import java.util.ArrayList;
import java.util.List;
-import org.forester.clade_analysis.Analysis;
-import org.forester.clade_analysis.Result;
+import org.forester.clade_analysis.AnalysisSingle;
+import org.forester.clade_analysis.ResultSingle;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
System.out.println( "\nCould not read \"" + intreefile + "\" [" + e.getMessage() + "]\n" );
System.exit( -1 );
}
- final Result res = Analysis.execute( p, query, separator );
+ final ResultSingle res = AnalysisSingle.execute( p, query, separator );
System.out.println();
System.out.println( "Result:" );
System.out.println( "Query : " + query );
import org.forester.phylogeny.data.Confidence;
import org.forester.util.ForesterUtil;
-public final class Analysis2 {
+public final class AnalysisMulti {
- public static Result2 execute( final Phylogeny p, final Pattern query, final String separator ) {
+ private final static String UNKNOWN = "?";
+ public final static double DEFAULT_CUTOFF_FOR_SPECIFICS = 0.5;
+ public final static String DEFAULT_SEPARATOR = ".";
+ public final static Pattern DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE = Pattern.compile( ".+#\\d+_M=(.+)" );
+
+
+ public static ResultMulti execute( final Phylogeny p ) {
+ return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, DEFAULT_SEPARATOR, DEFAULT_CUTOFF_FOR_SPECIFICS );
+ }
+
+ public static ResultMulti execute( final Phylogeny p, final String separator ) {
+ return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, separator , DEFAULT_CUTOFF_FOR_SPECIFICS );
+ }
+
+ public static ResultMulti execute( final Phylogeny p, final String separator, final double cutoff_for_specifics ) {
+ return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, separator , cutoff_for_specifics );
+ }
+
+ public static ResultMulti execute( final Phylogeny p, final double cutoff_for_specifics ) {
+ return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, DEFAULT_SEPARATOR , cutoff_for_specifics );
+ }
+
+ public static ResultMulti execute( final Phylogeny p,
+ final Pattern query,
+ final String separator,
+ final double cutoff_for_specifics ) {
final List<PhylogenyNode> qnodes = p.getNodes( query );
- final Result2 res = new Result2();
+ final ResultMulti res = new ResultMulti();
for( int i = 0; i < qnodes.size(); ++i ) {
final PhylogenyNode qnode = qnodes.get( i );
System.out.println( ">>" + qnode.getName() );
while ( qnode_pp.getNumberOfDescendants() == 1 ) {
qnode_pp = qnode_pp.getParent();
}
- // final List<PhylogenyNode> qnode_ext_nodes = new ArrayList<PhylogenyNode>();
final List<String> qnode_ext_nodes_names = new ArrayList<>();
for( final PhylogenyNode qnode_ext_node : qnode_pp.getAllExternalDescendants() ) {
final String name = qnode_ext_node.getName();
qnode_ext_nodes_names.add( name );
}
}
- //final int lec_ext_nodes = qnode_ext_nodes_names.size();
- //final int p_ext_nodes = p.getNumberOfExternalNodes() - 1;
final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( qnode_ext_nodes_names, separator );
// System.out.println( greatest_common_prefix );
Matcher matcher = query.matcher( qnode.getName() );
res.addGreatestCommonPrefix( greatest_common_prefix, conf );
}
else {
- res.addGreatestCommonPrefix( "?", conf );
+ res.addGreatestCommonPrefix( UNKNOWN, conf );
}
//final String greatest_common_prefix_up[] = analyzeSiblings( qnode_p, qnode_pp, separator, query, res );
final String greatest_common_prefix_up = analyzeSiblings( qnode_p, qnode_pp, separator, query );
- System.out.println( "greatest_common_prefix_up=" + greatest_common_prefix_up + " " + conf);
- if ( !ForesterUtil.isEmpty( greatest_common_prefix_up) ) {
+ System.out.println( "greatest_common_prefix_up=" + greatest_common_prefix_up + " " + conf );
+ if ( !ForesterUtil.isEmpty( greatest_common_prefix_up ) ) {
res.addGreatestCommonPrefixUp( greatest_common_prefix_up, conf );
}
else {
- res.addGreatestCommonPrefixUp( "?", conf );
+ res.addGreatestCommonPrefixUp( UNKNOWN, conf );
}
- // res.addGreatestCommonPrefixUp( greatest_common_prefix_up, conf );
- //res.addGreatestCommonPrefixUp( greatest_common_prefix_up[ 0 ], 0.1 );
- // res.setGreatestCommonPrefixUp( greatest_common_prefix_up[ 0 ] );
- //if ( greatest_common_prefix_up[ 1 ] != null ) {
- // res.setGreatestCommonCladeUpSubtreeConfidence( greatest_common_prefix_up[ 1 ] );
- // }
- // final String greatest_common_prefix_down[] = analyzeSiblings( qnode, qnode_p, separator,query, res );
- final String greatest_common_prefix_down = analyzeSiblings( qnode, qnode_p, separator, query );
- System.out.println( "greatest_common_prefix_down=" + greatest_common_prefix_down+ " " + conf);
- if ( !ForesterUtil.isEmpty( greatest_common_prefix_down) ) {
+ final String greatest_common_prefix_down = analyzeSiblings( qnode, qnode_p, separator, query );
+ System.out.println( "greatest_common_prefix_down=" + greatest_common_prefix_down + " " + conf );
+ if ( !ForesterUtil.isEmpty( greatest_common_prefix_down ) ) {
res.addGreatestCommonPrefixDown( greatest_common_prefix_down, conf );
}
else {
- res.addGreatestCommonPrefixDown( "?", conf );
- }
- //res.addGreatestCommonPrefixDown( greatest_common_prefix_down, conf );
- // res.setGreatestCommonPrefixDown( greatest_common_prefix_down[ 0 ] );
- // if ( greatest_common_prefix_down[ 1 ] != null ) {
- // res.setGreatestCommonCladeDownSubtreeConfidence( greatest_common_prefix_down[ 1 ] );
- // }
- }
