3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org/
27 package org.forester.io.parsers.util;
29 import java.io.BufferedReader;
31 import java.io.FileNotFoundException;
32 import java.io.FileReader;
33 import java.io.IOException;
34 import java.io.InputStream;
35 import java.io.InputStreamReader;
36 import java.io.StringReader;
38 import java.util.regex.Matcher;
39 import java.util.regex.Pattern;
41 import org.forester.io.parsers.PhylogenyParser;
42 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
43 import org.forester.io.parsers.nhx.NHXParser;
44 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
45 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
46 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
47 import org.forester.io.parsers.tol.TolParser;
48 import org.forester.phylogeny.Phylogeny;
49 import org.forester.phylogeny.PhylogenyMethods;
50 import org.forester.phylogeny.PhylogenyNode;
51 import org.forester.phylogeny.data.Identifier;
52 import org.forester.phylogeny.data.Taxonomy;
53 import org.forester.util.ForesterConstants;
54 import org.forester.util.ForesterUtil;
56 public final class ParserUtils {
58 final public static String TAX_CODE = "(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA";
59 final public static Pattern TAXOMONY_CODE_PATTERN_A = Pattern.compile( "(?:\\b|_)(" + TAX_CODE + ")\\b" );
60 final public static Pattern TAXOMONY_CODE_PATTERN_BRACKETED = Pattern.compile( "\\[(" + TAX_CODE + ")\\]" );
61 final public static Pattern TAXOMONY_CODE_PATTERN_PFR = Pattern.compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_("
62 + TAX_CODE + ")\\b" );
63 final public static Pattern TAXOMONY_SN_PATTERN = Pattern
64 .compile( "(?:\\b|_)[a-zA-Z0-9]{3,}_([A-Z][a-z]+_[a-z]{2,}(?:_[a-z][a-z0-9_]+)?)\\b" );
65 final public static Pattern TAXOMONY_SN_PATTERN_SN = Pattern
66 .compile( "\\b([A-Z][a-z]+_[a-z]{2,}(?:_[a-z][a-z0-9_]+)?)(?:\\b|_)" );
67 final private static Pattern TAXOMONY_CODE_PATTERN_PFS = Pattern.compile( "(?:\\b|_)[A-Z0-9]{4,}_("
68 + TAX_CODE + ")/\\d+-\\d+\\b" );
69 // final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_A = Pattern.compile( "(?:\\b|(?:[A-Z]_))(\\d{1,7})\\b" );
70 final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFR = Pattern
71 .compile( "(?:\\b|_)[A-Z0-9]{1,}_(\\d{1,7})\\b" );
72 final private static Pattern TAXOMONY_UNIPROT_ID_PATTERN_PFS = Pattern
73 .compile( "(?:\\b|_)[A-Z0-9]{4,}_(\\d{1,7})/\\d+-\\d+\\b" );
75 final public static PhylogenyParser createParserDependingFileContents( final File file,
76 final boolean phyloxml_validate_against_xsd )
77 throws FileNotFoundException, IOException {
78 PhylogenyParser parser = null;
79 final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
80 if ( first_line.startsWith( "<" ) ) {
81 parser = PhyloXmlParser.createPhyloXmlParser();
82 if ( phyloxml_validate_against_xsd ) {
83 final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
84 final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
85 if ( xsd_url != null ) {
86 ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
89 if ( ForesterConstants.RELEASE ) {
90 throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
91 + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
96 else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
97 || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
98 parser = new NexusPhylogeniesParser();
101 parser = new NHXParser();
106 final public static PhylogenyParser createParserDependingOnFileType( final File file,
107 final boolean phyloxml_validate_against_xsd )
108 throws FileNotFoundException, IOException {
109 PhylogenyParser parser = null;
110 parser = ParserUtils.createParserDependingOnSuffix( file.getName(), phyloxml_validate_against_xsd );
111 if ( parser == null ) {
112 parser = createParserDependingFileContents( file, phyloxml_validate_against_xsd );
114 if ( ( parser != null ) && file.toString().toLowerCase().endsWith( ".zip" ) ) {
115 if ( parser instanceof PhyloXmlParser ) {
116 ( ( PhyloXmlParser ) parser ).setZippedInputstream( true );
118 else if ( parser instanceof TolParser ) {
119 ( ( TolParser ) parser ).setZippedInputstream( true );
125 final public static PhylogenyParser createParserDependingOnUrlContents( final URL url,
126 final boolean phyloxml_validate_against_xsd )
127 throws FileNotFoundException, IOException {
128 final String lc_filename = url.getFile().toString().toLowerCase();
129 PhylogenyParser parser = createParserDependingOnSuffix( lc_filename, phyloxml_validate_against_xsd );
130 if ( parser == null ) {
131 final String first_line = ForesterUtil.getFirstLine( url ).trim().toLowerCase();
132 if ( first_line.startsWith( "<" ) ) {
133 parser = PhyloXmlParser.createPhyloXmlParser();
134 if ( phyloxml_validate_against_xsd ) {
135 final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
136 final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
137 if ( xsd_url != null ) {
138 ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
141 throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
142 + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
146 else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
147 || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
148 parser = new NexusPhylogeniesParser();
151 parser = new NHXParser();
154 if ( ( parser != null ) && lc_filename.endsWith( ".zip" ) ) {
155 if ( parser instanceof PhyloXmlParser ) {
156 ( ( PhyloXmlParser ) parser ).setZippedInputstream( true );
158 else if ( parser instanceof TolParser ) {
