phylotastic hackathon at NESCENT 120606

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index 674c9c6..019df24 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -38,6 +38,7 @@ import javax.swing.JOptionPane;
 
 import org.forester.archaeopteryx.MainFrameApplication;
 import org.forester.archaeopteryx.TreePanel;
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
 import org.forester.archaeopteryx.tools.RunnableProcess;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.phylogeny.Phylogeny;
@@ -521,7 +522,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
     }
 
     private final String getBaseUrl() {
-        return UniProtWsTools.BASE_URL;
+        return AncestralTaxonomyInferrer.getBaseUrl();
     }
 
     @Override

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index ac531ba..9a7619b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -954,9 +954,9 @@ public final class MainFrameApplication extends MainFrame {
         _obtain_detailed_taxonomic_information_deleting_jmi
                 .setToolTipText( "To add additional taxonomic information, deletes nodes for which taxonomy cannot found (from UniProt Taxonomy)" );
         _tools_menu
-                .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information (from UniProt)" ) );
+                .add( _obtain_uniprot_seq_information_jmi = new JMenuItem( "Obtain Sequence Information" ) );
         customizeJMenuItem( _obtain_uniprot_seq_information_jmi );
-        _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information (from UniProt)" );
+        _obtain_uniprot_seq_information_jmi.setToolTipText( "To add additional sequence information" );
         _tools_menu.addSeparator();
         if ( !Constants.__RELEASE ) {
             _tools_menu.add( _function_analysis = new JMenuItem( "Add UniProtKB Annotations" ) );

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
index 7475d1d..a42d1ec 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
@@ -48,8 +48,8 @@ public class AncestralTaxonomyInferrer extends RunnableProcess {
         _treepanel = treepanel;
     }
 
-    private String getBaseUrl() {
-        return UniProtWsTools.BASE_URL;
+    public static String getBaseUrl() {
+        return UniProtWsTools.BASE_UNIPROT_URL;
     }
 
     private void inferTaxonomies() {

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
index 21dcf1f..7423832 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
@@ -44,7 +44,6 @@ import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 import org.forester.util.SequenceIdParser;
-import org.forester.ws.uniprot.DatabaseTools;
 import org.forester.ws.uniprot.SequenceDatabaseEntry;
 import org.forester.ws.uniprot.UniProtWsTools;
 
@@ -53,7 +52,7 @@ public final class SequenceDataRetriver extends RunnableProcess {
     private final Phylogeny            _phy;
     private final MainFrameApplication _mf;
     private final TreePanel            _treepanel;
-    private final static boolean       DEBUG = false;
+    private final static boolean       DEBUG = true;
 
     private enum Db {
         UNKNOWN, UNIPROT, EMBL, NCBI;
@@ -65,10 +64,6 @@ public final class SequenceDataRetriver extends RunnableProcess {
         _treepanel = treepanel;
     }
 