- /* for( final PhylogenyNode qnode_ext_node : qnode_ext_nodes ) {
- String name = qnode_ext_node.getName();
- if ( ForesterUtil.isEmptyTrimmed( name ) ) {
- throw new IllegalArgumentException( "external node(s) with empty names found" );
- }
- name = name.trim();
- if ( !name.equals( query ) ) {
- qnode_ext_nodes_names.add( name );
+ res.addGreatestCommonPrefixDown( UNKNOWN, conf );
}
- }*/
- // if ( greatest_common_prefix.length() < 1 ) {
- // res.addWarning( "No greatest common prefix" );
- //res.setGreatestCommonPrefix( "" );
- // }
- // else {
- // // res.setGreatestCommonPrefix( greatest_common_prefix );
- // res.addGreatestCommonPrefix( prefix, confidence, separator ); //TODO
- // }
- // if ( qnode_pp.isRoot() ) {
- // res.addWarning( "Least Encompassing Clade is entire tree" );
- // }
- /* final String conf = obtainConfidence( qnode_pp );
- if ( conf != null ) {
- res.setGreatestCommonCladeSubtreeConfidence(conf);
- }*/
- /* final String greatest_common_prefix_up[] = analyzeSiblings( qnode_p, qnode_pp, separator );
- res.setGreatestCommonPrefixUp( greatest_common_prefix_up[ 0 ] );
- if ( greatest_common_prefix_up[ 1 ] != null ) {
- res.setGreatestCommonCladeUpSubtreeConfidence( greatest_common_prefix_up[ 1 ] );
}
- final String greatest_common_prefix_down[] = analyzeSiblings( qnode, qnode_p, separator );
- res.setGreatestCommonPrefixDown( greatest_common_prefix_down[ 0 ] );
- if ( greatest_common_prefix_down[ 1 ] != null ) {
- res.setGreatestCommonCladeDownSubtreeConfidence( greatest_common_prefix_down[ 1 ] );
- }*/
+ res.analyze( cutoff_for_specifics );
return res;
}
- private final static void analyzeSiblingsOLD( final PhylogenyNode child,
- final PhylogenyNode parent,
- final String separator,
- final Pattern query,
- Result2 res,
- double conf2 ) {
- final int child_index = child.getChildNodeIndex();
- final List<String> ext_nodes_names = new ArrayList<>();
- final List<PhylogenyNode> descs = parent.getDescendants();
- // String conf = null;
- for( int i = 0; i < descs.size(); ++i ) {
- if ( i != child_index ) {
- final PhylogenyNode d = descs.get( i );
- for( final PhylogenyNode n : d.getAllExternalDescendants() ) {
- final String name = n.getName();
- if ( ForesterUtil.isEmptyTrimmed( name ) ) {
- throw new IllegalArgumentException( "external node(s) with empty names found" );
- }
- ext_nodes_names.add( name.trim() );
- }
- // if ( descs.size() == 2 ) {
- // conf = obtainConfidence( d );
- // }
- }
- }
- ////////////////////////////////////////////////////////////
- /* Matcher matcher = query.matcher( child.getName() );
- String conf_str = null;
- if ( matcher.find() ) {
- conf_str = matcher.group( 1 );
- }
- else {
- throw new IllegalStateException( "pattern did not match for \"" + child.getName() + "\" -- this should have never happened!" );
- }*/
- ////////////////////////////////////////////////////////////
- final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( ext_nodes_names, separator );
- //final double conf = Double.parseDouble( conf_str );
- if ( !ForesterUtil.isEmpty( greatest_common_prefix ) ) {
- res.addGreatestCommonPrefix( greatest_common_prefix, conf2 );
- }
- else {
- res.addGreatestCommonPrefix( "?", conf2 );
- }
- }
-
private final static String analyzeSiblings( final PhylogenyNode child,
- final PhylogenyNode parent,
- final String separator,
- final Pattern query) {
+ final PhylogenyNode parent,
+ final String separator,
+ final Pattern query ) {
final int child_index = child.getChildNodeIndex();
final List<String> ext_nodes_names = new ArrayList<>();
final List<PhylogenyNode> descs = parent.getDescendants();
if ( ForesterUtil.isEmptyTrimmed( name ) ) {
throw new IllegalArgumentException( "external node(s) with empty names found" );
}
-
- ////
-
final Matcher m = query.matcher( name );
if ( !m.find() ) {
ext_nodes_names.add( name );
}
-
- ////
-
}
// if ( descs.size() == 2 ) {
// conf = obtainConfidence( d );
// }
}
}
- ////////////////////////////////////////////////////////////
- /* Matcher matcher = query.matcher( child.getName() );
- String conf_str = null;
- if ( matcher.find() ) {
- conf_str = matcher.group( 1 );
- }
- else {
- throw new IllegalStateException( "pattern did not match for \"" + child.getName() + "\" -- this should have never happened!" );
- }*/
- ////////////////////////////////////////////////////////////
final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( ext_nodes_names, separator );
- //final double conf = Double.parseDouble( conf_str );
return greatest_common_prefix;
}
import org.forester.phylogeny.data.Confidence;
import org.forester.util.ForesterUtil;
-public final class Analysis {
+public final class AnalysisSingle {
- public static Result execute( final Phylogeny p, final String query, final String separator ) {
+ public static ResultSingle execute( final Phylogeny p, final String query, final String separator ) {
final PhylogenyNode qnode = p.getNode( query );
if ( qnode.isRoot() ) {
throw new IllegalStateException( "Unexpected error: Query " + query
}
}
final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( qnode_ext_nodes_names, separator );
- final Result res = new Result();
+ final ResultSingle res = new ResultSingle();
if ( greatest_common_prefix.length() < 1 ) {
res.addWarning( "No greatest common prefix" );
res.setGreatestCommonPrefix( "" );
package org.forester.clade_analysis;
import java.io.File;
-import java.util.List;
