org.forester.util.ForesterUtil Maven / Gradle / Ivy
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// $Id:
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.util;
import java.awt.Color;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.io.Writer;
import java.math.BigDecimal;
import java.net.URL;
import java.net.URLConnection;
import java.text.DateFormat;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.forester.archaeopteryx.Constants;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Distribution;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.protein.BasicProtein;
import org.forester.protein.Domain;
import org.forester.protein.Protein;
import org.forester.sequence.MolecularSequence;
import org.forester.sequence.MolecularSequence.TYPE;
import org.forester.surfacing.SurfacingUtil;
public final class ForesterUtil {
public final static String FILE_SEPARATOR = System.getProperty( "file.separator" );
public static final NumberFormat FORMATTER_06;
public static final NumberFormat FORMATTER_3;
public static final NumberFormat FORMATTER_6;
public static final NumberFormat FORMATTER_9;
public final static String JAVA_VENDOR = System.getProperty( "java.vendor" );
public final static String JAVA_VERSION = System.getProperty( "java.version" );
public final static String LINE_SEPARATOR = System.getProperty( "line.separator" );
public static final String NCBI_GI = "http://www.ncbi.nlm.nih.gov/protein/gi:";
public static final String NCBI_NUCCORE = "http://www.ncbi.nlm.nih.gov/nuccore/";
public static final String NCBI_PROTEIN = "http://www.ncbi.nlm.nih.gov/protein/";
public static final BigDecimal NULL_BD = new BigDecimal( 0 );
public final static String OS_ARCH = System.getProperty( "os.arch" );
public final static String OS_NAME = System.getProperty( "os.name" );
public final static String OS_VERSION = System.getProperty( "os.version" );
public static final String PDB = "http://www.pdb.org/pdb/explore/explore.do?pdbId=";
public final static String UNIPROT_KB = "http://www.uniprot.org/uniprot/";
public final static double ZERO_DIFF = 1.0E-9;
private static final Pattern PARANTHESESABLE_NH_CHARS_PATTERN = Pattern.compile( "[(),;\\s:\\[\\]]" );
static {
final DecimalFormatSymbols dfs = new DecimalFormatSymbols();
dfs.setDecimalSeparator( '.' );
// dfs.setGroupingSeparator( ( char ) 0 );
FORMATTER_9 = new DecimalFormat( "#.#########", dfs );
FORMATTER_6 = new DecimalFormat( "#.######", dfs );
FORMATTER_06 = new DecimalFormat( "0.######", dfs );
FORMATTER_3 = new DecimalFormat( "#.###", dfs );
}
final public static void appendSeparatorIfNotEmpty( final StringBuffer sb, final char separator ) {
if ( sb.length() > 0 ) {
sb.append( separator );
}
}
/**
* This calculates a color. If value is equal to min the returned color is
* minColor, if value is equal to max the returned color is maxColor,
* otherwise a color 'proportional' to value is returned.
*
* @param value
* the value
* @param min
* the smallest value
* @param max
* the largest value
* @param minColor
* the color for min
* @param maxColor
* the color for max
* @return a Color
*/
final public static Color calcColor( double value,
final double min,
final double max,
final Color minColor,
final Color maxColor ) {
if ( value < min ) {
value = min;
}
if ( value > max ) {
value = max;
}
final double x = ForesterUtil.calculateColorFactor( value, max, min );
final int red = ForesterUtil.calculateColorComponent( minColor.getRed(), maxColor.getRed(), x );
final int green = ForesterUtil.calculateColorComponent( minColor.getGreen(), maxColor.getGreen(), x );
final int blue = ForesterUtil.calculateColorComponent( minColor.getBlue(), maxColor.getBlue(), x );
return new Color( red, green, blue );
}
/**
* This calculates a color. If value is equal to min the returned color is
* minColor, if value is equal to max the returned color is maxColor, if
* value is equal to mean the returned color is meanColor, otherwise a color
* 'proportional' to value is returned -- either between min-mean or
* mean-max
*
* @param value
* the value
* @param min
* the smallest value
* @param max
* the largest value
* @param mean
* the mean/median value
* @param minColor
* the color for min
* @param maxColor
* the color for max
* @param meanColor
* the color for mean
* @return a Color
*/
final public static Color calcColor( double value,
final double min,
final double max,
final double mean,
final Color minColor,
final Color maxColor,
final Color meanColor ) {
if ( value < min ) {
value = min;
}
if ( value > max ) {
value = max;
}
if ( value < mean ) {
final double x = ForesterUtil.calculateColorFactor( value, mean, min );
final int red = ForesterUtil.calculateColorComponent( minColor.getRed(), meanColor.getRed(), x );
final int green = ForesterUtil.calculateColorComponent( minColor.getGreen(), meanColor.getGreen(), x );
final int blue = ForesterUtil.calculateColorComponent( minColor.getBlue(), meanColor.getBlue(), x );
return new Color( red, green, blue );
}
else if ( value > mean ) {
final double x = ForesterUtil.calculateColorFactor( value, max, mean );
final int red = ForesterUtil.calculateColorComponent( meanColor.getRed(), maxColor.getRed(), x );
final int green = ForesterUtil.calculateColorComponent( meanColor.getGreen(), maxColor.getGreen(), x );
final int blue = ForesterUtil.calculateColorComponent( meanColor.getBlue(), maxColor.getBlue(), x );
return new Color( red, green, blue );
}
else {
return meanColor;
}
}
/**
* Helper method for calcColor methods.
