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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
sequence
/
Sequence.java
diff --git
a/forester/java/src/org/forester/sequence/Sequence.java
b/forester/java/src/org/forester/sequence/Sequence.java
index
fd13abf
..
cac6bcf
100644
(file)
--- a/
forester/java/src/org/forester/sequence/Sequence.java
+++ b/
forester/java/src/org/forester/sequence/Sequence.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;
@@
-37,7
+37,7
@@
public interface Sequence {
static final String DNA_REGEXP = "[^ACGTRYMKWSN\\-\\*]";
static final String RNA_REGEXP = "[^ACGURYMKWSN\\-\\*]";
static final String DNA_REGEXP = "[^ACGTRYMKWSN\\-\\*]";
static final String RNA_REGEXP = "[^ACGURYMKWSN\\-\\*]";
- public abstract Object getIdentifier();
+ public abstract String getIdentifier();
public abstract int getLength();
public abstract int getLength();
@@
-45,8
+45,12
@@
public interface Sequence {
public abstract char[] getMolecularSequence();
public abstract char[] getMolecularSequence();
+ public abstract String getMolecularSequenceAsString();
+
public abstract char getResidueAt( final int position );
public abstract char getResidueAt( final int position );
+ public abstract boolean isGapAt( final int position );
+
public abstract TYPE getType();
public enum TYPE {
public abstract TYPE getType();
public enum TYPE {