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more test for isDuplication() and isSpecation() added (phyloXML encoded
[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
f7a8917
..
6d339ca
100644
(file)
--- a/
forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/
forester/java/src/org/forester/sequence/BasicSequence.java
@@
-36,23
+36,27
@@
public class BasicSequence implements MolecularSequence {
/**
* 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 ) ) {
@@
-144,18
+148,21
@@
public class BasicSequence implements MolecularSequence {
}
public static MolecularSequence 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 MolecularSequence 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 MolecularSequence 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