Java command line arguments parser
Author: m | 2025-04-24
Download Java Command-Line Argument Parser latest version for Windows free. Java Command-Line Argument Parser latest update: J
onlycrab/argument-parser: JAVA command line argument 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
A Java command line parser that parse command line arguments
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 inJava Command Line Argument Parser - Jenkov.com
Order to satisfy them. In other words, it is unlikely that a preexisting JVM instance will have been started with the correct set of command-line arguments to satisfy the request. The rules for exactly when a new JVM instance is launched to start a given applet are deliberately left unspecified and may need to change in subsequent releases. Here is a rough set of guidelines for the sharing and creation of new JVM instances:If the command-line arguments used to start a preexisting JVM instance are a superset of the requested arguments, the preexisting JVM instance will be used.If a JVM instance is launched for the "default" set of command-line arguments (i.e., those specified in the Java Control Panel, with no java_arguments specified), then this JVM instance will never be used to launch any applet that has even one command-line argument specified via java_arguments.-Xmx is handled specially: if a preexisting JVM instance was started with for example -Xmx256m via java_arguments, and a new applet requests -Xmx128m, then new applet will very likely be run in the preexisting JVM instance. In other words, -Xmx specifications are matched with a greater-than-or-equal test.There is no way to "name" a JVM instance used to launch a particular applet and "force" subsequent applets into that JVM instance.See the section on the separate_jvm parameter to isolate a particular applet in its own JVM instance, separate from all other applets.. Download Java Command-Line Argument Parser latest version for Windows free. Java Command-Line Argument Parser latest update: JGitHub - silentsoft/arguments-parser: Java command line arguments
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: 16690args4j Alternatives - Java Command-line Argument Parsers
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() #Argparse4j - The Java command-line argument parser library
In the blog post Apache PDFBox 2, I demonstrated use of Apache PDFBox 2 as a library called from within Java code to manipulate PDFs. It turns out that Apache PDFBox 2 also provides command-line tools that can be used directly from the command-line as-is with no additional Java coding required. There are several command-line tools available and I will demonstrate some of them in this post.The PDFBox command-line tools are executed by taking advantage of PDFBox’s executable JAR (java -jar with Main-Class: org.apache.pdfbox.tools.PDFBox). This is the JAR with “app” in its name and, for this particular blog post, is pdfbox-app-2.0.2.jar. The general format used to invoke these tools in java -jar pdfbox-app-2.0.2.jar [options] [files].When the executable JAR is executed without arguments, a form of help is provided that lists the available commands. This is shown in the next screen snapshot.This screen snapshot shows that this version of Apache PDFBox (2.0.2) advertises support for the “Possible commands” of ConvertColorspace, Decrypt, Encrypt, ExtractText, ExtractImages, OverlayPDF, PrintPDF, PDFDebugger, PDFMerger, PDFReader, PDFSplit, PDFToImage, TextToPDF, and WriteDecodedDoc.Extracting Text: “ExtractText”The first command-line tool I am looking at is extracting text from a PDF. I demonstrated using PDFBox to do this from Java code in my previous blog post. Here, I will use PDFBox to do the same thing directly from the command-line with no Java source code in sight. The following operation extracts the text from the PDF Scala by Example. In my previous, post the Java code accessed this PDF online and used PDFBox to extract text from it. In this case, I’ve downloaded the Scala by Example and am running the PDFBox ExtractText command-line tool against that downloaded PDF stored on my hard drive at C:\pdf\ScalaByExample.pdf.The command to extract text from the PDF from the command-line using PDFBox is: java -jar pdfbox-app-2.0.2.jar ExtractText C:\pdf\ScalaByExample.pdf. The next two screen snapshots demonstrate running this command and the file it generates. From these screen snapshots, we can see that the text file generated by this command by default has the same name as the source PDF but with a .txt extension. This command supports multiple options. Download Java Command-Line Argument Parser latest version for Windows free. Java Command-Line Argument Parser latest update: JComments
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
2025-04-1312.3.3.2 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
2025-04-08Hello, 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
2025-04-01With 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() #