*
* @param smallercolor_component_x
* color component the smaller color
* @param largercolor_component_x
* color component the larger color
* @param x
* factor
* @return an int representing a color component
*/
final private static int calculateColorComponent( final double smallercolor_component_x,
final double largercolor_component_x,
final double x ) {
return ( int ) ( smallercolor_component_x + ( ( x * ( largercolor_component_x - smallercolor_component_x ) ) / 255.0 ) );
}
/**
* Helper method for calcColor methods.
*
*
* @param value
* the value
* @param larger
* the largest value
* @param smaller
* the smallest value
* @return a normalized value between larger and smaller
*/
final private static double calculateColorFactor( final double value, final double larger, final double smaller ) {
return ( 255.0 * ( value - smaller ) ) / ( larger - smaller );
}
public static int calculateOverlap( final Domain domain, final List covered_positions ) {
int overlap_count = 0;
for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
++overlap_count;
}
}
return overlap_count;
}
final public static String collapseWhiteSpace( final String s ) {
return s.replaceAll( "[\\s]+", " " );
}
final public static void collection2file( final File file, final Collection data, final String separator )
throws IOException {
final Writer writer = new BufferedWriter( new FileWriter( file ) );
collection2writer( writer, data, separator );
writer.close();
}
final public static void collection2writer( final Writer writer, final Collection data, final String separator )
throws IOException {
boolean first = true;
for( final Object object : data ) {
if ( !first ) {
writer.write( separator );
}
else {
first = false;
}
writer.write( object.toString() );
}
}
final public static String colorToHex( final Color color ) {
final String rgb = Integer.toHexString( color.getRGB() );
return rgb.substring( 2, rgb.length() );
}
synchronized public static void copyFile( final File in, final File out ) throws IOException {
final FileInputStream in_s = new FileInputStream( in );
final FileOutputStream out_s = new FileOutputStream( out );
try {
final byte[] buf = new byte[ 1024 ];
int i = 0;
while ( ( i = in_s.read( buf ) ) != -1 ) {
out_s.write( buf, 0, i );
}
}
catch ( final IOException e ) {
throw e;
}
finally {
if ( in_s != null ) {
in_s.close();
}
if ( out_s != null ) {
out_s.close();
}
}
}
final public static int countChars( final String str, final char c ) {
int count = 0;
for( int i = 0; i < str.length(); ++i ) {
if ( str.charAt( i ) == c ) {
++count;
}
}
return count;
}
final public static BufferedWriter createBufferedWriter( final File file ) throws IOException {
if ( file.exists() ) {
throw new IOException( "[" + file + "] already exists" );
}
return new BufferedWriter( new FileWriter( file ) );
}
final public static BufferedWriter createBufferedWriter( final String name ) throws IOException {
return new BufferedWriter( new FileWriter( createFileForWriting( name ) ) );
}
final public static EasyWriter createEasyWriter( final File file ) throws IOException {
return new EasyWriter( createBufferedWriter( file ) );
}
final public static BufferedWriter createEasyWriter( final String name ) throws IOException {
return createEasyWriter( createFileForWriting( name ) );
}
final public static File createFileForWriting( final String name ) throws IOException {
final File file = new File( name );
if ( file.exists() ) {
throw new IOException( "[" + name + "] already exists" );
}
return file;
}
final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
if ( !node.getNodeData().isHasDate() ) {
node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
}
}
final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
if ( !node.getNodeData().isHasDistribution() ) {
node.getNodeData().setDistribution( new Distribution( "" ) );
}
}
public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
if ( !node.getNodeData().isHasSequence() ) {
node.getNodeData().setSequence( new Sequence() );
}
}
public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
if ( !node.getNodeData().isHasTaxonomy() ) {
node.getNodeData().setTaxonomy( new Taxonomy() );
}
}
public static void fatalError( final String message ) {
System.err.println();
System.err.println( "error: " + message );
System.err.println();
System.exit( -1 );
}
public static void fatalError( final String prg_name, final String message ) {
System.err.println();
System.err.println( "[" + prg_name + "] > " + message );
System.err.println();
System.exit( -1 );
}
public static void fatalErrorIfFileNotReadable( final File file ) {
final String error = isReadableFile( file );
if ( !isEmpty( error ) ) {
System.err.println();
System.err.println( "error: " + error );
System.err.println();
System.exit( -1 );
}
}
