php preg_match_all Qt alternative

**alrawab** · 23rd June 2014, 03:45

hi
is there any way to use php preg_match_all in Qt .

**anda_skoa** · 23rd June 2014, 07:29

You'll need to be a bit more precise.

If you are looking for regular expression handling, see QRegularExpression

Cheers,
_

**alrawab** · 23rd June 2014, 10:51

thanks anda the original code is looks like :

Qt Code:

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while (preg_match_all("$pattren","$vary","$res")==1){$x++;}

while (preg_match_all("$pattren","$vary","$res")==1){$x++;}

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the problem is both QRegExp::exactMatch and regular QString.contains some times gives diffrent resault .

**anda_skoa** · 23rd June 2014, 12:37

Can you given an example?

Cheers,
_

**alrawab** · 23rd June 2014, 15:27

i'm trying to port biophp "Microsatellite repeats finder"
this is the link for demo http://collegesoftwareconnection.com...satellites.php

and this is the source code in php :

Qt Code:

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<html>
    <head>
        <meta charset="UTF-8">
        <title></title>
    </head>
    <body>
        <?php
 
      function includeN_1($primer,$minus) {
        $code=".".substr($primer,1);
        $wpos=1;
        while ($wpos<strlen($primer)-$minus){
        $code.="|".substr($primer,0,$wpos).".".substr($primer,$wpos+1);
        $wpos++;
        }
return ($code);
      }  
 
 
 
        function includeN_2($primer,$minus) {
        $max=strlen($primer)-$minus;
        $code="";
        for($i=0;$i<$max;$i++){
                for($j=0;$j<$max-$i-1;$j++){
                  $code.="|".substr($primer,0,$i).".";
                  $resto=substr($primer,$i+1);
                  $code.=substr($resto,0,$j).".".substr($resto,$j+1);
                }
                }
 
$code=substr($code,1);
return ($code);
}
 
function includeN_3($primer,$minus) {
        $max=strlen($primer)-$minus;
        $code="";
        for($i=0;$i<$max;$i++){
                for($j=0;$j<$max-$i-1;$j++){
                  $code.="|".substr($primer,0,$i).".";
                  $resto=substr($primer,$i+1);
                  $code.=substr($resto,0,$j).".".substr($resto,$j+1);
                }
                }
$code=substr($code,1);
return ($code);
}
 
function find_microsatellite_repeats($sequence,$min_length,$max_length,$min_repeats,$min_length_of_MR,$mismatches_allowed){
        $len_seq=strlen($sequence);
        $counter=0;
        for ($i=0;$i<$len_seq-3;$i++){
                for ($j=$min_length;$j<$max_length+1;$j++){
                        if (($i+$j)>$len_seq){break;}
                        $sub_seq=substr($sequence,$i,$j);
 
                        $len_sub_seq=strlen ($sub_seq);
                        $mismatches=floor($len_sub_seq*$mismatches_allowed/100);
                        if ($mismatches==1){$sub_seq_pattern=includeN_1($sub_seq,0);}
                        elseif ($mismatches==2){$sub_seq_pattern=includeN_2($sub_seq,0);}
                        elseif ($mismatches==3){$sub_seq_pattern=includeN_3($sub_seq,0);}
                        else {$sub_seq_pattern=$sub_seq;}
 
                        $matches=1;
 
                        while (preg_match_all("/($sub_seq_pattern)/",substr($sequence,($i+$j*$matches),$j),$out)==1){$matches++;}
echo $matches;
                        if ($matches>=$min_repeats and ($j*$matches)>=$min_length_of_MR){
 
                                $results[$counter]["start_position"]=$i;
                                $results[$counter]["length"]=$j;
                                $results[$counter]["repeats"]=$matches;
                                $results[$counter]["sequence"]=substr($sequence,$i,$j*$matches);
                                $counter++;
                                $i+=$j*$matches;
                                }
                }
        }
        return ($results);
}
//echo includeN_2("saifab",1);
//echo "\n";
//echo includeN_3("saifab",1);
 
  $sequence="AACAATGCCATGATGATGATTATTACGACACAACAACACCGCGCTTGACGGCGGCGGATGGATGCCGCGATCAGACGTTCAACGCCCACGTAACGTAACGCAACGTAACCTAACGACACTGTTAACGGTACGAT";
//print_r( find_microsatellite_repeats($sequence,2,6,3,6,0));
find_microsatellite_repeats($sequence,2,6,3,6,0);
        ?>
    </body>
</html>

