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Commit 80c29957 authored by marco's avatar marco
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update sequence unit tests 

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2522 5a81b35b-ba03-0410-adc8-b2c5c5119f08
parent 09f5c2b4
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modules/seq/base/src/impl/sequence_impl.cc
+ 1
− 1
View file @ 80c29957
...@@ -136,7 +136,7 @@ int SequenceImpl::GetPos(int index) const ...@@ -136,7 +136,7 @@ int SequenceImpl::GetPos(int index) const
int shifted_index=index-sequence_offset_; int shifted_index=index-sequence_offset_;
int pos=this->GetPosNoBounds(shifted_index); int pos=this->GetPosNoBounds(shifted_index);
if (pos<0 || pos>=static_cast<int>(seq_string_.length())) 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; return pos;
} }
......
modules/seq/base/src/impl/sequence_list_impl.hh
+ 2
− 2
View file @ 80c29957
...@@ -46,7 +46,7 @@ public: ...@@ -46,7 +46,7 @@ public:
if (index<list_.size()) { if (index<list_.size()) {
return list_[index]; 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 { const SequenceImplPtr& GetSequence(unsigned int i) const {
...@@ -54,7 +54,7 @@ public: ...@@ -54,7 +54,7 @@ public:
if (index<list_.size()) { if (index<list_.size()) {
return list_[index]; 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; int GetPos(int seq_index, int residue_index) const;
......
modules/seq/base/tests/test_alignment.cc
+ 13
− 13
View file @ 80c29957
...@@ -102,10 +102,10 @@ BOOST_AUTO_TEST_CASE(alignment_onelettercode) ...@@ -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(0,3),seq1.GetOneLetterCode(3));
BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,3),'w'); BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,3),'w');
BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,3),seq2.GetOneLetterCode(3)); BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,3),seq2.GetOneLetterCode(3));
BOOST_CHECK_THROW(a.GetOneLetterCode(0,-1),Error); BOOST_CHECK_THROW(a.GetOneLetterCode(0,-1),std::out_of_range);
BOOST_CHECK_THROW(a.GetOneLetterCode(1,6),Error); BOOST_CHECK_THROW(a.GetOneLetterCode(1,6),std::out_of_range);
BOOST_CHECK_THROW(a.GetOneLetterCode(2,0),Error); BOOST_CHECK_THROW(a.GetOneLetterCode(2,0),std::out_of_range);
BOOST_CHECK_THROW(a.GetOneLetterCode(-1,0),Error); BOOST_CHECK_THROW(a.GetOneLetterCode(-1,0), std::out_of_range);
} }
BOOST_AUTO_TEST_CASE(alignment_pos_and_index) BOOST_AUTO_TEST_CASE(alignment_pos_and_index)
...@@ -119,8 +119,8 @@ 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_EQUAL(a.GetResidueIndex(1,4), 2);
BOOST_CHECK_THROW(a.GetPos(0,-1),Error); BOOST_CHECK_THROW(a.GetPos(0,-1),Error);
BOOST_CHECK_THROW(a.GetPos(1,4),Error); BOOST_CHECK_THROW(a.GetPos(1,4),Error);
BOOST_CHECK_THROW(a.GetPos(2,0),Error); BOOST_CHECK_THROW(a.GetPos(2,0),std::out_of_range);
BOOST_CHECK_THROW(a.GetPos(-1,0),Error); BOOST_CHECK_THROW(a.GetPos(-1,0),std::out_of_range);
} }
BOOST_AUTO_TEST_CASE(alignment_getseq) BOOST_AUTO_TEST_CASE(alignment_getseq)
...@@ -132,8 +132,8 @@ BOOST_AUTO_TEST_CASE(alignment_getseq) ...@@ -132,8 +132,8 @@ BOOST_AUTO_TEST_CASE(alignment_getseq)
a.AddSequence(seq2); a.AddSequence(seq2);
BOOST_CHECK_EQUAL(a.GetSequence(0), seq1); BOOST_CHECK_EQUAL(a.GetSequence(0), seq1);
BOOST_CHECK_EQUAL(a.GetSequence(1), seq2); BOOST_CHECK_EQUAL(a.GetSequence(1), seq2);
BOOST_CHECK_THROW(a.GetSequence(-1), Error); BOOST_CHECK_THROW(a.GetSequence(-1), std::out_of_range);
BOOST_CHECK_THROW(a.GetSequence(2), Error); BOOST_CHECK_THROW(a.GetSequence(2), std::out_of_range);
} }
BOOST_AUTO_TEST_CASE(alignment_attach_view) BOOST_AUTO_TEST_CASE(alignment_attach_view)
...@@ -156,7 +156,7 @@ 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_NO_THROW(a.AttachView(0,EntityView()));
BOOST_CHECK_EQUAL(a.GetResidue(0,1), EntityView()); BOOST_CHECK_EQUAL(a.GetResidue(0,1), EntityView());
BOOST_CHECK_EQUAL(a.GetResidue(0,3), 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) BOOST_AUTO_TEST_CASE(alignment_cut)
...@@ -170,10 +170,10 @@ 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.GetLength(),2);
BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,0),'r'); BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,0),'r');
BOOST_CHECK_EQUAL(a.GetOneLetterCode(0,1),'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(1,0),'a');
BOOST_CHECK_EQUAL(a.GetOneLetterCode(1,1),'-'); 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) BOOST_AUTO_TEST_CASE(alignment_shift_region)
...@@ -194,8 +194,8 @@ 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(0).GetString(),"abefcd");
BOOST_CHECK_EQUAL(a.GetSequence(1).GetString(),"ghlkij"); 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),std::out_of_range);
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),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); BOOST_CHECK_THROW(a.ShiftRegion(0,5,2),std::out_of_range);
......
