Extracting information from String (regex, Beanshell)

[Mokita]

Hello,

I am working with Taverna to build a workflow. Taverna has a beanshell where I can program in java. I am having some problems in writing a script. I want to extract information from a string, separated by newline. For this i am using regex.

The String is given:

P48534
EXP value is: e-10
Q0543
EXP value is: 4e-07


My script look like this in Beanshell:

 import java.util.regex.Matcher;
import java.util.regex.Pattern;
 
Pattern pGI = Pattern.compile("(^.*?$)");
Pattern pEvaLue = Pattern.compile("is: (.*)$");
Matcher mGI;
Matcher mEvalue;
StringBuffer temp = new StringBuffer();
String [] line = BlastReport.split("\n");
int arraysize = line.length; 
 
for (int i=0; i<(arraysize-1); i+=2){
    String sGI = line[i];
    String sEvalue = line[i+1];    
    mGI = pGI.matcher(sGI);
    mEvalue = pEvalue.matcher(sEvalue);
    String gi="";
 
    if (mGI.find()){
        gi =mGI.group(1);
    }
    if (mEvalue.find()){
        String eval = mEvalue.group(1);
        if(eval.startsWith("e")){
            eval= "1".concat(eval);
        }
        Double d = new Double (eval);
        double Evalue = d.doubleValue();
        if (Evalue<=0.02){
            temp.append(gi + "\n");
        }
    }
}
 
String result = temp.toString().trim();

The error message is: "Attempt to resolve method: matcher() on undefined variable or class name: pEvalue: at Line: 16: pEvalue .matcher(sEvalu e)"


Can someone tell me why is giving me this error and how can i fix it.

Thank you in advance,

Mokita

[prometheuzz]

...
How can i change group 1 ([A-Z]\\d+) to catch: P00DF3 or 1234653 or Q5647GJD or A4658DF
It is not catching the ones with letters in the midle.

Thank you again,

Mokita

Try replacing "([A-Z]\\d+)" with "(\\w+)"