+ public final static String greatestCommonPrefix( final String a, final String b ) {
+ final int min_length = Math.min( a.length(), b.length() );
+ for( int i = 0; i < min_length; ++i ) {
+ if ( a.charAt( i ) != b.charAt( i ) ) {
+ return a.substring( 0, i );
+ }
+ }
+ 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 String[] as = a.split( Pattern.quote( separator ) );
+ final String[] bs = b.split( Pattern.quote( separator ) );
+ final int min_length = Math.min( as.length, bs.length );
+ for( int i = 0; i < min_length; ++i ) {
+ if ( !( as[ i ].equals( bs[ i ] ) ) ) {
+ final StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for( int j = 0; j < i; ++j ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( separator );
+ }
+ sb.append( as[ j ] );
+ }
+ return sb.toString();
+ }
+ }
+ final StringBuilder sb = new StringBuilder();
+ boolean first = true;
+ for( int j = 0; j < min_length; ++j ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( separator );
+ }
+ sb.append( as[ j ] );
+ }
+ return sb.toString();
+ }
+
+ public final static String greatestCommonPrefix( final List<String> strings ) {
+ if ( strings == null ) {
+ throw new IllegalArgumentException( "list of strings is null" );
+ }
+ if ( strings.isEmpty() ) {
+ throw new IllegalArgumentException( "list of strings is empty" );
+ }
+ String common = strings.get( 0 );
+ for( int i = 1; i < strings.size(); ++i ) {
+ common = greatestCommonPrefix( common, strings.get( i ) );
+ }
+ return common;
+ }
+
+ public final static String greatestCommonPrefix( final List<String> strings, final String separator ) {
+ if ( ForesterUtil.isEmpty( separator ) ) {
+ return greatestCommonPrefix( strings );
+ }
+ if ( strings == null ) {
+ throw new IllegalArgumentException( "list of strings is null" );
+ }
+ if ( strings.isEmpty() ) {
+ throw new IllegalArgumentException( "list of strings is empty" );
+ }
+ String common = strings.get( 0 );
+ for( int i = 1; i < strings.size(); ++i ) {
+ common = greatestCommonPrefix( common, strings.get( i ), separator );
+ }
+ return common;
+ }
+
+ 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<>();
+ for( int i = 0; i < a.length; ++i ) {
+ final StringBuilder sb = new StringBuilder();
+ for( int j = 0; j <= i; ++j ) {
+ sb.append( a[ j ] );
+ if ( j < i ) {
+ sb.append( separator );
+ }
+ }
+ 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( ">" ) ) );
+ }
+