSources.length; --i >= 0;)
     {
-      if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
+      if (ucversion.startsWith(allSources[i])) // BH 2019.01.25
+                                               // .toUpperCase(Locale.ROOT)
+                                               // unnecessary here for
+                                               // allSources
       {
         // by convention, many secondary references inherit the primary
         // reference's
@@ -190,9 +176,6 @@ public class DBRefSource
       }
     }
     return true;
-}
-
-
+  }
 
-  
 }