// Copyright (C) 2010 Christian M Zmasek
// Copyright (C) 2010 Sanford-Burnham Medical Research Institute
// All rights reserved
-//
+//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
-//
+//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.sequence;
-public class BasicSequence implements Sequence {
+import org.forester.util.ForesterUtil;
+
+public class BasicSequence implements MolecularSequence {
private final char[] _mol_sequence;
- private final Object _identifier;
+ private String _identifier;
private final TYPE _type;
- private BasicSequence( final Object 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;
}
- // Only use if you know what you are doing!
- public BasicSequence( final Object identifier, final char[] mol_sequence, final 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" );
+ }
+ }
+
+ /**
+ * 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;
}
- public Object getIdentifier() {
+ public void setIdentifier( final String id ) {
+ _identifier = id;
+ }
+
+ @Override
+ public String getIdentifier() {
return _identifier;
}
+ @Override
public int getLength() {
return _mol_sequence.length;
}
+ @Override
public char[] getMolecularSequence() {
return _mol_sequence;
}
+ @Override
public char getResidueAt( final int position ) {
return _mol_sequence[ position ];
}
+ @Override
public TYPE getType() {
return _type;
}
@Override
+ public int getNumberOfGapResidues() {
+ int gaps = 0;
+ for( final char element : _mol_sequence ) {
+ if ( element == GAP ) {
+ ++gaps;
+ }
+ }
+ return gaps;
+ }
+
+ @Override
+ public boolean equals( final Object obj ) {
+ if ( obj == null ) {
+ return false;
+ }
+ if ( obj.getClass() != getClass() ) {
+ return false;
+ }
+ final MolecularSequence other = ( MolecularSequence ) 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();
}
- public static Sequence createAaSequence( final Object identifier, final String mol_sequence ) {
+ 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 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 Object 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 Object 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;
}
}
git://source.jalview.org / jalview.git / blobdiff