From c21d1e7dc362723cdc55ab5ed9b6ad34237b7ee5 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Tue, 10 Jul 2012 10:23:41 +0200
Subject: [PATCH] document a few more AlignmentHandle methods
---
modules/seq/base/doc/seq.rst | 44 ++++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index 99f4c6b73..042f1d09c 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -388,3 +388,47 @@ an alignment:
:raises: In case one of the two sequences doesn't have an attached view, a
:exc:`RuntimeError` is raised.
+
+ .. method:: AddSequence(sequence)
+
+ Append a sequence to the alignment. The sequence must have the same length as
+ sequences already present in the alignment.
+
+ :raises: :exc:`RuntimeError` if the sequence length does not match
+ :param sequence: Sequence to be added
+ :type sequence: :class:`ConstSequenceHandle`
+
+ .. method:: GetSequenceOffset(index)
+ SetSequenceOffset(index, offset)
+
+ Get/set the offset for sequence at *index*.
+
+ :param index: The index of the sequence
+ :type index: :class:`int`
+ :param offset: The new offset
+ :type offset: :class:`int`
+ :rtype: :class:`int`
+
+ .. method:: GetSequenceRole(index)
+ SetSequenceRole(index, role)
+
+ Get/Set the sequence role for sequence at *index*.
+
+ :param index: The index of the sequence
+ :type index: :class:`int`
+ :param role: The new role
+ :type role: :class:`str`
+ :rtype: :class:`str`
+
+ .. method:: GetCoverage(index)
+
+ Get coverage of sequence at *index* to the first sequence.
+
+ :param index: The index of the sequence
+ :type index: :class:`int`
+ :returns: Coverage as a number between 0 and 1.
+
+ .. method:: RemoveSequence(index)
+
+ Remove sequence at *index* from the alignment.
+
--
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