<html>
    <head>
        <meta charset="UTF-8">
        <title></title>
    </head>
    <body>
        <?php
       
      function includeN_1($primer,$minus) {
        $code=".".substr($primer,1);
        $wpos=1;
        while ($wpos<strlen($primer)-$minus){
        $code.="|".substr($primer,0,$wpos).".".substr($primer,$wpos+1);
        $wpos++;
        }
return ($code);
      }  
        
        
        
        function includeN_2($primer,$minus) {
        $max=strlen($primer)-$minus;
        $code="";
        for($i=0;$i<$max;$i++){
                for($j=0;$j<$max-$i-1;$j++){
                  $code.="|".substr($primer,0,$i).".";
                  $resto=substr($primer,$i+1);
                  $code.=substr($resto,0,$j).".".substr($resto,$j+1);
                }
                }

$code=substr($code,1);
return ($code);
}

function includeN_3($primer,$minus) {
        $max=strlen($primer)-$minus;
        $code="";
        for($i=0;$i<$max;$i++){
                for($j=0;$j<$max-$i-1;$j++){
                  $code.="|".substr($primer,0,$i).".";
                  $resto=substr($primer,$i+1);
                  $code.=substr($resto,0,$j).".".substr($resto,$j+1);
                }
                }
$code=substr($code,1);
return ($code);
}

function find_microsatellite_repeats($sequence,$min_length,$max_length,$min_repeats,$min_length_of_MR,$mismatches_allowed){
        $len_seq=strlen($sequence);
        $counter=0;
        for ($i=0;$i<$len_seq-3;$i++){
                for ($j=$min_length;$j<$max_length+1;$j++){
                        if (($i+$j)>$len_seq){break;}
                        $sub_seq=substr($sequence,$i,$j);

                        $len_sub_seq=strlen ($sub_seq);
                        $mismatches=floor($len_sub_seq*$mismatches_allowed/100);
                        if ($mismatches==1){$sub_seq_pattern=includeN_1($sub_seq,0);}
                        elseif ($mismatches==2){$sub_seq_pattern=includeN_2($sub_seq,0);}
                        elseif ($mismatches==3){$sub_seq_pattern=includeN_3($sub_seq,0);}
                        else {$sub_seq_pattern=$sub_seq;}

                        $matches=1;

                        while (preg_match_all("/($sub_seq_pattern)/",substr($sequence,($i+$j*$matches),$j),$out)==1){$matches++;}
echo $matches;
                        if ($matches>=$min_repeats and ($j*$matches)>=$min_length_of_MR){
                        
                                $results[$counter]["start_position"]=$i;
                                $results[$counter]["length"]=$j;
                                $results[$counter]["repeats"]=$matches;
                                $results[$counter]["sequence"]=substr($sequence,$i,$j*$matches);
                                $counter++;
                                $i+=$j*$matches;
                                }
                }
        }
        return ($results);
}
//echo includeN_2("saifab",1);
//echo "\n";
//echo includeN_3("saifab",1);
 
  $sequence="AACAATGCCATGATGATGATTATTACGACACAACAACACCGCGCTTGACGGCGGCGGATGGATGCCGCGATCAGACGTTCAACGCCCACGTAACGTAACGCAACGTAACCTAACGACACTGTTAACGGTACGAT";
//print_r( find_microsatellite_repeats($sequence,2,6,3,6,0));
find_microsatellite_repeats($sequence,2,6,3,6,0);
        ?>
    </body>
</html>

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and this is my c++ port :

Qt Code:

Switch view

QString includeN_1(const QString & primer,int minus)
{
    QString code="."+primer.mid(1);
    int wpos=1;
 
    while (wpos<primer.size()-minus){
        code+="|"+primer.mid(0,wpos)+"."+primer.mid(wpos+1);
        wpos++;
    }
    return code;
}
 
QString includeN_2(const QString & primer,int minus)
{
    int max=primer.size()-minus;
    QString code="";
    for(int i=0;i<max;i++){
        for(int j=0; j<max-i-1;j++){
            code+="|"+primer.mid(0,i)+".";
            QString  resto=primer.mid(i+1);
            code+=resto.mid(0,j)+"."+resto.mid(j+1);
 
