CoolFace
Datasetpublic

SciCodePile/SciCode-Domain-Code

DATA1: Domain-Specific Code Dataset Dataset Overview DATA1 is a large-scale domain-specific code dataset focusing on code samples from interdisciplinary fields such as biology, chemistry, materials science, and related areas. The dataset is collected and organized from GitHub repositories, covering 178 different domain topics with over 1.1 billion lines of code. Dataset Statistics Total Datasets: 178 CSV files Total Data Size: ~115 GB Total Lines… See the full description on the dataset page: https://huggingface.co/datasets/SciCodePile/SciCode-Domain-Code.

sourceHugging Faceapache-2.0updated 6mo agoView on Hugging Face
4likes2.4kdownloads
rootdatadataset_Bio_foundation_model.csv
dataset_Bio_foundation_model.csv40327 linesDownload Raw Back to data
1"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language"
2"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/demo/ConsoleApp/src/net/sf/launch4j/example/ConsoleApp.java",".java","2858","73","/*3	Launch4j (http://launch4j.sourceforge.net/)4	Cross-platform Java application wrapper for creating Windows native executables.5 6	Copyright (c) 2004, 2007 Grzegorz Kowal7 8	All rights reserved.9 10	Redistribution and use in source and binary forms, with or without modification,11	are permitted provided that the following conditions are met:12 13	    * Redistributions of source code must retain the above copyright notice,14	      this list of conditions and the following disclaimer.15	    * Redistributions in binary form must reproduce the above copyright notice,16	      this list of conditions and the following disclaimer in the documentation17	      and/or other materials provided with the distribution.18	    * Neither the name of the Launch4j nor the names of its contributors19	      may be used to endorse or promote products derived from this software without20	      specific prior written permission.21 22	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS23	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT24	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR25	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR26	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,27	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,28	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR29	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF30	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING31	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS32	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.33*/34 35package net.sf.launch4j.example;36 37import java.io.BufferedReader;38import java.io.IOException;39import java.io.InputStreamReader;40 41/**42 * @author Copyright (C) 2005 Grzegorz Kowal43 */44public class ConsoleApp {45    public static void main(String[] args) {46		StringBuffer sb = new StringBuffer(""Hello World!\n\nJava version: "");47		sb.append(System.getProperty(""java.version""));48		sb.append(""\nJava home: "");49		sb.append(System.getProperty(""java.home""));50		sb.append(""\nCurrent dir: "");51		sb.append(System.getProperty(""user.dir""));52		if (args.length > 0) {53			sb.append(""\nArgs: "");54			for (int i = 0; i < args.length; i++) {55				sb.append(args[i]);56				sb.append(' ');57			}58		}59		sb.append(""\n\nEnter a line of text, Ctrl-C to stop.\n\n>"");60		System.out.print(sb.toString());61		try {62			BufferedReader is = new BufferedReader(new InputStreamReader(System.in));63			String line;64			while ((line = is.readLine()) != null && !line.equalsIgnoreCase(""quit"")) {65				System.out.print(""You wrote: "" + line + ""\n\n>"");66			}67			is.close();68			System.exit(123);69		} catch (IOException e) {70			System.err.print(e);71		}72    }73}74","Java"
75"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/demo/SimpleApp/src/net/sf/launch4j/example/SimpleApp.java",".java","3743","105","/*76	Launch4j (http://launch4j.sourceforge.net/)77	Cross-platform Java application wrapper for creating Windows native executables.78 79	Copyright (c) 2004, 2007 Grzegorz Kowal80 81	All rights reserved.82 83	Redistribution and use in source and binary forms, with or without modification,84	are permitted provided that the following conditions are met:85 86	    * Redistributions of source code must retain the above copyright notice,87	      this list of conditions and the following disclaimer.88	    * Redistributions in binary form must reproduce the above copyright notice,89	      this list of conditions and the following disclaimer in the documentation90	      and/or other materials provided with the distribution.91	    * Neither the name of the Launch4j nor the names of its contributors92	      may be used to endorse or promote products derived from this software without93	      specific prior written permission.94 95	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS96	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT97	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR98	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR99	