string_util.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   utility/string_util.cc
///
/// @brief  Some std::string helper functions.
/// @author Sergey Lyskov
#include <platform/types.hh>

#include <utility/numbers.hh>
#include <utility/exit.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/string.functions.hh>
#include <locale>

// C/C++ headers
#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
#include <cmath>
#include <boost/uuid/sha1.hpp>

namespace utility {

void ReadFromFileOrDie(const std::string& filename, std::string* contents) {
  using std::ifstream;
  using std::string;
  using std::stringstream;

  assert(contents);

  ifstream in(filename.c_str());
  if ( !in ) {
    stringstream ss;
    ss << "The specified file " << filename
      << "does not exist or lacks sufficient permissions";
    utility_exit_with_message(ss.str());
  }

  string line;
  while ( in.good() ) {
    getline(in, line);
    (*contents) +=line + "\n";
  }
  in.close();
}

utility::vector1< std::string > split(const std::string &s)
{
  utility::vector1<std::string> r;
  unsigned int start=0, i=0;
  while ( start < s.size() ) {
    if ( s[i] == ' ' /*|| i==s.size()-1 */ ) {
      std::string add(s.begin()+start, s.begin()+i);
      if ( add.size() != 0 ) r.push_back( add );
      start = i+1;
    }
    i++;
    if ( i == s.size() ) {
      std::string add(s.begin()+start, s.begin()+i);
      if ( add.size() != 0 ) r.push_back( add );
      break;
    }
  }
  return r;
}

utility::vector1< std::string > split_whitespace(const std::string &s){
  std::istringstream ss( s );
  utility::vector1<std::string> r;
  while ( !ss.fail() ) {
    std::string e;
    ss >> e;
    if ( ss.fail() ) break;
    r.push_back(e);
  }
  return r;
}

std::string join(utility::vector1<std::string> const & s, std::string const & connector){
  std::ostringstream os;
  utility::vector1<std::string>::const_iterator begin= s.begin();
  os << *begin++;
  for ( ; begin != s.end(); ++begin ) {
    os<< connector<< *begin;
  }
  return os.str();
}

std::string join(std::vector<std::string> const & s, std::string const & connector){
  std::ostringstream os;
  utility::vector1<std::string>::const_iterator begin= s.begin();
  os << *begin++;
  for ( ; begin != s.end(); ++begin ) {
    os<< connector<< *begin;
  }
  return os.str();
}

std::string replace_spaces(std::string const & string_w_spaces, std::string const & replacement){
  //std::string trimmed= trim(string_w_spaces);
  utility::vector1<std::string> pieces= split(string_w_spaces);
  return join(pieces, replacement);
}

/// @details split given std::string using ' ' symbol.
std::list< std::string > split_to_list(const std::string &s) {
  std::list<std::string> r;
  unsigned int start=0, i=0;
  while ( start < s.size() ) {
    if ( s[i] == ' ' /*|| i==s.size()-1 */ ) {
      std::string add(s.begin()+start, s.begin()+i);
      if ( add.size() != 0 ) r.push_back( add );
      start = i+1;
    }
    i++;
    if ( i == s.size() ) {
      std::string add(s.begin()+start, s.begin()+i);
      if ( add.size() != 0 ) r.push_back( add );
      break;
    }
  }
  return r;
}

/// @details split given std::string using ' ' symbol.
std::set< std::string > split_to_set(const std::string &s) {
  std::set<std::string> r;
  unsigned int start=0, i=0;
  while ( start < s.size() ) {
    if ( s[i] == ' ' /*|| i==s.size()-1 */ ) {
      std::string add(s.begin()+start, s.begin()+i);
      if ( add.size() != 0 ) r.insert( add );
      start = i+1;
    }
    i++;
    if ( i == s.size() ) {
      std::string add(s.begin()+start, s.begin()+i);
      if ( add.size() != 0 ) r.insert( add );
      break;
    }
  }
  return r;
}

utility::vector1< std::string >
string_split( std::string const & in, char splitchar /* = ' ' */ )
{
  utility::vector1< std::string > parts;
  size_t i(0), j(0);
  while ( j != std::string::npos ) {
    j = in.find( splitchar, i );
    std::string const part = in.substr(i,j-i);
    parts.push_back( part );
    i = j+1;
  }
  return parts;
}

