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 019df24..99c1de1 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -48,7 +48,7 @@ import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.uniprot.SequenceDbWsTools;
 
 public final class TaxonomyDataManager extends RunnableProcess {
 
@@ -176,19 +176,19 @@ public final class TaxonomyDataManager extends RunnableProcess {
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String query ) throws IOException {
-        return UniProtWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
+        return SequenceDbWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromId( final String query ) throws IOException {
-        return UniProtWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN );
+        return SequenceDbWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query ) throws IOException {
-        return UniProtWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
+        return SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
-        return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
+        return SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
     static final boolean isHasAppropriateId( final Taxonomy tax ) {

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
index a42d1ec..ec8ba76 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
@@ -34,7 +34,7 @@ import org.forester.analysis.AncestralTaxonomyInferenceException;
 import org.forester.archaeopteryx.MainFrameApplication;
 import org.forester.archaeopteryx.TreePanel;
 import org.forester.phylogeny.Phylogeny;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.uniprot.SequenceDbWsTools;
 
 public class AncestralTaxonomyInferrer extends RunnableProcess {
 
@@ -49,7 +49,7 @@ public class AncestralTaxonomyInferrer extends RunnableProcess {
     }
 
     public static String getBaseUrl() {
-        return UniProtWsTools.BASE_UNIPROT_URL;
+        return SequenceDbWsTools.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 507d28c..d389aec 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java
@@ -25,7 +25,6 @@
 
 package org.forester.archaeopteryx.tools;
 
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.UnknownHostException;
 import java.util.SortedSet;
@@ -45,7 +44,7 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.ForesterUtil;
 import org.forester.util.SequenceIdParser;
 import org.forester.ws.uniprot.SequenceDatabaseEntry;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.uniprot.SequenceDbWsTools;
 
 public final class SequenceDataRetriver extends RunnableProcess {
 
@@ -55,7 +54,7 @@ public final class SequenceDataRetriver extends RunnableProcess {
     private final static boolean       DEBUG = true;
 
     private enum Db {
-        UNIPROT, EMBL, NCBI, NONE;
+        UNIPROT, EMBL, NCBI, NONE, REFSEQ;
     }
 
     public SequenceDataRetriver( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
@@ -170,11 +169,18 @@ public final class SequenceDataRetriver extends RunnableProcess {
                 db = Db.EMBL;
             }
             else if ( !ForesterUtil.isEmpty( node.getName() ) ) {
-                if ( ( query = UniProtWsTools.parseUniProtAccessor( node.getName() ) ) != null ) {
+                if ( ( query = SequenceDbWsTools.parseUniProtAccessor( node.getName() ) ) != null ) {
                     db = Db.UNIPROT;
                 }
                 else if ( ( id = SequenceIdParser.parse( node.getName() ) ) != null ) {
-                    db = Db.NCBI;
+                    
+                    if ( id.getProvider().equalsIgnoreCase( Identifier.NCBI ) ) {
+                        db = Db.NCBI;
+                    }
+                    else if ( id.getProvider().equalsIgnoreCase( Identifier.REFSEQ ) ) {
+                        db = Db.REFSEQ;
+                    }
+                   
                 }
             }
             SequenceDatabaseEntry db_entry = null;
@@ -183,25 +189,23 @@ public final class SequenceDataRetriver extends RunnableProcess {
                     if ( DEBUG ) {
                         System.out.println( "uniprot: " + query );
                     }
-                  
-                    db_entry = UniProtWsTools.obtainUniProtEntry( query, 200 );
-                  
+                    db_entry = SequenceDbWsTools.obtainUniProtEntry( query, 200 );
                 }
                 if ( ( db == Db.EMBL ) || ( ( db == Db.UNIPROT ) && ( db_entry == null ) ) ) {
                     if ( DEBUG ) {
                         System.out.println( "embl: " + query );
                     }
-                    
-                    db_entry = UniProtWsTools.obtainEmblEntry( query, 200 );
-                   
+                    db_entry = SequenceDbWsTools.obtainEmblEntry(  new Identifier( query ), 200 );
                     if ( ( db == Db.UNIPROT ) && ( db_entry != null ) ) {
                         db = Db.EMBL;
                     }
                 }
             }
+            else if ( ( db == Db.REFSEQ ) && ( id != null ) ) {
+                db_entry = SequenceDbWsTools.obtainRefSeqEntryFromEmbl( id, 200 );
+            }
             else if ( ( db == Db.NCBI ) && ( id != null ) ) {
-                System.out.println( "db == Db.NCBI && id != null" );
-                db_entry = UniProtWsTools.obtainrefSeqentryFromEmbl( id, 200 );
+                db_entry = SequenceDbWsTools.obtainEmblEntry( id, 200 );
             }
             if ( ( db_entry != null ) && !db_entry.isEmpty() ) {
                 if ( !ForesterUtil.isEmpty( db_entry.getAccession() ) ) {
@@ -212,6 +216,12 @@ public final class SequenceDataRetriver extends RunnableProcess {
                     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() ) ) {

