Examples with FunctionFileGenerator cbit.vcell.solvers.FunctionFileGenerator used on opensource projects

Example 1 with FunctionFileGenerator

use of cbit.vcell.solvers.FunctionFileGenerator in project vcell by virtualcell.

the class FunctionFileCrawler method scan.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 */
private void scan(File userDir, File outputDir) throws Exception {
    File outputFile = null;
    java.io.PrintWriter pw = null;
    try {
        outputFile = new File(outputDir, "FunctionFileCrawler_" + userDir.getName() + ".txt");
        pw = new java.io.PrintWriter(new java.io.FileOutputStream(outputFile));
        // 
        // file filter for *.functions files
        // 
        java.io.FilenameFilter functionFileFilter = new java.io.FilenameFilter() {

            public boolean accept(File dir, String name) {
                return name.endsWith(".functions");
            }
        };
        // find all the log files
        File[] functionFiles = userDir.listFiles(functionFileFilter);
        // loop through all the functions files
        int filesWithSpaceInNames = 0;
        for (int i = 0; i < functionFiles.length; i++) {
            File fnFile = functionFiles[i];
            if (fnFile.exists()) {
                // read the functions from the function files and and check if they have spaces
                Vector<AnnotatedFunction> annotatedFnsVector = FunctionFileGenerator.readFunctionsFile(fnFile, null);
                boolean bNameHasSpaces = false;
                for (int j = 0; j < annotatedFnsVector.size(); j++) {
                    AnnotatedFunction afn = annotatedFnsVector.elementAt(j);
                    if (afn.getName().indexOf(" ") > 0) {
                        // if function name has space, mangle the name and store the function in a different list.
                        bNameHasSpaces = true;
                        String newName = TokenMangler.fixTokenStrict(afn.getName());
                        annotatedFnsVector.set(j, new AnnotatedFunction(newName, afn.getExpression(), afn.getDomain(), afn.getErrorString(), afn.getFunctionType(), afn.getFunctionCatogery()));
                    } else {
                        annotatedFnsVector.set(j, afn);
                    }
                }
                // If function file had function(s) with space(s), need to rewrite function file
                if (bNameHasSpaces) {
                    FunctionFileGenerator ffg = new FunctionFileGenerator(fnFile.getPath(), annotatedFnsVector);
                    ffg.generateFunctionFile();
                    filesWithSpaceInNames++;
                    totalNumOfFilesModified++;
                }
            } else {
                System.err.println("Function file : " + fnFile.getName() + " does not exist.");
            }
        }
        System.out.println("NUM Files with spaces in names : " + filesWithSpaceInNames + "; NUM Files with No spaces in names : " + (functionFiles.length - filesWithSpaceInNames));
    } finally {
        if (pw != null) {
            pw.close();
        }
        if (lg.isTraceEnabled())
            lg.trace("User " + userDir.getName() + ", See " + outputFile.getAbsolutePath() + " for details");
    }
}