All-vs-All blastP commands

Script

    String createBlastCommand(String blastBin, String fastaFile, String databaseName, String additionalCommands, String outPrefix){
        StringBuilder contents = new StringBuilder();
        contents.append(blastBin).append("blastp -query ").append(fastaFile);
        contents.append(" -db ").append(databaseName);
	contents.append(" -out ").append(outPrefix).append(".out");
        if (additionalCommands != null && !additionalCommands.isEmpty()) {
            contents.append(" ").append(additionalCommands);
        }
        return contents.toString();
    }

if(additionalCommands == void){
	additionalCommands = null;	
}

if(blastBin == void || blastBin == null){
	blastBin = "";	
}
if(!blastBin.isEmpty() && !blastBin.endsWith("/")){
	blastBin = blastBin + "/";
}

if(outPrefix == void || outPrefix == null){
	outPrefix = "blast";
}

List commandList = new LinkedList();
int i = 0;
for(String fasta : fastaFiles){
	String command = createBlastCommand(blastBin, fasta, databaseName, additionalCommands, outPrefix);
	commandList.add(command);
	i++;
}

Script

    String createBlastCommand(String blastBin, List fileNames, String databaseName, String additionalCommands){
	StringBuilder contents = new StringBuilder();
	contents.append(blastBin).append("makeblastdb -dbtype prot -in ");
        contents.append("\"");
        for (String fileName : fileNames) {
            contents.append(fileName).append(" ");
        }
        contents.replace(contents.length() - 1, contents.length(), "\"");
        contents.append(" -out ").append(databaseName);
        if (additionalCommands != null) {
            contents.append(" ").append(additionalCommands);
        }
	return contents.toString();
    }

if(blastBin == void || blastBin == null){
	blastBin = "";	
}
if(!blastBin.isEmpty() && !blastBin.endsWith("/")){
	blastBin = blastBin + "/";
}

if(additionalCommands == void){
	additionalCommands = null;	
}


command = createBlastCommand(blastBin, fastaFiles, databaseName, additionalCommands);

Value