Converting Perl to Java

Question

I have a Perl file which is actually calling some jar files and I'm trying to make it an all Java program and remove the Perl. So I came up through this lines which is:

$blammercommand="$javapath $javaparams -jar $blammerpath -conf $blammerconf $blammerparams -cpu $cpu -i \"".$tmpdir."blastresults/*.bls\" -db \"$infilename $blastdb\"";
(system($blammercommand)==0) or die "unable to do $blammercommand\n";

I've already decompressed the jar files and added the source codes to my Eclipse project and have access to the main function of the related jar file. I'm just trying to pass the arguments as inputs.

My problem is exactly here that I don't know what "\\"".$tmpdir."blastresults/*.bls\\"" and "\\"$infilename $blastdb\\"" mean. I know what exactly each one of this variables are but I don't know how those \\ , / and * are working and how should I convert them to Java.

Answer 1

Those are just shell escaping and shell globbing. Literally written, it would look like this:

${javapath} ${javaparams} -jar ${blammerpath} -conf ${blammerconf} ${blammerparams} -cpu ${cpu} -i "${tmpdir}blastresults/*.bls" -db "${infilename} ${blastdb}

Here, the syntax ${name} is meant to indicated an inserted value of the variable. The system command in Perl runs a system command through the default system shell, usually something like bash. The quotes are used to make several space-separated strings "stick together" as one argument. The * is a wildcard, which is replaced by all filenames in a given directory.