X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fclade_analysis%2FAnalysisMulti.java;h=3970e5d16310521b0fd7c34381aeb9d16fa3bd47;hb=1706deea223bc1a30d170596192d726b6847b7eb;hp=2654b8284f4ce9ba1a5cd04917d67e938f2dab72;hpb=efaea5057ced91f5d162cebb6459d206da1d3c82;p=jalview.git diff --git a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java index 2654b82..3970e5d 100644 --- a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java +++ b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java @@ -31,7 +31,6 @@ package org.forester.clade_analysis; import java.util.ArrayList; -import java.util.Collections; import java.util.List; import java.util.SortedMap; import java.util.regex.Matcher; @@ -39,7 +38,6 @@ import java.util.regex.Pattern; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyNode; -import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.util.ForesterUtil; import org.forester.util.UserException; @@ -49,7 +47,7 @@ public final class AnalysisMulti { 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 final static Pattern DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE = Pattern.compile( "_#\\d+_M=(.+)" ); public static ResultMulti execute( final Phylogeny p ) throws UserException { return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, DEFAULT_SEPARATOR, DEFAULT_CUTOFF_FOR_SPECIFICS ); @@ -73,9 +71,15 @@ public final class AnalysisMulti { final String separator, final double cutoff_for_specifics ) throws UserException { + if ( ForesterUtil.isEmpty( separator ) ) { + throw new IllegalArgumentException( "separator must not be null or empty" ); + } cleanUpExternalNames( p, separator ); final List qnodes = p.getNodes( query ); final ResultMulti res = new ResultMulti(); + res.setQueryNamePrefix( obtainQueryPrefix( query, qnodes ) ); + res.setTotalNumberOfMatches( qnodes.size() ); + res.setReferenceTreeNumberOfExternalNodes( p.getNumberOfExternalNodes() - qnodes.size() ); for( int i = 0; i < qnodes.size(); ++i ) { final PhylogenyNode qnode = qnodes.get( i ); if ( qnode.isRoot() ) { @@ -93,7 +97,7 @@ public final class AnalysisMulti { while ( qnode_pp.getNumberOfDescendants() == 1 ) { qnode_pp = qnode_pp.getParent(); } - final List qnode_ext_nodes_names = new ArrayList<>(); + final List qnode_ext_nodes_names = new ArrayList(); for( final PhylogenyNode qnode_ext_node : qnode_pp.getAllExternalDescendants() ) { final String name = qnode_ext_node.getName(); final Matcher m = query.matcher( name ); @@ -108,7 +112,7 @@ public final class AnalysisMulti { conf_str = matcher.group( 1 ); } else { - throw new IllegalStateException( "pattern did not match -- this should have never happened!" ); + throw new IllegalStateException( "query pattern does not match [this should have never happened!]" ); } final double conf = Double.parseDouble( conf_str ); if ( !ForesterUtil.isEmpty( greatest_common_prefix ) ) { @@ -136,6 +140,29 @@ public final class AnalysisMulti { return res; } + private final static String obtainQueryPrefix( final Pattern query, final List qnodes ) + throws UserException { + String query_name_prefix = null; + for( final PhylogenyNode n : qnodes ) { + final String name = n.getName(); + final Matcher matcher = query.matcher( name ); + if ( matcher.find() ) { + final String prefix = name.substring( 0, matcher.start() ); + if ( ForesterUtil.isEmpty( prefix ) ) { + throw new UserException( "query nodes with empty label prefix found: \"" + prefix + "\"" ); + } + if ( query_name_prefix == null ) { + query_name_prefix = prefix; + } + else if ( !query_name_prefix.equals( prefix ) ) { + throw new UserException( "query nodes with different label prefixes found: \"" + query_name_prefix + + "\" and \"" + prefix + "\"" ); + } + } + } + return query_name_prefix; + } + private final static void cleanUpExternalNames( final Phylogeny p, final String separator ) throws UserException { final Pattern pattern1 = Pattern.compile( "\\Q" + separator + "\\E" + "\\s+" ); final Pattern pattern2 = Pattern.compile( "\\s+" + "\\Q" + separator + "\\E" ); @@ -175,7 +202,7 @@ public final class AnalysisMulti { final String separator, final Pattern query ) { final int child_index = child.getChildNodeIndex(); - final List ext_nodes_names = new ArrayList<>(); + final List ext_nodes_names = new ArrayList(); final List descs = parent.getDescendants(); for( int i = 0; i < descs.size(); ++i ) { if ( i != child_index ) { @@ -193,30 +220,6 @@ public final class AnalysisMulti { return greatest_common_prefix; } - private final static String obtainConfidence( final PhylogenyNode n ) { - if ( ( n.getBranchData().getConfidences() != null ) && ( n.getBranchData().getConfidences().size() > 0 ) ) { - final List confidences = n.getBranchData().getConfidences(); - boolean not_first = false; - Collections.sort( confidences ); - final StringBuilder sb = new StringBuilder(); - for( final Confidence confidence : confidences ) { - final double value = confidence.getValue(); - if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - if ( not_first ) { - sb.append( " / " ); - } - else { - not_first = true; - } - sb.append( ( ForesterUtil.isEmpty( confidence.getType() ) ? "confidence: " - : confidence.getType() + ": " ) + value ); - } - } - return sb.toString(); - } - return null; - } - public final static void performMapping( final Pattern pattern, final SortedMap map, final Phylogeny p, @@ -249,7 +252,7 @@ public final class AnalysisMulti { } } - public final static void performExtraProcessing1( final Pattern pattern, + public final static void performExtraProcessing1( final Pattern query_pattern, final Phylogeny p, final String extra_sep, final boolean keep, @@ -267,14 +270,13 @@ public final class AnalysisMulti { if ( ForesterUtil.isEmpty( name ) ) { throw new UserException( "external node with empty name found" ); } - final Matcher m = pattern.matcher( name ); - if ( !m.find() ) { + if ( !query_pattern.matcher( name ).find() ) { final StringBuilder sb = new StringBuilder(); final int last_index = name.lastIndexOf( extra_sep ); if ( last_index >= 0 ) { final String annotation = name.substring( last_index + 1 ).trim(); if ( ForesterUtil.isEmptyTrimmed( annotation ) ) { - throw new UserException( "illegal format:" + name ); + throw new UserException( "llegally formatted annotation: " + name ); } if ( keep ) { final String extra = name.substring( 0, last_index ).trim(); @@ -298,4 +300,55 @@ public final class AnalysisMulti { System.out.println(); } } + + public final static void performSpecialProcessing1( final Pattern query_pattern, + final Phylogeny p, + final String annotation_sep, + final Pattern special_pattern, + final boolean verbose ) + throws UserException { + if ( verbose ) { + System.out.println(); + System.out.println( "Special annotation processing:" ); + } + final PhylogenyNodeIterator it = p.iteratorExternalForward(); + while ( it.hasNext() ) { + final PhylogenyNode node = it.next(); + final String name = node.getName().trim(); + if ( ForesterUtil.isEmpty( name ) ) { + throw new UserException( "external node with empty name found" ); + } + if ( !query_pattern.matcher( name ).find() ) { + final Matcher special_m = special_pattern.matcher( name ); + if ( special_m.matches() ) { + final int c = special_m.groupCount(); + if ( c < 1 ) { + throw new UserException( "illegal special pattern: " + special_pattern + + " (need at least one capturing group)" ); + } + final StringBuilder sb = new StringBuilder(); + for( int i = 1; i <= c; ++i ) { + final String g = special_m.group( i ); + if ( !ForesterUtil.isEmpty( g ) ) { + if ( i > 1 ) { + sb.append( annotation_sep ); + } + sb.append( special_m.group( i ) ); + } + } + node.setName( sb.toString() ); + if ( verbose ) { + System.out.println( name + " -> " + node.getName() ); + } + } + else { + throw new UserException( "illegally formatted annotation for special processing: " + name + + " (expected pattern: " + special_pattern + ")" ); + } + } + } + if ( verbose ) { + System.out.println(); + } + } }