2025-04-23Top 9 Java Command-line Argument Parser Projects picocli 1 31 5,044 7.8 JavaPicocli is a modern framework for building powerful, user-friendly, GraalVM-enabled command line apps with ease. It supports colors, autocompletion, subcommands, and more. In 1 source file so apps can include as source & avoid adding a dependency. Written in Java, usable from Groovy, Kotlin, Scala, etc.Project mention:Making Contributions|dev.to|2024-09-20His project uses picocli for argument parsing. I briefly looked through the documentation and realized it was pretty similar to the clap crate I used for my project. So I mimicked his other code as well as my own understanding of clap. This part was easy. CodeRabbitcoderabbit.aifeaturedCodeRabbit: AI Code Reviews for Developers.Revolutionize your code reviews with AI. CodeRabbit offers PR summaries, code walkthroughs, 1-click suggestions, and AST-based analysis. Boost productivity and code quality across all major languages with each PR. JCommander 2 0 1,987 8.0 JavaCommand line parsing framework for Java JLine 3 7 1,551 9.1 JavaJLine is a Java library for handling console input. Airline 4 0 846 0.0 JavaJava annotation-based framework for parsing Git like command line structures args4j 5 0 790 7.9 Javaargs4j JOpt Simple 7 0 353 3.3 JavaJava library for parsing command line options SaaSHubwww.saashub.comfeaturedSaaSHub - Software Alternatives and Reviews.SaaSHub helps you find the best software and product alternatives airline 8 0 137 6.5 JavaJava annotation-based framework for parsing Git like command line structures with deep extensibility (by rvesse) JewelCLI 9 0 61 0.0 JavaJewelCli uses an annotated interface definition to automatically parse and present command line argumentsNOTE:The open source projects on this list are ordered by number of github stars.The number of mentions indicates repo mentiontions in the last 12 Months orsince we started tracking (Dec 2020).Java Command-line Argument Parsers discussionJava Command-line Argument Parsers related postsMaking Contributions3 projects|dev.to|20 Sep 2024PicoCLI – Powerful command-line parsing library for JavaGraalVM for JDK 21 is here“Why I develop on Windows”Java 20 / JDK 20: General Availability3 projects|/r/java|21 Mar 2023any opinion good or bed about a code that smells?3 projects|/r/java|28 Jan 2023Building a Java CLI. How can I make it more powershell-friendlyA note from our sponsor - CodeRabbitcoderabbit.ai|23 Mar 2025Revolutionize your code reviews with AI. CodeRabbit offers PR summaries, code walkthroughs, 1-click suggestions, and AST-based analysis. Boost productivity and code quality across all major languages with each PR.Learn more →IndexSponsoredCodeRabbit: AI Code Reviews for DevelopersRevolutionize your code reviews with AI. CodeRabbit offers PR summaries, code walkthroughs, 1-click suggestions, and AST-based
2025-04-02“jps” is a command-line utility provided as part of the Java Development Kit (JDK), which displays information about Java Virtual Machine (JVM) processes currently running on the system. It stands for “Java Virtual Machine Process Status.” The tool is commonly used by developers, system administrators, and troubleshooting professionals to identify and monitor Java applications and processes. Here’s a more detailed explanation of its features and functionalities:Process Identification: “jps” lists Java processes running on the system along with their corresponding process IDs (PIDs) and descriptive information. This information helps users identify and distinguish between different Java applications and instances of the JVM running on the system.User-Specific Display: By default, “jps” displays information only about JVM processes associated with the current user. This helps users focus on relevant processes without being overwhelmed by system-wide information. However, users with appropriate permissions can use command-line options to view processes from all users or specific user accounts.Process Status Information: In addition to displaying process IDs, “jps” provides additional information about Java processes, such as the main class name or JAR file name associated with each process. This helps users identify the purpose or function of each Java application running on the system.Integration with Other Tools: “jps” integrates well with other Java diagnostic and troubleshooting tools, such as “jstat” for monitoring JVM statistics, “jstack” for thread analysis, “jmap” for memory mapping, and “jconsole” or “VisualVM” for visualizing and analyzing JVM metrics. This allows users to perform comprehensive monitoring and analysis of Java applications and JVM instances.Scripting and Automation: “jps” can be used in scripts and automated workflows to programmatically monitor and manage Java processes. Users can combine “jps” with other command-line utilities and shell scripts to create custom monitoring solutions or integrate process status checks into system administration tasks.Platform Support: “jps” is available on multiple platforms, including Linux, macOS, and Windows, ensuring compatibility with a wide range of development environments and operating systems. This cross-platform support makes “jps” a versatile tool for monitoring Java applications in diverse computing environments.Documentation and Resources: “jps” is documented as part of the JDK documentation, providing detailed information on its usage, command-line options, and output format. Additionally, there are numerous tutorials, guides, and online resources available that cover JVM monitoring and troubleshooting techniques using “jps” and other related tools.1. List all JVM processes:2. List all JVM processes with only PID:3. Display the arguments passed to the processes:4. Display the full package name of all processes:5. Display the arguments passed to the JVM:SummaryIn summary, “jps” is a useful command-line utility for displaying information about Java processes and JVM instances running on the system. Its user-specific display, process identification, status information, integration with other tools, scripting capabilities, platform support, and comprehensive documentation make it a valuable tool for monitoring and managing Java applications in various environments.
2025-04-15