public final class Result2 {
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<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 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 = "";
private List<Prefix> _all = null;
private List<Prefix> _collapsed = null;
private List<Prefix> _cleaned_spec = null;
- private boolean _has_specifics;
+ 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 ) {
_separator = separator;
_separator = ".";//TODO make const somewhere
}
+ public List<Prefix> getAllMultiHitPrefixesUp() {
+ return _all_up;
+ }
+
+ public List<Prefix> getCollapsedMultiHitPrefixesUp() {
+ return _collapsed_up;
+ }
+
+ public List<Prefix> getSpecificMultiHitPrefixesUp() {
+ return _cleaned_spec_up;
+ }
+
+ public boolean isHasSpecificMultiHitsPrefixesUp() {
+ return _has_specifics_up;
+ }
+
+ public List<Prefix> getAllMultiHitPrefixesDown() {
+ return _all_down;
+ }
+
+ public List<Prefix> getCollapsedMultiHitPrefixesDown() {
+ return _collapsed_down;
+ }
+
+ public List<Prefix> getSpecificMultiHitPrefixesDown() {
+ return _cleaned_spec_down;
+ }
+
+ public boolean isHasSpecificMultiHitsPrefixesDown() {
+ return _has_specifics_down;
+ }
+
public List<Prefix> getAllMultiHitPrefixes() {
return _all;
}
-
+
public List<Prefix> getCollapsedMultiHitPrefixes() {
return _collapsed;
}
-
+
public List<Prefix> getSpecificMultiHitPrefixes() {
return _cleaned_spec;
}
-
+
public boolean isHasSpecificMultiHitsPrefixes() {
return _has_specifics;
}
-
-
+
void addWarning( final String warning ) {
_warnings.add( warning );
}
_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;
+ void addGreatestCommonPrefixUp( final String prefix_up, final double confidence ) {
+ _greatest_common_prefixes_up.add( new Prefix( prefix_up, confidence, _separator ) );
}
- void setGreatestCommonPrefixDown( final String greatest_common_prefix_down ) {
- _greatest_common_prefix_down = greatest_common_prefix_down;
+ void addGreatestCommonPrefixDown( final String prefix_down, 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_down = greatest_common_clade_confidence_down;
}
- // public String getGreatestCommonPrefix() {
- // return _greatest_common_prefix;
- // }
- public String getGreatestCommonPrefixUp() {
- return _greatest_common_prefix_up;
- }
-
- public String getGreatestCommonPrefixDown() {
- return _greatest_common_prefix_down;
- }
-
public String getGreatestCommonCladeSubtreeConfidence() {
return _greatest_common_clade_subtree_confidence;
}
return _warnings;
}
- void setLeastEncompassingCladeSize( final int lec_ext_nodes ) {
- _lec_ext_nodes = lec_ext_nodes;
+ public void analyzeGreatestCommonPrefixes( final double cutoff_for_specifics ) {
+ 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 );
}
- void setTreeSize( final int p_ext_nodes ) {
- _p_ext_nodes = p_ext_nodes;
+ public void analyzeGreatestCommonPrefixes() {
+ analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, -1 );
}
- public int getLeastEncompassingCladeSize() {
- return _lec_ext_nodes;
+ private void analyzeGreatestCommonPrefixesUp( final double cutoff_for_specifics ) {
+ analyzeGreatestCommonPrefixesUp( _greatest_common_prefixes_up, _separator, cutoff_for_specifics );
}
- public int getTreeSize() {
- return _p_ext_nodes;
+ private void analyzeGreatestCommonPrefixesUp() {
+ analyzeGreatestCommonPrefixesUp( _greatest_common_prefixes_up, _separator, -1 );
}
- public void analyzeGreatestCommonPrefixes( final double cutoff ) {
- analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, cutoff );
+ private void analyzeGreatestCommonPrefixesDown( final double cutoff_for_specifics ) {
+ analyzeGreatestCommonPrefixesDown( _greatest_common_prefixes_down, _separator, cutoff_for_specifics );
}
- public void analyzeGreatestCommonPrefixes() {
- analyzeGreatestCommonPrefixes( _greatest_common_prefixes, _separator, -1 );
+ private void analyzeGreatestCommonPrefixesDown() {
+ analyzeGreatestCommonPrefixesDown( _greatest_common_prefixes_down, _separator, -1 );
}
private final void analyzeGreatestCommonPrefixes( final List<Prefix> greatest_common_prefixes,
}
}
+ 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;
+ }
+ }
+ else {
+ _cleaned_spec_up = null;
+ }
+ }
+
+ private 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;
+ }
+ }
+ else {
+ _cleaned_spec_down = null;
+ }
+ }
+
private final static List<Prefix> obtainSpecifics( final double cutoff,
final List<Prefix> cleaned,
final List<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 cleaned;
}
- private static void sortPrefixesAccordingToConfidence( final List<Prefix> l ) {
+ private final static void sortPrefixesAccordingToConfidence( final List<Prefix> l ) {
Collections.sort( l, new Comparator<Prefix>() {
@Override
sb.append( ForesterUtil.LINE_SEPARATOR );
}
sb.append( ForesterUtil.LINE_SEPARATOR );
- sb.append( "Collapsed with specifics:" );
+ sb.append( "Collapsed With Specifics:" );
sb.append( ForesterUtil.LINE_SEPARATOR );
for( final Prefix prefix : _collapsed ) {
sb.append( prefix );
}
}
}
+ //////
+ 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();
}
}
git://source.jalview.org / jalview.git / blobdiff