package org.forester.sequence;
+import org.forester.util.ForesterUtil;
+
public class BasicSequence implements Sequence {
private final char[] _mol_sequence;
private final TYPE _type;
private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
+ if ( ForesterUtil.isEmpty( identifier ) ) {
+ throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
+ }
+ if ( ForesterUtil.isEmpty( mol_sequence ) ) {
+ throw new IllegalArgumentException( "molecular sequence cannot be empty" );
+ }
_mol_sequence = mol_sequence.toCharArray();
_identifier = identifier;
_type = type;
// Only use if you know what you are doing!
public BasicSequence( final String identifier, final char[] mol_sequence, final TYPE type ) {
+ if ( ForesterUtil.isEmpty( identifier ) ) {
+ throw new IllegalArgumentException( "identifier of sequence cannot be empty" );
+ }
+ if ( ( mol_sequence == null ) || ( mol_sequence.length < 1 ) ) {
+ throw new IllegalArgumentException( "molecular sequence cannot be empty" );
+ }
_mol_sequence = mol_sequence;
_identifier = identifier;
_type = type;
}
@Override
+ public boolean equals( final Object obj ) {
+ if ( obj == null ) {
+ return false;
+ }
+ if ( obj.getClass() != getClass() ) {
+ return false;
+ }
+ final Sequence other = ( Sequence ) obj;
+ if ( getMolecularSequenceAsString().equals( other.getMolecularSequenceAsString() ) ) {
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public int hashCode() {
+ return getMolecularSequenceAsString().hashCode();
+ }
+
+ @Override
public String toString() {
final StringBuffer sb = new StringBuffer();
sb.append( _identifier.toString() );
- sb.append( " " );
- sb.append( new String( _mol_sequence ) );
+ sb.append( ": " );
+ sb.append( getMolecularSequenceAsString() );
return sb.toString();
}
return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
.replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
}
+
+ @Override
+ public String getMolecularSequenceAsString() {
+ return new String( getMolecularSequence() );
+ }
}