X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FCommandLineArguments.java;h=f75eb691d5d78a8c1f73d03888f45642a5175104;hb=e572f0142daf64409db0461f15215288137603f8;hp=0fc0485b750b34aa780be5f7016ae007d18c3792;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/util/CommandLineArguments.java b/forester/java/src/org/forester/util/CommandLineArguments.java
index 0fc0485..f75eb69 100644
--- a/forester/java/src/org/forester/util/CommandLineArguments.java
+++ b/forester/java/src/org/forester/util/CommandLineArguments.java
@@ -5,7 +5,7 @@
 // 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
@@ -15,13 +15,13 @@
 // 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: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.util;
 
@@ -93,7 +93,7 @@ public final class CommandLineArguments {
         if ( o.containsKey( option_name ) ) {
             final String value = o.get( option_name );
             if ( !ForesterUtil.isEmpty( value ) ) {
-                return value;
+                return value.replaceAll( "\\s+", " " ).trim();
             }
             else {
                 throw new IllegalArgumentException( "value for \"" + option_name + "\" is not set" );
@@ -106,12 +106,16 @@ public final class CommandLineArguments {
 
     /**
      * Removes quotes
-     * 
+     *
      */
     public String getOptionValueAsCleanString( final String option_name ) throws IllegalArgumentException {
         return getOptionValue( option_name ).replaceAll( "\"", "" ).replaceAll( "\'", "" );
     }
 
+    public char getOptionValueAsChar( final String option_name ) throws IllegalArgumentException {
+        return getOptionValue( option_name ).charAt( 0 );
+    }
+
     public double getOptionValueAsDouble( final String option_name ) throws IOException {
         double d = -Double.MAX_VALUE;
         try {
@@ -182,7 +186,7 @@ public final class CommandLineArguments {
         for( int i = 0; i < args.length; ++i ) {
             final String arg = args[ i ].trim();
             _command_line_str += arg;
-            if ( i < args.length - 1 ) {
+            if ( i < ( args.length - 1 ) ) {
                 _command_line_str += " ";
             }
             if ( arg.startsWith( CommandLineArguments.EXTENDED_OPTIONS_PREFIX ) ) {
@@ -220,7 +224,7 @@ public final class CommandLineArguments {
             //  }
             if ( getAllOptions().containsKey( key ) ) {
                 throw new IllegalArgumentException( "attempt to set option \"" + key + "\" mutiple times [" + option
-                        + "]" );
+                                                    + "]" );
             }
             options_map.put( key, value );
         }