From b1ba3664afa43da41a3520867f953e5750848c4d Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 11 May 2010 12:03:05 +0000
Subject: [PATCH] fix to replace function
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2235 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/seq/base/src/alignment_handle.cc | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/modules/seq/base/src/alignment_handle.cc b/modules/seq/base/src/alignment_handle.cc
index 39db09fa5..d4611b562 100644
--- a/modules/seq/base/src/alignment_handle.cc
+++ b/modules/seq/base/src/alignment_handle.cc
@@ -170,16 +170,17 @@ void AlignmentHandle::Replace(const AlignedRegion& aln_r, int start, int end){
this->CheckValidity();
//check that alignment handle and aligned region contain same number of sequences
if (impl_->GetCount() != aln_r.GetAlignmentHandle().GetCount()) {
- throw IntegrityError("alignment handle and aligned region are required "\
- "to share the same number of sequences");
+ throw IntegrityError("alignment handle and aligned region are required "
+ "to have the same number of sequences");
}
- int aln_rStart=aln_r.GetStart();
- int aln_rEnd=aln_r.GetEnd()-1;
+ int aln_r_start=aln_r.GetStart();
+ int aln_r_length=aln_r.GetLength();
AlignmentHandle aln=aln_r.GetAlignmentHandle();
//iterate over sequences and replace part of sequences with the substrings
//from aligned region
for (int i=0;i<impl_->GetCount() ;++i) {
- this->GetSequence(i).Impl()->Replace(aln.GetSequence(i).GetString().substr(aln_rStart,aln_rEnd), start, end);
+ String s=aln.GetSequence(i).GetString().substr(aln_r_start, aln_r_length);
+ this->GetSequence(i).Impl()->Replace(s, start, end);
}
}
--
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