public static void fatalErrorIfFileNotReadable( final String prg_name, final File file ) {
final String error = isReadableFile( file );
if ( !isEmpty( error ) ) {
System.err.println();
System.err.println( "[" + prg_name + "] > " + error );
System.err.println();
System.exit( -1 );
}
}
public static String[][] file22dArray( final File file ) throws IOException {
final List list = new ArrayList();
final BufferedReader in = new BufferedReader( new FileReader( file ) );
String str;
while ( ( str = in.readLine() ) != null ) {
str = str.trim();
if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
list.add( str );
}
}
in.close();
final String[][] ary = new String[ list.size() ][ 2 ];
final Pattern pa = Pattern.compile( "(\\S+)\\s+(\\S+)" );
int i = 0;
for( final String s : list ) {
final Matcher m = pa.matcher( s );
if ( m.matches() ) {
ary[ i ][ 0 ] = m.group( 1 );
ary[ i ][ 1 ] = m.group( 2 );
++i;
}
else {
throw new IOException( "unexpcted format: " + s );
}
}
return ary;
}
public static String[] file2array( final File file ) throws IOException {
final List list = file2list( file );
final String[] ary = new String[ list.size() ];
int i = 0;
for( final String s : list ) {
ary[ i++ ] = s;
}
return ary;
}
final public static List file2list( final File file ) throws IOException {
final List list = new ArrayList();
final BufferedReader in = new BufferedReader( new FileReader( file ) );
String str;
while ( ( str = in.readLine() ) != null ) {
str = str.trim();
if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
for( final String s : splitString( str ) ) {
list.add( s );
}
}
}
in.close();
return list;
}
final public static SortedSet file2set( final File file ) throws IOException {
final SortedSet set = new TreeSet();
final BufferedReader in = new BufferedReader( new FileReader( file ) );
String str;
while ( ( str = in.readLine() ) != null ) {
str = str.trim();
if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
for( final String s : splitString( str ) ) {
set.add( s );
}
}
}
in.close();
return set;
}
final public static String getCurrentDateTime() {
final DateFormat format = new SimpleDateFormat( "yyyy/MM/dd HH:mm:ss" );
return format.format( new Date() );
}
final public static String getFileSeparator() {
return ForesterUtil.FILE_SEPARATOR;
}
final public static String getFirstLine( final Object source ) throws FileNotFoundException, IOException {
BufferedReader reader = null;
if ( source instanceof File ) {
final File f = ( File ) 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 String ) {
reader = new BufferedReader( new StringReader( ( String ) source ) );
}
else if ( source instanceof StringBuffer ) {
reader = new BufferedReader( new StringReader( source.toString() ) );
}
else if ( source instanceof URL ) {
final URLConnection url_connection = ( ( URL ) source ).openConnection();
url_connection.setDefaultUseCaches( false );
reader = new BufferedReader( new InputStreamReader( url_connection.getInputStream() ) );
}
else {
throw new IllegalArgumentException( "dont know how to read [" + source.getClass() + "]" );
}
String line;
while ( ( line = reader.readLine() ) != null ) {
line = line.trim();
if ( !ForesterUtil.isEmpty( line ) ) {
if ( reader != null ) {
reader.close();
}
return line;
}
}
if ( reader != null ) {
reader.close();
}
return line;
}
final public static String getForesterLibraryInformation() {
return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")";
}
final public static String getLineSeparator() {
return ForesterUtil.LINE_SEPARATOR;
}
final public static MolecularSequence.TYPE guessMolecularSequenceType( final String mol_seq ) {
if ( mol_seq.contains( "L" ) || mol_seq.contains( "I" ) || mol_seq.contains( "E" ) || mol_seq.contains( "H" )
|| mol_seq.contains( "D" ) || mol_seq.contains( "Q" ) ) {
return TYPE.AA;
}
else {
if ( mol_seq.contains( "T" ) ) {
return TYPE.DNA;
}
else if ( mol_seq.contains( "U" ) ) {
return TYPE.RNA;
}
}
return null;
}
final public static void increaseCountingMap( final Map counting_map, final String item_name ) {
if ( !counting_map.containsKey( item_name ) ) {
counting_map.put( item_name, 1 );
}
else {
counting_map.put( item_name, counting_map.get( item_name ) + 1 );
}
}
final public static boolean isEmpty( final List l ) {
if ( ( l == null ) || l.isEmpty() ) {
return true;
}
for( final Object o : l ) {
if ( o != null ) {
return false;
}
}
return true;
}
final public static boolean isEmpty( final Set s ) {
if ( ( s == null ) || s.isEmpty() ) {
return true;
}
for( final Object o : s ) {
if ( o != null ) {
return false;
}
}
return true;
}
final public static boolean isEmpty( final String s ) {
return ( ( s == null ) || ( s.length() < 1 ) );
}
/**
* Returns true is Domain domain falls in an uninterrupted stretch of
* covered positions.