/// @details split to vector1< std::string > using arbitrary split character, but no empty strings (closer to python string::split)
utility::vector1< std::string >
string_split_simple( std::string const & in, char splitchar /* = ' ' */ )
{
  utility::vector1< std::string > parts;
  size_t i(0), j(0);
  while ( j != std::string::npos ) {
    j = in.find( splitchar, i );
    std::string const part = in.substr(i,j-i);
    if ( part.size() > 0 ) {
      parts.push_back( part );
    }
    i = j+1;
  }
  return parts;
}


//overloaded to split on any of an array of chars, useful to split on any whitespace
utility::vector1< std::string >
string_split_multi_delim( std::string const & in, std::string splitchars )
{
  utility::vector1< std::string > parts;
  size_t i(0), j(0);
  while ( j != std::string::npos ) {
    //find first instance of any of the splitchars
    j = in.find_first_of( splitchars, i );
    parts.push_back( in.substr(i,j-i) );
    i = j+1;
  }
  return parts;
}


/// @details convert a string to a float
float string2float( std::string st ){
  float i;
  std::stringstream ss( st );
  ss >> i;
  if ( !ss ) {
    return -1;
  }
  return i;
}

/// @details convert a string to an int
int string2int( std::string st ){
  int i;
  std::stringstream ss( st );
  ss >> i;
  if ( !ss ) {
    return -1;
  }
  return i;
}

/// @brief convert a string to a Size, returns numeric::get_undefined_size() on failure
platform::Size string2Size( std::string st ){
  platform::Size i;
  std::stringstream ss( st );
  ss >> i;
  if ( !ss ) {
    return get_undefined_size();
  }
  return i;
}

/// @brief convert a string to a Real, returns numeric::get_undefined_real() on failure
platform::Real string2Real( std::string st ){
  platform::Real i;
  std::stringstream ss( st );
  ss >> i;
  if ( !ss ) {
    return get_undefined_real();
  }
  return i;
}

// @brief Reads an unsigned int from string <x>, writing the result
// to output parameter <y>, which must be non-NULL. The result is
// undefined if the input string is malformed.
void string2uint(const std::string& x, unsigned int* y) {
  assert(y != NULL);
  std::stringstream ss(x);
  ss >> *y;
}

/// @details compares two strings ignoring leading and trailing spaces
bool trimmed_compare( std::string const & s1, std::string const & s2 )
{
  std::string const space( " " );

  std::size_t const s1_start( s1.find_first_not_of( space ) );
  std::size_t const s1_end( s1.find_last_not_of( space ) );
  std::size_t const s2_start( s2.find_first_not_of( space ) );
  std::size_t const s2_end( s2.find_last_not_of( space ) );

  std::size_t const s1_len( s1_end - s1_start + 1 );
  std::size_t const s2_len( s2_end - s2_start + 1 );

  return ( ( s1_len == s2_len ) && ( s1.compare( s1_start, s1_len, s2, s2_start, s2_len ) == 0 ) );
}

bool startswith(std::string const & haystack, std::string const & needle)
{
  if ( haystack.length() < needle.length() ) return false;
  else return ( haystack.compare(0, needle.length(), needle) == 0 );
}

bool endswith(std::string const & haystack, std::string const & needle)
{
  if ( haystack.length() < needle.length() ) return false;
  else return ( haystack.compare(haystack.size()-needle.size(),needle.size(),needle) == 0 );
}

