From: cmzmasek Date: Mon, 11 Sep 2017 23:02:28 +0000 (-0700) Subject: in progress... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=efaea5057ced91f5d162cebb6459d206da1d3c82;p=jalview.git in progress... --- diff --git a/forester/java/src/org/forester/application/cladinator.java b/forester/java/src/org/forester/application/cladinator.java index d1b4f44..d7f6e48 100644 --- a/forester/java/src/org/forester/application/cladinator.java +++ b/forester/java/src/org/forester/application/cladinator.java @@ -31,7 +31,6 @@ import java.text.DecimalFormat; import java.util.ArrayList; import java.util.List; import java.util.SortedMap; -import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; @@ -41,34 +40,39 @@ import org.forester.clade_analysis.ResultMulti; import org.forester.io.parsers.PhylogenyParser; import org.forester.io.parsers.util.ParserUtils; import org.forester.phylogeny.Phylogeny; -import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; -import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.util.BasicTable; import org.forester.util.BasicTableParser; import org.forester.util.CommandLineArguments; import org.forester.util.EasyWriter; import org.forester.util.ForesterUtil; +import org.forester.util.UserException; public final class cladinator { - final static private String PRG_NAME = "cladinator"; - final static private String PRG_VERSION = "1.01"; - final static private String PRG_DATE = "170906"; - final static private String PRG_DESC = "clades within clades of annotated labels -- analysis of pplacer-type outputs"; - final static private String E_MAIL = "phyloxml@gmail.com"; - final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String SEP_OPTION = "s"; - final static private String QUERY_PATTERN_OPTION = "q"; - final static private String SPECIFICS_CUTOFF_OPTION = "c"; - final static private String MAPPING_FILE_OPTION = "m"; - final static private double SPECIFICS_CUTOFF_DEFAULT = 0.8; - final static private String SEP_DEFAULT = "."; - final static private Pattern QUERY_PATTERN_DEFAULT = AnalysisMulti.DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE; - private final static DecimalFormat df = new DecimalFormat( "0.0#######" ); + final static private String PRG_NAME = "cladinator"; + final static private String PRG_VERSION = "1.02"; + final static private String PRG_DATE = "170912"; + final static private String PRG_DESC = "clades within clades of annotated labels -- analysis of pplacer-type outputs"; + final static private String E_MAIL = "phyloxml@gmail.com"; + final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String SEP_OPTION = "s"; + final static private String QUERY_PATTERN_OPTION = "q"; + final static private String SPECIFICS_CUTOFF_OPTION = "c"; + final static private String MAPPING_FILE_OPTION = "m"; + final static private String EXTRA_PROCESSING_OPTION1 = "x"; + final static private String EXTRA_PROCESSING1_SEP_OPTION = "xs"; + final static private String EXTRA_PROCESSING1_KEEP_EXTRA_OPTION = "xk"; + final static private String VERBOSE_OPTION = "v"; + final static private double SPECIFICS_CUTOFF_DEFAULT = 0.8; + final static private String SEP_DEFAULT = "."; + final static private Pattern QUERY_PATTERN_DEFAULT = AnalysisMulti.DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE; + final static private String EXTRA_PROCESSING1_SEP_DEFAULT = "|"; + final static private boolean EXTRA_PROCESSING1_KEEP_EXTRA_DEFAULT = false; + private final static DecimalFormat df = new DecimalFormat( "0.0#######" ); public static void main( final String args[] ) { try { @@ -100,6 +104,10 @@ public final class cladinator { allowed_options.add( QUERY_PATTERN_OPTION ); allowed_options.add( SPECIFICS_CUTOFF_OPTION ); allowed_options.add( MAPPING_FILE_OPTION ); + allowed_options.add( EXTRA_PROCESSING_OPTION1 ); + allowed_options.add( EXTRA_PROCESSING1_SEP_OPTION ); + allowed_options.add( EXTRA_PROCESSING1_KEEP_EXTRA_OPTION ); + allowed_options.add( VERBOSE_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); @@ -186,6 +194,47 @@ public final class cladinator { t = null; map = null; } + final boolean extra_processing1; + if ( cla.isOptionSet( EXTRA_PROCESSING_OPTION1 ) ) { + extra_processing1 = true; + } + else { + extra_processing1 = false; + } + String extra_processing1_sep = EXTRA_PROCESSING1_SEP_DEFAULT; + if ( cla.isOptionSet( EXTRA_PROCESSING1_SEP_OPTION ) ) { + if ( !extra_processing1 ) { + ForesterUtil.fatalError( PRG_NAME, + "extra processing is not enabled, cannot set -" + + EXTRA_PROCESSING1_SEP_OPTION + " option" ); + } + if ( cla.isOptionValueSet( EXTRA_PROCESSING1_SEP_OPTION ) ) { + extra_processing1_sep = cla.getOptionValue( EXTRA_PROCESSING1_SEP_OPTION ); + } + else { + ForesterUtil.fatalError( PRG_NAME, "no value for extra processing separator" ); + } + } + if ( extra_processing1_sep != null && extra_processing1_sep.equals( separator ) ) { + ForesterUtil.fatalError( PRG_NAME, + "extra processing separator must not be the same the annotation-separator" ); + } + boolean extra_processing1_keep = EXTRA_PROCESSING1_KEEP_EXTRA_DEFAULT; + if ( cla.isOptionSet( EXTRA_PROCESSING1_KEEP_EXTRA_OPTION ) ) { + if ( !extra_processing1 ) { + ForesterUtil.fatalError( PRG_NAME, + "extra processing is not enabled, cannot set -" + + EXTRA_PROCESSING1_KEEP_EXTRA_OPTION + " option" ); + } + extra_processing1_keep = true; + } + final boolean verbose; + if ( cla.isOptionSet( VERBOSE_OPTION ) ) { + verbose = true; + } + else { + verbose = false; + } System.out.println( "Input tree : " + intreefile ); System.out.println( "Specific-hit support cutoff: " + cutoff_specifics ); if ( mapping_file != null ) { @@ -194,6 +243,11 @@ public final class cladinator { } System.out.println( "Annotation-separator : " + separator ); System.out.println( "Query pattern : " + pattern ); + System.out.println( "Extra processing : " + extra_processing1 ); + if ( extra_processing1 ) { + System.out.println( "Extra processing separator : " + extra_processing1_sep ); + System.out.println( "Keep extra annotations : " + extra_processing1_keep ); + } if ( outtablefile != null ) { System.out.println( "Output table : " + outtablefile ); } @@ -209,7 +263,15 @@ public final class cladinator { } System.out.println( "Ext. nodes in input tree : " + p.getNumberOfExternalNodes() ); if ( map != null ) { - performMapping( pattern, map, p ); + AnalysisMulti.performMapping( pattern, map, p, verbose ); + } + if ( extra_processing1 ) { + AnalysisMulti.performExtraProcessing1( pattern, + p, + extra_processing1_sep, + extra_processing1_keep, + separator, + verbose ); } final ResultMulti res = AnalysisMulti.execute( p, pattern, separator, cutoff_specifics ); printResult( res ); @@ -217,7 +279,7 @@ public final class cladinator { writeResultToTable( res, outtablefile ); } } - catch ( final IllegalArgumentException e ) { + catch ( final UserException e ) { ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); } catch ( final IOException e ) { @@ -229,26 +291,6 @@ public final class cladinator { } } - private final static void performMapping( final Pattern pattern, - final SortedMap map, - Phylogeny p ) { - final PhylogenyNodeIterator it = p.iteratorExternalForward(); - while ( it.hasNext() ) { - final PhylogenyNode node = it.next(); - final String name = node.getName(); - if ( ForesterUtil.isEmpty( name ) ) { - ForesterUtil.fatalError( PRG_NAME, "external node with empty name found" ); - } - final Matcher m = pattern.matcher( name ); - if ( !m.find() ) { - if ( !map.containsKey( name ) ) { - ForesterUtil.fatalError( PRG_NAME, "no mapping for \"" + name + "\" found" ); - } - node.setName( map.get( name ) ); - } - } - } - private final static void printResult( final ResultMulti res ) { System.out.println(); System.out.println( "Result:" ); @@ -352,21 +394,31 @@ public final class cladinator { System.out.println(); System.out.println( " options:" ); System.out.println( " -" + SPECIFICS_CUTOFF_OPTION - + "=: the cutoff for \"specific-hit\" support values (default: " + SPECIFICS_CUTOFF_DEFAULT - + ")" ); - System.out.println( " -" + SEP_OPTION + "=: the annotation-separator to be used (default: " + + "= : the cutoff for \"specific-hit\" support values (default: " + + SPECIFICS_CUTOFF_DEFAULT + ")" ); + System.out.println( " -" + SEP_OPTION + "= : the annotation-separator to be used (default: " + SEP_DEFAULT + ")" ); System.out.println( " -" + MAPPING_FILE_OPTION + "=: to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)" ); System.out.println( " -" + QUERY_PATTERN_OPTION + "=: the regular expression for the query (default: \"" + QUERY_PATTERN_DEFAULT + "\" for pplacer output)" ); + System.out.println( " -" + EXTRA_PROCESSING_OPTION1 + + " : to enable extra processing of annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1\")" ); + System.out.println( " -" + EXTRA_PROCESSING1_SEP_OPTION + + "= : the separator for extra annotations (default: \"" + EXTRA_PROCESSING1_SEP_DEFAULT + + "\")" ); + System.out.println( " -" + EXTRA_PROCESSING1_KEEP_EXTRA_OPTION + + " : to keep extra annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1.Q16611\")" ); + System.out.println( " -" + VERBOSE_OPTION + " : verbose" ); System.out.println(); System.out.println( "Examples:" ); System.out.println(); System.out.println( " " + PRG_NAME + " my_tree.nh result.tsv" ); System.out.println( " " + PRG_NAME + " -c=0.5 -s=. my_tree.nh result.tsv" ); System.out.println( " " + PRG_NAME + " -c=0.9 -s=_ -m=map.tsv my_tree.nh result.tsv" ); + System.out.println( " " + PRG_NAME + " -x -xs=& -xk my_tree.nh result.tsv" ); + System.out.println( " " + PRG_NAME + " -x -xs=\"|\" my_tree.nh result.tsv" ); System.out.println(); } } diff --git a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java index d920d77..2654b82 100644 --- a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java +++ b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java @@ -33,52 +33,56 @@ 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; 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; 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 = "."; + 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 static ResultMulti execute( final Phylogeny p ) { + public static ResultMulti execute( final Phylogeny p ) throws UserException { return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, DEFAULT_SEPARATOR, DEFAULT_CUTOFF_FOR_SPECIFICS ); } - - public static ResultMulti execute( final Phylogeny p, final String separator ) { - return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, separator , DEFAULT_CUTOFF_FOR_SPECIFICS ); + + public static ResultMulti execute( final Phylogeny p, final String separator ) throws UserException { + return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, separator, DEFAULT_CUTOFF_FOR_SPECIFICS ); } - - public static ResultMulti execute( final Phylogeny p, final String separator, final double cutoff_for_specifics ) { - return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, separator , cutoff_for_specifics ); + + public static ResultMulti execute( final Phylogeny p, final String separator, final double cutoff_for_specifics ) + throws UserException { + return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, separator, cutoff_for_specifics ); } - - public static ResultMulti execute( final Phylogeny p, final double cutoff_for_specifics ) { - return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, DEFAULT_SEPARATOR , cutoff_for_specifics ); + + public static ResultMulti execute( final Phylogeny p, final double cutoff_for_specifics ) throws UserException { + return execute( p, DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE, DEFAULT_SEPARATOR, cutoff_for_specifics ); } public static ResultMulti execute( final Phylogeny p, - final Pattern query, - final String separator, - final double cutoff_for_specifics ) { + final Pattern query, + final String separator, + final double cutoff_for_specifics ) + throws UserException { + cleanUpExternalNames( p, separator ); final List qnodes = p.getNodes( query ); final ResultMulti res = new ResultMulti(); for( int i = 0; i < qnodes.size(); ++i ) { final PhylogenyNode qnode = qnodes.get( i ); - //System.out.println( ">>" + qnode.getName() ); if ( qnode.isRoot() ) { - throw new IllegalArgumentException( "Query " + query + " is root." ); + throw new UserException( "query " + query + " is root" ); } if ( qnode.getParent().isRoot() ) { - throw new IllegalArgumentException( "Parent of query " + query + " is root." ); + throw new UserException( "parent of query " + query + " is root" ); } PhylogenyNode qnode_p = qnode.getParent(); PhylogenyNode qnode_pp = qnode.getParent().getParent(); @@ -92,17 +96,13 @@ public final class AnalysisMulti { final List qnode_ext_nodes_names = new ArrayList<>(); for( final PhylogenyNode qnode_ext_node : qnode_pp.getAllExternalDescendants() ) { final String name = qnode_ext_node.getName(); - if ( ForesterUtil.isEmptyTrimmed( name ) ) { - throw new IllegalArgumentException( "external node(s) with empty names found" ); - } final Matcher m = query.matcher( name ); if ( !m.find() ) { qnode_ext_nodes_names.add( name ); } } final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( qnode_ext_nodes_names, separator ); - // System.out.println( greatest_common_prefix ); - Matcher matcher = query.matcher( qnode.getName() ); + final Matcher matcher = query.matcher( qnode.getName() ); String conf_str = null; if ( matcher.find() ) { conf_str = matcher.group( 1 ); @@ -117,9 +117,7 @@ public final class AnalysisMulti { else { res.addGreatestCommonPrefix( UNKNOWN, conf ); } - //final String greatest_common_prefix_up[] = analyzeSiblings( qnode_p, qnode_pp, separator, query, res ); final String greatest_common_prefix_up = analyzeSiblings( qnode_p, qnode_pp, separator, query ); - //System.out.println( "greatest_common_prefix_up=" + greatest_common_prefix_up + " " + conf ); if ( !ForesterUtil.isEmpty( greatest_common_prefix_up ) ) { res.addGreatestCommonPrefixUp( greatest_common_prefix_up, conf ); } @@ -127,7 +125,6 @@ public final class AnalysisMulti { res.addGreatestCommonPrefixUp( UNKNOWN, conf ); } final String greatest_common_prefix_down = analyzeSiblings( qnode, qnode_p, separator, query ); - // System.out.println( "greatest_common_prefix_down=" + greatest_common_prefix_down + " " + conf ); if ( !ForesterUtil.isEmpty( greatest_common_prefix_down ) ) { res.addGreatestCommonPrefixDown( greatest_common_prefix_down, conf ); } @@ -139,6 +136,40 @@ public final class AnalysisMulti { return res; } + 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" ); + final Pattern pattern3 = Pattern.compile( "\\Q" + separator + separator + "\\E" ); + 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(s) with empty annotation found" ); + } + if ( name.endsWith( separator ) ) { + throw new UserException( "illegally formatted annotation found: annotations cannot end with separator: " + + name ); + } + if ( name.startsWith( separator ) ) { + throw new UserException( "illegally formatted annotation found: annotations cannot start with separator: " + + name ); + } + if ( pattern1.matcher( name ).find() ) { + throw new UserException( "illegally formatted annotation found: separator followed by whitespace: " + + name ); + } + if ( pattern2.matcher( name ).find() ) { + throw new UserException( "illegally formatted annotation found: whitespace followed by separator: " + + name ); + } + if ( pattern3.matcher( name ).find() ) { + throw new UserException( "illegally formatted annotation found: empty annotation level: " + name ); + } + node.setName( name.replaceAll( "\\s+", " " ) ); + } + } + private final static String analyzeSiblings( final PhylogenyNode child, final PhylogenyNode parent, final String separator, @@ -146,23 +177,16 @@ public final class AnalysisMulti { final int child_index = child.getChildNodeIndex(); final List ext_nodes_names = new ArrayList<>(); final List descs = parent.getDescendants(); - // String conf = null; for( int i = 0; i < descs.size(); ++i ) { if ( i != child_index ) { final PhylogenyNode d = descs.get( i ); for( final PhylogenyNode n : d.getAllExternalDescendants() ) { final String name = n.getName(); - if ( ForesterUtil.isEmptyTrimmed( name ) ) { - throw new IllegalArgumentException( "external node(s) with empty names found" ); - } final Matcher m = query.matcher( name ); if ( !m.find() ) { ext_nodes_names.add( name ); } } - // if ( descs.size() == 2 ) { - // conf = obtainConfidence( d ); - // } } } final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( ext_nodes_names, separator ); @@ -170,7 +194,7 @@ public final class AnalysisMulti { } private final static String obtainConfidence( final PhylogenyNode n ) { - if ( n.getBranchData().getConfidences() != null && n.getBranchData().getConfidences().size() > 0 ) { + if ( ( n.getBranchData().getConfidences() != null ) && ( n.getBranchData().getConfidences().size() > 0 ) ) { final List confidences = n.getBranchData().getConfidences(); boolean not_first = false; Collections.sort( confidences ); @@ -192,4 +216,86 @@ public final class AnalysisMulti { } return null; } + + public final static void performMapping( final Pattern pattern, + final SortedMap map, + final Phylogeny p, + final boolean verbose ) + throws UserException { + if ( verbose ) { + System.out.println(); + System.out.println( "Id to annotation mapping:" ); + } + 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" ); + } + final Matcher m = pattern.matcher( name ); + if ( !m.find() ) { + if ( !map.containsKey( name ) ) { + throw new UserException( "no mapping for \"" + name + "\" found" ); + } + node.setName( map.get( name ).trim() ); + if ( verbose ) { + System.out.println( name + " -> " + node.getName() ); + } + } + } + if ( verbose ) { + System.out.println(); + } + } + + public final static void performExtraProcessing1( final Pattern pattern, + final Phylogeny p, + final String extra_sep, + final boolean keep, + final String annotation_sep, + final boolean verbose ) + throws UserException { + if ( verbose ) { + System.out.println(); + System.out.println( "Extra 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" ); + } + final Matcher m = pattern.matcher( name ); + if ( !m.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 ); + } + if ( keep ) { + final String extra = name.substring( 0, last_index ).trim(); + sb.append( annotation ); + if ( !ForesterUtil.isEmpty( extra ) ) { + sb.append( annotation_sep ); + sb.append( extra ); + } + } + else { + sb.append( annotation ); + } + node.setName( sb.toString() ); + if ( verbose ) { + System.out.println( name + " -> " + node.getName() ); + } + } + } + } + if ( verbose ) { + System.out.println(); + } + } } diff --git a/forester/java/src/org/forester/clade_analysis/ResultMulti.java b/forester/java/src/org/forester/clade_analysis/ResultMulti.java index 0fcda8b..e3b102e 100644 --- a/forester/java/src/org/forester/clade_analysis/ResultMulti.java +++ b/forester/java/src/org/forester/clade_analysis/ResultMulti.java @@ -36,6 +36,7 @@ import java.util.SortedMap; import java.util.TreeMap; import org.forester.util.ForesterUtil; +import org.forester.util.UserException; public final class ResultMulti { @@ -178,7 +179,7 @@ public final class ResultMulti { _greatest_common_prefixes_down.add( new Prefix( prefix_down, confidence, _separator ) ); } - final void analyze( final double cutoff_for_specifics ) { + 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 ); @@ -202,7 +203,8 @@ public final class ResultMulti { private final void analyzeGreatestCommonPrefixes( final List greatest_common_prefixes, final String separator, - final double cutoff ) { + final double cutoff ) + throws UserException { final List l = obtainAllPrefixes( greatest_common_prefixes, separator ); if ( !ForesterUtil.isEmpty( l ) ) { sortPrefixesAccordingToConfidence( l ); @@ -220,7 +222,8 @@ public final class ResultMulti { private final void analyzeGreatestCommonPrefixesUp( final List greatest_common_prefixes_up, final String separator, - final double cutoff ) { + final double cutoff ) + throws UserException { final List l = obtainAllPrefixes( greatest_common_prefixes_up, separator ); if ( !ForesterUtil.isEmpty( l ) ) { sortPrefixesAccordingToConfidence( l ); @@ -238,7 +241,8 @@ public final class ResultMulti { final void analyzeGreatestCommonPrefixesDown( final List greatest_common_prefixes_down, final String separator, - final double cutoff ) { + final double cutoff ) + throws UserException { final List l = obtainAllPrefixes( greatest_common_prefixes_down, separator ); if ( !ForesterUtil.isEmpty( l ) ) { sortPrefixesAccordingToConfidence( l ); @@ -283,7 +287,7 @@ public final class ResultMulti { return cleaned_spec; } - private final static List collapse( final List cleaned ) { + private final static List collapse( final List cleaned ) throws UserException { final List collapsed = new ArrayList<>(); final Set firsts = new HashSet<>(); double confidence_sum = 0; @@ -296,7 +300,7 @@ public final class ResultMulti { } } if ( !ForesterUtil.isEqual( confidence_sum, 1.0, 1E-5 ) ) { - throw new IllegalArgumentException( "Confidences add up to " + confidence_sum + " instead of 1.0" ); + throw new UserException( "confidences add up to " + confidence_sum + " instead of 1.0" ); } return collapsed; } diff --git a/forester/java/src/org/forester/util/UserException.java b/forester/java/src/org/forester/util/UserException.java new file mode 100644 index 0000000..7136b3f --- /dev/null +++ b/forester/java/src/org/forester/util/UserException.java @@ -0,0 +1,15 @@ + +package org.forester.util; + +public class UserException extends Exception { + + private static final long serialVersionUID = -4607485599991434499L; + + public UserException( final String message ) { + super( message ); + } + + public UserException() { + super(); + } +}