From 7e5f1c71fd89ae077d4b3e529f3d43bdd17699d2 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Mon, 5 Jun 2023 12:00:52 +0200
Subject: [PATCH] refactor: custom GetLine to handle \r characters
Removes code duplication
---
modules/io/src/mol/sdf_reader.cc | 39 +++++++++++++++++---------------
modules/io/src/mol/sdf_reader.hh | 4 ++++
2 files changed, 25 insertions(+), 18 deletions(-)
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index b45c8ac46..ed53e5a0f 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -55,21 +55,29 @@ SDFReader::SDFReader(std::istream& instream)
this->ClearState(boost::filesystem::path(""));
}
+boost::iostreams::filtering_stream<boost::iostreams::input>& SDFReader::GetLine(
+ boost::iostreams::filtering_stream<boost::iostreams::input>& in,
+ String& line)
+ // Read next line from in and place it in line.
+ // Remove trailing \r characters.
+{
+ std::getline(in, line);
+ size_t cr_pos = line.find("\r");
+ if (cr_pos != String::npos) {
+ LOG_TRACE( "Remove CR@" << cr_pos);
+ line.erase(cr_pos);
+ }
+ return in;
+}
+
// import data from provided stream
void SDFReader::Import(mol::EntityHandle& ent)
{
String line;
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
- while (std::getline(in_,line)) {
+ while (GetLine(in_,line)) {
++line_num;
- // std::getline removes EOL character but may leave a DOS CR (\r) in Unix
- size_t cr_pos = line.find("\r");
- if (cr_pos != String::npos) {
- LOG_TRACE( "Remove CR@" << cr_pos);
- line.erase(cr_pos);
- }
-
if (line_num<=4) {
ParseHeader(line, line_num, ent, editor);
} else if (version_ == "V2000" && line_num<=atom_count_+4) {
@@ -89,7 +97,7 @@ void SDFReader::Import(mol::EntityHandle& ent)
throw IOException(str(format(msg) % line_num));
}
String data_value="";
- while(std::getline(in_,line) && !boost::iequals(line, "")) {
+ while(GetLine(in_,line) && !boost::iequals(line, "")) {
data_value.append(line);
}
curr_chain_.SetStringProp(data_header, data_value);
@@ -438,15 +446,10 @@ String SDFReader::CleanupV3000Line(const String& line)
while (v30_line.find("-") == v30_line.length()-1) {
// Read and append the next line
String next_line;
- std::getline(in_,next_line);
- ++line_num;
- // std::getline removes EOL character but may leave a DOS CR (\r) in Unix
- size_t cr_pos = next_line.find("\r");
- if (cr_pos != String::npos) {
- LOG_TRACE( "Remove CR@" << cr_pos);
- next_line.erase(cr_pos);
- }
- // Ensure we have a valid line
+ GetLine(in_,next_line);
+ ++line_num; // Update class member
+
+ // Ensure we have a valid next_line
if (next_line.substr(0, 7) != "M V30 ") {
String msg="Bad V3000 line %d: starts with '%s'.";
throw IOException(str(format(msg) % line_num % next_line.substr(0, 6)));
diff --git a/modules/io/src/mol/sdf_reader.hh b/modules/io/src/mol/sdf_reader.hh
index ad8a6fff8..f684a5325 100644
--- a/modules/io/src/mol/sdf_reader.hh
+++ b/modules/io/src/mol/sdf_reader.hh
@@ -49,6 +49,10 @@ private:
typedef std::tuple<String, String, String> bond_data;
typedef std::tuple<std::vector<String>, std::map<String, String>> v3000_line_tokens;
+ boost::iostreams::filtering_stream<boost::iostreams::input>& GetLine(
+ boost::iostreams::filtering_stream<boost::iostreams::input>& in,
+ String& line);
+
void ClearState(const boost::filesystem::path& loc);
void NextMolecule();
--
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