inprogress

diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java
index bc90822..500ec78 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Constants.java
+++ b/forester/java/src/org/forester/archaeopteryx/Constants.java
@@ -42,7 +42,7 @@ public final class Constants {
     public final static boolean __SYNTH_LF                                                    = false;                                                               // TODO remove me
     public final static boolean ALLOW_DDBJ_BLAST                                              = false;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9805 A1ST";
+    final static String         VERSION                                                       = "0.9805+ A1ST";
     final static String         PRG_DATE                                                      = "130306";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { "Verdana", "Tahoma",

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index afab717..4a3e95b 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -9416,45 +9416,6 @@ public final class Test {
     }
 
     private static boolean testUniprotEntryRetrieval() {
-        if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
-            return false;
-        }
-        if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
-            return false;
-        }
-        if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
-            return false;
-        }
-        if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
-            return false;
-        }
-        if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
-            return false;
-        }
-        if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
-            return false;
-        }
-        if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
-            return false;
-        }
-        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
-            return false;
-        }
-        if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
-            return false;
-        }
-        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
-            return false;
-        }
-        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
-            return false;
-        }
-        if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
-            return false;
-        }
-        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
-            return false;
-        }
         try {
             final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
             if ( !entry.getAccession().equals( "P12345" ) ) {

diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
index c2258d6..e3b222b 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
+++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java
@@ -36,8 +36,6 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.SortedSet;
 import java.util.TreeSet;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
@@ -51,20 +49,13 @@ import org.forester.util.SequenceIdParser;
 
 public final class SequenceDbWsTools {
 
-    private static final boolean ALLOW_TAXONOMY_CODE_HACKS = true;                                                                                  //TODO turn off for final realease!
+    private static final boolean ALLOW_TAXONOMY_CODE_HACKS = true;                                         //TODO turn off for final realease!
     public final static String   BASE_UNIPROT_URL          = "http://www.uniprot.org/";
     public final static String   BASE_EMBL_DB_URL          = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/";
     public final static String   EMBL_DBS_EMBL             = "embl";
     public final static String   EMBL_DBS_REFSEQ_P         = "refseqp";
     public final static String   EMBL_DBS_REFSEQ_N         = "refseqn";
     private final static String  URL_ENC                   = "UTF-8";
-    // uniprot/expasy accession number format (6 chars):
-    // letter digit letter-or-digit letter-or-digit letter-or-digit digit
-    // ?: => no back-reference
-    // \A => begin of String
-    // \Z => end of String
-    private final static Pattern UNIPROT_AC_PATTERN        = Pattern
-                                                                   .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]\\d[A-Z0-9]{3}\\d)(?:[^a-zA-Z0-9]|\\Z)" );
     private final static boolean DEBUG                     = false;
 