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,100	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,101	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR102	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF103	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING104	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS105	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.106*/107 108package net.sf.launch4j.example;109 110import java.awt.Dimension;111import java.awt.Toolkit;112import java.awt.event.WindowAdapter;113import java.awt.event.WindowEvent;114 115import javax.swing.JFrame;116import javax.swing.JMenu;117import javax.swing.JMenuBar;118import javax.swing.JMenuItem;119import javax.swing.JOptionPane;120import javax.swing.UIManager;121 122public class SimpleApp extends JFrame {123    public SimpleApp(String[] args) {124        super(""Java Application"");125        final int inset = 100;126        Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();127		setBounds (inset, inset,128				screenSize.width - inset * 2, screenSize.height - inset * 2);129 130		JMenu menu = new JMenu(""File"");131		menu.add(new JMenuItem(""Open""));132		menu.add(new JMenuItem(""Save""));133		JMenuBar mb = new JMenuBar();134		mb.setOpaque(true);135		mb.add(menu);136		setJMenuBar(mb);137 138		this.addWindowListener(new WindowAdapter() {139	    	public void windowClosing(WindowEvent e) {140				System.exit(123);141		}});142		setVisible(true);143 144		StringBuffer sb = new StringBuffer(""Java version: "");145		sb.append(System.getProperty(""java.version""));146		sb.append(""\nJava home: "");147		sb.append(System.getProperty(""java.home""));148		sb.append(""\nCurrent dir: "");149		sb.append(System.getProperty(""user.dir""));150		if (args.length > 0) {151			sb.append(""\nArgs: "");152			for (int i = 0; i < args.length; i++) {153				sb.append(args[i]);154				sb.append(' ');155			}156		}157		JOptionPane.showMessageDialog(this,158				sb.toString(),159				""Info"",160				JOptionPane.INFORMATION_MESSAGE);161    }162 163	public static void setLAF() {164		JFrame.setDefaultLookAndFeelDecorated(true);165		Toolkit.getDefaultToolkit().setDynamicLayout(true);166		System.setProperty(""sun.awt.noerasebackground"",""true"");167		try {168			UIManager.setLookAndFeel(""com.sun.java.swing.plaf.windows.WindowsLookAndFeel"");169		} catch (Exception e) {170			System.err.println(""Failed to set LookAndFeel"");171		}172	}173 174   	public static void main(String[] args) {175   		setLAF();176		new SimpleApp(args);177	}178}179","Java"
180"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/Main.java",".java","3605","100","/*181	Launch4j (http://launch4j.sourceforge.net/)182	Cross-platform Java application wrapper for creating Windows native executables.183 184	Copyright (c) 2004, 2008 Grzegorz Kowal185 186	All rights reserved.187 188	Redistribution and use in source and binary forms, with or without modification,189	are permitted provided that the following conditions are met:190 191	    * Redistributions of source code must retain the above copyright notice,192	      this list of conditions and the following disclaimer.193	    * Redistributions in binary form must reproduce the above copyright notice,194	      this list of conditions and the following disclaimer in the documentation195	      and/or other materials provided with the distribution.196	    * Neither the name of the Launch4j nor the names of its contributors197	      may be used to endorse or promote products derived from this software without198	      specific prior written permission.199 200	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS201	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT202	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR203	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR204	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,205	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,206	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR207	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF208	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING209	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS210	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.211*/212 213/*214 * Created on Apr 21, 2005215 */216package net.sf.launch4j;217 218import java.io.File;219import java.io.InputStream;220import java.util.Properties;221 222import net.sf.launch4j.config.ConfigPersister;223import net.sf.launch4j.formimpl.MainFrame;224 225/**226 * @author Copyright (C) 2005 Grzegorz Kowal227 */228public class Main {229	private static String _name; 230	private static String _description;231 232	public static void main(String[] args) {233		try {234			Properties props = new Properties();235			InputStream in = Main.class.getClassLoader()236					.getResourceAsStream(""launch4j.properties"");237			props.load(in);238			in.close();239			setDescription(props);240 241			if (args.length == 0) {242				ConfigPersister.getInstance().createBlank();243				MainFrame.createInstance();244			} else if (args.length == 1 && !args[0].startsWith(""-"")) {245				