How to interpolatin in java regular expression

Question

Hello,
I am having a problem regarding variable interpotaion in java regex.
i am having a pattern file .
This is one of my Pattern from pattern file
(\{NP_PP_[0-9]+\}|\{NP_B_[0-9]+\}|\{NP_P_[0-9]+\}|\{NP_[0-9]+\})[^{}]*PHOSphorylatable amino[^{}]*(\{NP_PP_[0-9]+\}|\{NP_B_[0-9]+\}|\{NP_P_[0-9]+\}|\{NP_[0-9]+\}|\{NP_C_[0-9]+\}) on (\{NP_P_[0-9]+\}[^{}]+\{NP_P_[0-9]+\}|\{NP_B_[0-9]+\}[^{}]+\{NP_B_[0-9]+\}))(
In which amino has a separate set of values ,defined in program.
And i need to pass the value of amino from the program to the file during compilation. but it is getting compiled as a text..not as it's values defined in program.
so help me out how i can pass the values of amino to the file.

Answer 1

Hello,
I am having a problem regarding variable interpotaion in java regex.
i am having a pattern file .
This is one of my Pattern from pattern file named 'ultimatepat'(check RuleFile = "/home/texsieve/sample/src/ultimatepat")
((\{NP_PP_[0-9]+\}|\{NP_B_[0-9]+\}|\{NP_P_[0-9]+\}|\{NP_[0-9]+\})[^{}]*PHOSphorylatable amino*+[^{}]*(\{NP_PP_[0-9]+\}|\{NP_B_[0-9]+\}|\{NP_P_[0-9]+\}|\{NP_[0-9]+\}|\{NP_C_[0-9]+\}) on (\{NP_P_[0-9]+\}[^{}]+\{NP_P_[0-9]+\}|\{NP_B_[0-9]+\}[^{}]+\{NP_B_[0-9]+\}))
In which '_amino_' has a separate set of values ,defined in program.
my program is::
public class Ptmrules {
     public static void main(String[] args)
          try
               String InputFile = "/home/texsieve/sample/src/gt_bm.newtyp";
               String RuleFile = "/home/texsieve/sample/src/ultimatepat";
     String amino= "(valine|serine)";
     System.out.println("sites are"+amino);
               BufferedReader rd1=new BufferedReader(new FileReader(InputFile));
          BufferedReader rd2=new BufferedReader(new FileReader(RuleFile));
          ArrayList<String> phosPatterns = new ArrayList<String>();
          String line1=null;
          String line2=null;
          String l1="phosphorylatable";
          while((line2=rd2.readLine())!=null)
               phosPatterns.add(line2);
               Pattern pat1 = Pattern.compile(line2);
               System.out.println("PATTERN"+pat1);
          int len=phosPatterns.size();
          System.out.println("Total Patterns compiled::"+len);
          while((line1=rd1.readLine())!=null)
                    Pattern pat=Pattern.compile(l1);
                    Matcher mat=pat.matcher(line1);
                    while(mat.find())
                         line1=line1.replaceFirst("phosphorylatable","PHOSphorylatable");
                         for(int i=0;i<len;i++)
                              String phosRule=phosPatterns.get(i);
                              Pattern phosPattern=Pattern.compile(phosRule);
                         Matcher phosMatch=phosPattern.matcher(line1);
                         System.out.println("Patterns"+phosPattern);
                         if(phosMatch.find())
                                   System.out.println("LINE found::" +line1);
                                   System.out.println("Pattern found:: M"+i+" : "+phosMatch.group()+"\n");
                                   line1=line1.replace("PHOSphorylatable","phosphorylataBLE");
     catch(IOException ie)
               System.out.println("Match not found");
And i need to pass the value of '*amino*' from the program to the file during compilation. but it is getting compiled as a text..means getting read as 'amino' word only , not as a it's values defined in the program.
so please help me out ,how i can pass the values of amino to the file.and i should read the value of amino* when pattern is being compiled.and should not read as a text(amino word itself).
Edited by: GauravIT on Feb 8, 2008 4:11 AM