-import java.util.regex.Pattern;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.util.ParserUtils;
public static void main( final String[] args ) {
boolean failed = false;
- /* if ( !testCladeAnalysis1() ) {
+ if ( !testCladeAnalysis1() ) {
System.out.println( "Clade analysis 1 failed" );
failed = true;
}
if ( !testCladeAnalysis4() ) {
System.out.println( "Clade analysis 4 failed" );
failed = true;
- */
+ }
if ( !testCladeAnalysis5() ) {
System.out.println( "Clade analysis 5 failed" );
failed = true;
}
- /* if ( !testCladeAnalysis6() ) {
+ if ( !testCladeAnalysis6() ) {
System.out.println( "Clade analysis 6 failed" );
failed = true;
- }*/
+ }
if ( !failed ) {
System.out.println( "OK" );
}
+ else {
+ System.out.println( "NOT OK" );
+ }
}
public static boolean test() {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
- Result res = Analysis.execute( p1, "A.1.1.1", "." );
+ ResultSingle res = AnalysisSingle.execute( p1, "A.1.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.1.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.1.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.1.1.3", "." );
+ res = AnalysisSingle.execute( p1, "A.1.1.3", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.1.1.4", "." );
+ res = AnalysisSingle.execute( p1, "A.1.1.4", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.1.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.1.2.1", "." );
+ res = AnalysisSingle.execute( p1, "A.1.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.2.1.1", "." );
+ res = AnalysisSingle.execute( p1, "A.2.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.2.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.2.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.3.1.1", "." );
+ res = AnalysisSingle.execute( p1, "A.3.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.3.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.3.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.3.2.1", "." );
+ res = AnalysisSingle.execute( p1, "A.3.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.3.3.1", "." );
+ res = AnalysisSingle.execute( p1, "A.3.3.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.4.1.1", "." );
+ res = AnalysisSingle.execute( p1, "A.4.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.4.1.1.a", "." );
+ res = AnalysisSingle.execute( p1, "A.4.1.1.a", "." );
if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.4.1.2", "." );
- res = Analysis.execute( p1, "A.4.1.2.a", "." );
- res = Analysis.execute( p1, "A.5.1.1", "." );
+ res = AnalysisSingle.execute( p1, "A.4.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.4.1.2.a", "." );
+ res = AnalysisSingle.execute( p1, "A.5.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.5.1.2", "." );
+ res = AnalysisSingle.execute( p1, "A.5.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "A.6.3.12", "." );
+ res = AnalysisSingle.execute( p1, "A.6.3.12", "." );
if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "B.1.1.1", "." );
+ res = AnalysisSingle.execute( p1, "B.1.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
if ( res.getWarnings().size() != 2 ) {
return false;
}
- res = Analysis.execute( p1, "B.1.234.3", "." );
+ res = AnalysisSingle.execute( p1, "B.1.234.3", "." );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
if ( res.getWarnings().size() != 2 ) {
return false;
}
- res = Analysis.execute( p1, "C.1.1.1", "." );
+ res = AnalysisSingle.execute( p1, "C.1.1.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "C.1.1.2", "." );
+ res = AnalysisSingle.execute( p1, "C.1.1.2", "." );
if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "C.1.2.1", "." );
+ res = AnalysisSingle.execute( p1, "C.1.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "C.2.1", "." );
+ res = AnalysisSingle.execute( p1, "C.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "C.3", "." );
+ res = AnalysisSingle.execute( p1, "C.3", "." );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
if ( res.getWarnings().size() != 1 ) {
return false;
}
- res = Analysis.execute( p1, "QE.1.1.1.2.1", "." );
+ res = AnalysisSingle.execute( p1, "QE.1.1.1.2.1", "." );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
- Result res = Analysis.execute( p1, "6_DQ278891", null );
+ ResultSingle res = AnalysisSingle.execute( p1, "6_DQ278891", null );
if ( !res.getGreatestCommonPrefix().equals( "6_" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "6xa_EU408330", null );
+ res = AnalysisSingle.execute( p1, "6xa_EU408330", null );
if ( !res.getGreatestCommonPrefix().equals( "6xa_EU40833" ) ) {
return false;
}
if ( res.getWarnings().size() != 0 ) {
return false;
}
- res = Analysis.execute( p1, "7a_EF108306", null );
+ res = AnalysisSingle.execute( p1, "7a_EF108306", null );
if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
return false;
}
private static boolean testCladeAnalysis3() {
try {
- final Result2 res1 = new Result2();
+ final ResultMulti res1 = new ResultMulti();
res1.addGreatestCommonPrefix( "A.1.1", 0.3 );
res1.addGreatestCommonPrefix( "A.1.2", 0.3 );
res1.addGreatestCommonPrefix( "A.1.3", 0.3 );
res1.addGreatestCommonPrefix( "B.1", 0.1 );
- res1.analyzeGreatestCommonPrefixes( 0.5 );
- //res1.analyzeGreatestCommonPrefixesDown(0.5);
- //res1.analyzeGreatestCommonPrefixesUp(0.5);
- System.out.print( res1.toString());
- System.out.println( "------------------------- ");
+ res1.analyze( 0.5 );
+ System.out.print( res1.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res2 = new Result2( "." );