ConfigPersister.getInstance().load(new File(args[0]));246				Builder b = new Builder(Log.getConsoleLog());247				b.build();248			} else {249				System.out.println(_description250						+ Messages.getString(""Main.usage"")251						+ "": launch4j config.xml"");252			}253		} catch (Exception e) {254			Log.getConsoleLog().append(e.getMessage());255		} 256	}257 258	public static String getName() {259		return _name;260	}261 262	public static String getDescription() {263		return _description;264	}265 266	private static void setDescription(Properties props) {267		_name = ""Launch4j "" + props.getProperty(""version""); 268		_description = _name + 269				"" (http://launch4j.sourceforge.net/)\n"" +270				""Cross-platform Java application wrapper"" +271						"" for creating Windows native executables.\n\n"" +272				""Copyright (C) 2004, 2008 Grzegorz Kowal\n\n"" +273				""Launch4j comes with ABSOLUTELY NO WARRANTY.\n"" +274				""This is free software, licensed under the BSD License.\n"" +275				""This product includes software developed by the Apache Software Foundation"" +276						"" (http://www.apache.org/)."";277	}278}279","Java"
280"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/FileChooserFilter.java",".java","2639","77","/*281	Launch4j (http://launch4j.sourceforge.net/)282	Cross-platform Java application wrapper for creating Windows native executables.283 284	Copyright (c) 2004, 2007 Grzegorz Kowal285 286	All rights reserved.287 288	Redistribution and use in source and binary forms, with or without modification,289	are permitted provided that the following conditions are met:290 291	    * Redistributions of source code must retain the above copyright notice,292	      this list of conditions and the following disclaimer.293	    * Redistributions in binary form must reproduce the above copyright notice,294	      this list of conditions and the following disclaimer in the documentation295	      and/or other materials provided with the distribution.296	    * Neither the name of the Launch4j nor the names of its contributors297	      may be used to endorse or promote products derived from this software without298	      specific prior written permission.299 300	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS301	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT302	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR303	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR304	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,305	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,306	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR307	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF308	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING309	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS310	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.311*/312 313/*314 * Created on 2004-01-15315 */316package net.sf.launch4j;317 318import java.io.File;319 320import javax.swing.filechooser.FileFilter;321 322/**323 * @author Copyright (C) 2004 Grzegorz Kowal324 */325public class FileChooserFilter extends FileFilter {326	String _description;327	String[] _extensions;328 329	public FileChooserFilter(String description, String extension) {330		_description = description;331		_extensions = new String[] {extension};332	}333	334	public FileChooserFilter(String description, String[] extensions) {335		_description = description;336		_extensions = extensions;337	}338 339	public boolean accept(File f) {340		if (f.isDirectory()) {341			return true;342		}343		String ext = Util.getExtension(f);344		for (int i = 0; i < _extensions.length; i++) {345			if (ext.toLowerCase().equals(_extensions[i].toLowerCase())) {346				return true;347			}348		}349		return false;350	}351 352	public String getDescription() {353		return _description;354	}355}356","Java"
357"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/Builder.java",".java","6332","208","/*358	Launch4j (http://launch4j.sourceforge.net/)359	Cross-platform Java application wrapper for creating Windows native executables.360 361	Copyright (c) 2004, 2007 Grzegorz Kowal362 363	All rights reserved.364 365	Redistribution and use in source and binary forms, with or without modification,366	are permitted provided that the following conditions are met:367 368	    * Redistributions of source code must retain the above copyright notice,369	      this list of conditions and the following disclaimer.370	    * Redistributions in binary form must reproduce the above copyright notice,371	      this list of conditions and the following disclaimer in the documentation372	      and/or other materials provided with the distribution.373	    * Neither the name of the Launch4j nor the names of its contributors374	      may be used to endorse or promote products derived from this software without375	      specific prior written permission.376 377	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS378	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT379	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR380	