From 336f5fa9f62e8e13c7fad1bb745fa57e28bf535a Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Fri, 7 May 2010 15:19:32 +0000
Subject: [PATCH] Fixed, alignment and sequence impls (added more bounds
checks)
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2203 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/seq/base/src/alignment_handle.cc | 23 ++++++++++++-------
modules/seq/base/src/alignment_handle.hh | 3 +--
modules/seq/base/src/impl/sequence_impl.cc | 3 +++
.../seq/base/src/impl/sequence_list_impl.hh | 17 ++++++++++----
4 files changed, 32 insertions(+), 14 deletions(-)
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index ee21b144c..3ad612da9 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -62,9 +62,9 @@ int AlignmentHandle::GetResidueIndex(int seq_index, int pos) const
void AlignmentHandle::AddSequence(const ConstSequenceHandle& sequence)
{
this->CheckValidity();
- if (impl_->GetCount()>0 &&
- impl_->GetSequence(0)->GetLength()!=sequence.GetLength()) {
- throw InvalidAlignment();
+ if (!sequence.IsValid() || (impl_->GetCount()>0 &&
+ impl_->GetSequence(0)->GetLength()!=sequence.GetLength())) {
+ throw InvalidSequence();
}
return impl_->AddSequence(sequence.Impl());
}
@@ -124,7 +124,7 @@ int AlignmentHandle::GetCount() const
AlignmentHandle AlignmentFromSequenceList(const SequenceList& seq_list)
{
- if (seq_list.SequencesHaveEqualLength()) {
+ if (seq_list.IsValid() && seq_list.SequencesHaveEqualLength()) {
return AlignmentHandle(seq_list.Impl());
}
throw InvalidAlignment();
@@ -188,10 +188,14 @@ void AlignmentHandle::ShiftRegion(int start, int end, int amount,
{
this->CheckValidity();
int cnt=0;
- for (impl::SequenceListImpl::Iterator i=impl_->Begin(),
- e=impl_->End(); i!=e; ++i, ++cnt) {
- if (master==-1 || cnt==master) {
- (*i)->ShiftRegion(start, end, amount);
+ if(master!=-1){
+ impl::SequenceImplPtr handle = this->GetSequence(master).Impl();
+ handle->ShiftRegion(start, end, amount);
+ }
+ else{
+ for (impl::SequenceListImpl::Iterator i=impl_->Begin(),
+ e=impl_->End(); i!=e; ++i, ++cnt) {
+ (*i)->ShiftRegion(start, end, amount);
}
}
}
@@ -199,6 +203,9 @@ void AlignmentHandle::ShiftRegion(int start, int end, int amount,
AlignedRegion AlignmentHandle::MakeRegion(int start, int n, int master) const
{
this->CheckValidity();
+ if(start<0 || n < 0 || start >= n || start + n >= this->GetLength()){
+ throw std::out_of_range("Region not valid");
+ }
return AlignedRegion(*this, start, start+n, master);
}
diff --git a/modules/seq/base/src/alignment_handle.hh b/modules/seq/base/src/alignment_handle.hh
index e007b4fb3..998618b52 100644
--- a/modules/seq/base/src/alignment_handle.hh
+++ b/modules/seq/base/src/alignment_handle.hh
@@ -121,8 +121,7 @@ public:
/// If set to -1, no master sequence is defined and the operations will
/// affect all sequences
///
- /// This method does not throw any exceptions, even if the aligned region is
- /// out of bounds.
+ /// If the aligned region is out of bounds, a std::out_of_bounds exeception will be thrown.
AlignedRegion MakeRegion(int start, int n, int master=-1) const;
/// \brief get number of sequences in alignment
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index 070211924..5ce66685e 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/modules/seq/base/src/impl/sequence_impl.cc
@@ -280,6 +280,9 @@ void SequenceImpl::Replace(const String& str,int start, int end)
void SequenceImpl::ShiftRegion(int start, int end, int amount)
{
+ if(start <= end && end + amount > this->GetLength() || start + amount <= 0){
+ throw std::out_of_range("Region not valid");
+ }
String str1=seq_string_.substr(start, end-start);
if (amount<0) {
String str2=seq_string_.substr(start+amount, -amount);
diff --git a/modules/seq/base/src/impl/sequence_list_impl.hh b/modules/seq/base/src/impl/sequence_list_impl.hh
index 0911aa9b8..93bc07035 100644
--- a/modules/seq/base/src/impl/sequence_list_impl.hh
+++ b/modules/seq/base/src/impl/sequence_list_impl.hh
@@ -41,12 +41,21 @@ public:
/// \brief get number of sequences in list
int GetCount() const { return list_.size(); }
- SequenceImplPtr& GetSequence(int i)
- {
- return list_[i];
+ SequenceImplPtr& GetSequence(int i) {
+ unsigned int index = static_cast<unsigned int>(i);
+ if (index<list_.size()) {
+ return list_[index];
+ }
+ throw Error("Index not covered SequenceList");
}
- const SequenceImplPtr& GetSequence(int i) const { return list_[i]; }
+ const SequenceImplPtr& GetSequence(unsigned int i) const {
+ unsigned int index = static_cast<unsigned int>(i);
+ if (index<list_.size()) {
+ return list_[index];
+ }
+ throw Error("Index not covered SequenceList");
+ }
int GetPos(int seq_index, int residue_index) const;
--
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