void slurp(std::istream & in, std::string & out)
{
  std::string line;
  std::ostringstream os;
  while ( std::getline(in,line) ) {
    os << line << std::endl;
  }
  out.append( os.str());
}

void trim( std::string & s, const std::string & drop)
{
  std::string r = s.erase( s.find_last_not_of(drop)+1 );
  r.erase( 0, r.find_first_not_of(drop) );
  s = r;
}

std::string
trim( std::string const & s, std::string const & drop )
{
  std::string copystr( s );
  trim( copystr, drop );
  return copystr;
}

void add_spaces_left_align( std::string & st, std::size_t const newlen )
{
  std::size_t const to_add = newlen - st.length();
  if ( to_add > 0 ) {
    std::string st_to_add("");
    st_to_add.append(to_add,' ');
    st = st + st_to_add;
  }
}

void add_spaces_right_align( std::string & st, std::size_t const newlen )
{
  std::size_t const to_add = newlen - st.length();
  if ( to_add > 0 ) {
    std::string st_to_add("");
    st_to_add.append(to_add,' ');
    st = st_to_add + st;
  }
}

bool is_string_numeric(std::string const & input)
{
  std::locale loc;
  for ( platform::Size i = 0 ; i < input.size(); ++i ) {
    char current = input[i];
    if ( std::isdigit(current,loc) || current == '-' || current == '+' || current =='E' ||current=='e' ) {
      continue;
    } else {
      return false;
    }
  }
  return true;
}

std::string
file_contents( std::string const & file_name )
{
  vector1< std::string > text;
  std::string line;
  io::izstream textstream( file_name );
  if ( ! textstream ) {
    throw excn::EXCN_Msg_Exception( "Could not open file " + file_name  );
  }
  int strsize( 0 );
  while ( getline(textstream, line) ) {
    text.push_back(line + "\n");
    strsize += line.size() + 1;
  }
  textstream.close();

  std::string alltext;
  alltext.reserve( strsize );
  for ( unsigned int ii = 1; ii <= text.size(); ++ ii ) {
    alltext += text[ii];
  }
  return alltext;
}

std::string file_basename(const std::string& full_path) {
  return filename(full_path);
}

std::string filename(const std::string& path) {
  utility::file::FileName f(path);
  return f.base() + f.extension();
}

std::string pathname(const std::string& path) {
  return utility::file::FileName(path).path();
}

std::string replace_environment_variables(std::string input)
{
  const std::string start("${");
  const std::string end("}");

  platform::Size start_position = 0;
  while ( true )
      {
    start_position = input.find(start);
    if ( start_position != std::string::npos ) {
      platform::Size end_position = input.find(end,start_position);
      if ( start_position == std::string::npos ) {
        utility_exit_with_message("opening ${ but no closing } around an environment variable, check your options file");
      }

      platform::Size env_length = end_position-start_position;

      std::string env_name = input.substr(start_position+2,env_length-2);
      char * env_value = getenv(env_name.c_str());
      if ( !env_value ) {
        utility_exit_with_message("environment variable "+env_name+" does not exist");
      }

      input.replace(start_position, env_length+1,env_value);

    } else {
      return input;
    }
  }
}

std::string string_to_sha1(std::string const & input_string)
{
  //Based on https://gist.github.com/990731
  unsigned int digest[5];
  boost::uuids::detail::sha1 hasher;
  hasher.process_bytes(input_string.c_str(),input_string.size());


  char hash[20];
  std::stringstream output_hash;

  hasher.get_digest(digest);

  for ( int i = 0; i < 5; ++i ) {
    const char* tmp = reinterpret_cast<char*>(digest);
    hash[i*4] = tmp[i*4+3];
    hash[i*4+1] = tmp[i*4+2];
    hash[i*4+2] = tmp[i*4+1];
    hash[i*4+3] = tmp[i*4];
  }

  output_hash << std::hex;

