Lines Matching refs:out
70 System.out.println(str); in usage()
94 System.out.println("Could not open Property File " + propFile); in parsePropertyFile()
108 System.out.println("Missing listFile or missing pdb filenames in Property file " + propFile); in parsePropertyFile()
125 System.out.println("Output is written to log file... " + LOGFILE); in parsePropertyFile()
155 System.out.println("Could not create a File object for file " + filename); in validateAndCreateFile()
166 System.out.println("Could not get File Object instance for " + newFile); in validateAndCreateFile()
175 System.out.println("Could not get delete " + newFile); in validateAndCreateFile()
183 System.out.println("Could not rename " + filename + " to " + newFile ); in validateAndCreateFile()
187 System.out.println("SecurityException: " + s.toString()); in validateAndCreateFile()
190 System.out.println("NullPointerException: " + n.toString()); in validateAndCreateFile()
197 System.out.println("Could not create " + filename + " Check permissions.."); in validateAndCreateFile()
201 System.out.println("IOException: " + e.toString()); in validateAndCreateFile()
204 System.out.println("SecuriityException: " + s.toString() ); in validateAndCreateFile()
230 System.out.println("Could not create a File object for file " + filename); in checkFile()
236 System.out.println("File " + filename + " does not exist... "); in checkFile()
242 System.out.println("Cannot read file " + filename); in checkFile()
271 System.out.println("Could not open List File " + listFile); in populatePDBArray()
350 System.out.println("Could not parse PDB " + pdbname1); in comparePDB()
357 System.out.println("Could not parse PDB " + pdbname2); in comparePDB()
389 System.out.println ("Could not open file " + LOGFILE); in writeToLog()
399 System.out.println("ERROR: Could not write to File " + LOGFILE); in writeToLog()
427 System.out.println ("Could not open file " + OUTFILE); in writeToOutputFile()
438 System.out.println("ERROR: Could not write to File " + OUTFILE); in writeToOutputFile()
445 System.out.println("ERROR: Could not close File " + OUTFILE); in writeToOutputFile()
470 System.out.println("Incorrect no. of arguments passed..."); in main()
482 System.out.println("Exception: Could not open file " + propFile); in main()
487 System.out.println("Exception: " + propFile + " is not a file "); in main()
492 System.out.println("Exception: Cannot open file for reading. Please check permissions "); in main()
506 System.out.println("pdbArray is empty. No PDBS to compare... \n"); in main()