import java.util.TreeMap;
import org.forester.util.ForesterUtil;
+import org.forester.util.UserException;
public final class ResultMulti {
- private 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;
+ private final static double MIN_DIFF = 1E-5;
+ private 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;
+ private int _matches = 0;
+ private int _ref_tree_ext_nodes = 0;
+ private String _query_name_prefix = "";
ResultMulti( final String separator ) {
+ if ( ForesterUtil.isEmpty( separator ) ) {
+ throw new IllegalArgumentException( "separator must not be null or empty" );
+ }
_separator = separator;
reset();
}
return _has_specifics;
}
+ public String getQueryNamePrefix() {
+ return _query_name_prefix;
+ }
+
+ public int getNumberOfMatches() {
+ return _matches;
+ }
+
+ public int getReferenceTreeNumberOfExternalNodes() {
+ return _ref_tree_ext_nodes;
+ }
+
@Override
public final String toString() {
final StringBuilder sb = new StringBuilder();
- sb.append( "Cleaned:" );
+ sb.append( "Query: " );
+ sb.append( getQueryNamePrefix() );
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( "Matching Clade(s):" );
sb.append( ForesterUtil.LINE_SEPARATOR );
for( final Prefix prefix : _collapsed ) {
sb.append( prefix );
}
if ( _has_specifics ) {
sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Specifics:" );
+ sb.append( "Specific-hit(s):" );
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( "Matching Clade(s) with Specific-hit(s):" );
sb.append( ForesterUtil.LINE_SEPARATOR );
for( final Prefix prefix : _collapsed ) {
sb.append( prefix );
}
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( "Matching Down-tree Bracketing Clade(s):" );
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( "Matching Up-tree Bracketing Clade(s):" );
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 );
- }
- }
- }
- }
}
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ sb.append( "Total Number of Matches: " + getNumberOfMatches() + "/" + getReferenceTreeNumberOfExternalNodes() );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
return sb.toString();
}
_greatest_common_prefixes_down.add( new Prefix( prefix_down, confidence, _separator ) );
}
- final void analyze( final double cutoff_for_specifics ) {
+ void setQueryNamePrefix( final String query_name_prefix ) {
+ if ( !ForesterUtil.isEmpty( _query_name_prefix ) ) {
+ throw new IllegalStateException( "illegal attempt to change the query name prefix" );
+ }
+ _query_name_prefix = query_name_prefix;
+ }
+
+ void setTotalNumberOfMatches( final int matches ) {
+ if ( _matches > 0 ) {
+ throw new IllegalStateException( "illegal attempt to change the number of matches" );
+ }
+ _matches = matches;
+ }
+
+ public void setReferenceTreeNumberOfExternalNodes( final int ext_nodes ) {
+ if ( _ref_tree_ext_nodes > 0 ) {
+ throw new IllegalStateException( "illegal attempt to change the number of external nodes" );
+ }
+ _ref_tree_ext_nodes = ext_nodes;
+ }
+
+ final void analyze( final double cutoff_for_specifics ) throws UserException {
reset();
analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, cutoff_for_specifics );
analyzeGreatestCommonPrefixesUp( _greatest_common_prefixes_up, _separator, cutoff_for_specifics );
private final void analyzeGreatestCommonPrefixes( final List<Prefix> greatest_common_prefixes,
final String separator,
- final double cutoff ) {
+ final double cutoff )
+ throws UserException {
final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes, separator );
if ( !ForesterUtil.isEmpty( l ) ) {
sortPrefixesAccordingToConfidence( l );
- _all = removeLessSpecificPrefixes( l );
+ _all = removeLessSpecificPrefixes( l, separator );
_collapsed = collapse( _all );
_has_specifics = false;
if ( cutoff >= 0 ) {
- _cleaned_spec = obtainSpecifics( cutoff, _all, _collapsed );
+ _cleaned_spec = obtainSpecifics( cutoff, _all, _collapsed, separator );
if ( !ForesterUtil.isEmpty( _cleaned_spec ) ) {
_has_specifics = true;
}
private final void analyzeGreatestCommonPrefixesUp( final List<Prefix> greatest_common_prefixes_up,
final String separator,
- final double cutoff ) {
+ final double cutoff )
+ throws UserException {
final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes_up, separator );
if ( !ForesterUtil.isEmpty( l ) ) {
sortPrefixesAccordingToConfidence( l );
- _all_up = removeLessSpecificPrefixes( l );
+ _all_up = removeLessSpecificPrefixes( l, separator );
_collapsed_up = collapse( _all_up );
_has_specifics_up = false;
if ( cutoff >= 0 ) {
- _cleaned_spec_up = obtainSpecifics( cutoff, _all_up, _collapsed_up );
+ _cleaned_spec_up = obtainSpecifics( cutoff, _all_up, _collapsed_up, separator );
if ( !ForesterUtil.isEmpty( _cleaned_spec_up ) ) {