*
* @param domain
* @param covered_positions
* @return
*/
public static boolean isEngulfed( final Domain domain, final List covered_positions ) {
for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
return false;
}
}
return true;
}
final public static boolean isEqual( final double a, final double b ) {
return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
}
final public static boolean isEven( final int n ) {
return ( n % 2 ) == 0;
}
/**
* This determines whether String[] a and String[] b have at least one
* String in common (intersect). Returns false if at least one String[] is
* null or empty.
*
* @param a
* a String[] b a String[]
* @return true if both a and b or not empty or null and contain at least
* one element in common false otherwise
*/
final public static boolean isIntersecting( final String[] a, final String[] b ) {
if ( ( a == null ) || ( b == null ) ) {
return false;
}
if ( ( a.length < 1 ) || ( b.length < 1 ) ) {
return false;
}
for( final String ai : a ) {
for( final String element : b ) {
if ( ( ai != null ) && ( element != null ) && ai.equals( element ) ) {
return true;
}
}
}
return false;
}
final public static double isLargerOrEqualToZero( final double d ) {
if ( d > 0.0 ) {
return d;
}
else {
return 0.0;
}
}
public final static boolean isMac() {
try {
return OS_NAME.toLowerCase().startsWith( "mac" );
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
return false;
}
}
final public static boolean isNull( final BigDecimal s ) {
return ( ( s == null ) || ( s.compareTo( NULL_BD ) == 0 ) );
}
final public static String isReadableFile( final File f ) {
if ( !f.exists() ) {
return "file [" + f + "] does not exist";
}
if ( f.isDirectory() ) {
return "[" + f + "] is a directory";
}
if ( !f.isFile() ) {
return "[" + f + "] is not a file";
}
if ( !f.canRead() ) {
return "file [" + f + "] is not readable";
}
if ( f.length() < 1 ) {
return "file [" + f + "] is empty";
}
return null;
}
final public static String isReadableFile( final String s ) {
return isReadableFile( new File( s ) );
}
public final static boolean isWindows() {
try {
return OS_NAME.toLowerCase().indexOf( "win" ) > -1;
}
catch ( final Exception e ) {
ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
return false;
}
}
final public static String isWritableFile( final File f ) {
if ( f.isDirectory() ) {
return "[" + f + "] is a directory";
}
if ( f.exists() ) {
return "[" + f + "] already exists";
}
return null;
}
/**
* Helper for method "stringToColor".
*
* (Last modified: 12/20/03)
*/
final public static int limitRangeForColor( int i ) {
if ( i > 255 ) {
i = 255;
}
else if ( i < 0 ) {
i = 0;
}
return i;
}
final public static SortedMap listToSortedCountsMap( final List list ) {
final SortedMap map = new TreeMap();
for( final Object key : list ) {
if ( !map.containsKey( key ) ) {
map.put( key, 1 );
}
else {
map.put( key, map.get( key ) + 1 );
}
}
return map;
}
final public static void map2file( final File file,
final Map data,
final String entry_separator,
final String data_separator ) throws IOException {
final Writer writer = new BufferedWriter( new FileWriter( file ) );
map2writer( writer, data, entry_separator, data_separator );
writer.close();
}
final public static void map2writer( final Writer writer,
final Map data,
final String entry_separator,
final String data_separator ) throws IOException {
boolean first = true;
for( final Entry entry : data.entrySet() ) {
if ( !first ) {
writer.write( data_separator );
}
else {
first = false;
}
writer.write( entry.getKey().toString() );
writer.write( entry_separator );
writer.write( entry.getValue().toString() );
}
}
final public static StringBuffer mapToStringBuffer( final Map map, final String key_value_separator ) {
final StringBuffer sb = new StringBuffer();
for( final Object key : map.keySet() ) {
sb.append( key.toString() );
sb.append( key_value_separator );
sb.append( map.get( key ).toString() );
sb.append( ForesterUtil.getLineSeparator() );
}
return sb;
}
final public static String normalizeString( final String s,
final int length,
final boolean left_pad,
final char pad_char ) {
if ( s.length() > length ) {
return s.substring( 0, length );
}
else {
final StringBuffer pad = new StringBuffer( length - s.length() );
for( int i = 0; i < ( length - s.length() ); ++i ) {
pad.append( pad_char );
}
if ( left_pad ) {
return pad + s;
}
