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