-\r
- /*\r
- * @Override public List<String> getParameters(\r
- * compbio.runner.Executable.ExecProvider provider) { for (int i = 0; i <\r
- * param.size(); i++) { String par = param.get(i); if\r
- * (isMatrixParameter(par)) { String matrixName = getValue(i); if (new\r
- * File(matrixName).isAbsolute()) { // Matrix can be found so no actions\r
- * necessary // This method has been called already and the matrix name //\r
- * is modified to contain full path // no further actions is necessary\r
- * break; } String matrixPath = Util.getExecProperty("matrix.path", this);\r
- * String absMatrixPath = Util.convertToAbsolute(matrixPath); param.remove(i\r
- * + 1); param.remove(i); super.addParameter(MATRIX_PAR_NAME);\r
- * super.addParameter(absMatrixPath + File.separator + matrixName); break; }\r
- * } return super.getParameters(provider); }\r
- * \r
- * boolean isMatrixParameter(String parameter) { assert\r
- * !compbio.util.Util.isEmpty(parameter); if\r
- * (parameter.toUpperCase().startsWith(MATRIX_PAR_NAME)) { return true; }\r
- * return false; }\r
- * \r
- * String getValue(int i) { return param.get(i + 1); }\r
- */\r