From 80c29957f911279dd1a2aa288f0dbfebeed5045f Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 6 Jul 2010 07:46:34 +0000
Subject: [PATCH] update sequence unit tests
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2522 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/seq/base/src/impl/sequence_impl.cc | 2 +-
.../seq/base/src/impl/sequence_list_impl.hh | 4 +--
modules/seq/base/tests/test_alignment.cc | 26 +++++++++----------
modules/seq/base/tests/test_sequence.cc | 19 +++++++-------
4 files changed, 26 insertions(+), 25 deletions(-)
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index d584c3549..9539dd20c 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/modules/seq/base/src/impl/sequence_impl.cc
@@ -136,7 +136,7 @@ int SequenceImpl::GetPos(int index) const
int shifted_index=index-sequence_offset_;
int pos=this->GetPosNoBounds(shifted_index);
if (pos<0 || pos>=static_cast<int>(seq_string_.length()))
- throw std::out_of_range("number not covered in sequence");
+ throw Error("number not covered in sequence");
return pos;
}
diff --git a/modules/seq/base/src/impl/sequence_list_impl.hh b/modules/seq/base/src/impl/sequence_list_impl.hh
index 93bc07035..3f1970f51 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl.hh
@@ -46,7 +46,7 @@ public:
if (index<list_.size()) {
return list_[index];
}
- throw Error("Index not covered SequenceList");
+ throw std::out_of_range("Index not covered SequenceList");
}
const SequenceImplPtr& GetSequence(unsigned int i) const {
@@ -54,7 +54,7 @@ public:
if (index<list_.size()) {
return list_[index];
}
- throw Error("Index not covered SequenceList");
+ throw std::out_of_range("Index not covered SequenceList");
}
int GetPos(int seq_index, int residue_index) const;
diff --git a/modules/seq/base/tests/test_alignment.cc b/modules/seq/base/tests/test_alignment.cc
index 260ea5c23..0491f7d35 100644
--- a/modules/seq/base/tests/test_alignment.cc
+++ b/modules/seq/base/tests/test_alignment.cc
@@ -102,10 +102,10 @@ BOOST_AUTO_TEST_CASE(alignment_onelettercode)
BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,3),seq1.GetOneLetterCode(3));
BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,3),'w');
BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,3),seq2.GetOneLetterCode(3));
- BOOST_CHECK_THROW(a.GetOneLetterCode(0,-1),Error);
- BOOST_CHECK_THROW(a.GetOneLetterCode(1,6),Error);
- BOOST_CHECK_THROW(a.GetOneLetterCode(2,0),Error);
- BOOST_CHECK_THROW(a.GetOneLetterCode(-1,0),Error);
+ BOOST_CHECK_THROW(a.GetOneLetterCode(0,-1),std::out_of_range);
+ BOOST_CHECK_THROW(a.GetOneLetterCode(1,6),std::out_of_range);
+ BOOST_CHECK_THROW(a.GetOneLetterCode(2,0),std::out_of_range);
+ BOOST_CHECK_THROW(a.GetOneLetterCode(-1,0), std::out_of_range);
}
BOOST_AUTO_TEST_CASE(alignment_pos_and_index)
@@ -119,8 +119,8 @@ BOOST_AUTO_TEST_CASE(alignment_pos_and_index)
BOOST_CHECK_EQUAL(a.GetResidueIndex(1,4), 2);
BOOST_CHECK_THROW(a.GetPos(0,-1),Error);
BOOST_CHECK_THROW(a.GetPos(1,4),Error);
- BOOST_CHECK_THROW(a.GetPos(2,0),Error);
- BOOST_CHECK_THROW(a.GetPos(-1,0),Error);
+ BOOST_CHECK_THROW(a.GetPos(2,0),std::out_of_range);
+ BOOST_CHECK_THROW(a.GetPos(-1,0),std::out_of_range);
}
BOOST_AUTO_TEST_CASE(alignment_getseq)
@@ -132,8 +132,8 @@ BOOST_AUTO_TEST_CASE(alignment_getseq)
a.AddSequence(seq2);
BOOST_CHECK_EQUAL(a.GetSequence(0), seq1);
BOOST_CHECK_EQUAL(a.GetSequence(1), seq2);
- BOOST_CHECK_THROW(a.GetSequence(-1), Error);
- BOOST_CHECK_THROW(a.GetSequence(2), Error);
+ BOOST_CHECK_THROW(a.GetSequence(-1), std::out_of_range);
+ BOOST_CHECK_THROW(a.GetSequence(2), std::out_of_range);
}
BOOST_AUTO_TEST_CASE(alignment_attach_view)
@@ -156,7 +156,7 @@ BOOST_AUTO_TEST_CASE(alignment_attach_view)
BOOST_CHECK_NO_THROW(a.AttachView(0,EntityView()));
BOOST_CHECK_EQUAL(a.GetResidue(0,1), EntityView());
BOOST_CHECK_EQUAL(a.GetResidue(0,3), EntityView());