        }//j
    }
    code=code.mid(1);
    return code;
}
 
QString includeN_3(const QString & primer,int minus)
{
    int max=primer.size()-minus;
    QString code="";
    for(int i=0;i<max;i++){
        for(int j=0;j<max-i-1;j++){
            code+="|"+primer.mid(0,i)+".";
            QString resto=primer.mid(i+1);
            code+=resto.mid(0,j)+"."+resto.mid(j+1);
        }
    }
    code=code.mid(1);
    return code;
}
 
void FindMicrosatelliteRepeats(QString &seq,int MinLen,int MaxLen,int MinRepeat,int MRMinLen,int MismatchesAllowed)
{
 
    int len_seq=seq.size();
    int counter=0;
  //  QString sub_seq_pattern;
    for (int i=0;i<len_seq-3;i++){
        for (int j=MinLen;j<MaxLen+1;j++){
 
            if ((i+j)>len_seq)
          {break;}
            QString sub_seq_pattern;
            QString sub_seq=seq.mid(i,j) ;  
 
            int len_sub_seq=sub_seq.size();
 
            int mismatches=floor(len_sub_seq*MismatchesAllowed/100);
 
            if (mismatches==1)
            {
                sub_seq_pattern=includeN_1(sub_seq,0);
            }
            else if (mismatches==2){sub_seq_pattern=includeN_2(sub_seq,0);}
            else if (mismatches==3){sub_seq_pattern=includeN_3(sub_seq,0);}
            else {sub_seq_pattern=sub_seq;}
            int             matches=1;
            if(seq.mid(i+j*matches,j)==sub_seq_pattern==1)
                matches++;
 
          //  qDebug()<<matches;
            if(matches >=MinRepeat && (j*matches) >=MRMinLen)
            {
                qDebug()<<"yes";
                qDebug()<<"start postion = "<<i;
                qDebug()<<"length = "<<j;
                qDebug()<<"repeats = "<<matches;
                qDebug()<<"sequence = "<<seq.mid(i,j*matches);
                counter++;
                i+=j*matches;
 
            }//j
}
 
        }//i
 
    }
 
 
//================================================================
 
int main(int argc, char *argv[])
{
    QCoreApplication a(argc, argv);
 
    QString primer="AACAATGCCATGATGATGATTATTACGACACAACAACACCGCGCTTGACGGCGGCGGATGGATGCCGCGATCAGACGTTCAACGCCCACGTAACGTAACGCAACGTAACCTAACGACACTGTTAACGGTACGAT";
 
    FindMicrosatelliteRepeats(primer,2,6,3,6,0);
    return a.exec();
}

QString includeN_1(const QString & primer,int minus)
{
    QString code="."+primer.mid(1);
    int wpos=1;

    while (wpos<primer.size()-minus){
        code+="|"+primer.mid(0,wpos)+"."+primer.mid(wpos+1);
        wpos++;
    }
    return code;
}

QString includeN_2(const QString & primer,int minus)
{
    int max=primer.size()-minus;
    QString code="";
    for(int i=0;i<max;i++){
        for(int j=0; j<max-i-1;j++){
            code+="|"+primer.mid(0,i)+".";
            QString  resto=primer.mid(i+1);
            code+=resto.mid(0,j)+"."+resto.mid(j+1);

        }//j
    }
    code=code.mid(1);
    return code;
}

QString includeN_3(const QString & primer,int minus)
{
    int max=primer.size()-minus;
    QString code="";
    for(int i=0;i<max;i++){
        for(int j=0;j<max-i-1;j++){
            code+="|"+primer.mid(0,i)+".";
            QString resto=primer.mid(i+1);
            code+=resto.mid(0,j)+"."+resto.mid(j+1);
        }
    }
    code=code.mid(1);
    return code;
}

void FindMicrosatelliteRepeats(QString &seq,int MinLen,int MaxLen,int MinRepeat,int MRMinLen,int MismatchesAllowed)
{

    int len_seq=seq.size();
    int counter=0;
  //  QString sub_seq_pattern;
    for (int i=0;i<len_seq-3;i++){
        for (int j=MinLen;j<MaxLen+1;j++){

            if ((i+j)>len_seq)
          {break;}
            QString sub_seq_pattern;
            QString sub_seq=seq.mid(i,j) ;  

            int len_sub_seq=sub_seq.size();

            int mismatches=floor(len_sub_seq*MismatchesAllowed/100);

            if (mismatches==1)
            {
                sub_seq_pattern=includeN_1(sub_seq,0);
            }
            else if (mismatches==2){sub_seq_pattern=includeN_2(sub_seq,0);}
            else if (mismatches==3){sub_seq_pattern=includeN_3(sub_seq,0);}
            else {sub_seq_pattern=sub_seq;}
            int             matches=1;
            if(seq.mid(i+j*matches,j)==sub_seq_pattern==1)
                matches++;
            