diff --git a/forester/java/src/org/forester/phylogeny/data/Identifier.java b/forester/java/src/org/forester/phylogeny/data/Identifier.java
index 555743e..d3b4437 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Identifier.java
+++ b/forester/java/src/org/forester/phylogeny/data/Identifier.java
@@ -34,7 +34,7 @@ import org.forester.util.ForesterUtil;
 
 public final class Identifier implements PhylogenyData {
 
-    final  public static String NCBI = "ncbi";
+    final public static String NCBI = "ncbi";
     final public static String REFSEQ = "refseq";
     
     final private String _value;

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index cdad772..5704870 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -107,7 +107,7 @@ import org.forester.util.SequenceIdParser;
 import org.forester.ws.uniprot.DatabaseTools;
 import org.forester.ws.uniprot.SequenceDatabaseEntry;
 import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.uniprot.SequenceDbWsTools;
 import org.forester.ws.wabi.TxSearch;
 import org.forester.ws.wabi.TxSearch.RANKS;
 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
@@ -7850,7 +7850,7 @@ public final class Test {
 
     private static boolean testUniprotTaxonomySearch() {
         try {
-            List<UniProtTaxonomy> results = UniProtWsTools
+            List<UniProtTaxonomy> results = SequenceDbWsTools
                     .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
             if ( results.size() != 1 ) {
                 return false;
@@ -7871,7 +7871,7 @@ public final class Test {
                 return false;
             }
             results = null;
-            results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
+            results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
             if ( results.size() != 1 ) {
                 return false;
             }
@@ -7891,7 +7891,7 @@ public final class Test {
                 return false;
             }
             results = null;
-            results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
+            results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
             if ( results.size() != 1 ) {
                 return false;
             }
@@ -7911,7 +7911,7 @@ public final class Test {
                 return false;
             }
             results = null;
-            results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
+            results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
             if ( results.size() != 1 ) {
                 return false;
             }
@@ -8002,47 +8002,47 @@ public final class Test {
     }
 
     private static boolean testUniprotEntryRetrieval() {
-        if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
             return false;
         }
         try {
-            final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
+            final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
             if ( !entry.getAccession().equals( "P12345" ) ) {
                 return false;
             }

diff --git a/forester/java/src/org/forester/util/SequenceIdParser.java b/forester/java/src/org/forester/util/SequenceIdParser.java
index 767a310..d75a6dd 100644 (file)
--- a/forester/java/src/org/forester/util/SequenceIdParser.java
+++ b/forester/java/src/org/forester/util/SequenceIdParser.java
@@ -32,7 +32,6 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;\r
 \r
 import org.forester.phylogeny.data.Identifier;\r
-import org.forester.ws.uniprot.DatabaseTools;\r
 \r
 public final class SequenceIdParser {\r
 \r
@@ -65,11 +64,7 @@ public final class SequenceIdParser {
     private final static Pattern REFSEQ_PATTERN      = Pattern\r
     .compile( "(?:\\A|.*[^a-zA-Z0-9])([A-Z]{2}_\\d{6,})(?:[^a-zA-Z0-9]|\\Z)" );\r
 \r
-    \r
-    private final static boolean DEBUG                           = true;\r
-    \r
-  \r
-\r
+   \r
     \r
     /**\r
      * Returns null if no match.\r
@@ -78,6 +73,7 @@ public final class SequenceIdParser {
     public final static Identifier parse( final String s ) {\r
         String v = parseGenbankAccessor( s );\r
         if ( !ForesterUtil.isEmpty( v ) ) {\r
+\r
             return new Identifier( v, Identifier.NCBI );\r
         }\r
         v = parseRefSeqAccessor( s );\r

diff --git a/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java b/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java
index 735d68f..c840dff 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java
+++ b/forester/java/src/org/forester/ws/uniprot/EbiDbEntry.java
@@ -37,6 +37,7 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
     private String _os;
     private String _tax_id;
     private String _symbol;
+    private String _provider;
 
     private EbiDbEntry() {
     }
@@ -47,10 +48,10 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
     }
 
