+// $Id:
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// Copyright (C) 2010 Christian M Zmasek
+// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.ws.uniprot;
+
+import java.util.List;
+
+import sun.reflect.generics.reflectiveObjects.NotImplementedException;
+
+public final class EbiDbEntry implements SequenceDatabaseEntry {
+//http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/emb/AAR37336/
+
+
+ private String _pa;
+ private String _de;
+ private String _os;
+ private String _tax_id;
+ private String _symbol;
+
+ private EbiDbEntry() {
+ }
+
+
+ public Object clone() {
+ throw new NotImplementedException();
+ }
+
+ 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", "(" ) );
+ }
+ else {
+ e.setOs( DatabaseTools.extract( line, "OS" ) );
+ }
+ }
+ else if ( line.startsWith( "OX" ) ) {
+ if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
+ e.setTaxId( DatabaseTools.extract( line, "NCBI_TaxID=", ";" ) );
+ }
+ }
+ }
+ return e;
+ }
+
+ @Override
+ public String getAccession() {
+ return _pa;
+ }
+
+ private void setPA( final String pa ) {
+ if ( _pa == null ) {
+ _pa= pa;
+ }
+ }
+
+ @Override
+ public String getSequenceName() {
+ return _de;
+ }
+
+ private void setDe( final String rec_name ) {
+ if ( _de == null ) {
+ _de = rec_name;
+ }
+ }
+
+ @Override
+ public String getTaxonomyScientificName() {
+ return _os;
+ }
+
+ private void setOs( final String os ) {
+ if ( _os== null ) {
+ _os = os;
+ }
+ }
+
+ @Override
+ public String getTaxonomyIdentifier() {
+ return _tax_id;
+ }
+
+ private void setTaxId( final String tax_id ) {
+ if ( _tax_id == null ) {
+ _tax_id = tax_id;
+ }
+ }
+
+ @Override
+ public String getSequenceSymbol() {
+ return _symbol;
+ }
+
+ private void setSymbol( final String symbol ) {
+ if ( _symbol == null ) {
+ _symbol = symbol;
+ }
+ }
+}