else {
return s + pad;
}
}
}
public final static Color obtainColorDependingOnTaxonomyGroup( final String tax_group ) {
if ( !ForesterUtil.isEmpty( tax_group ) ) {
if ( tax_group.equals( TaxonomyGroups.DEUTEROSTOMIA ) ) {
return TaxonomyColors.DEUTEROSTOMIA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.PROTOSTOMIA ) ) {
return TaxonomyColors.PROTOSTOMIA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.CNIDARIA ) ) {
return TaxonomyColors.CNIDARIA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.PLACOZOA ) ) {
return TaxonomyColors.PLACOZOA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.CTENOPHORA ) ) {
return TaxonomyColors.CTENOPHORA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.PORIFERA ) ) {
return TaxonomyColors.PORIFERA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
return TaxonomyColors.CHOANOFLAGELLIDA;
}
else if ( tax_group.equals( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA ) ) {
return TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA;
}
else if ( tax_group.equals( TaxonomyGroups.DIKARYA ) ) {
return TaxonomyColors.DIKARYA_COLOR;
}
else if ( tax_group.equalsIgnoreCase( TaxonomyGroups.FUNGI )
|| tax_group.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
return TaxonomyColors.OTHER_FUNGI_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP ) ) {
return TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.AMOEBOZOA ) ) {
return TaxonomyColors.AMOEBOZOA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.EMBRYOPHYTA ) ) {
return TaxonomyColors.EMBRYOPHYTA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.CHLOROPHYTA ) ) {
return TaxonomyColors.CHLOROPHYTA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.RHODOPHYTA ) ) {
return TaxonomyColors.RHODOPHYTA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.HACROBIA ) ) {
return TaxonomyColors.HACROBIA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) ) {
return TaxonomyColors.GLAUCOPHYTA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.STRAMENOPILES ) ) {
return TaxonomyColors.STRAMENOPILES_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.ALVEOLATA ) ) {
return TaxonomyColors.ALVEOLATA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.RHIZARIA ) ) {
return TaxonomyColors.RHIZARIA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.EXCAVATA ) ) {
return TaxonomyColors.EXCAVATA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.APUSOZOA ) ) {
return TaxonomyColors.APUSOZOA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.ARCHAEA ) ) {
return TaxonomyColors.ARCHAEA_COLOR;
}
else if ( tax_group.equals( TaxonomyGroups.BACTERIA ) ) {
return TaxonomyColors.BACTERIA_COLOR;
}
}
return null;
}
public final static String obtainNormalizedTaxonomyGroup( final String tax ) {
if ( tax.equalsIgnoreCase( TaxonomyGroups.DEUTEROSTOMIA ) ) {
return TaxonomyGroups.DEUTEROSTOMIA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.PROTOSTOMIA ) ) {
return TaxonomyGroups.PROTOSTOMIA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.CNIDARIA ) ) {
return TaxonomyGroups.CNIDARIA;
}
else if ( tax.toLowerCase().startsWith( "trichoplax" ) || tax.equalsIgnoreCase( TaxonomyGroups.PLACOZOA ) ) {
return TaxonomyGroups.PLACOZOA;
}
else if ( tax.toLowerCase().startsWith( "mnemiopsis" ) || tax.equalsIgnoreCase( TaxonomyGroups.CTENOPHORA ) ) {
return TaxonomyGroups.CTENOPHORA;
}
else if ( tax.toLowerCase().startsWith( "amphimedon" ) || tax.equalsIgnoreCase( TaxonomyGroups.PORIFERA ) ) {
return TaxonomyGroups.PORIFERA;
}
else if ( tax.equalsIgnoreCase( "codonosigidae" ) || tax.equalsIgnoreCase( TaxonomyGroups.CHOANOFLAGELLIDA ) ) {
return TaxonomyGroups.CHOANOFLAGELLIDA;
}
else if ( tax.toLowerCase().startsWith( TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA )
|| tax.toLowerCase().startsWith( "ichthyophonida and filasterea" )
|| tax.toLowerCase().startsWith( "ichthyosporea & filasterea" )
|| tax.toLowerCase().startsWith( "ichthyosporea and filasterea" ) ) {
return TaxonomyGroups.ICHTHYOPHONIDA_FILASTEREA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.DIKARYA ) ) {
return TaxonomyGroups.DIKARYA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.FUNGI ) || tax.equalsIgnoreCase( TaxonomyGroups.OTHER_FUNGI ) ) {
return TaxonomyGroups.OTHER_FUNGI;
}
else if ( tax.toLowerCase().startsWith( "nucleariidae and fonticula" ) ) {