     public static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String cn, final int max_taxonomies_return )
@@ -202,7 +193,7 @@ public final class SequenceDbWsTools {
                 db = Db.EMBL;
             }
             else if ( !ForesterUtil.isEmpty( node.getName() ) ) {
-                if ( ( query = parseUniProtAccessor( node.getName() ) ) != null ) {
+                if ( ( query = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node ) ) != null ) {
                     db = Db.UNIPROT;
                 }
                 else if ( ( id = SequenceIdParser.parse( node.getName() ) ) != null ) {
@@ -240,50 +231,50 @@ public final class SequenceDbWsTools {
             }
             else if ( ( db == Db.NCBI ) && ( id != null ) ) {
                 db_entry = obtainEmblEntry( id, lines_to_return );
-                if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
-                    final Sequence seq = node.getNodeData().isHasSequence() ? node.getNodeData().getSequence()
-                            : new Sequence();
-                    if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) {
-                        String type = null;
-                        if ( db == Db.EMBL ) {
-                            type = "embl";
-                        }
-                        else if ( db == Db.UNIPROT ) {
-                            type = "uniprot";
-                        }
-                        else if ( db == Db.NCBI ) {
-                            type = "ncbi";
-                        }
-                        else if ( db == Db.REFSEQ ) {
-                            type = "refseq";
-                        }
-                        seq.setAccession( new Accession( db_entry.getAccession(), type ) );
-                    }
-                    if ( !ForesterUtil.isEmpty( db_entry.getSequenceName() ) ) {
-                        seq.setName( db_entry.getSequenceName() );
+            }
+            if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
+                final Sequence seq = node.getNodeData().isHasSequence() ? node.getNodeData().getSequence()
+                        : new Sequence();
+                if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) {
+                    String type = null;
+                    if ( db == Db.EMBL ) {
+                        type = "embl";
                     }
-                    if ( !ForesterUtil.isEmpty( db_entry.getSequenceSymbol() ) ) {
-                        seq.setSymbol( db_entry.getSequenceSymbol() );
+                    else if ( db == Db.UNIPROT ) {
+                        type = "uniprot";
                     }
-                    final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy()
-                            : new Taxonomy();
-                    if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
-                        tax.setScientificName( db_entry.getTaxonomyScientificName() );
+                    else if ( db == Db.NCBI ) {
+                        type = "ncbi";
                     }
-                    if ( allow_to_set_taxonomic_data && !ForesterUtil.isEmpty( db_entry.getTaxonomyIdentifier() ) ) {
-                        tax.setIdentifier( new Identifier( db_entry.getTaxonomyIdentifier(), "uniprot" ) );
+                    else if ( db == Db.REFSEQ ) {
+                        type = "refseq";
                     }
-                    node.getNodeData().setTaxonomy( tax );
-                    node.getNodeData().setSequence( seq );
+                    seq.setAccession( new Accession( db_entry.getAccession(), type ) );
                 }
-                else if ( db != Db.NONE ) {
-                    not_found.add( node.getName() );
+                if ( !ForesterUtil.isEmpty( db_entry.getSequenceName() ) ) {
+                    seq.setName( db_entry.getSequenceName() );
                 }
-                try {
-                    Thread.sleep( 10 );// Sleep for 10 ms
+                if ( !ForesterUtil.isEmpty( db_entry.getSequenceSymbol() ) ) {
+                    seq.setSymbol( db_entry.getSequenceSymbol() );
                 }
-                catch ( final InterruptedException ie ) {
+                final Taxonomy tax = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy()
+                        : new Taxonomy();
+                if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
+                    tax.setScientificName( db_entry.getTaxonomyScientificName() );
                 }
+                if ( allow_to_set_taxonomic_data && !ForesterUtil.isEmpty( db_entry.getTaxonomyIdentifier() ) ) {
+                    tax.setIdentifier( new Identifier( db_entry.getTaxonomyIdentifier(), "uniprot" ) );
+                }
+                node.getNodeData().setTaxonomy( tax );
+                node.getNodeData().setSequence( seq );
+            }
+            else if ( db != Db.NONE ) {
+                not_found.add( node.getName() );
+            }
+            try {
+                Thread.sleep( 10 );// Sleep for 10 ms
+            }
+            catch ( final InterruptedException ie ) {
             }
         }
         return not_found;
@@ -295,23 +286,6 @@ public final class SequenceDbWsTools {
         return UniProtEntry.createInstanceFromPlainText( lines );
     }
 
-    /**
-     * Returns null if no match.
-     * 
-     * @param query
-     * @param db 
-     * @return
-     */
-    static public String parseUniProtAccessor( final String query ) {
-        final Matcher m = UNIPROT_AC_PATTERN.matcher( query );
-        if ( m.lookingAt() ) {
-            return m.group( 1 );
-        }
-        else {
-            return null;
-        }
-    }
-
     public static List<String> queryDb( final String query, int max_lines_to_return, final String base_url )
             throws IOException {
         if ( ForesterUtil.isEmpty( query ) ) {

diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
index 263a115..05e2e59 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
+++ b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
@@ -32,10 +32,9 @@ import org.forester.util.ForesterUtil;
 public final class UniProtEntry implements SequenceDatabaseEntry {
 
     private String _ac;
-    private String _rec_name;
+    private String _name;
     private String _os_scientific_name;
     private String _tax_id;
-    private String _symbol;
 
     private UniProtEntry() {
     }
@@ -51,14 +50,12 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
             if ( line.startsWith( "AC" ) ) {
                 e.setAc( DatabaseTools.extract( line, "AC", ";" ) );
             }
-            else if ( line.startsWith( "DE" ) ) {
+            else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceName() ) ) {
                 if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
-                    e.setRecName( DatabaseTools.extract( line, "Full=", ";" ) );
+                    e.setSequenceName( DatabaseTools.extract( line, "Full=", ";" ) );
                 }
-            }
-            else if ( line.startsWith( "GN" ) ) {
-                if ( ( line.indexOf( "Name=" ) > 0 ) ) {
-                    e.setSymbol( DatabaseTools.extract( line, "Name=", ";" ) );
+                else if ( ( line.indexOf( "SubName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
+                    e.setSequenceName( DatabaseTools.extract( line, "Full=", ";" ) );
                 }
             }
             else if ( line.startsWith( "OS" ) ) {
@@ -91,12 +88,12 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
 
     @Override
     public String getSequenceName() {
-        return _rec_name;
+        return _name;
     }
 
-    private void setRecName( final String rec_name ) {
-        if ( _rec_name == null ) {
-            _rec_name = rec_name;
+    private void setSequenceName( final String name ) {
+        if ( _name == null ) {
+            _name = name;
         }
     }
 
@@ -124,13 +121,7 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
 
     @Override
     public String getSequenceSymbol() {
-        return _symbol;
-    }
-
-    private void setSymbol( final String symbol ) {
-        if ( _symbol == null ) {
-            _symbol = symbol;
-        }
+        return "";
     }
 
     @Override