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;
public Result2( final String separator ) {
_separator = separator;
return _p_ext_nodes;
}
+ public void analyzeGreatestCommonPrefixes( final double cutoff ) {
+ analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, cutoff );
+ }
+
public void analyzeGreatestCommonPrefixes() {
- analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, 0.3 );
+ analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, -1 );
}
- public final static void analyzeGreatestCommonPrefixes( final List<Prefix> greatest_common_prefixes,
- final String separator,
- final double cutoff ) {
+ 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 );
- System.out.println();
- System.out.println( "All:" );
- for( final Prefix prefix : l ) {
- System.out.println( prefix );
- }
- final List<Prefix> cleaned = removeLessSpecificPrefixes( l );
- System.out.println();
- System.out.println( "Cleaned:" );
- for( final Prefix prefix : cleaned ) {
- System.out.println( prefix );
- }
- final List<Prefix> collapsed = collapse( cleaned );
- System.out.println();
- System.out.println( "Collapsed:" );
- for( final Prefix prefix : collapsed ) {
- System.out.println( prefix );
- }
+ _all = removeLessSpecificPrefixes( l );
+ _collapsed = collapse( _all );
+ _has_specifics = false;
if ( cutoff >= 0 ) {
- System.out.println();
- System.out.println( "Specifics:" );
- final List<Prefix> cleaned_spec = obtainSpecifics( cutoff, cleaned, collapsed );
- for( final Prefix prefix : cleaned_spec ) {
- System.out.println( prefix );
+ _cleaned_spec = obtainSpecifics( cutoff, _all, _collapsed );
+ if ( _cleaned_spec != null && _cleaned_spec.size() > 0 ) {
+ _has_specifics = true;
}
}
- System.out.println( "------" );
+ else {
+ _cleaned_spec = null;
+ }
}
private final static List<Prefix> obtainSpecifics( final double cutoff,
- final List<Prefix> cleaned,
- final List<Prefix> collapsed ) {
+ 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 ) {
final List<Prefix> spec = new ArrayList<>();
for( final Prefix prefix : cleaned ) {
if ( ( prefix.getConfidence() >= cutoff ) && !collapsed_set.contains( prefix.getPrefix() ) ) {
- // System.out.println( prefix );
spec.add( prefix );
}
}
}
}
if ( ok ) {
- //System.out.println(">" + o );
cleaned_spec.add( o );
}
}
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 ) {
map.put( p, 0.0 );
}
}
- // System.out.println( map );
for( final String key : map.keySet() ) {
- //System.out.println(key);
for( final Prefix prefix : greatest_common_prefixes ) {
if ( prefix.getPrefix().startsWith( key ) ) {
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 ) );
}
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 );
+ }
+ }
+ }
+ }
+ return sb.toString();
+ }
}