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.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Date;
import java.util.Iterator;
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;
sb.append( separator );
}
}
+
+ final public static String getForesterLibraryInformation() {
+ return "forester " + ForesterConstants.FORESTER_VERSION + " (" + ForesterConstants.FORESTER_DATE + ")";
+ }
+
+ 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;
+ }
/**
* This calculates a color. If value is equal to min the returned color is
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() );
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 Iterator iter = map.keySet().iterator(); iter.hasNext(); ) {
}
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 int l = prg_name.length() + prg_version.length() + date.length() + 4;
+ 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( prg_name + " " + prg_version + " (" + date + ")" );
+ 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 );
+ 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 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 printWarningMessage( final String prg_name, final String message ) {
System.out.println( "[" + prg_name + "] > warning: " + message );
}
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 ) ) {
return sb.toString();
}
+ final public static String[] stringListToArray( final List<String> 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<String> l, final String separator ) {
final StringBuilder sb = new StringBuilder();
if ( ( l != null ) && ( l.size() > 0 ) ) {
return sb.toString();
}
- final public static String stringArrayToString( final String[] a ) {
- return stringArrayToString( a, ", " );
- }
-
final public static String[] stringSetToArray( final Set<String> strings ) {
final String[] str_array = new String[ strings.size() ];
int i = 0;
return str_array;
}
- final public static String[] stringListToArray( final List<String> 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 void unexpectedFatalError( final String prg_name, final Exception e ) {
System.err.println();
System.err.println( "[" + prg_name
git://source.jalview.org / jalview.git / blobdiff