public interface AlignmentI extends AnnotatedCollectionI
{
/**
- * Calculates the number of sequences in an alignment
+ * Calculates the number of sequences in an alignment, excluding hidden
+ * sequences
*
* @return Number of sequences in alignment
*/
int getHeight();
/**
+ * Calculates the number of sequences in an alignment, including hidden
+ * sequences
+ *
+ * @return Number of sequences in alignment
+ */
+ int getAbsoluteHeight();
+
+ /**
*
* Calculates the maximum width of the alignment, including gaps.
*
boolean isAligned(boolean includeHidden);
/**
+ * Answers if the sequence at alignmentIndex is hidden
+ *
+ * @param alignmentIndex
+ * the index to check
+ * @return true if the sequence is hidden
+ */
+ boolean isHidden(int alignmentIndex);
+
+ /**
* Gets sequences as a Synchronized collection
*
* @return All sequences in alignment.
SequenceI getSequenceAt(int i);
/**
+ * Find a specific sequence in this alignment.
+ *
+ * @param i
+ * Index of required sequence in full alignment, i.e. if all columns
+ * were visible
+ *
+ * @return SequenceI at given index.
+ */
+ SequenceI getSequenceAtAbsoluteIndex(int i);
+
+ /**
* Returns a map of lists of sequences keyed by sequence name.
*
* @return
SequenceI replaceSequenceAt(int i, SequenceI seq);
/**
- * Deletes a sequence from the alignment
+ * Deletes a sequence from the alignment. Updates hidden sequences to account
+ * for the removed sequence. Do NOT use this method to delete sequences which
+ * are just hidden.
*
* @param s
* Sequence to be deleted.
void deleteSequence(SequenceI s);
/**
- * Deletes a sequence from the alignment.
+ * Deletes a sequence from the alignment. Updates hidden sequences to account
+ * for the removed sequence. Do NOT use this method to delete sequences which
+ * are just hidden.
*
* @param i
* Index of sequence to be deleted.
void deleteSequence(int i);
/**
+ * Deletes a sequence in the alignment which has been hidden.
+ *
+ * @param i
+ * Index of sequence to be deleted
+ */
+ void deleteHiddenSequence(int i);
+
+ /**
* Finds sequence in alignment using sequence name as query.
*
* @param name
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.
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
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
* @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.
* @return
*/
public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
}