159 ( ( TolParser ) parser ).setZippedInputstream( true );
165 public static BufferedReader createReader( final Object source ) throws IOException, FileNotFoundException {
166 BufferedReader reader = null;
167 if ( ( source instanceof File ) || ( source instanceof String ) ) {
169 if ( source instanceof File ) {
173 f = new File( ( String ) source );
176 throw new IOException( "[" + f.getAbsolutePath() + "] does not exist" );
178 else if ( !f.isFile() ) {
179 throw new IOException( "[" + f.getAbsolutePath() + "] is not a file" );
181 else if ( !f.canRead() ) {
182 throw new IOException( "[" + f.getAbsolutePath() + "] is not a readable" );
184 reader = new BufferedReader( new FileReader( f ) );
186 else if ( source instanceof InputStream ) {
187 reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) );
189 else if ( ( source instanceof StringBuffer ) || ( source instanceof StringBuilder ) ) {
190 reader = new BufferedReader( new StringReader( source.toString() ) );
193 throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass()
194 + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" );
199 public final static String extractScientificNameFromNodeName( final String name ) {
200 final Matcher m = TAXOMONY_SN_PATTERN.matcher( name );
202 return m.group( 1 ).replace( '_', ' ' );
204 final Matcher m_sn = TAXOMONY_SN_PATTERN_SN.matcher( name );
206 return m_sn.group( 1 ).replace( '_', ' ' );
211 public final static String extractTaxonomyCodeFromNodeName( final String name,
212 final TAXONOMY_EXTRACTION taxonomy_extraction ) {
213 Matcher m = TAXOMONY_CODE_PATTERN_PFS.matcher( name );
217 else if ( ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
218 || ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) ) {
219 m = TAXOMONY_CODE_PATTERN_PFR.matcher( name );
223 else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) {
224 m = TAXOMONY_CODE_PATTERN_A.matcher( name );
233 public final static String extractTaxonomyDataFromNodeName( final PhylogenyNode node,
234 final NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction )
235 throws PhyloXmlDataFormatException {
236 if ( taxonomy_extraction == TAXONOMY_EXTRACTION.NO ) {
237 throw new IllegalArgumentException();
239 final String id = extractUniprotTaxonomyIdFromNodeName( node.getName(), taxonomy_extraction );
240 if ( !ForesterUtil.isEmpty( id ) ) {
241 if ( !node.getNodeData().isHasTaxonomy() ) {
242 node.getNodeData().setTaxonomy( new Taxonomy() );
244 node.getNodeData().getTaxonomy().setIdentifier( new Identifier( id, "uniprot" ) );
248 final String code = extractTaxonomyCodeFromNodeName( node.getName(), taxonomy_extraction );
249 if ( !ForesterUtil.isEmpty( code ) ) {
250 if ( !node.getNodeData().isHasTaxonomy() ) {
251 node.getNodeData().setTaxonomy( new Taxonomy() );
253 node.getNodeData().getTaxonomy().setTaxonomyCode( code );
256 else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) {
257 final String sn = extractScientificNameFromNodeName( node.getName() );
258 if ( !ForesterUtil.isEmpty( sn ) ) {
259 if ( !node.getNodeData().isHasTaxonomy() ) {
260 node.getNodeData().setTaxonomy( new Taxonomy() );
262 node.getNodeData().getTaxonomy().setScientificName( sn );
270 public final static String extractUniprotTaxonomyIdFromNodeName( final String name,
271 final TAXONOMY_EXTRACTION taxonomy_extraction ) {
272 Matcher m = TAXOMONY_UNIPROT_ID_PATTERN_PFS.matcher( name );
276 else if ( ( taxonomy_extraction == TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED )
277 || ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) ) {
278 m = TAXOMONY_UNIPROT_ID_PATTERN_PFR.matcher( name );
282 //else if ( taxonomy_extraction == TAXONOMY_EXTRACTION.AGGRESSIVE ) {
283 // m = TAXOMONY_UNIPROT_ID_PATTERN_A.matcher( name );
285 // return m.group( 1 );
292 public final static Phylogeny[] readPhylogenies( final File file ) throws FileNotFoundException, IOException {
293 return PhylogenyMethods.readPhylogenies( ParserUtils.createParserDependingOnFileType( file, true ), file );
296 public final static Phylogeny[] readPhylogenies( final String file_name ) throws FileNotFoundException, IOException {
297 return readPhylogenies( new File( file_name ) );
301 * Return null if it can not guess the parser to use based on name suffix.
306 final private static PhylogenyParser createParserDependingOnSuffix( final String filename,
307 final boolean phyloxml_validate_against_xsd ) {
308 PhylogenyParser parser = null;
309 final String filename_lc = filename.toLowerCase();
310 if ( filename_lc.endsWith( ".tol" ) || filename_lc.endsWith( ".tolxml" ) || filename_lc.endsWith( ".tol.zip" ) ) {
311 parser = new TolParser();
313 else if ( filename_lc.endsWith( ".xml" ) || filename_lc.endsWith( "phyloxml" ) || filename_lc.endsWith( ".zip" ) ) {
314 parser = PhyloXmlParser.createPhyloXmlParser();
315 if ( phyloxml_validate_against_xsd ) {
316 final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
317 final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
318 if ( xsd_url != null ) {
319 ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
322 if ( ForesterConstants.RELEASE ) {
323 throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
324 + ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
329 else if ( filename_lc.endsWith( ".nexus" ) || filename_lc.endsWith( ".nex" ) || filename_lc.endsWith( ".nx" ) ) {
330 parser = new NexusPhylogeniesParser();
332 else if ( filename_lc.endsWith( ".nhx" ) || filename_lc.endsWith( ".nh" ) || filename_lc.endsWith( ".newick" )
333 || filename_lc.endsWith( ".nwk" ) ) {
334 parser = new NHXParser();