return TaxonomyGroups.NUCLEARIIDAE_AND_FONTICULA_GROUP;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.AMOEBOZOA ) ) {
return TaxonomyGroups.AMOEBOZOA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.EMBRYOPHYTA ) ) {
return TaxonomyGroups.EMBRYOPHYTA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.CHLOROPHYTA ) ) {
return TaxonomyGroups.CHLOROPHYTA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHODOPHYTA ) ) {
return TaxonomyGroups.RHODOPHYTA;
}
else if ( tax.toLowerCase().startsWith( TaxonomyGroups.HACROBIA ) ) {
return TaxonomyGroups.HACROBIA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.GLAUCOCYSTOPHYCEAE ) || tax.equalsIgnoreCase( "glaucophyta" ) ) {
return TaxonomyGroups.GLAUCOCYSTOPHYCEAE;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.STRAMENOPILES ) ) {
return TaxonomyGroups.STRAMENOPILES;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.ALVEOLATA ) ) {
return TaxonomyGroups.ALVEOLATA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.RHIZARIA ) ) {
return TaxonomyGroups.RHIZARIA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.EXCAVATA ) ) {
return TaxonomyGroups.EXCAVATA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.APUSOZOA ) ) {
return TaxonomyGroups.APUSOZOA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.ARCHAEA ) ) {
return TaxonomyGroups.ARCHAEA;
}
else if ( tax.equalsIgnoreCase( TaxonomyGroups.BACTERIA ) ) {
return TaxonomyGroups.BACTERIA;
}
return null;
}
final public static BufferedReader obtainReader( final Object source ) throws IOException, FileNotFoundException {
BufferedReader reader = null;
if ( source instanceof File ) {
final File f = ( File ) 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 String ) {
reader = new BufferedReader( new StringReader( ( String ) source ) );
}
else if ( source instanceof StringBuffer ) {
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, InputStream, String, or StringBuffer)" );
}
return reader;
}
public final static void outOfMemoryError( final OutOfMemoryError e ) {
System.err.println();
System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
System.err.println();
e.printStackTrace( System.err );
System.err.println();
System.exit( -1 );
}
final public static StringBuffer pad( final double number, final int size, final char pad, final boolean left_pad ) {
return pad( new StringBuffer( number + "" ), size, pad, left_pad );
}
final public static StringBuffer pad( final String string, final int size, final char pad, final boolean left_pad ) {
return pad( new StringBuffer( string ), size, pad, left_pad );
}
final public static StringBuffer pad( final StringBuffer string,
final int size,
final char pad,
final boolean left_pad ) {
final StringBuffer padding = new StringBuffer();
final int s = size - string.length();
if ( s < 1 ) {
return new StringBuffer( string.substring( 0, size ) );
}
for( int i = 0; i < s; ++i ) {
padding.append( pad );
}
if ( left_pad ) {
return padding.append( string );
}
else {
return string.append( padding );
}
}
final public static double parseDouble( final String str ) throws ParseException {
if ( ForesterUtil.isEmpty( str ) ) {
return 0.0;
}
return Double.parseDouble( str );
}
final public static int parseInt( final String str ) throws ParseException {
if ( ForesterUtil.isEmpty( str ) ) {
return 0;
}
return Integer.parseInt( str );
}
final public static void printArray( final Object[] a ) {
for( int i = 0; i < a.length; ++i ) {
System.out.println( "[" + i + "]=" + a[ i ] );
}
}
final public static void printCountingMap( final Map counting_map ) {
for( final String key : counting_map.keySet() ) {
System.out.println( key + ": " + counting_map.get( key ) );
}
}
final public static void printErrorMessage( final String prg_name, final String message ) {
System.err.println( "[" + prg_name + "] > error: " + message );
}
final public static void printProgramInformation( final String prg_name, final String prg_version, final String date ) {
final int l = prg_name.length() + prg_version.length() + date.length() + 4;
System.out.println();
System.out.println( prg_name + " " + prg_version + " (" + date + ")" );
for( int i = 0; i < l; ++i ) {
System.out.print( "_" );
}
System.out.println();
}
final public static void printProgramInformation( final String prg_name,
final String prg_version,
final String date,
final String email,
final String www ) {
