Java command line arguments parser

Revision: 53Author: maka82Date: Fri Aug 21 17:04:14 2009Log: Comments in whole project have been write down according to javadoc standard trying to give more informations about parameters and about returning informations for functions.Some misspelled words have been written correct now.Also, CamelCases are used now in a project where it is needed.Some TODOs are fixed. /trunk/src/main/java/org/apache/rat/pd/core/PdCommandLine.java /trunk/src/main/java/org/apache/rat/pd/core/PlagiarismDetector.java /trunk/src/main/java/org/apache/rat/pd/core/SourceCodeAnalyser.java /trunk/src/main/java/org/apache/rat/pd/engines/ISearchEngine.java /trunk/src/main/java/org/apache/rat/pd/engines/KodersCodeSearchParser.java /trunk/src/main/java/org/apache/rat/pd/engines/Managable.java /trunk/src/main/java/org/apache/rat/pd/engines/RetryManager.java /trunk/src/main/java/org/apache/rat/pd/engines/google/GoogleCodeSearchParser.java /trunk/src/main/java/org/apache/rat/pd/engines/google/MultilineRegexGenerator.java /trunk/src/main/java/org/apache/rat/pd/heuristic/functions/CPPFunctionHeuristicChecker.java /trunk/src/main/java/org/apache/rat/pd/heuristic/functions/FortranFunctionHeuristicChecker.java /trunk/src/main/java/org/apache/rat/pd/heuristic/misspellings/MisspellingsHeuristicChecker.java /trunk/src/main/java/org/apache/rat/pd/util/FileManipulator.java /trunk/src/test/java/org/apache/rat/pd/core/SlidingWindowAlgorithmTest.java /trunk/src/test/java/org/apache/rat/pd/engines/google/RegexGeneratorTest.java /trunk/src/test/java/org/apache/rat/pd/heuristic/functions/CPPFunctionHeuristicCheckerTest.java=======================================--- /trunk/src/main/java/org/apache/rat/pd/core/PdCommandLine.java Fri Aug 21 06:53:09 2009+++ /trunk/src/main/java/org/apache/rat/pd/core/PdCommandLine.java Fri Aug 21 17:04:14 2009@@ -173,7 +173,7 @@ } catch (Exception e) { // oops, something went wrong this.out.println("Parsing failed. Reason: " + e.getMessage());- // if any error is happened, we can say that not all arguments are+ // if any error happened, we can say that not all arguments are // correct allArgumentsCorrect = false; }@@ -194,6 +194,8 @@ * Parse arguments and gets parameters from them. * * @param args command line arguments+ * @throws ParseException+ * @throws NumberFormatException */ private void parseArguments(String[] args) throws ParseException, NumberFormatException { CommandLineParser parser = new GnuParser();@@ -260,7 +262,8 @@ * If some property is invalid an exception is thrown. * * @param line CommandLine- * @throws NumberFormatException , IllegalArgumentException+ * @throws NumberFormatException+ * @throws IllegalArgumentException */ private void parseCommandLineArguments(CommandLine line) throws NumberFormatException, IllegalArgumentException {=======================================--- /trunk/src/main/java/org/apache/rat/pd/core/PlagiarismDetector.java Fri Aug 21 06:53:09 2009+++ /trunk/src/main/java/org/apache/rat/pd/core/PlagiarismDetector.java Fri Aug 21 17:04:14 2009@@ -91,6 +91,7 @@ /** * @param args * @throws RatReportFailedException+ * @throws IOException */ public static void main(String[] args) throws RatReportFailedException, IOException { // instance of PlagiarismDetector@@ -129,7 +130,7 @@ * Decide which format of report will be used. * * @param pdCommandLine command line object to read report format from- * @return+ * @return which format of report will be used */ private Report configureReport(PdCommandLine pdCommandLine) { Report reportDocument;=======================================--- /trunk/src/main/java/org/apache/rat/pd/core/SourceCodeAnalyser.java Fri Aug 21 06:53:09 2009+++ /trunk/src/main/java/org/apache/rat/pd/core/SourceCodeAnalyser.java Fri Aug 21 17:04:14 2009@@ -58,7 +58,7 @@ * @param searchEngines list of chosen search engine parsers * @param algorithmsForChecking list of chosen heuristic algorithms * @param reportDocument chosen report- * @param out printStream wnere current information are be printed+ * @param out printStream where current information are to be printed */ public SourceCodeAnalyser(List searchEngines, List algorithmsForChecking, Report reportDocument, PrintStream out) {@@ -133,18 +133,18 @@ * @throws IOException */ private String readFile(Reader reader) throws IOException {- String toret = "";+ String toRet = ""; // TODO encoding is system default now!!!! BufferedReader input = new BufferedReader(reader); try { String line = null; while ((line = input.readLine()) != null) {- toret += line + "\n";+ toRet += line + "\n"; } } finally { input.close(); }- return toret;+ return toRet; } /**@@ -209,16 +209,16 @@ } /**- * Search for code in all engines. If code is found, an reportEntry will be- * returned Otherwise, null will be returned.+ * Search for code in all engines. If code is found, a reportEntry will be+ * returned. Otherwise, null will be returned. * * @param searchEngines list of chosen search engine parsers * @param code code to be checked * @param fileName source

