From 54b004566a3ec88f306ddaa4658178caca98ef1a Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 30 Aug 2010 07:30:37 +0000
Subject: [PATCH] speedup and unit test for sequence identity calculation
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2676 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/seq/alg/pymod/wrap_seq_alg.cc | 4 +-
modules/seq/alg/src/sequence_identity.cc | 33 +++--
modules/seq/alg/tests/CMakeLists.txt | 1 +
.../seq/alg/tests/test_sequence_identity.cc | 132 ++++++++++++++++++
4 files changed, 159 insertions(+), 11 deletions(-)
create mode 100644 modules/seq/alg/tests/test_sequence_identity.cc
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index 7ec249db1..f632d3d6e 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -35,8 +35,8 @@ BOOST_PYTHON_MODULE(_seq_alg)
.value("LONGER_SEQUENCE", RefMode::LONGER_SEQUENCE)
.export_values()
;
- def("SequenceIdentity", &SequenceIdentity, arg("seq_a")=0, arg("seq_b")=1);
-
+ def("SequenceIdentity", &SequenceIdentity,
+ (arg("ref_mode")=RefMode::ALIGNMENT, arg("seq_a")=0, arg("seq_b")=1));
class_<AlignedRegionList>("AlignedRegionList", init<>())
.def(vector_indexing_suite<AlignedRegionList>())
;
diff --git a/modules/seq/alg/src/sequence_identity.cc b/modules/seq/alg/src/sequence_identity.cc
index 855d3ec48..5d0a7dc2d 100644
--- a/modules/seq/alg/src/sequence_identity.cc
+++ b/modules/seq/alg/src/sequence_identity.cc
@@ -30,28 +30,43 @@ Real SequenceIdentity(const AlignmentHandle& aln, RefMode::Type ref_mode,
{
int non_gap_count=0;
int identical_count=0;
- for (AlignedColumnIterator i=aln.begin(), e=aln.end(); i!=e; ++i) {
- AlignedColumn col=*i;
- if (!(col[seq_a] == '-' && col[seq_b]=='-')) {
+ const String& sa=aln.GetSequence(seq_a).GetString();
+ const String& sb=aln.GetSequence(seq_b).GetString();
+ for (String::const_iterator
+ i=sa.begin(), e=sa.end(), j=sb.begin(); i!=e; ++i, ++j) {
+ if (!((*i)== '-' || (*j)=='-')) {
non_gap_count++;
}
- if (col[seq_a]!='-' && col[seq_a]==col[seq_b]) {
+ if ((*i)!='-' && (*i)==(*j)) {
identical_count++;
}
}
Real seq_id=0.0;
- // devide by length of longer sequence:
+ // divide by length of longer sequence:
if (ref_mode==RefMode::LONGER_SEQUENCE) {
int wo_gaps_a=aln.GetSequence(seq_a).GetGaplessString().length();
int wo_gaps_b=aln.GetSequence(seq_b).GetGaplessString().length();
if(wo_gaps_a>=wo_gaps_b) {
- seq_id=100*static_cast<Real>(identical_count)/wo_gaps_a;
+ if (wo_gaps_a==0) {
+ seq_id=0;
+ } else {
+ seq_id=100*static_cast<Real>(identical_count)/wo_gaps_a;
+ }
+
} else {
- seq_id=100*static_cast<Real>(identical_count)/wo_gaps_b;
+ if (wo_gaps_b==0) {
+ seq_id=0;
+ } else {
+ seq_id=100*static_cast<Real>(identical_count)/wo_gaps_b;
+ }
}
} else {
- // divide by alignment length:
- seq_id=100*static_cast<Real>(identical_count)/non_gap_count;
+ if (non_gap_count==0) {
+ seq_id=0;
+ } else {
+ // divide by alignment length:
+ seq_id=100*static_cast<Real>(identical_count)/non_gap_count;
+ }
}
return seq_id;
}
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 512de0856..37969a869 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -1,5 +1,6 @@
set(OST_SEQ_ALG_UNIT_TESTS
test_merge_pairwise_alignments.cc
+ test_sequence_identity.cc
tests.cc
)
diff --git a/modules/seq/alg/tests/test_sequence_identity.cc b/modules/seq/alg/tests/test_sequence_identity.cc
new file mode 100644
index 000000000..fa2d58eaf
--- /dev/null
+++ b/modules/seq/alg/tests/test_sequence_identity.cc
@@ -0,0 +1,132 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+/*
+ * Authors: Marco Biasini
+ */
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+
+#include <ost/seq/alg/sequence_identity.hh>
+
+
+
+using namespace ost;
+using namespace ost::seq;
+
+BOOST_AUTO_TEST_SUITE(ost_seq_alg)
+
+BOOST_AUTO_TEST_CASE(seqid_one)
+{
+ SequenceHandle s1=CreateSequence("S1", "abcdefgh");
+ SequenceHandle s2=CreateSequence("S2", "abcd----");
+
+ AlignmentHandle aln=CreateAlignment();
+ aln.AddSequence(s1);
+ aln.AddSequence(s2);
+
+ Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
+ BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+ // check the default sequence indices
+ seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
+ BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+ // check the default value for reference mode
+ seqid=alg::SequenceIdentity(aln);
+ BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+ seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
+ BOOST_CHECK_CLOSE(seqid, 100.0, 1e-6);
+}
+
+BOOST_AUTO_TEST_CASE(seqid_two)
+{
+ SequenceHandle s1=CreateSequence("S1", "abcd");
+ SequenceHandle s2=CreateSequence("S2", "xbcx");
+
+ AlignmentHandle aln=CreateAlignment();
+ aln.AddSequence(s1);
+ aln.AddSequence(s2);
+
+ Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
+ BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+ // check the default sequence indices
+ seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
+ BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+ // check the default value for reference mode
+ seqid=alg::SequenceIdentity(aln);
+ BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+
+ seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
+ BOOST_CHECK_CLOSE(seqid, 50.0, 1e-6);
+}
+
+BOOST_AUTO_TEST_CASE(seqid_three)
+{
+ SequenceHandle s1=CreateSequence("S1", "a--d");
+ SequenceHandle s2=CreateSequence("S2", "x--x");
+
+ AlignmentHandle aln=CreateAlignment();
+ aln.AddSequence(s1);
+ aln.AddSequence(s2);
+
+ Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
+ BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+ // check the default sequence indices
+ seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
+ BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+ // check the default value for reference mode
+ seqid=alg::SequenceIdentity(aln);
+ BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+ seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
+ BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+}
+
+BOOST_AUTO_TEST_CASE(seqid_empty)
+{
+ SequenceHandle s1=CreateSequence("S1", "---");
+ SequenceHandle s2=CreateSequence("S2", "---");
+
+ AlignmentHandle aln=CreateAlignment();
+ aln.AddSequence(s1);
+ aln.AddSequence(s2);
+
+ Real seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE, 0, 1);
+ BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+ // check the default sequence indices
+ seqid=alg::SequenceIdentity(aln, alg::RefMode::LONGER_SEQUENCE);
+ BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+ // check the default value for reference mode
+ seqid=alg::SequenceIdentity(aln);
+ BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+
+ seqid=alg::SequenceIdentity(aln, alg::RefMode::ALIGNMENT);
+ BOOST_CHECK_CLOSE(seqid, 0.0, 1e-6);
+}
+
+
+BOOST_AUTO_TEST_SUITE_END()
--
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