From 4ac959df53fa2050b46127c753c36a129e619e10 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 19 Aug 2010 11:00:47 +0000
Subject: [PATCH] added import of PIR files
This is BZDNG-153
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2656 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/src/seq/pir_io_handler.cc | 89 +++++++++++++-------
modules/io/tests/CMakeLists.txt | 1 +
modules/io/tests/test_pir.cc | 73 ++++++++++++++++
modules/io/tests/testfiles/pir/no-star.pir | 21 +++++
modules/io/tests/testfiles/pir/seq-types.pir | 21 +++++
modules/io/tests/testfiles/pir/simple.pir | 4 +
modules/seq/base/src/invalid_sequence.hh | 1 +
7 files changed, 180 insertions(+), 30 deletions(-)
create mode 100644 modules/io/tests/test_pir.cc
create mode 100644 modules/io/tests/testfiles/pir/no-star.pir
create mode 100644 modules/io/tests/testfiles/pir/seq-types.pir
create mode 100644 modules/io/tests/testfiles/pir/simple.pir
diff --git a/modules/io/src/seq/pir_io_handler.cc b/modules/io/src/seq/pir_io_handler.cc
index a5d07c9ee..2974dcd51 100644
--- a/modules/io/src/seq/pir_io_handler.cc
+++ b/modules/io/src/seq/pir_io_handler.cc
@@ -72,50 +72,79 @@ bool PirIOHandler::ProvidesExport(const boost::filesystem::path& loc,
return PirIOHandler::ProvidesImport(loc, format);
}
-void PirIOHandler::Import(seq::SequenceList& aln,
- std::istream& instream)
+void PirIOHandler::Import(seq::SequenceList& aln, std::istream& instream)
{
- const char* error_msg="Bad Pir file: Expected '>', but '%1%' found.";
-
+ const char* error_msg="Expected %1%, but '%2%' found.";
+ const char* premature_end="Premature end in PIR file on line %1%";
+ const char* empty_seq="PIR file contains empty sequence on line %1%";
String line;
- std::getline(instream, line);
- int seq_count=0;
- //not yet supported
- throw IOException("Import of PIR format is not yet supported!");
+ int line_num=1, seq_count=0;
+ // we can't use a normal while(std::getline(...)) here, because the PIR format
+ // requires us to perform a one-line look-ahead.
+ std::getline(instream, line);
while (!instream.eof()) {
- // parse header information. cut after first "|"
+ // skip empty lines
if (line.find_first_not_of("\n\t ")==String::npos) {
- std::getline(instream, line);
continue;
}
- if (line.length()==0 || line[0]!='>') {
- String error=str(format(error_msg) % line);
+ if (line[0]!='>') {
+ String error=str(format(error_msg) % "'>'" % line);
+ throw IOException(error);
+ }
+ if (line.length()<4) {
+ String error=str(format(error_msg) % "seq-type;identifier" % line);
throw IOException(error);
}
- String identifier=line.substr(1);
- String sequence_str;
- while (std::getline(instream, line) && line.size()>0 && line[0]!='>') {
- if (line.find_first_not_of("\n\t ")==String::npos) {
- continue;
+ String seq_type=line.substr(1, 2);
+ if (!(seq_type=="P1" || seq_type=="F1" || seq_type=="DL" ||
+ seq_type=="DC" || seq_type=="RL" || seq_type=="RC" ||
+ seq_type=="XX")) {
+ throw IOException("Bad PIR file: Unknown sequence type"/*" '%1%' on line %2%" % seq_type % line_nu*m*/);
+ }
+ String name=line.substr(4);
+ int subject_line_num=line_num;
+ if (!std::getline(instream, line)) {
+ throw IOException(str(format(premature_end) % line_num));
+ }
+ line_num+=1;
+ std::stringstream seq_string;
+ bool end_seq=false;
+ while (!end_seq && std::getline(instream, line)) {
+ line_num+=1;
+ for (String::iterator i=line.begin(), e=line.end(); i!=e; ++i) {
+ if (isspace(*i)) {
+ continue;
+ }
+ if (*i=='*') {
+ end_seq=true;
+ break;
+ }
+ seq_string << *i;
}
- sequence_str+=line;
}
- if (sequence_str.length()>0) {
- try {
- seq::SequenceHandle seq=seq::CreateSequence(identifier, sequence_str);
- aln.AddSequence(seq);
- seq_count+=1;
- } catch (seq::InvalidSequence& e) {
- throw e;
+ while (std::getline(instream, line)) {
+ line_num+=1;
+ if (!line.empty() && line[0]=='>') {
+ break;
}
- } else {
- throw IOException("Bad Pir file: Sequence is empty.");
}
- }
+ if (!end_seq) {
+ throw IOException(str(format(premature_end) % line_num));
+ }
+ if (seq_string.str().empty()) {
+ throw IOException(str(format(empty_seq) % subject_line_num));
+ }
+ try {