  for ( int i = 0; i < 20 ; ++i ) {
    output_hash << ((hash[i] & 0x000000F0) >> 4) <<  (hash[i] & 0x0000000F);
  }

  return output_hash.str();
}

////////////////////////////////////////////////////////////////////////////
// Compactifies vectors of ints:  1 2 3 9 10 11 to "1-3 9-11"
// The function to go the other way (from string to vector) is available in
// ObjexxFCL::get_ints(), I think.
//
std::string
make_tag_with_dashes( utility::vector1< int > res_vector,
  char const delimiter /* = ' ' */){
  utility::vector1< char > chains;
  for ( platform::Size n = 0; n < res_vector.size(); n++ ) chains.push_back( ' ' );
  return make_tag_with_dashes( res_vector, chains, delimiter );
}

////////////////////////////////////////////////////////////////////////////
// Compactifies vectors of ints and chars (resnum and chain):  1A 2A 3A 9B 10B 11B to "A:1-3 B:9-11"
// The function to go the other way (from string to two vectors) is available below in get_resnum_and_chain()
//
std::string
make_tag_with_dashes( utility::vector1< int > res_vector,
  utility::vector1< char > chain_vector,
  char const delimiter /* = ' ' */){

  using namespace ObjexxFCL;
  std::string tag = "";

  if ( res_vector.size() == 0 ) return tag;
  runtime_assert( res_vector.size() == chain_vector.size() );

  int start_segment = res_vector[1];
  int last_res = res_vector[1];
  int last_chain = chain_vector[1];
  utility::vector1< std::pair<int,int> > res_vector_segments;
  utility::vector1< char > chains_for_segments;
  for ( platform::Size n = 2; n<= res_vector.size(); n++ ) {
    if ( res_vector[n] != last_res+1  || chain_vector[n] != last_chain ) {
      res_vector_segments.push_back( std::make_pair( start_segment, last_res ) );
      chains_for_segments.push_back( last_chain );
      start_segment = res_vector[n];
    }
    last_res = res_vector[n];
    last_chain = chain_vector[n];
  }
  res_vector_segments.push_back( std::make_pair( start_segment, last_res ) );
  chains_for_segments.push_back( last_chain );

  for ( platform::Size n = 1; n <= res_vector_segments.size(); n++ ) {
    if ( n > 1 ) tag += delimiter;
    std::pair< int, int > const & segment = res_vector_segments[n];
    if ( chains_for_segments[n] != '\0' &&
        chains_for_segments[n] != ' '  &&
        chains_for_segments[n] != '_' ) tag += std::string(1,chains_for_segments[n]) + ":";
    if ( segment.first == segment.second ) {
      tag += string_of( segment.first );
    } else {
      tag += string_of( segment.first )+"-"+string_of(segment.second);
    }
  }

  return tag;
}

/////////////////////////////////////////////////////////////////////////////////////////
// @brief Demands four-character seg ids. Output looks like "SEG1:3-4 SEG2:1-12    :1-3"
std::string
make_segtag_with_dashes( utility::vector1< int > res_vector,
  utility::vector1< std::string > segid_vector,
  char const delimiter /* = ' ' */){

  using namespace ObjexxFCL;
  std::string tag = "";

  if ( res_vector.size() == 0 ) return tag;
  runtime_assert( res_vector.size() == segid_vector.size() );

  int start_segment = res_vector[1];
  int last_res = res_vector[1];
  std::string last_segid = segid_vector[1];
  runtime_assert( segid_vector[1].size() == 4 );
  utility::vector1< std::pair<int,int> > res_vector_segments;
  utility::vector1< std::string > segids_for_segments;
  for ( platform::Size n = 2; n<= res_vector.size(); n++ ) {
    runtime_assert( segid_vector[n].size() == 4 );
    if ( res_vector[n] != last_res+1  || segid_vector[n] != last_segid ) {
      res_vector_segments.push_back( std::make_pair( start_segment, last_res ) );
      segids_for_segments.push_back( last_segid );
      start_segment = res_vector[n];
    }
    last_res = res_vector[n];
    last_segid = segid_vector[n];
  }
  res_vector_segments.push_back( std::make_pair( start_segment, last_res ) );
  segids_for_segments.push_back( last_segid );

