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JAL-2446 FeatureStore with NCList - work in progress
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
c15bb99
..
5d185cd
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-41,7
+41,8
@@
public interface AlignmentI extends AnnotatedCollectionI
*
* Calculates the maximum width of the alignment, including gaps.
*
*
* Calculates the maximum width of the alignment, including gaps.
*
- * @return Greatest sequence length within alignment.
+ * @return Greatest sequence length within alignment, or -1 if no sequences
+ * present
*/
@Override
int getWidth();
*/
@Override
int getWidth();
@@
-107,11
+108,14
@@
public interface AlignmentI extends AnnotatedCollectionI
* Used to set a particular index of the alignment with the given sequence.
*
* @param i
* Used to set a particular index of the alignment with the given sequence.
*
* @param i
- * Index of sequence to be updated.
+ * Index of sequence to be updated. if i>length, sequence will be
+ * added to end, with no intervening positions.
* @param seq
* @param seq
- * New sequence to be inserted.
+ * New sequence to be inserted. The existing sequence at position i
+ * will be replaced.
+ * @return existing sequence (or null if i>current length)
*/
*/
- void setSequenceAt(int i, SequenceI seq);
+ SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
* Deletes a sequence from the alignment
/**
* Deletes a sequence from the alignment
@@
-152,15
+156,17
@@
public interface AlignmentI extends AnnotatedCollectionI
int findIndex(SequenceI s);
/**
int findIndex(SequenceI s);
/**
- * Finds group that given sequence is part of.
+ * Returns the first group (in the order in which groups were added) that
+ * includes the given sequence instance and aligned position (base 0), or null
+ * if none found
*
*
- * @param s
- * Sequence in alignment.
+ * @param seq
+ * - must be contained in the alignment (not a dataset sequence)
+ * @param position
*
*
- * @return First group found for sequence. WARNING : Sequences may be members
- * of several groups. This method is incomplete.
+ * @return
*/
*/
- SequenceGroup findGroup(SequenceI s);
+ SequenceGroup findGroup(SequenceI seq, int position);
/**
* Finds all groups that a given sequence is part of.
/**
* Finds all groups that a given sequence is part of.
@@
-280,13
+286,6
@@
public interface AlignmentI extends AnnotatedCollectionI
char getGapCharacter();
/**
char getGapCharacter();
/**
- * Test for all nucleotide alignment
- *
- * @return true if alignment is nucleotide sequence
- */
- boolean isNucleotide();
-
- /**
* Test if alignment contains RNA structure
*
* @return true if RNA structure AligmnentAnnotation was added to alignment
* Test if alignment contains RNA structure
*
* @return true if RNA structure AligmnentAnnotation was added to alignment
@@
-294,12
+293,6
@@
public interface AlignmentI extends AnnotatedCollectionI
boolean hasRNAStructure();
/**
boolean hasRNAStructure();
/**
- * Set alignment to be a nucleotide sequence
- *
- */
- void setNucleotide(boolean b);
-
- /**
* Get the associated dataset for the alignment.
*
* @return Alignment containing dataset sequences or null of this is a
* Get the associated dataset for the alignment.
*
* @return Alignment containing dataset sequences or null of this is a
@@
-422,7
+415,7
@@
public interface AlignmentI extends AnnotatedCollectionI
* @param results
* @return -1 or index of sequence in alignment
*/
* @param results
* @return -1 or index of sequence in alignment
*/
- int findIndex(SearchResults results);
+ int findIndex(SearchResultsI results);
/**
* append sequences and annotation from another alignment object to this one.
/**
* append sequences and annotation from another alignment object to this one.