          //  qDebug()<<matches;
            if(matches >=MinRepeat && (j*matches) >=MRMinLen)
            {
                qDebug()<<"yes";
                qDebug()<<"start postion = "<<i;
                qDebug()<<"length = "<<j;
                qDebug()<<"repeats = "<<matches;
                qDebug()<<"sequence = "<<seq.mid(i,j*matches);
                counter++;
                i+=j*matches;

            }//j
}

        }//i

    }


//================================================================

int main(int argc, char *argv[])
{
    QCoreApplication a(argc, argv);
    
    QString primer="AACAATGCCATGATGATGATTATTACGACACAACAACACCGCGCTTGACGGCGGCGGATGGATGCCGCGATCAGACGTTCAACGCCCACGTAACGTAACGCAACGTAACCTAACGACACTGTTAACGGTACGAT";
    
    FindMicrosatelliteRepeats(primer,2,6,3,6,0);
    return a.exec();
}

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the problem in variable matches dont give the same waht the original do (due to preg_match_all).
regards

**anda_skoa** · 23rd June 2014, 17:42

Hmm, your C++ code doesn't seem to have any usage of regular expressions or I am not seeing it.

Cheers,
_

**alrawab** · 23rd June 2014, 19:18

yes the original code comparing the pattrern with chunks from the original string
seq.mid(i+j*matches,j).contains( QRegExp("["+sub_seq_pattern+"]") will gives the same effect.

**anda_skoa** · 23rd June 2014, 20:20

Ah, ok. Misunderstanding. I thought there was still an open question.

Cheers,
_

**alrawab** · 23rd June 2014, 23:23

thanks for your help the problem is solved and this the php port of Microsatellite repeats finder

Qt Code:

Switch view

#include <QCoreApplication>
#include <QtCore>
 
//======================================================================
//**************************Find Microsatellite Repeats****************
//======================================================================
QString includeN_1(const QString & primer,int minus)
{
    QString code="."+primer.mid(1);
    int wpos=1;
 
    while (wpos<primer.size()-minus){
        code+="|"+primer.mid(0,wpos)+"."+primer.mid(wpos+1);
        wpos++;
    }
    return code;
}
//----------------------------------------------------------
QString includeN_2(const QString & primer,int minus)
{
    int max=primer.size()-minus;
    QString code="";
    for(int i=0;i<max;i++){
        for(int j=0; j<max-i-1;j++){
            code+="|"+primer.mid(0,i)+".";
            QString  resto=primer.mid(i+1);
            code+=resto.mid(0,j)+"."+resto.mid(j+1);
 
        }//j
    }
    code=code.mid(1);
    return code;
}
//---------------------------------------------------------------------
QString includeN_3(const QString & primer,int minus)
{
    int max=primer.size()-minus;
    QString code="";
    for(int i=0;i<max;i++){
        for(int j=0;j<max-i-1;j++){
            code+="|"+primer.mid(0,i)+".";
            QString resto=primer.mid(i+1);
            code+=resto.mid(0,j)+"."+resto.mid(j+1);
        }
    }
    code=code.mid(1);
    return code;
}
//--------------------------------------------------------------------------
void FindMicrosatelliteRepeats(QString &sequence,int min_length,int max_length,int min_repeats,int min_length_of_MR,int mismatches_allowed)
{
    int len_seq= sequence.size();
    int counter=0;
 
    for (int i=0;i<len_seq-3;i++){
 
                    for (int j=min_length;j<max_length+1;j++){
 
                        if ((i+j)>len_seq){break;}
                        QString sub_seq=sequence.mid(i,j);
                        int len_sub_seq=sub_seq.size();
                        int mismatches=floor(len_sub_seq*mismatches_allowed/100);
                        QString sub_seq_pattern;
                        if (mismatches==1){sub_seq_pattern=includeN_1(sub_seq,0);}
                        else if(mismatches==2){sub_seq_pattern=includeN_2(sub_seq,0);}
                        else if(mismatches==3){sub_seq_pattern=includeN_3(sub_seq,0);}
                        else {sub_seq_pattern=sub_seq;}
int matches=1;
                      while(sequence.mid((i+j*matches),j).contains(QRegExp("("+sub_seq_pattern+")"))==true)matches++;
 