-    private String getBaseUrl() {
-        return UniProtWsTools.BASE_URL;
-    }
-
     private void execute() {
         start( _mf, "sequence data" );
         SortedSet<String> not_found = null;
@@ -76,8 +71,9 @@ public final class SequenceDataRetriver extends RunnableProcess {
             not_found = obtainSeqInformation( _phy );
         }
         catch ( final UnknownHostException e ) {
+            final String what = "_"; //TODO FIXME 
             JOptionPane.showMessageDialog( _mf,
-                                           "Could not connect to \"" + getBaseUrl() + "\"",
+                                           "Could not connect to \"" + what + "\"",
                                            "Network error during taxonomic information gathering",
                                            JOptionPane.ERROR_MESSAGE );
             return;
@@ -165,6 +161,7 @@ public final class SequenceDataRetriver extends RunnableProcess {
                 tax = new Taxonomy();
             }
             String query = null;
+            Identifier id = null;
             Db db = Db.UNKNOWN;
             if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )
                     && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
@@ -186,12 +183,12 @@ public final class SequenceDataRetriver extends RunnableProcess {
                 if ( ( query = UniProtWsTools.parseUniProtAccessor( node.getName() ) ) != null ) {
                     db = Db.UNIPROT;
                 }
-                else if ( ( query = SequenceIdParser.parseGenbankAccessor( node.getName() ) ) != null ) {
+                else if ( ( id = SequenceIdParser.parse( node.getName() ) ) != null ) {
                     db = Db.NCBI;
                 }
             }
+            SequenceDatabaseEntry db_entry = null;
             if ( !ForesterUtil.isEmpty( query ) ) {
-                SequenceDatabaseEntry db_entry = null;
                 if ( db == Db.UNIPROT ) {
                     if ( DEBUG ) {
                         System.out.println( "uniprot: " + query );
@@ -217,35 +214,39 @@ public final class SequenceDataRetriver extends RunnableProcess {
                         db = Db.EMBL;
                     }
                 }
-                if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
-                    if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) {
-                        String type = null;
-                        if ( db == Db.EMBL ) {
-                            type = "embl";
-                        }
-                        else if ( db == Db.UNIPROT ) {
-                            type = "uniprot";
-                        }
-                        seq.setAccession( new Accession( db_entry.getAccession(), type ) );
-                    }
-                    if ( !ForesterUtil.isEmpty( db_entry.getSequenceName() ) ) {
-                        seq.setName( db_entry.getSequenceName() );
-                    }
-                    if ( !ForesterUtil.isEmpty( db_entry.getSequenceSymbol() ) ) {
-                        seq.setSymbol( db_entry.getSequenceSymbol() );
-                    }
-                    if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
-                        tax.setScientificName( db_entry.getTaxonomyScientificName() );
+            }
+            else if ( ( db == Db.NCBI ) && ( id != null ) ) {
+                System.out.println( "db == Db.NCBI && id != null" );
+                db_entry = UniProtWsTools.obtainrefSeqentryFromEmbl( id, 200 );
+            }
+            if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
+                if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) {
+                    String type = null;
+                    if ( db == Db.EMBL ) {
+                        type = "embl";
                     }
-                    if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyIdentifier() ) ) {
-                        tax.setIdentifier( new Identifier( db_entry.getTaxonomyIdentifier(), "uniprot" ) );
+                    else if ( db == Db.UNIPROT ) {
+                        type = "uniprot";
                     }
-                    node.getNodeData().setTaxonomy( tax );
-                    node.getNodeData().setSequence( seq );
+                    seq.setAccession( new Accession( db_entry.getAccession(), type ) );
+                }
+                if ( !ForesterUtil.isEmpty( db_entry.getSequenceName() ) ) {
+                    seq.setName( db_entry.getSequenceName() );
+                }
+                if ( !ForesterUtil.isEmpty( db_entry.getSequenceSymbol() ) ) {
+                    seq.setSymbol( db_entry.getSequenceSymbol() );
                 }
-                else {
-                    not_found.add( node.getName() );
+                if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyScientificName() ) ) {
+                    tax.setScientificName( db_entry.getTaxonomyScientificName() );
                 }
+                if ( !ForesterUtil.isEmpty( db_entry.getTaxonomyIdentifier() ) ) {
+                    tax.setIdentifier( new Identifier( db_entry.getTaxonomyIdentifier(), "uniprot" ) );
+                }
+                node.getNodeData().setTaxonomy( tax );
+                node.getNodeData().setSequence( seq );
+            }
+            else {
+                not_found.add( node.getName() );
             }
         }
         return not_found;

diff --git a/forester/java/src/org/forester/phylogeny/data/Identifier.java b/forester/java/src/org/forester/phylogeny/data/Identifier.java
index cd58bad..555743e 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Identifier.java
+++ b/forester/java/src/org/forester/phylogeny/data/Identifier.java
@@ -34,9 +34,14 @@ import org.forester.util.ForesterUtil;
 
 public final class Identifier implements PhylogenyData {
 
+    final  public static String NCBI = "ncbi";
+    final public static String REFSEQ = "refseq";
+    
     final private String _value;
     final private String _provider;
     final private String _value_provider;
+    
+   
 
     public Identifier() {
         _value = "";

