// 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.surfacing;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.BinaryCharacters;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
nodes.add( n );
}
}
- for( int i = 0; i < nodes.size() - 1; ++i ) {
+ for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
for( int j = i + 1; j < nodes.size(); ++j ) {
- final PhylogenyNode lca = PhylogenyMethods.obtainLCA( nodes.get( i ), nodes.get( j ) );
+ final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
String rank = "unknown";
if ( lca.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
+ all_pfams_encountered.size() );
ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping : "
+ pfams_without_mappings_counter + " ["
- + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
+ + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
+ pfams_without_mappings_to_bp_or_mf_counter + " ["
- + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME,
- "Pfams with a mapping : " + pfams_with_mappings_counter
- + " ["
- + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() )
- + "%]" );
+ + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping : "
+ + pfams_with_mappings_counter + " ["
+ + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func. : "
+ pfams_with_mappings_to_bp_or_mf_counter + " ["
- + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME,
- "Pfams with mapping to biological process: " + biological_process_counter
- + " ["
- + ( 100 * biological_process_counter / all_pfams_encountered.size() )
- + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME,
- "Pfams with mapping to molecular function: " + molecular_function_counter
- + " ["
- + ( 100 * molecular_function_counter / all_pfams_encountered.size() )
- + "%]" );
- ForesterUtil.programMessage( surfacing.PRG_NAME,
- "Pfams with mapping to cellular component: " + cellular_component_counter
- + " ["
- + ( 100 * cellular_component_counter / all_pfams_encountered.size() )
- + "%]" );
+ + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
+ + biological_process_counter + " ["
+ + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
+ + molecular_function_counter + " ["
+ + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
+ + cellular_component_counter + " ["
+ + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Sum of Pfams encountered : " + all_pfams_encountered.size() );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams without a mapping : " + pfams_without_mappings_counter
- + " [" + ( 100 * pfams_without_mappings_counter / all_pfams_encountered.size() ) + "%]" );
+ + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams without mapping to proc. or func. : "
+ pfams_without_mappings_to_bp_or_mf_counter + " ["
- + ( 100 * pfams_without_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
+ + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with a mapping : " + pfams_with_mappings_counter + " ["
- + ( 100 * pfams_with_mappings_counter / all_pfams_encountered.size() ) + "%]" );
+ + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with a mapping to proc. or func. : "
+ pfams_with_mappings_to_bp_or_mf_counter + " ["
- + ( 100 * pfams_with_mappings_to_bp_or_mf_counter / all_pfams_encountered.size() ) + "%]" );
+ + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
- + ( 100 * biological_process_counter / all_pfams_encountered.size() ) + "%]" );
+ + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
- + ( 100 * molecular_function_counter / all_pfams_encountered.size() ) + "%]" );
+ + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
- + ( 100 * cellular_component_counter / all_pfams_encountered.size() ) + "%]" );
+ + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
summary_writer.write( ForesterUtil.LINE_SEPARATOR );
summary_writer.close();
}