 
                      if (matches>=min_repeats && (j*matches)>=min_length_of_MR){
                                                     qDebug()<<"start_position"<<i;
                                                     qDebug()<<"length"<<j;
                                                     qDebug()<<"repeats"<<matches;
                                                     qDebug()<<"sequence"<<sequence.mid(i,j*matches);
                                                      counter++;
                                                      i+=j*matches;
                                                      }
 
 
                    }//j
 
    }//i
 
 
}
 
//========================================================================
 
int main(int argc, char *argv[])
{
    QCoreApplication a(argc, argv);
 
    QString primer="AACAATGCCATGATGATGATTATTACGACACAACAACACCGCGCTTGACGGCGGCGGATGGATGCCGCGATCAGACGTTCAACGCCCACGTAACGTAACGCAACGTAACCTAACGACACTGTTAACGGTACGAT";
 
    FindMicrosatelliteRepeats(primer,2,6,3,6,0);
    return a.exec();
}

#include <QCoreApplication>
#include <QtCore>

//======================================================================
//**************************Find Microsatellite Repeats****************
//======================================================================
QString includeN_1(const QString & primer,int minus)
{
    QString code="."+primer.mid(1);
    int wpos=1;

    while (wpos<primer.size()-minus){
        code+="|"+primer.mid(0,wpos)+"."+primer.mid(wpos+1);
        wpos++;
    }
    return code;
}
//----------------------------------------------------------
QString includeN_2(const QString & primer,int minus)
{
    int max=primer.size()-minus;
    QString code="";
    for(int i=0;i<max;i++){
        for(int j=0; j<max-i-1;j++){
            code+="|"+primer.mid(0,i)+".";
            QString  resto=primer.mid(i+1);
            code+=resto.mid(0,j)+"."+resto.mid(j+1);

        }//j
    }
    code=code.mid(1);
    return code;
}
//---------------------------------------------------------------------
QString includeN_3(const QString & primer,int minus)
{
    int max=primer.size()-minus;
    QString code="";
    for(int i=0;i<max;i++){
        for(int j=0;j<max-i-1;j++){
            code+="|"+primer.mid(0,i)+".";
            QString resto=primer.mid(i+1);
            code+=resto.mid(0,j)+"."+resto.mid(j+1);
        }
    }
    code=code.mid(1);
    return code;
}
//--------------------------------------------------------------------------
void FindMicrosatelliteRepeats(QString &sequence,int min_length,int max_length,int min_repeats,int min_length_of_MR,int mismatches_allowed)
{
    int len_seq= sequence.size();
    int counter=0;

    for (int i=0;i<len_seq-3;i++){

                    for (int j=min_length;j<max_length+1;j++){

                        if ((i+j)>len_seq){break;}
                        QString sub_seq=sequence.mid(i,j);
                        int len_sub_seq=sub_seq.size();
                        int mismatches=floor(len_sub_seq*mismatches_allowed/100);
                        QString sub_seq_pattern;
                        if (mismatches==1){sub_seq_pattern=includeN_1(sub_seq,0);}
                        else if(mismatches==2){sub_seq_pattern=includeN_2(sub_seq,0);}
                        else if(mismatches==3){sub_seq_pattern=includeN_3(sub_seq,0);}
                        else {sub_seq_pattern=sub_seq;}
int matches=1;
                      while(sequence.mid((i+j*matches),j).contains(QRegExp("("+sub_seq_pattern+")"))==true)matches++;
                   

                      if (matches>=min_repeats && (j*matches)>=min_length_of_MR){
                                                     qDebug()<<"start_position"<<i;
                                                     qDebug()<<"length"<<j;
                                                     qDebug()<<"repeats"<<matches;
                                                     qDebug()<<"sequence"<<sequence.mid(i,j*matches);
                                                      counter++;
                                                      i+=j*matches;
                                                      }


                    }//j

    }//i


}

//========================================================================

int main(int argc, char *argv[])
{
    QCoreApplication a(argc, argv);
    
    QString primer="AACAATGCCATGATGATGATTATTACGACACAACAACACCGCGCTTGACGGCGGCGGATGGATGCCGCGATCAGACGTTCAACGCCCACGTAACGTAACGCAACGTAACCTAACGACACTGTTAACGGTACGAT";

    FindMicrosatelliteRepeats(primer,2,6,3,6,0);
    return a.exec();
}

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