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index bbfa6dd..cdad772 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -9021,7 +9021,7 @@ public final class Test {
                  || ForesterUtil.isEmpty( id.getValue() )
                  || ForesterUtil.isEmpty( id.getProvider() )
                  || !id.getValue().equals( "XP_002434188" )
-                 || !id.getProvider().equals( "ncbi" ) ) {
+                 || !id.getProvider().equals( "refseq" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
                     System.out.println( "provider=" + id.getProvider() );
@@ -9034,7 +9034,7 @@ public final class Test {
                  || ForesterUtil.isEmpty( id.getValue() )
                  || ForesterUtil.isEmpty( id.getProvider() )
                  || !id.getValue().equals( "XP_002434188" )
-                 || !id.getProvider().equals( "ncbi" ) ) {
+                 || !id.getProvider().equals( "refseq" ) ) {
                 if ( id != null ) {
                     System.out.println( "value   =" + id.getValue() );
                     System.out.println( "provider=" + id.getProvider() );

diff --git a/forester/java/src/org/forester/util/SequenceIdParser.java b/forester/java/src/org/forester/util/SequenceIdParser.java
index 2f50f63..767a310 100644 (file)
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -67,6 +67,8 @@ public final class SequenceIdParser {
 \r
     \r
     private final static boolean DEBUG                           = true;\r
+    \r
+  \r
 \r
     \r
     /**\r
@@ -76,11 +78,11 @@ public final class SequenceIdParser {
     public final static Identifier parse( final String s ) {\r
         String v = parseGenbankAccessor( s );\r
         if ( !ForesterUtil.isEmpty( v ) ) {\r
-            return new Identifier( v, "ncbi" );\r
+            return new Identifier( v, Identifier.NCBI );\r
         }\r
         v = parseRefSeqAccessor( s );\r
         if ( !ForesterUtil.isEmpty( v ) ) {\r
-            return new Identifier( v, "ncbi" );\r
+            return new Identifier( v, Identifier.REFSEQ );\r
         }\r
         return null;\r
     }\r
@@ -89,7 +91,7 @@ public final class SequenceIdParser {
      * Returns null if no match.\r
      * \r
      */\r
-    static public String parseGenbankAccessor( final String query ) {\r
+    public static String parseGenbankAccessor( final String query ) {\r
         Matcher m = GENBANK_NUCLEOTIDE_AC_PATTERN_1.matcher( query );\r
         if ( m.lookingAt() ) {\r
             return m.group( 1 );\r
@@ -115,7 +117,7 @@ public final class SequenceIdParser {
      * Returns null if no match.\r
      * \r
      */\r
-    public final static String parseRefSeqAccessor( final String query ) {\r
+    private final static String parseRefSeqAccessor( final String query ) {\r
         Matcher m = REFSEQ_PATTERN.matcher( query );\r
         if ( m.lookingAt() ) {\r
             return m.group( 1 );\r

diff --git a/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java b/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java
index 5f0d599..ef44f38 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java
+++ b/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java
@@ -46,9 +46,44 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
         throw new CloneNotSupportedException();
     }
 
