import org.forester.util.ForesterUtil;
-public class BasicSequence implements Sequence {
+public class BasicSequence implements MolecularSequence {
private final char[] _mol_sequence;
- private final String _identifier;
+ private String _identifier;
private final TYPE _type;
- private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
+ /**
+ * Only use if you know what you are doing!
+ *
+ */
+ public BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
+ check( identifier, mol_sequence );
+ _mol_sequence = mol_sequence.toCharArray();
+ _identifier = identifier;
+ _type = type;
+ }
+
+ private static final void check( final String identifier, final String mol_sequence ) {
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!
+ /**
+ * 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" );
_type = type;
}
+ public void setIdentifier( final String id ) {
+ _identifier = id;
+ }
+
@Override
public String getIdentifier() {
return _identifier;
if ( obj.getClass() != getClass() ) {
return false;
}
- final Sequence other = ( Sequence ) obj;
+ final MolecularSequence other = ( MolecularSequence ) obj;
if ( getMolecularSequenceAsString().equals( other.getMolecularSequenceAsString() ) ) {
return true;
}
return sb.toString();
}
- public static Sequence copySequence( final Sequence seq ) {
+ public static MolecularSequence copySequence( final MolecularSequence seq ) {
final char[] s = new char[ seq.getMolecularSequence().length ];
for( int i = 0; i < seq.getMolecularSequence().length; i++ ) {
s[ i ] = seq.getMolecularSequence()[ i ];
return new BasicSequence( new String( seq.getIdentifier() ), s, seq.getType() );
}
- public static Sequence createAaSequence( final String identifier, final String mol_sequence ) {
+ public static MolecularSequence createSequence( final String identifier, final String mol_sequence ) {
+ check( identifier, mol_sequence );
+ final TYPE type = ForesterUtil.guessMolecularSequenceType( mol_sequence );
+ final String re;
+ final char repl;
+ if ( type == TYPE.AA ) {
+ re = AA_REGEXP;
+ repl = UNSPECIFIED_AA;
+ }
+ else if ( type == TYPE.DNA ) {
+ re = DNA_REGEXP;
+ repl = UNSPECIFIED_NUC;
+ }
+ else if ( type == TYPE.RNA ) {
+ re = RNA_REGEXP;
+ repl = UNSPECIFIED_NUC;
+ }
+ else {
+ throw new IllegalArgumentException( "could not determine sequence type for: " + mol_sequence);
+ }
+ return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
+ .replaceAll( re, Character.toString( repl ) ), type );
+ }
+
+ public static MolecularSequence createGeneralSequence( final String identifier, final String mol_sequence ) {
+ check( identifier, mol_sequence );
+ return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR
+ ), TYPE.GENERAL );
+ }
+
+ public static MolecularSequence createAaSequence( final String identifier, final String mol_sequence ) {
+ check( identifier, mol_sequence );
return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
- .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA );
+ .replaceAll( AA_REGEXP, Character.toString( UNSPECIFIED_AA ) ), TYPE.AA );
}
- public static Sequence createDnaSequence( final String identifier, final String mol_sequence ) {
+ public static MolecularSequence createDnaSequence( final String identifier, final String mol_sequence ) {
+ check( identifier, mol_sequence );
return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
- .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA );
+ .replaceAll( DNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.DNA );
}
- public static Sequence createRnaSequence( final String identifier, final String mol_sequence ) {
+ public static MolecularSequence createRnaSequence( final String identifier, final String mol_sequence ) {
+ check( identifier, mol_sequence );
return new BasicSequence( identifier, mol_sequence.toUpperCase().replaceAll( "\\.", GAP_STR )
- .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
+ .replaceAll( RNA_REGEXP, Character.toString( UNSPECIFIED_NUC ) ), TYPE.RNA );
}
@Override
public String getMolecularSequenceAsString() {
return new String( getMolecularSequence() );
}
+
+ @Override
+ public boolean isGapAt( final int position ) {
+ return getResidueAt( position ) == GAP;
+ }
}