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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
pfam_go.java
diff --git
a/forester/java/src/org/forester/application/pfam_go.java
b/forester/java/src/org/forester/application/pfam_go.java
index
07e22bb
..
df679e1
100644
(file)
--- a/
forester/java/src/org/forester/application/pfam_go.java
+++ b/
forester/java/src/org/forester/application/pfam_go.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;
@@
-49,8
+49,9
@@
public class pfam_go {
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "www.phylosoft.org";
final static private String E_MAIL = "czmasek@burnham.org";
final static private String WWW = "www.phylosoft.org";
- private static void process( final File pfams_file, final List<PfamToGoMapping> mappings, boolean allow_duplicates )
- throws IOException {
+ private static void process( final File pfams_file,
+ final List<PfamToGoMapping> mappings,
+ final boolean allow_duplicates ) throws IOException {
final BufferedReader reader = ForesterUtil.obtainReader( pfams_file );
String line = "";
int found_count = 0;
final BufferedReader reader = ForesterUtil.obtainReader( pfams_file );
String line = "";
int found_count = 0;
@@
-77,7
+78,7
@@
public class pfam_go {
encountered_domains.add( line );
boolean found = false;
for( final PfamToGoMapping mapping : mappings ) {
encountered_domains.add( line );
boolean found = false;
for( final PfamToGoMapping mapping : mappings ) {
- if ( mapping.getKey().getId().equals( line ) ) {
+ if ( mapping.getKey().equals( line ) ) {
System.out.println( mapping.getValue() );
found = true;
}
System.out.println( mapping.getValue() );
found = true;
}
@@
-113,7
+114,7
@@
public class pfam_go {
}
final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( ALLOW_DUPLICATES_OPTION );
}
final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( ALLOW_DUPLICATES_OPTION );
- if ( cla.getNumberOfNames() != 2 && cla.getNumberOfNames() != 3 ) {
+ if ( ( cla.getNumberOfNames() != 2 ) && ( cla.getNumberOfNames() != 3 ) ) {
printHelp();
System.exit( -1 );
}
printHelp();
System.exit( -1 );
}
@@
-149,7
+150,7
@@
public class pfam_go {
System.out.println( "Usage:" );
System.out.println();
System.out.println( PRG_NAME + " [-" + ALLOW_DUPLICATES_OPTION
System.out.println( "Usage:" );
System.out.println();
System.out.println( PRG_NAME + " [-" + ALLOW_DUPLICATES_OPTION
- + " to allow duplicates] <pfam2go file> <file with pfams>" );
+ + " to allow duplicates] <pfam2go file> <file with pfams>" );
System.out.println();
System.out.println();
}
System.out.println();
System.out.println();
}