import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.parsers.phyloxml.PhyloXmlParser;
import org.forester.io.parsers.tol.TolParser;
+import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
public final class ParserUtils {
- final public static PhylogenyParser createParserDependingOnUrlContents( final URL url,
- final boolean phyloxml_validate_against_xsd )
+ final public static PhylogenyParser createParserDependingFileContents( final File file,
+ final boolean phyloxml_validate_against_xsd )
throws FileNotFoundException, IOException {
- final String lc_filename = url.getFile().toString().toLowerCase();
- PhylogenyParser parser = createParserDependingOnSuffix( lc_filename, phyloxml_validate_against_xsd );
- if ( ( parser != null ) && lc_filename.endsWith( ".zip" ) ) {
- if ( parser instanceof PhyloXmlParser ) {
- ( ( PhyloXmlParser ) parser ).setZippedInputstream( true );
- }
- else if ( parser instanceof TolParser ) {
- ( ( TolParser ) parser ).setZippedInputstream( true );
- }
- }
- if ( parser == null ) {
- final String first_line = ForesterUtil.getFirstLine( url ).trim().toLowerCase();
- if ( first_line.startsWith( "<" ) ) {
- parser = new PhyloXmlParser();
- if ( phyloxml_validate_against_xsd ) {
- final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
- final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
- if ( xsd_url != null ) {
- ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
- }
- else {
+ PhylogenyParser parser = null;
+ final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
+ if ( first_line.startsWith( "<" ) ) {
+ parser = new PhyloXmlParser();
+ if ( phyloxml_validate_against_xsd ) {
+ final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
+ final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
+ if ( xsd_url != null ) {
+ ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
+ }
+ else {
+ if ( ForesterConstants.RELEASE ) {
throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
+ ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
}
}
}
- else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
- || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
- parser = new NexusPhylogeniesParser();
- }
- else {
- parser = new NHXParser();
- }
+ }
+ else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
+ || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
+ parser = new NexusPhylogeniesParser();
+ }
+ else {
+ parser = new NHXParser();
+ }
+ return parser;
+ }
+
+ final public static PhylogenyParser createParserDependingOnFileType( final File file,
+ final boolean phyloxml_validate_against_xsd )
+ throws FileNotFoundException, IOException {
+ PhylogenyParser parser = null;
+ parser = ParserUtils.createParserDependingOnSuffix( file.getName(), phyloxml_validate_against_xsd );
+ if ( parser == null ) {
+ parser = createParserDependingFileContents( file, phyloxml_validate_against_xsd );
}
return parser;
}
return parser;
}
- final public static PhylogenyParser createParserDependingOnFileType( final File file,
- final boolean phyloxml_validate_against_xsd )
+ final public static PhylogenyParser createParserDependingOnUrlContents( final URL url,
+ final boolean phyloxml_validate_against_xsd )
throws FileNotFoundException, IOException {
- PhylogenyParser parser = null;
- parser = ParserUtils.createParserDependingOnSuffix( file.getName(), phyloxml_validate_against_xsd );
- if ( parser == null ) {
- parser = createParserDependingFileContents( file, phyloxml_validate_against_xsd );
+ final String lc_filename = url.getFile().toString().toLowerCase();
+ PhylogenyParser parser = createParserDependingOnSuffix( lc_filename, phyloxml_validate_against_xsd );
+ if ( ( parser != null ) && lc_filename.endsWith( ".zip" ) ) {
+ if ( parser instanceof PhyloXmlParser ) {
+ ( ( PhyloXmlParser ) parser ).setZippedInputstream( true );
+ }
+ else if ( parser instanceof TolParser ) {
+ ( ( TolParser ) parser ).setZippedInputstream( true );
+ }
}
- return parser;
- }
-
- final public static PhylogenyParser createParserDependingFileContents( final File file,
- final boolean phyloxml_validate_against_xsd )
- throws FileNotFoundException, IOException {
- PhylogenyParser parser = null;
- final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
- if ( first_line.startsWith( "<" ) ) {
- parser = new PhyloXmlParser();
- if ( phyloxml_validate_against_xsd ) {
- final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
- final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
- if ( xsd_url != null ) {
- ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
- }
- else {
- if ( ForesterConstants.RELEASE ) {
+ if ( parser == null ) {
+ final String first_line = ForesterUtil.getFirstLine( url ).trim().toLowerCase();
+ if ( first_line.startsWith( "<" ) ) {
+ parser = new PhyloXmlParser();
+ if ( phyloxml_validate_against_xsd ) {
+ final ClassLoader cl = PhyloXmlParser.class.getClassLoader();
+ final URL xsd_url = cl.getResource( ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE );
+ if ( xsd_url != null ) {