printProgramInformation( prg_name, null, prg_version, date, email, www, null );
}
final public static void printProgramInformation( final String prg_name,
final String desc,
final String prg_version,
final String date,
final String email,
final String www,
final String based_on ) {
String my_prg_name = new String( prg_name );
if ( !ForesterUtil.isEmpty( desc ) ) {
my_prg_name += ( " - " + desc );
}
final int l = my_prg_name.length() + prg_version.length() + date.length() + 4;
System.out.println();
System.out.println( my_prg_name + " " + prg_version + " (" + date + ")" );
for( int i = 0; i < l; ++i ) {
System.out.print( "_" );
}
System.out.println();
System.out.println();
System.out.println( "WWW : " + www );
System.out.println( "Contact : " + email );
if ( !ForesterUtil.isEmpty( based_on ) ) {
System.out.println( "Based on: " + based_on );
}
if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
System.out.println();
System.out.println( "[running on Java " + ForesterUtil.JAVA_VERSION + " " + ForesterUtil.JAVA_VENDOR + "]" );
}
System.out.println();
}
final public static void printWarningMessage( final String prg_name, final String message ) {
System.out.println( "[" + prg_name + "] > warning: " + message );
}
final public static void programMessage( final String prg_name, final String message ) {
System.out.println( "[" + prg_name + "] > " + message );
}
public static List readUrl( final String url_str ) throws IOException {
final URL url = new URL( url_str );
final URLConnection urlc = url.openConnection();
//urlc.setRequestProperty( "User-Agent", "" );
final BufferedReader in = new BufferedReader( new InputStreamReader( urlc.getInputStream() ) );
String line;
final List result = new ArrayList();
while ( ( line = in.readLine() ) != null ) {
result.add( line );
}
in.close();
return result;
}
/**
*
* Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
* domain with 0.3 is ignored
*
* -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
*
*
* ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
* ignored
*
* @param max_allowed_overlap
* maximal allowed overlap (inclusive) to be still considered not
* overlapping (zero or negative value to allow any overlap)
* @param remove_engulfed_domains
* to remove domains which are completely engulfed by coverage of
* domains with better support
* @param protein
* @return
*/
public static Protein removeOverlappingDomains( final int max_allowed_overlap,
final boolean remove_engulfed_domains,
final Protein protein ) {
final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
.getSpeciesId(), protein.getLength() );
final List sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
final List covered_positions = new ArrayList();
for( final Domain domain : sorted ) {
if ( ( ( max_allowed_overlap < 0 ) || ( ForesterUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
&& ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
final int covered_positions_size = covered_positions.size();
for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
covered_positions.add( false );
}
final int new_covered_positions_size = covered_positions.size();
for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
if ( i < new_covered_positions_size ) {
covered_positions.set( i, true );
}
else {
covered_positions.add( true );
}
}
pruned_protein.addProteinDomain( domain );
}
}
return pruned_protein;
}
final public static String removeSuffix( final String file_name ) {
final int i = file_name.lastIndexOf( '.' );
if ( i > 1 ) {
return file_name.substring( 0, i );
}
return file_name;
}
/**
* Removes all white space from String s.
*
* @return String s with white space removed
*/
final public static String removeWhiteSpace( String s ) {
int i;
for( i = 0; i <= ( s.length() - 1 ); i++ ) {
if ( ( s.charAt( i ) == ' ' ) || ( s.charAt( i ) == '\t' ) || ( s.charAt( i ) == '\n' )
|| ( s.charAt( i ) == '\r' ) ) {
s = s.substring( 0, i ) + s.substring( i + 1 );
i--;
}
}
return s;
}
final public static String replaceIllegalNhxCharacters( final String nhx ) {
if ( nhx == null ) {
return "";
}
return nhx.trim().replaceAll( "[\\[\\]']+", "_" );
}
final public static double round( final double value, final int decimal_place ) {
BigDecimal bd = new BigDecimal( value );
bd = bd.setScale( decimal_place, BigDecimal.ROUND_HALF_UP );
return bd.doubleValue();
}
/**
* Rounds d to an int.
