// $Id: CommandLineArguments.java,v 1.16 2009/10/26 23:29:40 cmzmasek Exp $
// 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: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.util;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
public final class CommandLineArguments {
private final static String OPTIONS_PREFIX = "-";
private final static String EXTENDED_OPTIONS_PREFIX = "--";
private final static String OPTIONS_SEPARATOR = "=";
private Map<String, String> _options;
private Map<String, String> _extended_options;
private List<String> _names;
private String _command_line_str;
public CommandLineArguments( final String[] args ) throws IOException {
init();
parseCommandLineArguments( args );
}
private Map<String, String> getAllOptions() {
final Map<String, String> o = new HashMap<String, String>();
o.putAll( getOptionsList() );
o.putAll( getExtendedOptionsList() );
return o;
}
public String getCommandLineArgsAsString() {
return _command_line_str;
}
private Map<String, String> getExtendedOptionsList() {
return _extended_options;
}
public File getFile( final int i ) {
return new File( getNames()[ i ] );
}
public String getName( final int i ) {
return getNames()[ i ];
}
public String[] getNames() {
final String[] a = new String[ getNamesList().size() ];
return getNamesList().toArray( a );
}
private List<String> getNamesList() {
return _names;
}
public int getNumberOfNames() {
return getNames().length;
}
private Map<String, String> getOptionsList() {
return _options;
}
public String getOptionValue( final String option_name ) throws IllegalArgumentException {
final Map<String, String> o = getAllOptions();
if ( o.containsKey( option_name ) ) {
final String value = o.get( option_name );
if ( !ForesterUtil.isEmpty( value ) ) {
return value;
}
else {
throw new IllegalArgumentException( "value for \"" + option_name + "\" is not set" );
}
}
else {
throw new IllegalArgumentException( "option \"" + option_name + "\" is not set" );
}
}
/**
* Removes quotes
*
*/
public String getOptionValueAsCleanString( final String option_name ) throws IllegalArgumentException {
return getOptionValue( option_name ).replaceAll( "\"", "" ).replaceAll( "\'", "" );
}
public double getOptionValueAsDouble( final String option_name ) throws IOException {
double d = -Double.MAX_VALUE;
try {
d = new Double( getOptionValue( option_name ) ).doubleValue();
}
catch ( final NumberFormatException e ) {
throw new IOException( "value for option \"" + option_name + "\" is expected to be of type double" );
}
return d;
}
public int getOptionValueAsInt( final String option_name ) throws IOException {
int i = Integer.MIN_VALUE;
try {
i = new Integer( getOptionValue( option_name ) ).intValue();
}
catch ( final NumberFormatException e ) {
throw new IOException( "value for option \"" + option_name + "\" is expected to be of type integer" );
}
return i;
}
public long getOptionValueAsLong( final String option_name ) throws IOException {
long l = Long.MIN_VALUE;
try {
l = new Long( getOptionValue( option_name ) ).longValue();
}
catch ( final NumberFormatException e ) {
throw new IOException( "value for option \"" + option_name + "\" is expected to be of type long" );
}
return l;
}
private void init() {
_options = new HashMap<String, String>();
_extended_options = new HashMap<String, String>();
_names = new ArrayList<String>();
_command_line_str = "";
}
public boolean isOptionHasAValue( final String option_name ) {
final Map<String, String> o = getAllOptions();
if ( o.containsKey( option_name ) ) {
final String value = o.get( option_name );
return ( !ForesterUtil.isEmpty( value ) );
}
else {
throw new IllegalArgumentException( "option \"" + option_name + "\" is not set" );
}
}
public boolean isOptionSet( final String option_name ) {
final Map<String, String> o = getAllOptions();
return ( o.containsKey( option_name ) );
}
public boolean isOptionValueSet( final String option_name ) throws IllegalArgumentException {
final Map<String, String> o = getAllOptions();
if ( o.containsKey( option_name ) ) {
return !( ForesterUtil.isEmpty( o.get( option_name ) ) );
}
else {
throw new IllegalArgumentException( "option \"" + option_name + "\" is not set" );
}
}
private void parseCommandLineArguments( final String[] args ) throws IOException {
for( int i = 0; i < args.length; ++i ) {
final String arg = args[ i ].trim();
_command_line_str += arg;
if ( i < args.length - 1 ) {
_command_line_str += " ";
}
if ( arg.startsWith( CommandLineArguments.EXTENDED_OPTIONS_PREFIX ) ) {
parseOption( arg.substring( CommandLineArguments.EXTENDED_OPTIONS_PREFIX.length() ),
getExtendedOptionsList() );
}
else if ( arg.startsWith( CommandLineArguments.OPTIONS_PREFIX ) ) {
parseOption( arg.substring( CommandLineArguments.OPTIONS_PREFIX.length() ), getOptionsList() );
}
else {
getNamesList().add( arg );
}
}
}
private void parseOption( final String option, final Map<String, String> options_map ) throws IOException {
final int sep_index = option.indexOf( CommandLineArguments.OPTIONS_SEPARATOR );
if ( sep_index < 1 ) {
if ( ForesterUtil.isEmpty( option ) ) {
throw new IOException( "attempt to set option with an empty name" );
}
if ( getAllOptions().containsKey( option ) ) {
throw new IOException( "attempt to set option \"" + option + "\" mutiple times" );
}
options_map.put( option, null );
}
else {
final String key = option.substring( 0, sep_index );
final String value = option.substring( sep_index + 1 );
if ( ForesterUtil.isEmpty( key ) ) {
throw new IllegalArgumentException( "attempt to set option with an empty name" );
}
// if ( ForesterUtil.isEmpty( value ) ) {
// throw new IllegalArgumentException( "attempt to set option with an empty value" );
// }
if ( getAllOptions().containsKey( key ) ) {
throw new IllegalArgumentException( "attempt to set option \"" + key + "\" mutiple times [" + option
+ "]" );
}
options_map.put( key, value );
}
}
public List<String> validateAllowedOptions( final List<String> allowed_options ) {
final Map<String, String> options = getAllOptions();
final List<String> dissallowed = new ArrayList<String>();
for( final String o : options.keySet() ) {
if ( !allowed_options.contains( o ) ) {
dissallowed.add( o );
}
}
return dissallowed;
}
public String validateAllowedOptionsAsString( final List<String> allowed_options ) {
final List<String> dissallowed = validateAllowedOptions( allowed_options );
String dissallowed_string = "";
for( final Iterator<String> iter = dissallowed.iterator(); iter.hasNext(); ) {
dissallowed_string += "\"" + iter.next();
if ( iter.hasNext() ) {
dissallowed_string += "\", ";
}
else {
dissallowed_string += "\"";
}
}
return dissallowed_string;
}
public List<String> validateMandatoryOptions( final List<String> mandatory_options ) {
final Map<String, String> options = getAllOptions();
final List<String> missing = new ArrayList<String>();
for( final String string : mandatory_options ) {
final String ma = string;
if ( !options.containsKey( ma ) ) {
missing.add( ma );
}
}
return missing;
}
public String validateMandatoryOptionsAsString( final List<String> mandatory_options ) {
final List<String> missing = validateMandatoryOptions( mandatory_options );
String missing_string = "";
for( final Iterator<String> iter = missing.iterator(); iter.hasNext(); ) {
missing_string += "\"" + iter.next();
if ( iter.hasNext() ) {
missing_string += "\", ";
}
else {
missing_string += "\"";
}
}
return missing_string;
}
}