+ ( ( PhyloXmlParser ) parser ).setValidateAgainstSchema( xsd_url.toString() );
+ }
+ else {
throw new RuntimeException( "failed to get URL for phyloXML XSD from jar file from ["
+ ForesterConstants.LOCAL_PHYLOXML_XSD_RESOURCE + "]" );
}
}
}
+ else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
+ || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
+ parser = new NexusPhylogeniesParser();
+ }
+ else {
+ parser = new NHXParser();
+ }
}
- else if ( ( first_line.startsWith( "nexus" ) ) || ( first_line.startsWith( "#nexus" ) )
- || ( first_line.startsWith( "# nexus" ) ) || ( first_line.startsWith( "begin" ) ) ) {
- parser = new NexusPhylogeniesParser();
+ return parser;
+ }
+
+ public static BufferedReader createReader( final Object source ) throws IOException, FileNotFoundException {
+ BufferedReader reader = null;
+ if ( ( source instanceof File ) || ( source instanceof String ) ) {
+ File f = null;
+ if ( source instanceof File ) {
+ f = ( File ) source;
+ }
+ else {
+ f = new File( ( String ) source );
+ }
+ if ( !f.exists() ) {
+ throw new IOException( "[" + f.getAbsolutePath() + "] does not exist" );
+ }
+ else if ( !f.isFile() ) {
+ throw new IOException( "[" + f.getAbsolutePath() + "] is not a file" );
+ }
+ else if ( !f.canRead() ) {
+ throw new IOException( "[" + f.getAbsolutePath() + "] is not a readable" );
+ }
+ reader = new BufferedReader( new FileReader( f ) );
+ }
+ else if ( source instanceof InputStream ) {
+ reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) );
+ }
+ else if ( ( source instanceof StringBuffer ) || ( source instanceof StringBuilder ) ) {
+ reader = new BufferedReader( new StringReader( source.toString() ) );
}
else {
- parser = new NHXParser();
+ throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass()
+ + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" );
}
- return parser;
+ return reader;
}
/**
final boolean limit_to_five,
final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction ) {
if ( ( name.indexOf( "_" ) > 0 )
- && ( name.length() < 25 )
- && ( name.lastIndexOf( "_" ) == name.indexOf( "_" ) )
+ && ( name.length() < 31 )
+ // && ( name.lastIndexOf( "_" ) == name.indexOf( "_" ) )
&& ( name.indexOf( "|" ) < 0 )
&& ( name.indexOf( "." ) < 0 )
&& ( ( taxonomy_extraction != PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY ) || ( name
final String[] s = name.split( "[_/]" );
if ( s.length > 1 ) {
String str = s[ 1 ];
- if ( limit_to_five ) {
- if ( str.length() > 5 ) {
- str = str.substring( 0, 5 );
- }
- else if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) {
+ if ( ( str.length() < 6 ) || ( !limit_to_five && ( str.length() < 7 ) ) ) {
+ if ( ( str.length() < 5 ) && ( str.startsWith( "RAT" ) || str.startsWith( "PIG" ) ) ) {
str = str.substring( 0, 3 );
}
+ final Matcher uc_letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str );
+ if ( !uc_letters_and_numbers.matches() ) {
+ return null;
+ }
+ final Matcher numbers_only = NHXParser.NUMBERS_ONLY_PATTERN.matcher( str );
+ if ( numbers_only.matches() ) {
+ return null;
+ }
+ return str;
}
- final Matcher letters_and_numbers = NHXParser.UC_LETTERS_NUMBERS_PATTERN.matcher( str );
- if ( !letters_and_numbers.matches() ) {
- return null;
- }
- final Matcher numbers_only = NHXParser.NUMBERS_ONLY_PATTERN.matcher( str );
- if ( numbers_only.matches() ) {
- return null;
- }
- return str;
}
}
return null;
}
- public static BufferedReader createReader( final Object source ) throws IOException, FileNotFoundException {
- BufferedReader reader = null;
- if ( ( source instanceof File ) || ( source instanceof String ) ) {
- File f = null;
- if ( source instanceof File ) {
- f = ( File ) source;
- }
- else {
- f = new File( ( String ) source );
- }
- if ( !f.exists() ) {
- throw new IOException( "[" + f.getAbsolutePath() + "] does not exist" );
- }
- else if ( !f.isFile() ) {
- throw new IOException( "[" + f.getAbsolutePath() + "] is not a file" );
- }
- else if ( !f.canRead() ) {
- throw new IOException( "[" + f.getAbsolutePath() + "] is not a readable" );
- }
- reader = new BufferedReader( new FileReader( f ) );
- }
- else if ( source instanceof InputStream ) {
- reader = new BufferedReader( new InputStreamReader( ( InputStream ) source ) );
- }
- else if ( ( source instanceof StringBuffer ) || ( source instanceof StringBuilder ) ) {
- reader = new BufferedReader( new StringReader( source.toString() ) );
- }
- else {
- throw new IllegalArgumentException( "attempt to parse object of type [" + source.getClass()
- + "] (can only parse objects of type File/String, InputStream, StringBuffer, or StringBuilder)" );
- }
- return reader;
+ public final static Phylogeny[] readPhylogenies( final File file ) throws FileNotFoundException, IOException {
+ return PhylogenyMethods.readPhylogenies( ParserUtils.createParserDependingOnFileType( file, true ), file );
+ }
+
+ public final static Phylogeny[] readPhylogenies( final String file_name ) throws FileNotFoundException, IOException {
+ return readPhylogenies( new File( file_name ) );
}
}
git://source.jalview.org / jalview.git / blobdiff