+ final ResultMulti res2 = new ResultMulti( "." );
res2.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
res2.addGreatestCommonPrefix( "A.1", 0.7 );
res2.addGreatestCommonPrefix( "A.1.2", 0.1 );
res2.addGreatestCommonPrefix( "B.1", 0.1 );
- res2.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res2.toString());
- System.out.println( "------------------------- ");
+ res2.analyze( 0.3 );
+ System.out.print( res2.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res3 = new Result2( "." );
+ final ResultMulti res3 = new ResultMulti( "." );
res3.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
res3.addGreatestCommonPrefix( "A.1.1.1.1", 0.6 );
res3.addGreatestCommonPrefix( "A.1", 0.1 );
res3.addGreatestCommonPrefix( "A.1.2", 0.1 );
res3.addGreatestCommonPrefix( "B.1", 0.1 );
- res3.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res3.toString());
- System.out.println( "------------------------- ");
+ res3.analyze( 0.3 );
+ System.out.print( res3.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res33 = new Result2( "." );
+ final ResultMulti res33 = new ResultMulti( "." );
res33.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
res33.addGreatestCommonPrefix( "A.1.1.1.1", 0.3 );
res33.addGreatestCommonPrefix( "A.1", 0.1 );
res33.addGreatestCommonPrefix( "A.1.2", 0.1 );
res33.addGreatestCommonPrefix( "B.1", 0.1 );
res33.addGreatestCommonPrefix( "B.1.1.1", 0.3 );
- res33.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res33.toString());
- System.out.println( "------------------------- ");
+ res33.analyze( 0.3 );
+ System.out.print( res33.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res4 = new Result2();
+ final ResultMulti res4 = new ResultMulti();
res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35 );
res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 );
res4.addGreatestCommonPrefix( "A.1", 0.1 );
res4.addGreatestCommonPrefix( "A.1.2", 0.1 );
res4.addGreatestCommonPrefix( "B.1", 0.1 );
- res4.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res4.toString());
- System.out.println( "------------------------- ");
+ res4.analyze( 0.3 );
+ System.out.print( res4.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res5 = new Result2();
+ final ResultMulti res5 = new ResultMulti();
res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2 );
res5.addGreatestCommonPrefix( "C.2.3", 0.2 );
res5.addGreatestCommonPrefix( "A.1.5", 0.1 );
res5.addGreatestCommonPrefix( "B.1.1", 0.2 );
res5.addGreatestCommonPrefix( "B.1.2", 0.09 );
res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 );
- res5.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res5.toString());
- System.out.println( "------------------------- ");
+ res5.analyze( 0.3 );
+ System.out.print( res5.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res6 = new Result2();
+ final ResultMulti res6 = new ResultMulti();
res6.addGreatestCommonPrefix( "A.1.1.1", 0.05 );
res6.addGreatestCommonPrefix( "A.1.1.1.1", 0.65 );
res6.addGreatestCommonPrefix( "A.1", 0.1 );
res6.addGreatestCommonPrefix( "A.1.2", 0.1 );
res6.addGreatestCommonPrefix( "B.1", 0.1 );
- res6.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res6.toString());
- System.out.println( "------------------------- ");
+ res6.analyze( 0.3 );
+ System.out.print( res6.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res7 = new Result2();
+ final ResultMulti res7 = new ResultMulti();
res7.addGreatestCommonPrefix( "A.1.1.1", 0.07 );
res7.addGreatestCommonPrefix( "A.1.1.1.1", 0.9 );
res7.addGreatestCommonPrefix( "A.1", 0.01 );
res7.addGreatestCommonPrefix( "A.1.2", 0.01 );
res7.addGreatestCommonPrefix( "B.1", 0.01 );
- res7.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res7.toString());
- System.out.println( "------------------------- ");
+ res7.analyze( 0.3 );
+ System.out.print( res7.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res8 = new Result2( "_/_" );
+ final ResultMulti res8 = new ResultMulti( "_/_" );
res8.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
res8.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.9 );
res8.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
res8.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
res8.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
- res8.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res8.toString());
- System.out.println( "------------------------- ");
+ res8.analyze( 0.3 );
+ System.out.print( res8.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- final Result2 res9 = new Result2( "_/_" );
+ final ResultMulti res9 = new ResultMulti( "_/_" );
res9.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
res9.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.6 );
res9.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
res9.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
res9.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
res9.addGreatestCommonPrefix( "BB_/_fke_/_dme_/_nx2", 0.3 );
- res9.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res9.toString());
- System.out.println( "------------------------- ");
+ res9.analyze( 0.3 );
+ System.out.print( res9.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
}
catch ( final Exception e ) {
}
return true;
}
-
+
private static boolean testCladeAnalysis4() {
try {
final File intreefile1 = new File( PATH_TO_TEST_DATA + "pplacer_2.tre" );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
- Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
- Result2 res = Analysis2.execute( p1, query, "." );
-
- res.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res.toString());
- System.out.println( "------------------------- ");
+ ResultMulti res2 = AnalysisMulti.execute( p1 );
+ res2.analyze( 0.3 );
+ System.out.print( res2.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- // Result res = Analysis.execute( p1, "A.1.1.1", "." );
- /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
- return false;
- }
- if ( res.getLeastEncompassingCladeSize() != 4 ) {
- return false;
- }
- if ( res.getTreeSize() != 25 ) {
- return false;
- }
- if ( res.getWarnings().size() != 0 ) {
- return false;
- }*/
-
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
return true;
}
-
+
private static boolean testCladeAnalysis5() {
try {
final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_3.xml" );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
- Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
- Result2 res = Analysis2.execute( p1, query, "." );
-
- res.analyzeGreatestCommonPrefixes( 0.3 );
- System.out.print( res.toString());
- System.out.println( "------------------------- ");
+ ResultMulti res = AnalysisMulti.execute( p1 );
+ res.analyze( 0.3 );
+ System.out.print( res.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- // Result res = Analysis.execute( p1, "A.1.1.1", "." );
- /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
- return false;
- }
- if ( res.getLeastEncompassingCladeSize() != 4 ) {
- return false;
- }
- if ( res.getTreeSize() != 25 ) {
- return false;
- }
- if ( res.getWarnings().size() != 0 ) {
- return false;
- }*/
-
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
}
return true;
}
-
+
private static boolean testCladeAnalysis6() {
try {
final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_4.xml" );
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
- Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
- Result2 res = Analysis2.execute( p1, query, "." );
-
- res.analyzeGreatestCommonPrefixes( 0.45 );
- System.out.print( res.toString());
- System.out.println( "------------------------- ");
+ ResultMulti res = AnalysisMulti.execute( p1, 0.45 );
+ System.out.print( res.toString() );
+ System.out.println( "------------------------- " );
System.out.println();
-
- // Result res = Analysis.execute( p1, "A.1.1.1", "." );
- /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
- return false;
- }
- if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
- return false;
- }
- if ( res.getLeastEncompassingCladeSize() != 4 ) {
- return false;
- }
- if ( res.getTreeSize() != 25 ) {
- return false;
- }
- if ( res.getWarnings().size() != 0 ) {
- return false;
- }*/
-
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
import org.forester.util.ForesterUtil;
-public final class Result2 {
+public final class ResultMulti {
private final String _separator;
- private final List<Prefix> _greatest_common_prefixes = new ArrayList<Prefix>();
- private List<Prefix> _greatest_common_prefixes_up = new ArrayList<Prefix>();
- private List<Prefix> _greatest_common_prefixes_down = new ArrayList<Prefix>();
- private final List<String> _warnings = new ArrayList<>();
- private String _greatest_common_clade_subtree_confidence = "";
- private String _greatest_common_clade_subtree_confidence_up = "";
- private String _greatest_common_clade_subtree_confidence_down = "";
- private List<Prefix> _all = null;
- private List<Prefix> _collapsed = null;
- private List<Prefix> _cleaned_spec = null;
- private boolean _has_specifics = false;
- private List<Prefix> _all_up = null;
- private List<Prefix> _collapsed_up = null;
- private List<Prefix> _cleaned_spec_up = null;
- private boolean _has_specifics_up = false;
- private List<Prefix> _all_down = null;
- private List<Prefix> _collapsed_down = null;
- private List<Prefix> _cleaned_spec_down = null;
- private boolean _has_specifics_down = false;
-
- public Result2( final String separator ) {
+ private final List<Prefix> _greatest_common_prefixes = new ArrayList<Prefix>();
+ private final List<Prefix> _greatest_common_prefixes_up = new ArrayList<Prefix>();
+ private final List<Prefix> _greatest_common_prefixes_down = new ArrayList<Prefix>();
+ private List<Prefix> _all = null;
+ private List<Prefix> _collapsed = null;
+ private List<Prefix> _cleaned_spec = null;
+ private boolean _has_specifics = false;
+ private List<Prefix> _all_up = null;
+ private List<Prefix> _collapsed_up = null;
+ private List<Prefix> _cleaned_spec_up = null;
+ private boolean _has_specifics_up = false;
+ private List<Prefix> _all_down = null;
+ private List<Prefix> _collapsed_down = null;
+ private List<Prefix> _cleaned_spec_down = null;
+ private boolean _has_specifics_down = false;
+
+ ResultMulti( final String separator ) {
_separator = separator;
+ reset();
}
- public Result2() {
- _separator = ".";//TODO make const somewhere
+ ResultMulti() {
+ _separator = AnalysisMulti.DEFAULT_SEPARATOR;
+ reset();
}
public List<Prefix> getAllMultiHitPrefixesUp() {
return _has_specifics;
}
- void addWarning( final String warning ) {
- _warnings.add( warning );
+ @Override
+ public final String toString() {
+ final StringBuilder sb = new StringBuilder();