  for ( platform::Size n = 1; n <= res_vector_segments.size(); n++ ) {
    if ( n > 1 ) tag += delimiter;
    std::pair< int, int > const & segment = res_vector_segments[n];
    tag += segids_for_segments[n] + ":";
    if ( segment.first == segment.second ) {
      tag += string_of( segment.first );
    } else {
      tag += string_of( segment.first )+"-"+string_of(segment.second);
    }
  }

  return tag;
}

/////////////////////////////////////////////////////////////////////////////////
std::string
make_tag( utility::vector1< int > res_vector ){

  using namespace ObjexxFCL;
  std::string tag = "";

  for ( platform::Size n = 1; n <= res_vector.size(); ++n ) {
    if ( n > 1 ) tag += " ";
    tag += string_of( res_vector[n] );
  }

  return tag;
}

/// @brief  converts string like "1-3 20-22" or "A:1-5 B:20-22" to vectors containing resnums and chains.
/// @author rhiju
//
//  #detailed  several kinds of tags are OK, including "A:1-5 B:20-22" and "A1-5 B20,21,22".
//
std::pair< std::vector< int >, std::vector< char > >
get_resnum_and_chain( std::string const & s, bool & string_is_ok ){

  string_is_ok = true;
  std::vector< int  > resnum;
  std::vector< char > chain;

  std::string s_nocommas = replace_in( s, ",", " " ); // order of operations issue?
  utility::vector1< std::string > const tags = utility::string_split( s_nocommas );
  for ( platform::Size n = 1; n <= tags.size(); n++ ) {
    string_is_ok = get_resnum_and_chain_from_one_tag( tags[n], resnum, chain );
    if ( !string_is_ok ) break;
  }
  return std::make_pair( resnum,chain );
}

std::pair< std::vector< int >, std::vector< char > >
get_resnum_and_chain( std::string const & s ){
  bool string_is_ok;
  return get_resnum_and_chain( s, string_is_ok );
}

std::pair< std::vector< int >, std::vector< std::string > >
get_resnum_and_segid( std::string const & s, bool & string_is_ok ){

  string_is_ok = true;
  std::vector< int  > resnum;
  std::vector< std::string > segid;

  std::string s_nocommas = replace_in( s, ",", " " ); // order of operations issue?
  // Each tag looks like
  // abcd:n-m, bcd could be spaces...
  // Strategy: add substring from start to colon (skips spaces!)
  // then from the space on forward.
  // utility::string_split( s_nocommas );
  utility::vector1< std::string > tags;

  // populate tags
  while ( true ) {
    // get rid of spaces (will get filled back in by get_resnum_and_segid_from_one_tag)
    while ( s_nocommas.size() > 0 && s_nocommas[0]==' ' ) s_nocommas = s_nocommas.substr(1);

    std::string tag = s_nocommas.substr( 0, s_nocommas.find_first_of( ':' )+1 );
    s_nocommas = s_nocommas.substr( s_nocommas.find_first_of( ':' ) +1 );

    platform::Size space_pos( s_nocommas.find_first_of( ' ' ) );
    if ( space_pos == std::string::npos ) {
      tag += s_nocommas;
      tags.push_back( tag );
      break;
    } else {
      tag += s_nocommas.substr( 0, space_pos );
      tags.push_back( tag );
      s_nocommas = s_nocommas.substr( space_pos +1 );
    }
  }

  for ( platform::Size n = 1; n <= tags.size(); n++ ) {
    string_is_ok = get_resnum_and_segid_from_one_tag( tags[n], resnum, segid );
    if ( !string_is_ok ) break;
  }
  return std::make_pair( resnum, segid );
}

