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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
ws
/
seqdb
/
UniProtEntry.java
diff --git
a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
index
4a8d158
..
4ba10de
100644
(file)
--- a/
forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
+++ b/
forester/java/src/org/forester/ws/seqdb/UniProtEntry.java
@@
-174,24
+174,24
@@
public final class UniProtEntry implements SequenceDatabaseEntry {
for( final String line : lines ) {
//System.out.println( line );
if ( line.startsWith( "AC" ) ) {
for( final String line : lines ) {
//System.out.println( line );
if ( line.startsWith( "AC" ) ) {
- e.setAc( DatabaseTools.extract( line, "AC", ";" ) );
+ e.setAc( SequenceDbWsTools.extractFromTo( line, "AC", ";" ) );
}
else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceName() ) ) {
if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
}
else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceName() ) ) {
if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
- e.setSequenceName( DatabaseTools.extract( line, "Full=", ";" ) );
+ e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
}
else if ( ( line.indexOf( "SubName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
}
else if ( ( line.indexOf( "SubName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
- e.setSequenceName( DatabaseTools.extract( line, "Full=", ";" ) );
+ e.setSequenceName( SequenceDbWsTools.extractFromTo( line, "Full=", ";" ) );
}
}
else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceSymbol() ) ) {
if ( line.indexOf( "Short=" ) > 0 ) {
}
}
else if ( line.startsWith( "DE" ) && ForesterUtil.isEmpty( e.getSequenceSymbol() ) ) {
if ( line.indexOf( "Short=" ) > 0 ) {
- e.setSequenceSymbol( DatabaseTools.extract( line, "Short=", ";" ) );
+ e.setSequenceSymbol( SequenceDbWsTools.extractFromTo( line, "Short=", ";" ) );
}
}
else if ( line.startsWith( "GN" ) && ForesterUtil.isEmpty( e.getGeneName() ) ) {
if ( line.indexOf( "Name=" ) > 0 ) {
}
}
else if ( line.startsWith( "GN" ) && ForesterUtil.isEmpty( e.getGeneName() ) ) {
if ( line.indexOf( "Name=" ) > 0 ) {
- e.setGeneName( DatabaseTools.extract( line, "Name=", ";" ) );
+ e.setGeneName( SequenceDbWsTools.extractFromTo( line, "Name=", ";" ) );
}
}
else if ( line.startsWith( "DR" ) ) {
}
}
else if ( line.startsWith( "DR" ) ) {
@@
-274,15
+274,15
@@
public final class UniProtEntry implements SequenceDatabaseEntry {
}
else if ( line.startsWith( "OS" ) ) {
if ( line.indexOf( "(" ) > 0 ) {
}
else if ( line.startsWith( "OS" ) ) {
if ( line.indexOf( "(" ) > 0 ) {
- e.setOsScientificName( DatabaseTools.extract( line, "OS", "(" ) );
+ e.setOsScientificName( SequenceDbWsTools.extractFromTo( line, "OS", "(" ) );
}
else {
}
else {
- e.setOsScientificName( DatabaseTools.extract( line, "OS", "." ) );
+ e.setOsScientificName( SequenceDbWsTools.extractFromTo( line, "OS", "." ) );
}
}
else if ( line.startsWith( "OX" ) ) {
if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
}
}
else if ( line.startsWith( "OX" ) ) {
if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
- e.setTaxId( DatabaseTools.extract( line, "NCBI_TaxID=", ";" ) );
+ e.setTaxId( SequenceDbWsTools.extractFromTo( line, "NCBI_TaxID=", ";" ) );
}
}
}
}
}
}