+ sb.append( "Cleaned:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _all ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Collapsed:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _collapsed ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ if ( _has_specifics ) {
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Specifics:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _cleaned_spec ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Collapsed With Specifics:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _collapsed ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix spec : _cleaned_spec ) {
+ if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
+ sb.append( " " + spec );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ }
+ }
+ if ( !ForesterUtil.isEmpty( _all_down ) ) {
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Cleaned Down:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _all_down ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Collapsed Down:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _collapsed_down ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ if ( _has_specifics_down ) {
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Specifics Down:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _cleaned_spec_down ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Collapsed With Specifics Down:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _collapsed_down ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix spec : _cleaned_spec_down ) {
+ if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
+ sb.append( " " + spec );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ }
+ }
+ }
+ if ( !ForesterUtil.isEmpty( _all_up ) ) {
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Cleaned Up:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _all_up ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Collapsed Up:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _collapsed_up ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ if ( _has_specifics ) {
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Specifics Up:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _cleaned_spec_up ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Collapsed With Specifics Up:" );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix prefix : _collapsed_up ) {
+ sb.append( prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ for( final Prefix spec : _cleaned_spec_up ) {
+ if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
+ sb.append( " " + spec );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ }
+ }
+ }
+ return sb.toString();
}
void addGreatestCommonPrefix( final String prefix, final double confidence ) {
_greatest_common_prefixes_down.add( new Prefix( prefix_down, confidence, _separator ) );
}
- void setGreatestCommonCladeSubtreeConfidence( final String greatest_common_clade_confidence ) {
- _greatest_common_clade_subtree_confidence = greatest_common_clade_confidence;
- }
-
- void setGreatestCommonCladeUpSubtreeConfidence( final String greatest_common_clade_confidence_up ) {
- _greatest_common_clade_subtree_confidence_up = greatest_common_clade_confidence_up;
- }
-
- void setGreatestCommonCladeDownSubtreeConfidence( final String greatest_common_clade_confidence_down ) {
- _greatest_common_clade_subtree_confidence_down = greatest_common_clade_confidence_down;
- }
-
- public String getGreatestCommonCladeSubtreeConfidence() {
- return _greatest_common_clade_subtree_confidence;
- }
-
- public String getGreatestCommonCladeUpSubtreeConfidence() {
- return _greatest_common_clade_subtree_confidence_up;
- }
-
- public String getGreatestCommonCladeDownSubtreeConfidence() {
- return _greatest_common_clade_subtree_confidence_down;
- }
-
- public List<String> getWarnings() {
- return _warnings;
- }
-
- public void analyzeGreatestCommonPrefixes( final double cutoff_for_specifics ) {
+ final void analyze( final double cutoff_for_specifics ) {
+ reset();
analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, cutoff_for_specifics );
analyzeGreatestCommonPrefixesUp( _greatest_common_prefixes_up, _separator, cutoff_for_specifics );
analyzeGreatestCommonPrefixesDown( _greatest_common_prefixes_down, _separator, cutoff_for_specifics );
}
- public void analyzeGreatestCommonPrefixes() {
- analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, -1 );
- }
-
- private void analyzeGreatestCommonPrefixesUp( final double cutoff_for_specifics ) {
- analyzeGreatestCommonPrefixesUp( _greatest_common_prefixes_up, _separator, cutoff_for_specifics );
- }
-
- private void analyzeGreatestCommonPrefixesUp() {
- analyzeGreatestCommonPrefixesUp( _greatest_common_prefixes_up, _separator, -1 );
- }
-
- private void analyzeGreatestCommonPrefixesDown( final double cutoff_for_specifics ) {
- analyzeGreatestCommonPrefixesDown( _greatest_common_prefixes_down, _separator, cutoff_for_specifics );
- }
-
- private void analyzeGreatestCommonPrefixesDown() {
- analyzeGreatestCommonPrefixesDown( _greatest_common_prefixes_down, _separator, -1 );
+ private final void reset() {
+ _all = new ArrayList<Prefix>();
+ _collapsed = new ArrayList<Prefix>();
+ _cleaned_spec = new ArrayList<Prefix>();
+ _has_specifics = false;
+ _all_up = new ArrayList<Prefix>();
+ _collapsed_up = new ArrayList<Prefix>();
+ _cleaned_spec_up = new ArrayList<Prefix>();
+ _has_specifics_up = false;
+ _all_down = new ArrayList<Prefix>();
+ _collapsed_down = new ArrayList<Prefix>();