+ seq::SequenceHandle ss=seq::CreateSequence(name, seq_string.str());
+ aln.AddSequence(ss);
+ seq_count+=1;
+ } catch (seq::InvalidSequence& e) {
+ throw e;
+ }
+ }
if (seq_count==0) {
throw IOException("Bad Pir file: File is empty");
- }
-
+ }
}
void PirIOHandler::Export(const seq::ConstSequenceList& seqs,
diff --git a/modules/io/tests/CMakeLists.txt b/modules/io/tests/CMakeLists.txt
index f0c230801..1cb26f5fd 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -3,6 +3,7 @@ set(OST_IO_UNIT_TESTS
test_io_pdb.cc
test_io_crd.cc
test_io_sdf.cc
+ test_pir.cc
test_iomanager.cc
tests.cc
)
diff --git a/modules/io/tests/test_pir.cc b/modules/io/tests/test_pir.cc
new file mode 100644
index 000000000..1829404cc
--- /dev/null
+++ b/modules/io/tests/test_pir.cc
@@ -0,0 +1,73 @@
+//------------------------------------------------------------------------------
+// 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
+//------------------------------------------------------------------------------
+
+/*
+ Author: Marco Biasini
+ */
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <ost/seq/invalid_sequence.hh>
+#include <ost/io/seq/pir_io_handler.hh>
+#include <ost/io/seq/load.hh>
+#include <ost/io/io_exception.hh>
+
+
+using namespace ost;
+using namespace ost::io;
+
+
+BOOST_AUTO_TEST_SUITE( io )
+
+
+BOOST_AUTO_TEST_CASE(pir_filetypes)
+{
+ BOOST_CHECK(PirIOHandler::ProvidesImport("","pir"));
+ BOOST_CHECK(PirIOHandler::ProvidesImport("alignment.pir"));
+}
+
+BOOST_AUTO_TEST_CASE(pir_simple)
+{
+ seq::SequenceHandle s=LoadSequence("testfiles/pir/simple.pir");
+ BOOST_CHECK_EQUAL(s.GetName(), "name");
+ BOOST_CHECK_EQUAL(s.GetString(), "ABCDEFGHIJKLMNOP");
+}
+
+BOOST_AUTO_TEST_CASE(pir_seq_types)
+{
+ seq::SequenceList s=LoadSequenceList("testfiles/pir/seq-types.pir");
+}
+
+BOOST_AUTO_TEST_CASE(pir_errors)
+{
+ BOOST_CHECK_THROW(SequenceFromString(">", "pir"), IOException);
+ BOOST_CHECK_THROW(SequenceFromString(">P1", "pir"), IOException);
+ BOOST_CHECK_THROW(SequenceFromString(">P1;", "pir"), IOException);
+ BOOST_CHECK_THROW(SequenceFromString(">P1;name\n", "pir"), IOException);
+ BOOST_CHECK_THROW(SequenceFromString(">P1;name\ndescription\n", "pir"),
+ IOException);
+}
+
+BOOST_AUTO_TEST_CASE(pir_no_star)
+{
+ BOOST_CHECK_THROW(LoadSequence("testfiles/pir/no-star.pir"),
+ seq::InvalidSequence);
+}
+
+BOOST_AUTO_TEST_SUITE_END()
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pir/no-star.pir b/modules/io/tests/testfiles/pir/no-star.pir
new file mode 100644
index 000000000..98bc371aa
--- /dev/null
+++ b/modules/io/tests/testfiles/pir/no-star.pir
@@ -0,0 +1,21 @@
+>P1;name
+description
+ABCD EFGH*
+>F1;name
+description
+ABCD EFGH
+>DL;name*
+description
+ABCD EFGH
+>DC;name*
+description
+ABCD EFGH
+>RL;name*
+description
+ABCD EFGH
+>RC;name*
+description
+ABCD EFGH
+>XX;name*
+description
+ABCD EFGH*
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pir/seq-types.pir b/modules/io/tests/testfiles/pir/seq-types.pir
new file mode 100644
index 000000000..ed8569f43
--- /dev/null
+++ b/modules/io/tests/testfiles/pir/seq-types.pir
@@ -0,0 +1,21 @@
+>P1;name
+description
+ABCD EFGH*
+>F1;name
+description
+ABCD EFGH*
+>DL;name
+description
+ABCD EFGH*
+>DC;name
+description
+ABCD EFGH*
+>RL;name
+description
+ABCD EFGH*
+>RC;name*
+description
+ABCD EFGH*
+>XX;name
+description
+ABCD EFGH*
\ No newline at end of file
diff --git a/modules/io/tests/testfiles/pir/simple.pir b/modules/io/tests/testfiles/pir/simple.pir
new file mode 100644
index 000000000..6e8f03e4e
--- /dev/null
+++ b/modules/io/tests/testfiles/pir/simple.pir
@@ -0,0 +1,4 @@
+>P1;name
+description
+ABCD EFGH
+IJKL MNOP*
\ No newline at end of file
diff --git a/modules/seq/base/src/invalid_sequence.hh b/modules/seq/base/src/invalid_sequence.hh
index b112df8f3..453916403 100644
--- a/modules/seq/base/src/invalid_sequence.hh
+++ b/modules/seq/base/src/invalid_sequence.hh
@@ -23,6 +23,7 @@
Author: Marco Biasini
*/
#include <ost/seq/module_config.hh>
+#include <ost/message.hh>
namespace ost { namespace seq {
class DLLEXPORT InvalidSequence : public Error {
--
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