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[jalview.git] / forester / java / src / org / forester / ws / seqdb / SequenceDbWsTools.java

diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
index da16246..9106c38 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -55,20 +55,21 @@ import org.forester.util.SequenceAccessionTools;
 
 public final class SequenceDbWsTools {
 
-    public final static String   BASE_UNIPROT_URL        = "http://www.uniprot.org/";
-    public final static int      DEFAULT_LINES_TO_RETURN = 4000;
-    public final static String   EMBL_DBS_REFSEQ_N       = "refseqn";
-    public final static String   EMBL_DBS_REFSEQ_P       = "refseqp";
-    public final static String   EMBL_GENBANK            = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
-    public final static String   EMBL_REFSEQ             = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=";
-    public final static String   EMBL_EMBL               = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id=";
-    private final static boolean DEBUG                   = true;
-    private final static String  URL_ENC                 = "UTF-8";
-    private final static int     SLEEP                   = 200;
+    public final static String   BASE_UNIPROT_URL           = "http://www.uniprot.org/";
+    public final static int      DEFAULT_LINES_TO_RETURN    = 4000;
+    public final static String   EMBL_DBS_REFSEQ_N          = "refseqn";
+    public final static String   EMBL_DBS_REFSEQ_P          = "refseqp";
+    public final static String   EMBL_GENBANK               = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=";
+    public final static String   EMBL_REFSEQ                = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=";
+    public final static String   EMBL_EMBL                  = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id=";
+    private final static boolean DEBUG                      = true;
+    private final static String  URL_ENC                    = "UTF-8";
+    private final static int     SLEEP                      = 200;
+    private static final boolean ALLOW_TO_OVERWRITE_MOL_SEQ = false;
 
     public static List<UniProtTaxonomy> getTaxonomiesFromCommonNameStrict( final String cn,
                                                                            final int max_taxonomies_return )
-            throws IOException {
+                                                                                   throws IOException {
         final List<UniProtTaxonomy> taxonomies = getTaxonomiesFromCommonName( cn, max_taxonomies_return );
         if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
             final List<UniProtTaxonomy> filtered_taxonomies = new ArrayList<UniProtTaxonomy>();
@@ -95,11 +96,11 @@ public final class SequenceDbWsTools {
      * Does not return "sub-types".
      * For example, for "Mus musculus" only returns "Mus musculus"
      * and not "Mus musculus", "Mus musculus bactrianus", ...
-     * 
+     *
      */
     public static List<UniProtTaxonomy> getTaxonomiesFromScientificNameStrict( final String sn,
                                                                                final int max_taxonomies_return )
-            throws IOException {
+                                                                                       throws IOException {
         final List<UniProtTaxonomy> taxonomies = getTaxonomiesFromScientificName( sn, max_taxonomies_return );
         if ( ( taxonomies != null ) && ( taxonomies.size() > 0 ) ) {
             final List<UniProtTaxonomy> filtered_taxonomies = new ArrayList<UniProtTaxonomy>();
@@ -115,7 +116,7 @@ public final class SequenceDbWsTools {
 
     public static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String code,
                                                                        final int max_taxonomies_return )
-            throws IOException {
+                                                                               throws IOException {
         final String my_code = new String( code );
         final List<String> result = getTaxonomyStringFromTaxonomyCode( my_code, max_taxonomies_return );
         if ( result.size() > 0 ) {
@@ -141,7 +142,7 @@ public final class SequenceDbWsTools {
         final Accession acc = SequenceAccessionTools.parseAccessorFromString( acc_str );
         if ( acc == null ) {
             throw new IllegalArgumentException( "could not extract acceptable sequence db accessor from \"" + acc_str
-                    + "\"" );
+                                                + "\"" );
         }
         if ( acc.getSource().equals( Source.REFSEQ.toString() ) || acc.getSource().equals( Source.EMBL.toString() )
                 || acc.getSource().equals( Source.NCBI.toString() ) ) {
@@ -152,7 +153,7 @@ public final class SequenceDbWsTools {
         }
         else {
             throw new IllegalArgumentException( "don't know how to handle request for source \"" + acc.getSource()
-                    + "\"" );
+                                                + "\"" );
         }
     }
 
@@ -250,7 +251,7 @@ public final class SequenceDbWsTools {
         }
         in.close();
         try {
-            // To prevent accessing online dbs in too quick succession. 
+            // To prevent accessing online dbs in too quick succession.
             Thread.sleep( SLEEP );
         }
         catch ( final InterruptedException e ) {
@@ -300,7 +301,7 @@ public final class SequenceDbWsTools {
         final int i_b = target.indexOf( b );
         if ( ( i_a < 0 ) || ( i_b < i_a ) ) {
             throw new IllegalArgumentException( "attempt to extract from \"" + target + "\" between \"" + a
-                    + "\" and \"" + b + "\"" );
+                                                + "\" and \"" + b + "\"" );
         }
         return target.substring( i_a + a.length(), i_b ).trim();
     }
@@ -383,7 +384,7 @@ public final class SequenceDbWsTools {
             }
             if ( ( db_entry.getMolecularSequence() != null )
                     && !ForesterUtil.isEmpty( db_entry.getMolecularSequence().getMolecularSequenceAsString() )
-                    && seq.getMolecularSequence().isEmpty() ) {
+                    && ( ALLOW_TO_OVERWRITE_MOL_SEQ || seq.getMolecularSequence().isEmpty() ) ) {
                 seq.setMolecularSequence( db_entry.getMolecularSequence().getMolecularSequenceAsString() );
                 seq.setMolecularSequenceAligned( false );
                 if ( db_entry.getMolecularSequence().getType() == TYPE.AA ) {
@@ -454,7 +455,7 @@ public final class SequenceDbWsTools {
 
     private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String sn,
                                                                           final int max_taxonomies_return )
-            throws IOException {
+                                                                                  throws IOException {
         final List<String> result = getTaxonomyStringFromScientificName( sn, max_taxonomies_return );
         if ( result.size() > 0 ) {
             return parseUniProtTaxonomy( result );
@@ -486,7 +487,7 @@ public final class SequenceDbWsTools {
         return ( !( ( acc == null ) || ForesterUtil.isEmpty( acc.getSource() ) || ForesterUtil.isEmpty( acc.getValue() ) || ( ( acc
                 .getSource().equals( Source.UNIPROT.toString() ) )
                 && ( acc.getSource().toString().equals( Source.EMBL.toString() ) ) && ( acc.getSource().toString()
-                .equals( Source.REFSEQ.toString() ) ) ) ) );
+                        .equals( Source.REFSEQ.toString() ) ) ) ) );
     }
 
     private static List<UniProtTaxonomy> parseUniProtTaxonomy( final List<String> result ) throws IOException {