+ _cleaned_spec_down = new ArrayList<Prefix>();
+ _has_specifics_down = false;
}
private final void analyzeGreatestCommonPrefixes( final List<Prefix> greatest_common_prefixes,
final String separator,
final double cutoff ) {
final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes, separator );
- sortPrefixesAccordingToConfidence( l );
- _all = removeLessSpecificPrefixes( l );
- _collapsed = collapse( _all );
- _has_specifics = false;
- if ( cutoff >= 0 ) {
- _cleaned_spec = obtainSpecifics( cutoff, _all, _collapsed );
- if ( _cleaned_spec != null && _cleaned_spec.size() > 0 ) {
- _has_specifics = true;
+ if ( !ForesterUtil.isEmpty( l ) ) {
+ sortPrefixesAccordingToConfidence( l );
+ _all = removeLessSpecificPrefixes( l );
+ _collapsed = collapse( _all );
+ _has_specifics = false;
+ if ( cutoff >= 0 ) {
+ _cleaned_spec = obtainSpecifics( cutoff, _all, _collapsed );
+ if ( !ForesterUtil.isEmpty( _cleaned_spec ) ) {
+ _has_specifics = true;
+ }
}
}
- else {
- _cleaned_spec = null;
- }
}
private final void analyzeGreatestCommonPrefixesUp( final List<Prefix> greatest_common_prefixes_up,
final String separator,
final double cutoff ) {
final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes_up, separator );
- sortPrefixesAccordingToConfidence( l );
- _all_up = removeLessSpecificPrefixes( l );
- _collapsed_up = collapse( _all_up );
- _has_specifics_up = false;
- if ( cutoff >= 0 ) {
- _cleaned_spec_up = obtainSpecifics( cutoff, _all_up, _collapsed_up );
- if ( _cleaned_spec_up != null && _cleaned_spec_up.size() > 0 ) {
- _has_specifics_up = true;
+ if ( !ForesterUtil.isEmpty( l ) ) {
+ sortPrefixesAccordingToConfidence( l );
+ _all_up = removeLessSpecificPrefixes( l );
+ _collapsed_up = collapse( _all_up );
+ _has_specifics_up = false;
+ if ( cutoff >= 0 ) {
+ _cleaned_spec_up = obtainSpecifics( cutoff, _all_up, _collapsed_up );
+ if ( !ForesterUtil.isEmpty( _cleaned_spec_up ) ) {
+ _has_specifics_up = true;
+ }
}
}
- else {
- _cleaned_spec_up = null;
- }
}
- private final void analyzeGreatestCommonPrefixesDown( final List<Prefix> greatest_common_prefixes_down,
- final String separator,
- final double cutoff ) {
+ final void analyzeGreatestCommonPrefixesDown( final List<Prefix> greatest_common_prefixes_down,
+ final String separator,
+ final double cutoff ) {
final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes_down, separator );
- sortPrefixesAccordingToConfidence( l );
- _all_down = removeLessSpecificPrefixes( l );
- _collapsed_down = collapse( _all_down );
- _has_specifics_down = false;
- if ( cutoff >= 0 ) {
- _cleaned_spec_down = obtainSpecifics( cutoff, _all_down, _collapsed_down );
- if ( _cleaned_spec_down != null && _cleaned_spec_down.size() > 0 ) {
- _has_specifics_down = true;
+ if ( !ForesterUtil.isEmpty( l ) ) {
+ sortPrefixesAccordingToConfidence( l );
+ _all_down = removeLessSpecificPrefixes( l );
+ _collapsed_down = collapse( _all_down );
+ _has_specifics_down = false;
+ if ( cutoff >= 0 ) {
+ _cleaned_spec_down = obtainSpecifics( cutoff, _all_down, _collapsed_down );
+ if ( !ForesterUtil.isEmpty( _cleaned_spec_down ) ) {
+ _has_specifics_down = true;
+ }
}
}
- else {
- _cleaned_spec_down = null;
- }
}
- private final static List<Prefix> obtainSpecifics( final double cutoff,
- final List<Prefix> cleaned,
- final List<Prefix> collapsed ) {
+ final static List<Prefix> obtainSpecifics( final double cutoff,
+ final List<Prefix> cleaned,
+ final List<Prefix> collapsed ) {
final List<Prefix> cleaned_spec = new ArrayList<>();
final Set<String> collapsed_set = new HashSet<>();
for( final Prefix prefix : collapsed ) {
}
}
if ( !ForesterUtil.isEqual( confidence_sum, 1.0, 1E-5 ) ) {
- // throw new IllegalArgumentException( "Confidences add up to " + confidence_sum + " instead of 1.0" );
+ throw new IllegalArgumentException( "Confidences add up to " + confidence_sum + " instead of 1.0" );
}
return collapsed;
}
}
return l;
}
-
- public final String toString() {
- final StringBuilder sb = new StringBuilder();
- //TODO add all other stuff
- sb.append( "Cleaned:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _all ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Collapsed:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _collapsed ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- if ( _has_specifics ) {
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Specifics:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _cleaned_spec ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Collapsed With Specifics:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _collapsed ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix spec : _cleaned_spec ) {
- if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
- sb.append( " " + spec );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- }
- }
- }
- //////
- if ( _all_down != null ) {
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Cleaned Down:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _all_down ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Collapsed Down:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _collapsed_down ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- if ( _has_specifics_down ) {
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Specifics Down:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _cleaned_spec_down ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Collapsed With Specifics Down:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _collapsed_down ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix spec : _cleaned_spec_down ) {
