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[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
// 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;
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 {
import org.forester.util.ForesterUtil;
public final class EbiDbEntry implements SequenceDatabaseEntry {
@@
-47,11
+49,10
@@
public final class EbiDbEntry implements SequenceDatabaseEntry {
throw new CloneNotSupportedException();
}
throw new CloneNotSupportedException();
}
-
public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List<String> lines ) {
final EbiDbEntry e = new EbiDbEntry();
for( final String line : 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" ) );
}
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 {
e.setDe( DatabaseTools.extract( line, "DEFINITION" ) );
}
-
-
}
}
-
else if ( line.startsWith( "SOURCE" ) ) {
if ( line.indexOf( "(" ) > 0 ) {
e.setOs( DatabaseTools.extract( line, "SOURCE", "(" ) );
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" ) );
}
}
e.setOs( DatabaseTools.extract( line, "SOURCE" ) );
}
}
-
}
return e;
}
}
return e;
}
-
-
-
+
public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
final EbiDbEntry e = new EbiDbEntry();
for( final String line : lines ) {
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.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" ) );
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 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;
}
return _symbol;
}
- private void setSymbol( final String symbol ) {
- if ( _symbol == null ) {
- _symbol = symbol;
- }
- }
-
@Override
public boolean isEmpty() {
return ( ForesterUtil.isEmpty( getAccession() ) && ForesterUtil.isEmpty( getSequenceName() )
@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 String getProvider() {
return _provider;
}
-
+
public void setProvider( final String 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;
}
}
}
}