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;
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 {
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 );
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 ) {
}
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 );
}
}
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 );
writeResultToTable( res, outtablefile );
}
}
- catch ( final IllegalArgumentException e ) {
+ catch ( final UserException e ) {
ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
}
catch ( final IOException e ) {
}
}
- private final static void performMapping( final Pattern pattern,
- final SortedMap<String, String> 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:" );
System.out.println();
System.out.println( " options:" );
System.out.println( " -" + SPECIFICS_CUTOFF_OPTION
- + "=<double>: the cutoff for \"specific-hit\" support values (default: " + SPECIFICS_CUTOFF_DEFAULT
- + ")" );
- System.out.println( " -" + SEP_OPTION + "=<separator>: the annotation-separator to be used (default: "
+ + "=<double> : the cutoff for \"specific-hit\" support values (default: "
+ + SPECIFICS_CUTOFF_DEFAULT + ")" );
+ System.out.println( " -" + SEP_OPTION + "=<separator> : the annotation-separator to be used (default: "
+ SEP_DEFAULT + ")" );
System.out.println( " -" + MAPPING_FILE_OPTION
+ "=<mapping table>: to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)" );
System.out.println( " -" + QUERY_PATTERN_OPTION
+ "=<query pattern>: 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
+ + "=<separator> : 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();
}
}
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<PhylogenyNode> 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();
final List<String> 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 );
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 );
}
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 );
}
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,
final int child_index = child.getChildNodeIndex();
final List<String> ext_nodes_names = new ArrayList<>();
final List<PhylogenyNode> 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 );
}
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<Confidence> confidences = n.getBranchData().getConfidences();
boolean not_first = false;
Collections.sort( confidences );
}
return null;
}
+
+ public final static void performMapping( final Pattern pattern,
+ final SortedMap<String, String> 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();
+ }
+ }
}
import java.util.TreeMap;
import org.forester.util.ForesterUtil;
+import org.forester.util.UserException;
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 );
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 );
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 );
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 );
return cleaned_spec;
}
- private final static List<Prefix> collapse( final List<Prefix> cleaned ) {
+ private final static List<Prefix> collapse( final List<Prefix> cleaned ) throws UserException {
final List<Prefix> collapsed = new ArrayList<>();
final Set<String> firsts = new HashSet<>();
double confidence_sum = 0;
}
}
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;
}
--- /dev/null
+
+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();
+ }
+}
git://source.jalview.org / jalview.git / commitdiff