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR381	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,382	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,383	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR384	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF385	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING386	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS387	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.388*/389 390/*391 * Created on 2005-04-24392 */393package net.sf.launch4j;394 395import java.io.File;396import java.io.FileInputStream;397import java.io.FileOutputStream;398import java.io.IOException;399import java.util.ArrayList;400import java.util.Iterator;401import java.util.List;402import java.util.StringTokenizer;403 404import net.sf.launch4j.binding.InvariantViolationException;405import net.sf.launch4j.config.Config;406import net.sf.launch4j.config.ConfigPersister;407 408/**409 * @author Copyright (C) 2005 Grzegorz Kowal410 */411public class Builder {412	private final Log _log;413	private final File _basedir;414 415	public Builder(Log log) {416		_log = log;417		_basedir = Util.getJarBasedir();418	}419 420	public Builder(Log log, File basedir) {421		_log = log;422		_basedir = basedir;423	}424 425	/**426	 * @return Output file path.427	 */428	public File build() throws BuilderException {429		final Config c = ConfigPersister.getInstance().getConfig();430		try {431			c.validate();432		} catch (InvariantViolationException e) {433			throw new BuilderException(e.getMessage());434		}435		File rc = null;436		File ro = null;437		File outfile = null;438		FileInputStream is = null;439		FileOutputStream os = null;440		final RcBuilder rcb = new RcBuilder();441		try {442			rc = rcb.build(c);443			ro = Util.createTempFile(""o"");444			outfile = ConfigPersister.getInstance().getOutputFile();445 446			Cmd resCmd = new Cmd(_basedir);447			resCmd.addExe(""windres"")448					.add(Util.WINDOWS_OS ? ""--preprocessor=type"" : ""--preprocessor=cat"")449					.add(""-J rc -O coff -F pe-i386"")450					.addAbsFile(rc)451					.addAbsFile(ro);452			_log.append(Messages.getString(""Builder.compiling.resources""));453			resCmd.exec(_log);454 455			Cmd ldCmd = new Cmd(_basedir);456			ldCmd.addExe(""ld"")457					.add(""-mi386pe"")458					.add(""--oformat pei-i386"")459					.add((c.getHeaderType().equals(Config.GUI_HEADER))460							? ""--subsystem windows"" : ""--subsystem console"")461					.add(""-s"")		// strip symbols462					.addFiles(c.getHeaderObjects())463					.addAbsFile(ro)464					.addFiles(c.getLibs())465					.add(""-o"")466					.addAbsFile(outfile);467			_log.append(Messages.getString(""Builder.linking""));468			ldCmd.exec(_log);469 470			if (!c.isDontWrapJar()) {471				_log.append(Messages.getString(""Builder.wrapping""));472				int len;473				byte[] buffer = new byte[1024];474				is = new FileInputStream(Util.getAbsoluteFile(475						ConfigPersister.getInstance().getConfigPath(),	c.getJar()));476				os = new FileOutputStream(outfile, true);477				while ((len = is.read(buffer)) > 0) {478					os.write(buffer, 0, len);479				}480			}481			_log.append(Messages.getString(""Builder.success"") + outfile.getPath());482			return outfile;483		} catch (IOException e) {484			Util.delete(outfile);485			_log.append(e.getMessage());486			throw new BuilderException(e);487		} catch (ExecException e) {488			Util.delete(outfile);489			String msg = e.getMessage(); 490			if (msg != null && msg.indexOf(""windres"") != -1) {491				if (e.getErrLine() != -1) {492					_log.append(Messages.getString(""Builder.line.has.errors"",493							String.valueOf(e.getErrLine())));494					_log.append(rcb.getLine(e.getErrLine()));495				} else {496					_log.append(Messages.getString(""Builder.generated.resource.file""));497					_log.append(rcb.getContent());498				}499			}500			throw new BuilderException(e);501		} finally {502			Util.close(is);503			Util.close(os);504			Util.delete(rc);505			Util.delete(ro);506		}507	}508}509 510class Cmd {511	private final List _cmd = new ArrayList();512	private final File _basedir;513	private final File _bindir;514 515	public Cmd(File basedir) {516		_basedir = basedir;517		String path = System.getProperty(""launch4j.bindir"");518		if (path == null) {519			_bindir = new File(basedir, ""bin"");520		} else {521			File bindir = new File(path);522			_bindir = bindir.isAbsolute() ? bindir : new File(basedir, path);523		}524	}525 526	public Cmd add(String s) {527		StringTokenizer st = new StringTokenizer(s);528		while (st.hasMoreTokens()) {529			_cmd.add(st.nextToken());530		}531		return this;532	}533 534	public Cmd addAbsFile(File file) {535		_cmd.add(file.getPath());536		return this;537	}538 539	public Cmd addFile(String pathname) {540		_cmd.add(new File(_basedir, pathname).getPath());541		return this;542	}543 544	public Cmd addExe(String pathname) {545		if (Util.WINDOWS_OS) {546			pathname += "".exe"";547		}548		_cmd.add(new File(_bindir, pathname).getPath());549		return this;550	}551 552	public Cmd addFiles(List files) {553		for (Iterator iter = files.iterator(); iter.hasNext();) {554			addFile((String) iter.next());555		}556		return this;557	}558 559	public void exec(Log log) throws ExecException {560		String[] cmd = (String[]) _cmd.toArray(new String[_cmd.size()]);561		Util.exec(cmd, log);562	}563}564","Java"