modules/seq/base/tests/test_sequence.cc
+ 10
− 9
View file @ 80c29957
...@@ -94,16 +94,16 @@ BOOST_AUTO_TEST_CASE(seq_onelettercode) ...@@ -94,16 +94,16 @@ BOOST_AUTO_TEST_CASE(seq_onelettercode)
BOOST_CHECK_EQUAL(s.GetOneLetterCode(0),'a'); BOOST_CHECK_EQUAL(s.GetOneLetterCode(0),'a');
BOOST_CHECK_EQUAL(s.GetOneLetterCode(3),'c'); BOOST_CHECK_EQUAL(s.GetOneLetterCode(3),'c');
BOOST_CHECK_EQUAL(s.GetOneLetterCode(9),'f'); BOOST_CHECK_EQUAL(s.GetOneLetterCode(9),'f');
BOOST_CHECK_THROW(s.GetOneLetterCode(-1),Error); BOOST_CHECK_THROW(s.GetOneLetterCode(-1),std::out_of_range);
BOOST_CHECK_THROW(s.GetOneLetterCode(10),Error); BOOST_CHECK_THROW(s.GetOneLetterCode(10),std::out_of_range);
s=CreateSequence("S1", "-afc--de-f"); s=CreateSequence("S1", "-afc--de-f");
BOOST_CHECK_EQUAL(s.GetOneLetterCode(0),'-'); BOOST_CHECK_EQUAL(s.GetOneLetterCode(0),'-');
BOOST_CHECK_EQUAL(s.GetOneLetterCode(1),'a'); BOOST_CHECK_EQUAL(s.GetOneLetterCode(1),'a');
BOOST_CHECK_EQUAL(s.GetOneLetterCode(9),'f'); BOOST_CHECK_EQUAL(s.GetOneLetterCode(9),'f');
BOOST_CHECK_THROW(s.GetOneLetterCode(-1),Error); BOOST_CHECK_THROW(s.GetOneLetterCode(-1),std::out_of_range);
BOOST_CHECK_THROW(s.GetOneLetterCode(10),Error); BOOST_CHECK_THROW(s.GetOneLetterCode(10),std::out_of_range);
s=CreateSequence("S1", ""); 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) BOOST_AUTO_TEST_CASE(seq_getnum)
...@@ -116,8 +116,8 @@ 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(6),4-1);
BOOST_CHECK_EQUAL(s.GetResidueIndex(7),5-1); BOOST_CHECK_EQUAL(s.GetResidueIndex(7),5-1);
BOOST_CHECK_EQUAL(s.GetResidueIndex(9),6-1); BOOST_CHECK_EQUAL(s.GetResidueIndex(9),6-1);
BOOST_CHECK_THROW(s.GetResidueIndex(-1), Error); BOOST_CHECK_THROW(s.GetResidueIndex(-1), std::out_of_range);
BOOST_CHECK_THROW(s.GetResidueIndex(10), Error); BOOST_CHECK_THROW(s.GetResidueIndex(10), std::out_of_range);
} }
BOOST_AUTO_TEST_CASE(seq_getpos) BOOST_AUTO_TEST_CASE(seq_getpos)
...@@ -152,7 +152,8 @@ BOOST_AUTO_TEST_CASE(seq_offset) ...@@ -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(1),s2.GetResidueIndex(1)+2);
BOOST_CHECK_EQUAL(s.GetResidueIndex(6), 5); BOOST_CHECK_EQUAL(s.GetResidueIndex(6), 5);
BOOST_CHECK_EQUAL(s.GetResidueIndex(6),s2.GetResidueIndex(6)+2); 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); s.SetSequenceOffset(-1);
BOOST_CHECK_THROW(s.GetPos(-2), Error); BOOST_CHECK_THROW(s.GetPos(-2), Error);
...@@ -169,7 +170,7 @@ BOOST_AUTO_TEST_CASE(seq_offset) ...@@ -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(1),s2.GetResidueIndex(1)-1);
BOOST_CHECK_EQUAL(s.GetResidueIndex(6), 2); BOOST_CHECK_EQUAL(s.GetResidueIndex(6), 2);
BOOST_CHECK_EQUAL(s.GetResidueIndex(6),s2.GetResidueIndex(6)-1); 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) BOOST_AUTO_TEST_CASE(seq_gaps)
......
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