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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
6b76f92
..
a172221
100644
(file)
--- a/
forester/java/src/org/forester/sequence/BasicSequence.java
+++ b/
forester/java/src/org/forester/sequence/BasicSequence.java
@@
-22,7
+22,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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;
package org.forester.sequence;
@@
-31,7
+31,7
@@
import org.forester.util.ForesterUtil;
public class BasicSequence implements Sequence {
private final char[] _mol_sequence;
public class BasicSequence implements Sequence {
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 ) {
private final TYPE _type;
private BasicSequence( final String identifier, final String mol_sequence, final TYPE type ) {
@@
-59,6
+59,10
@@
public class BasicSequence implements Sequence {
_type = type;
}
_type = type;
}
+ public void setIdentifier( final String id ) {
+ _identifier = id;
+ }
+
@Override
public String getIdentifier() {
return _identifier;
@Override
public String getIdentifier() {
return _identifier;
@@
-151,4
+155,9
@@
public class BasicSequence implements Sequence {
public String getMolecularSequenceAsString() {
return new String( getMolecularSequence() );
}
public String getMolecularSequenceAsString() {
return new String( getMolecularSequence() );
}
+
+ @Override
+ public boolean isGapAt( final int position ) {
+ return getResidueAt( position ) == GAP;
+ }
}
}