     
-    public static SequenceDatabaseEntry createInstanceForRefSeq( final List<String> lines ) {
+    public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List<String> lines ) {
         final EbiDbEntry e = new EbiDbEntry();
         for( final String line : lines ) {
-            System.out.println( "-" + line );
+          //  System.out.println( "-" + line );
             if ( line.startsWith( "ACCESSION" ) ) {
                 e.setPA( DatabaseTools.extract( line, "ACCESSION" ) );
             }
@@ -83,7 +84,7 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
     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" ) );
             }
@@ -175,4 +176,13 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
                 && ForesterUtil.isEmpty( getTaxonomyScientificName() )
                 && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
     }
+
+    @Override
+    public String getProvider() {
+        return _provider;
+    }
+    
+    public void setProvider( final String provider ) {
+         _provider = provider;
+    }
 }

diff --git a/forester/java/src/org/forester/ws/uniprot/SequenceDatabaseEntry.java b/forester/java/src/org/forester/ws/uniprot/SequenceDatabaseEntry.java
index 9089737..a98c004 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/SequenceDatabaseEntry.java
+++ b/forester/java/src/org/forester/ws/uniprot/SequenceDatabaseEntry.java
@@ -30,6 +30,8 @@ public interface SequenceDatabaseEntry {
     public boolean isEmpty();
 
     public String getAccession();
+    
+    public String getProvider();
 
     public String getSequenceName();
 

diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java b/forester/java/src/org/forester/ws/uniprot/SequenceDbWsTools.java
similarity index 96%
rename from forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java
rename to forester/java/src/org/forester/ws/uniprot/SequenceDbWsTools.java
index 65bea2d..83f3c6f 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/UniProtWsTools.java
+++ b/forester/java/src/org/forester/ws/uniprot/SequenceDbWsTools.java
@@ -40,7 +40,7 @@ import java.util.regex.Pattern;
 import org.forester.phylogeny.data.Identifier;
 import org.forester.util.ForesterUtil;
 
-public final class UniProtWsTools {
+public final class SequenceDbWsTools {
 
     private static final boolean ALLOW_TAXONOMY_CODE_HACKS = true; //TODO turn off for final realease!
 
@@ -333,19 +333,19 @@ public final class UniProtWsTools {
         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( SequenceDbWsTools.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( SequenceDbWsTools.EMBL_DBS_REFSEQ_P );
                 url_sb.append( '/');
             }
             else {
-                url_sb.append( '/');
-                url_sb.append( UniProtWsTools.EMBL_DBS_REFSEQ_N );
+               
+                url_sb.append( SequenceDbWsTools.EMBL_DBS_REFSEQ_N );
                 url_sb.append( '/');
             }
         }
@@ -391,15 +391,15 @@ public final class UniProtWsTools {
         return UniProtEntry.createInstanceFromPlainText( lines );
     }
 
-    public static SequenceDatabaseEntry obtainrefSeqentryFromEmbl( final Identifier id, final int max_lines_to_return )
+    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 );
+        return EbiDbEntry.createInstanceFromPlainTextForRefSeq( lines );
     }
 
-    public static SequenceDatabaseEntry obtainEmblEntry( final String query, final int max_lines_to_return )
+    public static SequenceDatabaseEntry obtainEmblEntry( final Identifier id, final int max_lines_to_return )
             throws IOException {
-        final List<String> lines = queryEmblDb( new Identifier( query ), max_lines_to_return );
+        final List<String> lines = queryEmblDb( id , max_lines_to_return );
         return EbiDbEntry.createInstanceFromPlainText( lines );
     }
 }

diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java b/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java
index cd5d541..d5056e6 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java
+++ b/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java
@@ -139,4 +139,9 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
                 && ForesterUtil.isEmpty( getTaxonomyScientificName() )
                 && ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
     }
+
+    @Override
+    public String getProvider() {
+        return "uniprot";
+    }
 }