inprogress

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

diff --git a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
index 2f1a64e..8172d3d 100644 (file)
--- a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
+++ b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
@@ -21,12 +21,14 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.ws.seqdb;
 
 import java.util.List;
 
+import org.forester.go.GoTerm;
+import org.forester.phylogeny.data.Accession;
 import org.forester.util.ForesterUtil;
 
 public final class EbiDbEntry implements SequenceDatabaseEntry {
@@ -47,11 +49,10 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
         throw new CloneNotSupportedException();
     }
 
-    
     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" ) );
             }
@@ -62,10 +63,7 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
                 else {
                     e.setDe( DatabaseTools.extract( line, "DEFINITION" ) );
                 }
-               
-                
             }
-         
             else if ( line.startsWith( "SOURCE" ) ) {
                 if ( line.indexOf( "(" ) > 0 ) {
                     e.setOs( DatabaseTools.extract( line, "SOURCE", "(" ) );
@@ -74,30 +72,19 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
                     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 ) {
-            
             if ( line.startsWith( "PA" ) ) {
                 e.setPA( DatabaseTools.extract( line, "PA" ) );
             }
             else if ( line.startsWith( "DE" ) ) {
-                // if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
                 e.setDe( DatabaseTools.extract( line, "DE" ) );
-                //}
             }
-            //  else if ( line.startsWith( "GN" ) ) {
-            //      if ( ( line.indexOf( "Name=" ) > 0 ) ) {
-            //          e.setSymbol( extract( line, "Name=", ";" ) );
-            //      }
-            //  }
             else if ( line.startsWith( "OS" ) ) {
                 if ( line.indexOf( "(" ) > 0 ) {
                     e.setOs( DatabaseTools.extract( line, "OS", "(" ) );
@@ -164,12 +151,6 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
         return _symbol;
     }
 
-    private void setSymbol( final String symbol ) {
-        if ( _symbol == null ) {
-            _symbol = symbol;
-        }
-    }
-
     @Override
     public boolean isEmpty() {
         return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
@@ -181,8 +162,23 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
     public String getProvider() {
         return _provider;
     }
-    
+
     public void setProvider( final String provider ) {
-         _provider = provider;
+        _provider = provider;
+    }
+
+    @Override
+    public String getGeneName() {
+        return null;
+    }
+
+    @Override
+    public List<GoTerm> getGoTerms() {
+        return null;
+    }
+
+    @Override
+    public List<Accession> getCrossReferences() {
+        return null;
     }
 }