- if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
- sb.append( " " + spec );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- }
- }
- }
- }
- //////
- if ( _all_up != null ) {
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Cleaned Up:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _all_up ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Collapsed Up:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _collapsed_up ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- if ( _has_specifics ) {
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Specifics Up:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _cleaned_spec_up ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Collapsed With Specifics Up:" );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix prefix : _collapsed_up ) {
- sb.append( prefix );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- for( final Prefix spec : _cleaned_spec_up ) {
- if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
- sb.append( " " + spec );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- }
- }
- }
- }
- /////
- return sb.toString();
- }
}
import java.util.ArrayList;
import java.util.List;
-public final class Result {
-
- private String _greatest_common_prefix = "";
- private String _greatest_common_prefix_up = "";
- private String _greatest_common_prefix_down = "";
- private final List<String> _warnings = new ArrayList<>();
- private int _lec_ext_nodes = 0;
- private int _p_ext_nodes = 0;
+import org.forester.util.ForesterUtil;
+
+public final class ResultSingle {
+
+ private String _greatest_common_prefix = "";
+ private String _greatest_common_prefix_up = "";
+ private String _greatest_common_prefix_down = "";
+ private final List<String> _warnings = new ArrayList<>();
+ private int _lec_ext_nodes = 0;
+ private int _p_ext_nodes = 0;
private String _greatest_common_clade_subtree_confidence = "";
private String _greatest_common_clade_subtree_confidence_up = "";
private String _greatest_common_clade_subtree_confidence_down = "";
- void addWarning( final String warning ) {
- _warnings.add( warning );
- }
-
- void setGreatestCommonPrefix( final String greatest_common_prefix ) {
- _greatest_common_prefix = greatest_common_prefix;
- }
-
- void setGreatestCommonPrefixUp( final String greatest_common_prefix_up ) {
- _greatest_common_prefix_up = greatest_common_prefix_up;
- }
-
- void setGreatestCommonPrefixDown( final String greatest_common_prefix_down ) {
- _greatest_common_prefix_down = greatest_common_prefix_down;
- }
-
- void setGreatestCommonCladeSubtreeConfidence( final String greatest_common_clade_confidence ) {
- _greatest_common_clade_subtree_confidence = greatest_common_clade_confidence;
- }
-
- void setGreatestCommonCladeUpSubtreeConfidence( final String greatest_common_clade_confidence_up ) {
- _greatest_common_clade_subtree_confidence_up = greatest_common_clade_confidence_up;
- }
-
- void setGreatestCommonCladeDownSubtreeConfidence( final String greatest_common_clade_confidence_down ) {
- _greatest_common_clade_subtree_confidence_down = greatest_common_clade_confidence_down;
- }
-
public String getGreatestCommonPrefix() {
return _greatest_common_prefix;
}
return _warnings;
}
- void setLeastEncompassingCladeSize( final int lec_ext_nodes ) {
- _lec_ext_nodes = lec_ext_nodes;
- }
-
- void setTreeSize( final int p_ext_nodes ) {
- _p_ext_nodes = p_ext_nodes;
- }
-
public int getLeastEncompassingCladeSize() {
return _lec_ext_nodes;
}
public int getTreeSize() {
return _p_ext_nodes;
}
+
+ public final String toString() {
+ final StringBuilder sb = new StringBuilder();
+ sb.append( "Greatest common prefix : " + _greatest_common_prefix );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Greatest common prefix down: " + _greatest_common_prefix_down );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Greatest common prefix up : " + _greatest_common_prefix_up );
+ return sb.toString();
+ }
+
+ void addWarning( final String warning ) {
+ _warnings.add( warning );
+ }
+
+ void setGreatestCommonPrefix( final String greatest_common_prefix ) {
+ _greatest_common_prefix = greatest_common_prefix;
+ }
+
+ void setGreatestCommonPrefixUp( final String greatest_common_prefix_up ) {
+ _greatest_common_prefix_up = greatest_common_prefix_up;
+ }
+
+ void setGreatestCommonPrefixDown( final String greatest_common_prefix_down ) {
+ _greatest_common_prefix_down = greatest_common_prefix_down;
+ }
+
+ void setGreatestCommonCladeSubtreeConfidence( final String greatest_common_clade_confidence ) {
+ _greatest_common_clade_subtree_confidence = greatest_common_clade_confidence;
+ }
+
+ void setGreatestCommonCladeUpSubtreeConfidence( final String greatest_common_clade_confidence_up ) {
+ _greatest_common_clade_subtree_confidence_up = greatest_common_clade_confidence_up;
+ }
+
+ void setGreatestCommonCladeDownSubtreeConfidence( final String greatest_common_clade_confidence_down ) {
+ _greatest_common_clade_subtree_confidence_down = greatest_common_clade_confidence_down;
+ }
+
+ void setLeastEncompassingCladeSize( final int lec_ext_nodes ) {
+ _lec_ext_nodes = lec_ext_nodes;
+ }
+
+ void setTreeSize( final int p_ext_nodes ) {
+ _p_ext_nodes = p_ext_nodes;
+ }
}
git://source.jalview.org / jalview.git / commitdiff