*/
final public static int roundToInt( final double d ) {
return ( int ) ( d + 0.5 );
}
final public static int roundToInt( final float f ) {
return ( int ) ( f + 0.5f );
}
final public static short roundToShort( final double d ) {
return ( short ) ( d + 0.5 );
}
final public static String sanitizeString( final String s ) {
if ( s == null ) {
return "";
}
else {
return s.trim();
}
}
public final static StringBuilder santitizeStringForNH( String data ) {
data = data.replaceAll( "\\s+", " " ).trim();
final StringBuilder sb = new StringBuilder();
if ( data.length() > 0 ) {
final boolean single_pars = data.indexOf( '\'' ) > -1;
final boolean double_pars = data.indexOf( '"' ) > -1;
if ( single_pars && double_pars ) {
data = data.replace( '\'', '`' );
sb.append( '\'' );
sb.append( data );
sb.append( '\'' );
}
else if ( single_pars ) {
sb.append( '"' );
sb.append( data );
sb.append( '"' );
}
else if ( PARANTHESESABLE_NH_CHARS_PATTERN.matcher( data ).find() ) {
sb.append( '\'' );
sb.append( data );
sb.append( '\'' );
}
else {
sb.append( data );
}
}
return sb;
}
public static boolean seqIsLikelyToBeAa( final String s ) {
final String seq = s.toLowerCase();
if ( ( seq.indexOf( 'r' ) > -1 ) || ( seq.indexOf( 'd' ) > -1 ) || ( seq.indexOf( 'e' ) > -1 )
|| ( seq.indexOf( 'q' ) > -1 ) || ( seq.indexOf( 'h' ) > -1 ) || ( seq.indexOf( 'k' ) > -1 )
|| ( seq.indexOf( 'w' ) > -1 ) || ( seq.indexOf( 's' ) > -1 ) || ( seq.indexOf( 'm' ) > -1 )
|| ( seq.indexOf( 'p' ) > -1 ) || ( seq.indexOf( 'v' ) > -1 ) ) {
return true;
}
return false;
}
final private static String[] splitString( final String str ) {
final String regex = "[\\s;,]+";
return str.split( regex );
}
final public static String stringArrayToString( final String[] a ) {
return stringArrayToString( a, ", " );
}
final public static String stringArrayToString( final String[] a, final String separator ) {
final StringBuilder sb = new StringBuilder();
if ( ( a != null ) && ( a.length > 0 ) ) {
for( int i = 0; i < ( a.length - 1 ); ++i ) {
sb.append( a[ i ] + separator );
}
sb.append( a[ a.length - 1 ] );
}
return sb.toString();
}
final public static String[] stringListToArray( final List list ) {
if ( list != null ) {
final String[] str = new String[ list.size() ];
int i = 0;
for( final String l : list ) {
str[ i++ ] = l;
}
return str;
}
return null;
}
final public static String stringListToString( final List l, final String separator ) {
final StringBuilder sb = new StringBuilder();
if ( ( l != null ) && ( l.size() > 0 ) ) {
for( int i = 0; i < ( l.size() - 1 ); ++i ) {
sb.append( l.get( i ) + separator );
}
sb.append( l.get( l.size() - 1 ) );
}
return sb.toString();
}
final public static String[] stringSetToArray( final Set strings ) {
final String[] str_array = new String[ strings.size() ];
int i = 0;
for( final String e : strings ) {
str_array[ i++ ] = e;
}
return str_array;
}
final public static void unexpectedFatalError( final Error e ) {
System.err.println();
System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
e.printStackTrace( System.err );
System.err.println();
System.exit( -1 );
}
final public static void unexpectedFatalError( final Exception e ) {
System.err.println();
System.err.println( "unexpected exception: should not have occured! Please contact program author(s)." );
e.printStackTrace( System.err );
System.err.println();
System.exit( -1 );
}
final public static void unexpectedFatalError( final String message ) {
System.err.println();
System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
System.err.println( message );
System.err.println();
System.exit( -1 );
}
final public static void unexpectedFatalError( final String prg_name, final Exception e ) {
System.err.println();
System.err.println( "[" + prg_name
+ "] > unexpected error; should not have occured! Please contact program author(s)." );
e.printStackTrace( System.err );
System.err.println();
System.exit( -1 );
}
final public static void unexpectedFatalError( final String prg_name, final String message ) {
System.err.println();
System.err.println( "[" + prg_name
+ "] > unexpected error: should not have occured! Please contact program author(s)." );
System.err.println( message );
System.err.println();
System.exit( -1 );
}
final public static void unexpectedFatalError( final String prg_name, final String message, final Exception e ) {
System.err.println();
System.err.println( "[" + prg_name
+ "] > unexpected error: should not have occured! Please contact program author(s)." );
System.err.println( message );
e.printStackTrace( System.err );
System.err.println();
System.exit( -1 );
}
public final static void updateProgress( final double progress_percentage ) {
final int width = 50;
System.out.print( "\r[" );
int i = 0;
for( ; i <= ForesterUtil.roundToInt( progress_percentage * width ); i++ ) {
System.out.print( "." );
}
for( ; i < width; i++ ) {
System.out.print( " " );
}
System.out.print( "]" );
}
public final static void updateProgress( final int i, final DecimalFormat f ) {
System.out.print( "\r[" + f.format( i ) + "]" );
}
public final static String wordWrap( final String str, final int width ) {
final StringBuilder sb = new StringBuilder( str );
int start = 0;
int ls = -1;
int i = 0;
while ( i < sb.length() ) {
if ( sb.charAt( i ) == ' ' ) {
ls = i;
}
if ( sb.charAt( i ) == '\n' ) {
ls = -1;
start = i + 1;
}
if ( i > ( ( start + width ) - 1 ) ) {
if ( ls != -1 ) {
sb.setCharAt( ls, '\n' );
start = ls + 1;
ls = -1;
}
else {
sb.insert( i, '\n' );
start = i + 1;
}
}
i++;
}
return sb.toString();
}
private ForesterUtil() {
}
}