}
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" ) ) {
+ final String s = mol_seq.toUpperCase();
+ if ( s.contains( "L" ) || s.contains( "I" ) || s.contains( "E" ) || s.contains( "H" ) || s.contains( "D" )
+ || s.contains( "Q" ) ) {
return TYPE.AA;
}
else {
- if ( mol_seq.contains( "T" ) ) {
+ if ( s.contains( "T" ) ) {
return TYPE.DNA;
}
- else if ( mol_seq.contains( "U" ) ) {
+ else if ( s.contains( "U" ) ) {
return TYPE.RNA;
}
}
final public static boolean isEqual( final double a, final double b ) {
return ( ( Math.abs( a - b ) ) < ZERO_DIFF );
}
-
+
final public static boolean isEqual( final double a, final double b, final double tolerance ) {
return ( ( Math.abs( a - b ) ) < tolerance );
}
return null;
}
+ final public static String isWritableFile( final String s ) {
+ return isWritableFile( new File( s ) );
+ }
+
/**
* Helper for method "stringToColor".
* <p>
is.close();
}
catch ( final Exception e ) {
- // ignore
+ // ignore
}
return trees;
}
File the_one = null;
do {
int matches = 0;
- for( File file : files ) {
+ for( final File file : files ) {
if ( file.getName().startsWith( my_prefix ) ) {
matches++;
if ( matches > 1 ) {
return a.substring( 0, min_length );
}
+ public final static boolean isContainsPrefix( final String word, final String prefix, final String separator ) {
+ if ( ForesterUtil.isEmpty( separator ) ) {
+ throw new IllegalArgumentException( "separator must not be null or empty" );
+ }
+ final String[] word_ary = word.split( Pattern.quote( separator ) );
+ final String[] prefix_ary = prefix.split( Pattern.quote( separator ) );
+ if ( word_ary.length < prefix_ary.length ) {
+ return false;
+ }
+ final int prefix_ary_length = prefix_ary.length;
+ for( int i = 0; i < prefix_ary_length; ++i ) {
+ if ( !( word_ary[ i ].equals( prefix_ary[ i ] ) ) ) {
+ return false;
+ }
+ }
+ return true;
+ }
+
public final static String greatestCommonPrefix( final String a, final String b, final String separator ) {
if ( ForesterUtil.isEmpty( separator ) ) {
throw new IllegalArgumentException( "separator must not be null or empty" );
final int min_length = Math.min( as.length, bs.length );
for( int i = 0; i < min_length; ++i ) {
if ( !( as[ i ].equals( bs[ i ] ) ) ) {
- StringBuilder sb = new StringBuilder();
+ final StringBuilder sb = new StringBuilder();
boolean first = true;
for( int j = 0; j < i; ++j ) {
if ( first ) {
return sb.toString();
}
}
- StringBuilder sb = new StringBuilder();
+ final StringBuilder sb = new StringBuilder();
boolean first = true;
for( int j = 0; j < min_length; ++j ) {
if ( first ) {
return common;
}
- private ForesterUtil() {
- }
-
- public static List<String> spliIntoPrefixes(final String prefix, final String separator ) {
+ public static List<String> spliIntoPrefixes( final String prefix, final String separator ) {
final String[] a = prefix.split( Pattern.quote( separator ) );
- final List<String> l= new ArrayList<String>();
+ final List<String> l = new ArrayList<String>();
for( int i = 0; i < a.length; ++i ) {
final StringBuilder sb = new StringBuilder();
for( int j = 0; j <= i; ++j ) {
sb.append( separator );
}
}
- //System.out.println( sb.toString() );
- l.add( sb.toString());
+ l.add( sb.toString() );
}
return l;
}
+
+ public static boolean isLooksLikeFasta( final File file ) throws IOException {
+ final String first_line = ForesterUtil.getFirstLine( file ).trim().toLowerCase();
+ return ( ( !isEmptyTrimmed( first_line ) && first_line.trim().startsWith( ">" ) ) );
+ }
+
+ private ForesterUtil() {
+ }
}