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JAL-2110 cross-refs from protein to show cds not non-coding sequences
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
4ae8ba2
..
c15bb99
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-305,7
+305,7
@@
public interface AlignmentI extends AnnotatedCollectionI
* @return Alignment containing dataset sequences or null of this is a
* dataset.
*/
* @return Alignment containing dataset sequences or null of this is a
* dataset.
*/
- Alignment getDataset();
+ AlignmentI getDataset();
/**
* Set the associated dataset for the alignment, or create one.
/**
* Set the associated dataset for the alignment, or create one.
@@
-313,7
+313,7
@@
public interface AlignmentI extends AnnotatedCollectionI
* @param dataset
* The dataset alignment or null to construct one.
*/
* @param dataset
* The dataset alignment or null to construct one.
*/
- void setDataset(Alignment dataset);
+ void setDataset(AlignmentI dataset);
/**
* pads sequences with gaps (to ensure the set looks like an alignment)
/**
* pads sequences with gaps (to ensure the set looks like an alignment)
@@
-363,14
+363,6
@@
public interface AlignmentI extends AnnotatedCollectionI
void addCodonFrame(AlignedCodonFrame codons);
/**
void addCodonFrame(AlignedCodonFrame codons);
/**
- * add a set of aligned codons mappings for this alignment, apart from any
- * duplicates which are ignored
- *
- * @param codons
- */
- void addCodonFrames(Iterable<AlignedCodonFrame> codons);
-
- /**
* remove a particular codon frame reference from this alignment
*
* @param codons
* remove a particular codon frame reference from this alignment
*
* @param codons