565"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/OptionParser.java",".java","2772","72","/*566	Launch4j (http://launch4j.sourceforge.net/)567	Cross-platform Java application wrapper for creating Windows native executables.568 569	Copyright (c) 2004, 2007 Grzegorz Kowal570 571	All rights reserved.572 573	Redistribution and use in source and binary forms, with or without modification,574	are permitted provided that the following conditions are met:575 576	    * Redistributions of source code must retain the above copyright notice,577	      this list of conditions and the following disclaimer.578	    * Redistributions in binary form must reproduce the above copyright notice,579	      this list of conditions and the following disclaimer in the documentation580	      and/or other materials provided with the distribution.581	    * Neither the name of the Launch4j nor the names of its contributors582	      may be used to endorse or promote products derived from this software without583	      specific prior written permission.584 585	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS586	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT587	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR588	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR589	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,590	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,591	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR592	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF593	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING594	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS595	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.596*/597 598/*599 * Created on 2005-04-24600 */601package net.sf.launch4j;602 603//import net.sf.launch4j.config.Config;604 605//import org.apache.commons.cli.CommandLine;606//import org.apache.commons.cli.CommandLineParser;607//import org.apache.commons.cli.HelpFormatter;608//import org.apache.commons.cli.Options;609//import org.apache.commons.cli.ParseException;610//import org.apache.commons.cli.PosixParser;611 612/**613 * @author Copyright (C) 2005 Grzegorz Kowal614 */615public class OptionParser {616 617//	private final Options _options;618//619//	public OptionParser() {620//		_options = new Options();621//		_options.addOption(""h"", ""header"", true, ""header"");622//	}623//624//	public Config parse(Config c, String[] args) throws ParseException {625//		CommandLineParser parser = new PosixParser();626//		CommandLine cl = parser.parse(_options, args);627//		c.setJar(getFile(props, Config.JAR));628//		c.setOutfile(getFile(props, Config.OUTFILE));629//	}630//631//	public void printHelp() {632//		HelpFormatter formatter = new HelpFormatter();633//		formatter.printHelp(""launch4j"", _options);634//	}635}636","Java"
637"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/Messages.java",".java","2978","79","/*638	Launch4j (http://launch4j.sourceforge.net/)639	Cross-platform Java application wrapper for creating Windows native executables.640 641	Copyright (c) 2004, 2007 Grzegorz Kowal642 643	All rights reserved.644 645	Redistribution and use in source and binary forms, with or without modification,646	are permitted provided that the following conditions are met:647 648	    * Redistributions of source code must retain the above copyright notice,649	      this list of conditions and the following disclaimer.650	    * Redistributions in binary form must reproduce the above copyright notice,651	      this list of conditions and the following disclaimer in the documentation652	      and/or other materials provided with the distribution.653	    * Neither the name of the Launch4j nor the names of its contributors654	      may be used to endorse or promote products derived from this software without655	      specific prior written permission.656 657	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS658	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT659	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR660	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR661	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,662	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,663	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR664	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF665	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING666	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS667	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.668*/669 670package net.sf.launch4j;671 672import java.text.MessageFormat;673import java.util.MissingResourceException;674import java.util.ResourceBundle;675 676public class Messages {677	private static final String BUNDLE_NAME = ""net.sf.launch4j.messages"";678 679	private static final ResourceBundle RESOURCE_BUNDLE = ResourceBundle680			