private int determineMaxIdLength() {
int max = 0;
- for( int row = 0; row < _data.length; ++row ) {
- final int l = _identifiers[ row ].toString().length();
+ for( int row = 0; row < getNumberOfSequences(); ++row ) {
+ final int l = getIdentifier(row).length();
if ( l > max ) {
max = l;
}
@Override
public Sequence getSequence( final int row ) {
- return new BasicSequence( getIdentifier( row ), _data[ row ], getType() );
+ return new BasicSequence( getIdentifier( row ), getSequenceAsArray( row ), getType() );
}
@Override
public StringBuffer getSequenceAsString( final int row ) {
- final StringBuffer sb = new StringBuffer( _data[ 0 ].length );
- for( int col = 0; col < _data[ 0 ].length; ++col ) {
+ final StringBuffer sb = new StringBuffer(getLength() );
+ for( int col = 0; col < getLength(); ++col ) {
sb.append( getResidueAt( row, col ) );
}
return sb;
}
+
+ @Override
+ public char[] getSequenceAsArray( final int row ) {
+ return _data[ row ];
+ }
@Override
public TYPE getType() {
public String toString() {
final int max = determineMaxIdLength() + 1;
final StringBuffer sb = new StringBuffer();
- for( int row = 0; row < _data.length; ++row ) {
- sb.append( ForesterUtil.pad( _identifiers[ row ].toString(), max, ' ', false ) );
- for( int col = 0; col < _data[ 0 ].length; ++col ) {
+ for( int row = 0; row < getNumberOfSequences(); ++row ) {
+ sb.append( ForesterUtil.pad( getIdentifier( row ).toString(), max, ' ', false ) );
+ for( int col = 0; col < getLength(); ++col ) {
sb.append( getResidueAt( row, col ) );
}
sb.append( ForesterUtil.LINE_SEPARATOR );
private void writeToPhylip( final Writer w ) throws IOException {
final int max = determineMaxIdLength() + 1;
- for( int row = 0; row < _data.length; ++row ) {
- w.write( ForesterUtil.pad( _identifiers[ row ].toString(), max, ' ', false ).toString() );
- for( int col = 0; col < _data[ 0 ].length; ++col ) {
+ for( int row = 0; row < getNumberOfSequences(); ++row ) {
+ w.write( ForesterUtil.pad( getIdentifier( row ), max, ' ', false ).toString() );
+ for( int col = 0; col < getLength(); ++col ) {
w.write( getResidueAt( row, col ) );
}
w.write( ForesterUtil.LINE_SEPARATOR );