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v40
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
pfam2go_extractor.java
diff --git
a/forester/java/src/org/forester/application/pfam2go_extractor.java
b/forester/java/src/org/forester/application/pfam2go_extractor.java
index
02e26fb
..
f086af3
100644
(file)
--- a/
forester/java/src/org/forester/application/pfam2go_extractor.java
+++ b/
forester/java/src/org/forester/application/pfam2go_extractor.java
@@
-21,7
+21,7
@@
// 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.application;
package org.forester.application;
@@
-39,7
+39,6
@@
import org.forester.go.GoUtils;
import org.forester.go.OBOparser;
import org.forester.go.PfamToGoMapping;
import org.forester.go.PfamToGoParser;
import org.forester.go.OBOparser;
import org.forester.go.PfamToGoMapping;
import org.forester.go.PfamToGoParser;
-import org.forester.surfacing.DomainId;
public class pfam2go_extractor {
public class pfam2go_extractor {
@@
-79,12
+78,12
@@
public class pfam2go_extractor {
}
final SortedSet<String> pfams = new TreeSet<String>();
for( final PfamToGoMapping pfam_to_go_mapping : pfam2go ) {
}
final SortedSet<String> pfams = new TreeSet<String>();
for( final PfamToGoMapping pfam_to_go_mapping : pfam2go ) {
- final DomainId domain_id = pfam_to_go_mapping.getKey();
+ final String domain_id = pfam_to_go_mapping.getKey();
final GoId go_id = pfam_to_go_mapping.getValue();
final Set<GoId> supers = GoUtils.getAllSuperGoIds( go_id, goid_to_term_map );
supers.add( go_id );
final GoId go_id = pfam_to_go_mapping.getValue();
final Set<GoId> supers = GoUtils.getAllSuperGoIds( go_id, goid_to_term_map );
supers.add( go_id );
- for( int i = 0; i < queries.length; ++i ) {
- if ( supers.contains( queries[ i ] ) ) {
+ for( final GoId querie : queries ) {
+ if ( supers.contains( querie ) ) {
pfams.add( domain_id.toString() );
}
}
pfams.add( domain_id.toString() );
}
}
@@
-97,7
+96,7
@@
public class pfam2go_extractor {
private static void printHelp() {
System.out.println();
System.out.println( PRG_NAME
private static void printHelp() {
System.out.println();
System.out.println( PRG_NAME
- + " <pfam2go mapping file> <file with all GO terms, in 'obo' format> <GO id> [more GO ids]" );
+ + " <pfam2go mapping file> <file with all GO terms, in 'obo' format> <GO id> [more GO ids]" );
System.out.println();
}
}
System.out.println();
}
}