/// @brief helper function for get_resnum_and_chain
bool
get_resnum_and_chain_from_one_tag( std::string const & tag,
  std::vector< int > & resnum,
  std::vector< char > & chains ){
  bool string_is_ok( false );
  std::vector< int > resnum_from_tag;
  char chain( ' ' );
  std::string const numerical("-0123456789");

  if ( tag.size() == 0 ) return true;

  size_t found_colon = tag.find( ":" );
  if ( found_colon == std::string::npos ) {
    if ( numerical.find( tag[0] ) == std::string::npos ) { // looks like a chain character at beginning
      chain= tag[0];
      resnum_from_tag = ObjexxFCL::ints_of( tag.substr(1), string_is_ok );
    } else {
      resnum_from_tag = ObjexxFCL::ints_of( tag, string_is_ok );
    }
  } else {
    if ( found_colon == 0 ) {
      chain = ' ';
      resnum_from_tag = ObjexxFCL::ints_of( tag.substr(1), string_is_ok );
    } else if ( found_colon == 1 ) {
      chain = tag[0];
      resnum_from_tag = ObjexxFCL::ints_of( tag.substr(2), string_is_ok );
    } else {
      return false;
    }
  }

  for ( platform::Size n = 0; n < resnum_from_tag.size(); n++ ) {
    resnum.push_back( resnum_from_tag[ n ] );
    chains.push_back( chain );
  }

  return string_is_ok;
}

bool
get_resnum_and_segid_from_one_tag( std::string const & tag,
  std::vector< int > & resnum,
  std::vector< std::string > & segids ){
  bool string_is_ok( false );
  std::vector< int > resnum_from_tag;
  std::string segid( "" );

  if ( tag.size() == 0 ) return true;

  size_t found_colon = tag.find( ":" );

  if ( found_colon == std::string::npos || found_colon > 4 ) return false;

  for ( size_t n = found_colon; n < 4; n++ ) {
    segid += ' ';
  }
  if ( found_colon > 0 ) segid += tag.substr(0,found_colon);
  runtime_assert( segid.size() == 4 );

  resnum_from_tag = ObjexxFCL::ints_of( tag.substr( found_colon + 1 ), string_is_ok );

  for ( platform::Size n = 0; n < resnum_from_tag.size(); n++ ) {
    resnum.push_back( resnum_from_tag[ n ] );
    segids.push_back( segid );
  }

  return string_is_ok;
}

platform::Size
get_num_digits( platform::Size value){
  return (platform::Size)ceil( std::log10(value + 1.) );
}

std::string
replace_in( std::string const & name_in, std::string const & find_string, std::string const & replace_string ){
  std::string name = name_in;
  // WARNING WARNING WARNING: Do not change pos back to platform::Size. In general platform::Size type
  //                          is not the same as size_t and algorithm below is sensitive to this
  // platform::Size pos = name.find( find_string );
  size_t pos = name.find( find_string );
  while ( pos != std::string::npos ) {
    name = name.replace( pos, find_string.size(), replace_string );

    //pos = name.find( find_string );

    // No, need to look for LATER instances of the replacement string.
    pos = name.find( find_string, pos + replace_string.size() );
  }
  return name;
}


// @brief Return a copy of the string with leading and trailing characters removed
std::string strip(std::string const & source, char c)
{
  std::string::const_iterator begin = source.begin();
  std::string::const_iterator end = source.end();
  for ( std::string::const_iterator p = source.begin(); p!=source.end(); ++p ) {
    if ( *p == c ) begin = p+1;
    else break;
  }

  for ( std::string::const_iterator p = source.end(); p!=begin; --p ) {
    if ( *(p-1) == c ) end = p-1;
    else break;
  }

  return std::string(begin, end);
}


} // namespace utility