- BOOST_CHECK_THROW(a.GetResidue(-1,0),Error)
+ BOOST_CHECK_THROW(a.GetResidue(-1,0),std::out_of_range)
}
BOOST_AUTO_TEST_CASE(alignment_cut)
@@ -170,10 +170,10 @@ BOOST_AUTO_TEST_CASE(alignment_cut)
BOOST_CHECK_EQUAL(a.GetLength(),2);
BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,0),'r');
BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,1),'r');
- BOOST_CHECK_THROW(a.GetOneLetterCode(0,2),Error);
+ BOOST_CHECK_THROW(a.GetOneLetterCode(0,2),std::out_of_range);
BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,0),'a');
BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,1),'-');
- BOOST_CHECK_THROW(a.GetOneLetterCode(1,2),Error);
+ BOOST_CHECK_THROW(a.GetOneLetterCode(1,2),std::out_of_range);
}
BOOST_AUTO_TEST_CASE(alignment_shift_region)
@@ -194,8 +194,8 @@ BOOST_AUTO_TEST_CASE(alignment_shift_region)
BOOST_CHECK_EQUAL(a.GetSequence(0).GetString(),"abefcd");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"ghlkij");
- BOOST_CHECK_THROW(a.ShiftRegion(0,2,1,2),Error);
- BOOST_CHECK_THROW(a.ShiftRegion(0,2,1,-2),Error);
+ BOOST_CHECK_THROW(a.ShiftRegion(0,2,1,2),std::out_of_range);
+ BOOST_CHECK_THROW(a.ShiftRegion(0,2,1,-2),std::out_of_range);
BOOST_CHECK_THROW(a.ShiftRegion(0,2,-1),std::out_of_range);
BOOST_CHECK_THROW(a.ShiftRegion(0,5,2),std::out_of_range);
diff --git a/modules/seq/base/tests/test_sequence.cc b/modules/seq/base/tests/test_sequence.cc
index 97997f915..d97152f00 100644
--- a/modules/seq/base/tests/test_sequence.cc
+++ b/modules/seq/base/tests/test_sequence.cc
@@ -94,16 +94,16 @@ BOOST_AUTO_TEST_CASE(seq_onelettercode)
BOOST_CHECK_EQUAL(s.GetOneLetterCode(0),'a');
BOOST_CHECK_EQUAL(s.GetOneLetterCode(3),'c');
BOOST_CHECK_EQUAL(s.GetOneLetterCode(9),'f');
- BOOST_CHECK_THROW(s.GetOneLetterCode(-1),Error);
- BOOST_CHECK_THROW(s.GetOneLetterCode(10),Error);
+ BOOST_CHECK_THROW(s.GetOneLetterCode(-1),std::out_of_range);
+ BOOST_CHECK_THROW(s.GetOneLetterCode(10),std::out_of_range);
s=CreateSequence("S1", "-afc--de-f");
BOOST_CHECK_EQUAL(s.GetOneLetterCode(0),'-');
BOOST_CHECK_EQUAL(s.GetOneLetterCode(1),'a');
BOOST_CHECK_EQUAL(s.GetOneLetterCode(9),'f');
- BOOST_CHECK_THROW(s.GetOneLetterCode(-1),Error);
- BOOST_CHECK_THROW(s.GetOneLetterCode(10),Error);
+ BOOST_CHECK_THROW(s.GetOneLetterCode(-1),std::out_of_range);
+ BOOST_CHECK_THROW(s.GetOneLetterCode(10),std::out_of_range);
s=CreateSequence("S1", "");
- BOOST_CHECK_THROW(s.GetOneLetterCode(0),Error);
+ BOOST_CHECK_THROW(s.GetOneLetterCode(0), std::out_of_range);
}
BOOST_AUTO_TEST_CASE(seq_getnum)
@@ -116,8 +116,8 @@ BOOST_AUTO_TEST_CASE(seq_getnum)
BOOST_CHECK_EQUAL(s.GetResidueIndex(6),4-1);
BOOST_CHECK_EQUAL(s.GetResidueIndex(7),5-1);
BOOST_CHECK_EQUAL(s.GetResidueIndex(9),6-1);
- BOOST_CHECK_THROW(s.GetResidueIndex(-1), Error);
- BOOST_CHECK_THROW(s.GetResidueIndex(10), Error);
+ BOOST_CHECK_THROW(s.GetResidueIndex(-1), std::out_of_range);
+ BOOST_CHECK_THROW(s.GetResidueIndex(10), std::out_of_range);
}
BOOST_AUTO_TEST_CASE(seq_getpos)
@@ -152,7 +152,8 @@ BOOST_AUTO_TEST_CASE(seq_offset)
BOOST_CHECK_EQUAL(s.GetResidueIndex(1),s2.GetResidueIndex(1)+2);
BOOST_CHECK_EQUAL(s.GetResidueIndex(6), 5);
BOOST_CHECK_EQUAL(s.GetResidueIndex(6),s2.GetResidueIndex(6)+2);
- BOOST_CHECK_THROW(s.GetResidueIndex(10), Error);
+ BOOST_CHECK_THROW(s.GetResidueIndex(10), std::out_of_range);
+ BOOST_CHECK_THROW(s.GetResidueIndex(-1), std::out_of_range);
s.SetSequenceOffset(-1);
BOOST_CHECK_THROW(s.GetPos(-2), Error);
@@ -169,7 +170,7 @@ BOOST_AUTO_TEST_CASE(seq_offset)
BOOST_CHECK_EQUAL(s.GetResidueIndex(1),s2.GetResidueIndex(1)-1);
BOOST_CHECK_EQUAL(s.GetResidueIndex(6), 2);
BOOST_CHECK_EQUAL(s.GetResidueIndex(6),s2.GetResidueIndex(6)-1);
- BOOST_CHECK_THROW(s.GetResidueIndex(10), Error);
+ BOOST_CHECK_THROW(s.GetResidueIndex(10), std::out_of_range);
}
BOOST_AUTO_TEST_CASE(seq_gaps)
--
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