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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
sequence
/
BasicSequence.java
diff --git
a/forester/java/src/org/forester/sequence/BasicSequence.java
b/forester/java/src/org/forester/sequence/BasicSequence.java
index
dccc191
..
6d339ca
100644
(file)
--- a/
forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/
forester/java/src/org/forester/sequence/BasicSequence.java
@@
-28,7
+28,7
@@
package org.forester.sequence;
import org.forester.util.ForesterUtil;
import org.forester.util.ForesterUtil;
-public class BasicSequence implements Sequence {
+public class BasicSequence implements MolecularSequence {
private final char[] _mol_sequence;
private String _identifier;
private final char[] _mol_sequence;
private String _identifier;
@@
-36,23
+36,27
@@
public class BasicSequence implements Sequence {
/**
* Only use if you know what you are doing!
/**
* Only use if you know what you are doing!
- *
+ *
*/
public BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
*/
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" );
}
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 ) ) {
*/
public BasicSequence( final String identifier, final char[] mol_sequence, final TYPE type ) {
if ( ForesterUtil.isEmpty( identifier ) ) {
@@
-114,7
+118,7
@@
public class BasicSequence implements Sequence {
if ( obj.getClass() != getClass() ) {
return false;
}
if ( obj.getClass() != getClass() ) {
return false;
}
- final Sequence other = ( Sequence ) obj;
+ final MolecularSequence other = ( MolecularSequence ) obj;
if ( getMolecularSequenceAsString().equals( other.getMolecularSequenceAsString() ) ) {
return true;
}
if ( getMolecularSequenceAsString().equals( other.getMolecularSequenceAsString() ) ) {
return true;
}
@@
-135,7
+139,7
@@
public class BasicSequence implements Sequence {
return sb.toString();
}
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 ];
final char[] s = new char[ seq.getMolecularSequence().length ];
for( int i = 0; i < seq.getMolecularSequence().length; i++ ) {
s[ i ] = seq.getMolecularSequence()[ i ];
@@
-143,19
+147,22
@@
public class BasicSequence implements Sequence {
return new BasicSequence( new String( seq.getIdentifier() ), s, seq.getType() );
}
return new BasicSequence( new String( seq.getIdentifier() ), s, seq.getType() );
}
- public static Sequence createAaSequence( final String identifier, final String mol_sequence ) {
+ 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 )
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 )
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 )
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
}
@Override