_has_specifics_up = true;
}
final void analyzeGreatestCommonPrefixesDown( final List<Prefix> greatest_common_prefixes_down,
final String separator,
- final double cutoff ) {
+ final double cutoff )
+ throws UserException {
final List<Prefix> l = obtainAllPrefixes( greatest_common_prefixes_down, separator );
if ( !ForesterUtil.isEmpty( l ) ) {
sortPrefixesAccordingToConfidence( l );
- _all_down = removeLessSpecificPrefixes( l );
+ _all_down = removeLessSpecificPrefixes( l, separator );
_collapsed_down = collapse( _all_down );
_has_specifics_down = false;
if ( cutoff >= 0 ) {
- _cleaned_spec_down = obtainSpecifics( cutoff, _all_down, _collapsed_down );
+ _cleaned_spec_down = obtainSpecifics( cutoff, _all_down, _collapsed_down, separator );
if ( !ForesterUtil.isEmpty( _cleaned_spec_down ) ) {
_has_specifics_down = true;
}
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<>();
+ final List<Prefix> collapsed,
+ final String separator ) {
+ final List<Prefix> cleaned_spec = new ArrayList<Prefix>();
+ final Set<String> collapsed_set = new HashSet<String>();
for( final Prefix prefix : collapsed ) {
collapsed_set.add( prefix.getPrefix() );
}
- final List<Prefix> spec = new ArrayList<>();
+ final List<Prefix> spec = new ArrayList<Prefix>();
for( final Prefix prefix : cleaned ) {
if ( ( prefix.getConfidence() >= cutoff ) && !collapsed_set.contains( prefix.getPrefix() ) ) {
spec.add( prefix );
for( final Prefix o : spec ) {
boolean ok = true;
for( final Prefix i : spec ) {
- if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) ) ) {
+ if ( ( !o.getPrefix().equals( i.getPrefix() ) )
+ && ( ForesterUtil.isContainsPrefix( i.getPrefix(), o.getPrefix(), separator ) ) ) {
ok = false;
break;
}
+ /* if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) ) ) {
+ ok = false;
+ break;
+ }*/
}
if ( ok ) {
cleaned_spec.add( o );
return cleaned_spec;
}
- private final static List<Prefix> collapse( final List<Prefix> cleaned ) {
- final List<Prefix> collapsed = new ArrayList<>();
- final Set<String> firsts = new HashSet<>();
+ private final static List<Prefix> collapse( final List<Prefix> cleaned ) throws UserException {
+ final List<Prefix> collapsed = new ArrayList<Prefix>();
+ final Set<String> firsts = new HashSet<String>();
double confidence_sum = 0;
for( final Prefix prefix : cleaned ) {
final String f = prefix.getPrefixFirstElement();
confidence_sum += prefix.getConfidence();
}
}
- if ( !ForesterUtil.isEqual( confidence_sum, 1.0, 1E-5 ) ) {
- throw new IllegalArgumentException( "Confidences add up to " + confidence_sum + " instead of 1.0" );
+ if ( !ForesterUtil.isEqual( confidence_sum, 1.0, MIN_DIFF ) ) {
+ throw new UserException( "confidences add up to " + confidence_sum + " instead of 1.0" );
}
return collapsed;
}
* I.e. it removes less specific prefixes.
*
*/
- private final static List<Prefix> removeLessSpecificPrefixes( final List<Prefix> l ) {
- final List<Prefix> cleaned = new ArrayList<>();
+ private final static List<Prefix> removeLessSpecificPrefixes( final List<Prefix> l, final String separator ) {
+ final List<Prefix> cleaned = new ArrayList<Prefix>();
for( final Prefix o : l ) {
boolean ok = true;
for( final Prefix i : l ) {
- if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) )
+ /*if ( ( !o.getPrefix().equals( i.getPrefix() ) ) && ( i.getPrefix().startsWith( o.getPrefix() ) )
+ && ForesterUtil.isEqual( i.getConfidence(),
+ o.getConfidence() ) ) {
+ ok = false;
+ break;
+ }*/
+ if ( ( !o.getPrefix().equals( i.getPrefix() ) )
+ && ( ForesterUtil.isContainsPrefix( i.getPrefix(), o.getPrefix(), separator ) )
&& ForesterUtil.isEqual( i.getConfidence(),
o.getConfidence() ) ) {
ok = false;
private final static List<Prefix> obtainAllPrefixes( final List<Prefix> greatest_common_prefixes,
final String separator ) {
- final SortedMap<String, Double> map = new TreeMap<>();
+ final SortedMap<String, Double> map = new TreeMap<String, Double>();
for( final Prefix prefix : greatest_common_prefixes ) {
final List<String> prefixes = ForesterUtil.spliIntoPrefixes( prefix.getPrefix(), separator );
for( final String p : prefixes ) {
}
for( final String key : map.keySet() ) {
for( final Prefix prefix : greatest_common_prefixes ) {
- if ( prefix.getPrefix().startsWith( key ) ) {
+ if ( ForesterUtil.isContainsPrefix( prefix.getPrefix(), key, separator ) ) {
map.put( key, map.get( key ) + prefix.getConfidence() );
}
}
}
- final List<Prefix> l = new ArrayList<>();
+ final List<Prefix> l = new ArrayList<Prefix>();
for( final Entry<String, Double> entry : map.entrySet() ) {
l.add( new Prefix( entry.getKey(), entry.getValue(), separator ) );
}
git://source.jalview.org / jalview.git / blobdiff