12.3.3.2 Other ExamplesSpecifying a larger-than-default maximum heap size: Specifying a non-default heap size and a Java 2D hardware acceleration option typically used for applets using OpenGL via Java Binding for the OpenGL API (JOGL): Enabling verbose output of the garbage collector, and the assertion facility in the Java programming language: A set of "secure" JVM command-line arguments and system properties is defined in the JNLP File Syntax section of the Java Web Start Developers' Guide. In the Java Plug-in, as long as all of the JVM command-line arguments specified via the java_arguments parameter are secure, then the applet, or any classes it loads, may run without permissions.Insecure JVM command-line arguments (in other words, those not on the secure list) may also be specified via the java_arguments parameter. In this case, there is the potential for a security risk, so the Java Plug-In enforces the rule that no unsigned classes may be loaded. In other words, only trusted code, for which the user has accepted the security dialog, may be loaded by such a JVM instance. If an attempt is made to load an unsigned or untrusted class in a JVM instance for which insecure system properties have been specified, a ClassNotFoundException will be thrown indicating that the given class could not be loaded because it was not signed.There are relatively few restrictions on what command-line arguments may be passed via the java_arguments parameter. In general, the -Xbootclasspath argument is forbidden, as well as any command-line argument used to specify a path, such as -classpath or -jar. All other command-line arguments, present and future, should be supported, with the caveat about secure and insecure command-line arguments described above.The command-line arguments passed via the java_arguments parameter are added to any specified via the Java Runtime Environment Settings dialog in the Java Control Panel. The command-line arguments from the control panel are used for all JVM instances of the version for which they are specified; the java_arguments parameters do not completely replace them.When JVM command-line arguments are specified, it is likely that the Java Plug-in will need to launch another JVM instance in

Hello, I have a project with 11 mgf files searched with 4 search engines run by SearchGUI. I am not able to load those results in peptide shaker. Below is the Error log I copied out of the Bug Report Window.Do you have any advice how to proceed? Thank you.Thu Nov 10 08:40:53 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95162336.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 49.8/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 95379 and start tag from line 95371 and start tag from line 95267 and start tag from line 95266 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...\r\n at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1679)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:450)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:179)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Fri Nov 11 08:41:18 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95386640.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 47.4/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 3375096 and start tag from line 3374999 and start tag from line 3374998 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:142)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_12_C_04.mgf_cus_File230304 Spectrum29926 scans: 16690

With ZIP archives, providing features such as creating, extracting, and managing ZIP files with encryption and compression support:$ pip install pyzipper coloramaNext up, we import the necessary libraries in our newly created file named zip_file_locker.py for instance:# Import the necessary libraries.import pyzipper, argparse, sys, re, getpassfrom colorama import Fore, initinit()We already talked about what pyzipper does. I’m not repeating that :)argparse is a Python library used for parsing command-line arguments and options. We have a tutorial on this library.sys is a Python library that provides access to various runtime system functions and variables. One key one is exiting a program.re is the Python regular expression library for working with regular expressions.colorama is a library that simplifies colored text output in the terminal, enhancing the visual presentation of text with foreground and background colors. We also have a detailed tutorial on Colorama.getpass: is a Python library that lets us enter our passwords without displaying them on the screen. Similar to the way we enter our passwords on the Linux terminal. This is for security purposes.The init() function initializes colorama.This program is CLI-based. Next, we create a function that accepts user arguments from the command line:# Define a function to get CLI commands.def get_cli_arguments(): parser = argparse.ArgumentParser(description="A program to lock a ZIP File.") # Collect user arguments. parser.add_argument('--zipfile', '-z', dest='zip_file', help='Specify the ZIP file to create or update.') parser.add_argument('--addfile', '-a', dest='add_files', nargs='+', help='Specify one or more files to add to the ZIP file(s).') # Parse the collected arguments. args = parser.parse_args() #