package org.forester.clade_analysis;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashSet;
import java.util.List;
import java.util.Map.Entry;
+import java.util.Set;
import java.util.SortedMap;
import java.util.TreeMap;
public final class Result2 {
- private List<Prefix> _greatest_common_prefix = new ArrayList<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 final String _separator;
+ private final List<Prefix> _greatest_common_prefixes = new ArrayList<>();
+ 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 = "";
+
+ public Result2(final String separator) {
+ _separator = separator;
+ }
+
+ public Result2() {
+ _separator = ".";//TODO make const somewhere
+ }
void addWarning( final String warning ) {
_warnings.add( warning );
}
void addGreatestCommonPrefix( final String prefix, final double confidence ) {
- _greatest_common_prefix.add( new Prefix(prefix, confidence) );
+ _greatest_common_prefixes.add( new Prefix( prefix, confidence, _separator ) );
}
+
+
void setGreatestCommonPrefixUp( final String greatest_common_prefix_up ) {
_greatest_common_prefix_up = greatest_common_prefix_up;
}
_greatest_common_clade_subtree_confidence_down = greatest_common_clade_confidence_down;
}
- // public String getGreatestCommonPrefix() {
- // return _greatest_common_prefix;
- // }
-
+ // public String getGreatestCommonPrefix() {
+ // return _greatest_common_prefix;
+ // }
public String getGreatestCommonPrefixUp() {
return _greatest_common_prefix_up;
}
return _p_ext_nodes;
}
- public void analyzeGreatestCommonPrefixes(final String separator ) {
- final SortedMap<String,Double> map = new TreeMap<String,Double>();
- for( final Prefix prefix : _greatest_common_prefix ) {
- List<String> prefixes = ForesterUtil.spliIntoPrefixes( prefix.getPrefix(), separator );
+ public void analyzeGreatestCommonPrefixes( ) {
+ analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator );
+ }
+
+ public final static void analyzeGreatestCommonPrefixes( List<Prefix> greatest_common_prefixes, final String separator ) {
+ final SortedMap<String, Double> map = new TreeMap<>();
+ for( final Prefix prefix : greatest_common_prefixes ) {
+ final List<String> prefixes = ForesterUtil.spliIntoPrefixes( prefix.getPrefix(), separator );
for( final String p : prefixes ) {
map.put( p, 0.0 );
}
}
- // System.out.println( map );
- for (final String key : map.keySet()) {
+ // System.out.println( map );
+ for( final String key : map.keySet() ) {
//System.out.println(key);
- for( final Prefix prefix : _greatest_common_prefix ) {
+ for( final Prefix prefix : greatest_common_prefixes ) {
if ( prefix.getPrefix().startsWith( key ) ) {
- map.put( key, map.get( key ) + prefix.getConfidence() );
+ map.put( key, map.get( key ) + prefix.getConfidence() );
+ }
+ }
+ }
+ //System.out.println( map );
+ final List<Prefix> l = new ArrayList<>();
+ for( final Entry<String, Double> entry : map.entrySet() ) {
+ // System.out.println( entry.getKey() + "->" + entry.getValue() );
+ l.add( new Prefix( entry.getKey(), entry.getValue(), separator ) );
+ }
+ Collections.sort( l, new Comparator<Prefix>() {
+
+ @Override
+ public int compare( final Prefix x, final Prefix y ) {
+ final int start_comparison = compare( x.getConfidence(), y.getConfidence() );
+ return start_comparison;
+ //return startComparison != 0 ? startComparison
+ // : compare(x.timeEnded, y.timeEnded);
+ }
+
+ private int compare( final double a, final double b ) {
+ return a > b ? -1 : a > b ? 1 : 0;
+ }
+ } );
+ System.out.println();
+ for( final Prefix prefix : l ) {
+ // System.out.println( prefix );
+ }
+ final List<Prefix> cleaned = new ArrayList<>();
+ for( final Prefix o : l ) {
+ boolean ok = true;
+ for( final Prefix i : l ) {
+ if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) )
+ && ForesterUtil.isEqual( i.getConfidence(),
+ o.getConfidence() ) ) {
+ ok = false;
+ break;
}
}
+ if ( ok ) {
+ cleaned.add( o );
+ }
+ }
+ System.out.println();
+ for( final Prefix prefix : cleaned ) {
+ System.out.println( prefix );
+ }
+ final List<Prefix> collapsed = new ArrayList<>();
+ final Set<String> firsts = new HashSet<>();
+ double confidence_sum = 0;
+ for( final Prefix prefix : cleaned ) {
+ final String f = prefix.getPrefixFirstElement();
+ if ( !firsts.contains( f ) ) {
+ firsts.add( f );
+ collapsed.add( prefix );
+ confidence_sum += prefix.getConfidence();
+ }
+ }
+ if ( !ForesterUtil.isEqual( confidence_sum, 1.0 ) ) {
+ throw new IllegalArgumentException( "Confidences add up to " + confidence_sum + " instead of 1.0" );
+ }
+ System.out.println();
+ for( final Prefix prefix : collapsed ) {
+ System.out.println( prefix );
}
- System.out.println( map );
}
-
-
}
git://source.jalview.org / jalview.git / blobdiff