+    
+    public static SequenceDatabaseEntry createInstanceForRefSeq( final List<String> lines ) {
+        final EbiDbEntry e = new EbiDbEntry();
+        for( final String line : lines ) {
+            System.out.println( "-" + line );
+            if ( line.startsWith( "ACCESSION" ) ) {
+                e.setPA( DatabaseTools.extract( line, "ACCESSION" ) );
+            }
+            else if ( line.startsWith( "DEFINITION" ) ) {
+                if ( line.indexOf( "[" ) > 0 ) {
+                    e.setDe( DatabaseTools.extract( line, "DEFINITIO", "[" ) );
+                }
+                else {
+                    e.setDe( DatabaseTools.extract( line, "DEFINITION" ) );
+                }
+               
+                
+            }
+         
+            else if ( line.startsWith( "SOURCE" ) ) {
+                if ( line.indexOf( "(" ) > 0 ) {
+                    e.setOs( DatabaseTools.extract( line, "SOURCE", "(" ) );
+                }
+                else {
+                    e.setOs( DatabaseTools.extract( line, "SOURCE" ) );
+                }
+            }
+            
+        }
+        return e;
+    }
+    
+    
+    
     public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
         final EbiDbEntry e = new EbiDbEntry();
         for( final String line : lines ) {
+            System.out.println( "->" + line );
             if ( line.startsWith( "PA" ) ) {
                 e.setPA( DatabaseTools.extract( line, "PA" ) );
             }

diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java b/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java
index bec583f..65bea2d 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java
+++ b/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java
@@ -37,6 +37,7 @@ import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.forester.phylogeny.data.Identifier;
 import org.forester.util.ForesterUtil;
 
 public final class UniProtWsTools {
@@ -46,8 +47,12 @@ public final class UniProtWsTools {
     public enum Db {
         UNKNOWN, UNIPROT;
     }
-    public final static String   BASE_URL           = "http://www.uniprot.org/";
-    public final static String   BASE_EMBL_DB_URL   = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/";
+    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
@@ -322,12 +327,33 @@ public final class UniProtWsTools {
         return taxonomies;
     }
 
-    public static List<String> queryEmblDb( final String query, final int max_lines_to_return ) throws IOException {
-        return queryDb( query, max_lines_to_return, BASE_EMBL_DB_URL );
+    public static List<String> queryEmblDb( final Identifier id, final int max_lines_to_return ) throws IOException {
+        
+        StringBuilder url_sb = new StringBuilder();
+        url_sb.append( BASE_EMBL_DB_URL );
+        
+        if ( ForesterUtil.isEmpty(  id.getProvider() ) ||  id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+            url_sb.append( '/');
+            url_sb.append( UniProtWsTools.EMBL_DBS_EMBL );
+            url_sb.append( '/');
+        }
+        else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+            if ( id.getValue().toUpperCase().indexOf( 'P' ) == 1 ) {
+                url_sb.append( '/');
+                url_sb.append( UniProtWsTools.EMBL_DBS_REFSEQ_P );
+                url_sb.append( '/');
+            }
+            else {
+                url_sb.append( '/');
+                url_sb.append( UniProtWsTools.EMBL_DBS_REFSEQ_N );
+                url_sb.append( '/');
+            }
+        }
+        return queryDb( id.getValue(), max_lines_to_return, url_sb.toString() );
     }
 
     public static List<String> queryUniprot( final String query, final int max_lines_to_return ) throws IOException {
-        return queryDb( query, max_lines_to_return, BASE_URL );
+        return queryDb( query, max_lines_to_return, BASE_UNIPROT_URL );
     }
 
     public static List<String> queryDb( final String query, int max_lines_to_return, final String base_url )
@@ -365,9 +391,15 @@ public final class UniProtWsTools {
         return UniProtEntry.createInstanceFromPlainText( lines );
     }
 
+    public static SequenceDatabaseEntry obtainrefSeqentryFromEmbl( final Identifier id, final int max_lines_to_return )
+            throws IOException {
+        final List<String> lines = queryEmblDb( id, max_lines_to_return );
+        return EbiDbEntry.createInstanceForRefSeq( lines );
+    }
+
     public static SequenceDatabaseEntry obtainEmblEntry( final String query, final int max_lines_to_return )
             throws IOException {
-        final List<String> lines = queryEmblDb( query, max_lines_to_return );
+        final List<String> lines = queryEmblDb( new Identifier( query ), max_lines_to_return );
         return EbiDbEntry.createInstanceFromPlainText( lines );
     }
 }