.getBundle(BUNDLE_NAME);681	private static final MessageFormat FORMATTER = new MessageFormat("""");682 683	private Messages() {684	}685 686	public static String getString(String key) {687		try {688			return RESOURCE_BUNDLE.getString(key);689		} catch (MissingResourceException e) {690			return '!' + key + '!';691		}692	}693	694	public static String getString(String key, String arg0) {695		return getString(key, new Object[] {arg0});696	}697 698	public static String getString(String key, String arg0, String arg1) {699		return getString(key, new Object[] {arg0, arg1});700	}701 702	public static String getString(String key, String arg0, String arg1, String arg2) {703		return getString(key, new Object[] {arg0, arg1, arg2});704	}705 706	public static String getString(String key, Object[] args) {707		try {708			FORMATTER.applyPattern(RESOURCE_BUNDLE.getString(key));709			return FORMATTER.format(args);710		} catch (MissingResourceException e) {711			return '!' + key + '!';712		}713	}714}715","Java"
716"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/Util.java",".java","5877","198","/*717	Launch4j (http://launch4j.sourceforge.net/)718	Cross-platform Java application wrapper for creating Windows native executables.719 720	Copyright (c) 2004, 2007 Grzegorz Kowal721 722	All rights reserved.723 724	Redistribution and use in source and binary forms, with or without modification,725	are permitted provided that the following conditions are met:726 727	    * Redistributions of source code must retain the above copyright notice,728	      this list of conditions and the following disclaimer.729	    * Redistributions in binary form must reproduce the above copyright notice,730	      this list of conditions and the following disclaimer in the documentation731	      and/or other materials provided with the distribution.732	    * Neither the name of the Launch4j nor the names of its contributors733	      may be used to endorse or promote products derived from this software without734	      specific prior written permission.735 736	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS737	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT738	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR739	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR740	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,741	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,742	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR743	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF744	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING745	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS746	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.747*/748 749/*750 * Created on 2005-04-24751 */752package net.sf.launch4j;753 754import java.io.BufferedReader;755import java.io.File;756import java.io.IOException;757import java.io.InputStream;758import java.io.InputStreamReader;759import java.io.OutputStream;760import java.io.Reader;761import java.io.Writer;762import java.util.regex.Matcher;763import java.util.regex.Pattern;764 765/**766 * @author Copyright (C) 2005 Grzegorz Kowal767 */768public class Util {769	public static final boolean WINDOWS_OS = System.getProperty(""os.name"")770			.toLowerCase().startsWith(""windows"");771 772	private Util() {}773 774	public static File createTempFile(String suffix) throws IOException {775		String tmpdir = System.getProperty(""launch4j.tmpdir"");776		if (tmpdir != null) {777			if (tmpdir.indexOf(' ') != -1) {778				throw new IOException(Messages.getString(""Util.tmpdir""));779			}780			return File.createTempFile(""launch4j"", suffix, new File(tmpdir));781		} else {782			return File.createTempFile(""launch4j"", suffix);783		}784	}785 786	/**787	 * Returns the base directory of a jar file or null if the class is a standalone file. 788	 * @return System specific path789	 * 790	 * Based on a patch submitted by Josh Elsasser791	 */792	public static File getJarBasedir() {793		String url = Util.class.getClassLoader()794				.getResource(Util.class.getName().replace('.', '/') + "".class"")795				.getFile()796				.replaceAll(""%20"", "" "");797		if (url.startsWith(""file:"")) {798			String jar = url.substring(5, url.lastIndexOf('!'));799			int x = jar.lastIndexOf('/');800			if (x == -1) {801				x = jar.lastIndexOf('\\');	802			}803			String basedir = jar.substring(0, x + 1);804			return new File(basedir);805		} else {806			return new File(""."");807		}808	}809 810	public static File getAbsoluteFile(File basepath, File f) {811		return f.isAbsolute() ? f : new File(basepath, f.getPath());812	}813 814	public static String getExtension(File f) {815		String name = f.getName();816		int x = name.lastIndexOf('.');817		if (x != -1) {818			return name.substring(x);819		} else {820			return """";821		}822	}823 824	public static void exec(String[] cmd, Log log) throws ExecException {825		BufferedReader is = null;826		try {827			if (WINDOWS_OS) {828				for (int i = 0; i < cmd.length; i++) {829					cmd[i] = cmd[i].replaceAll(""/"", ""\\\\"");830				}831			}832			Process p = Runtime.getRuntime().exec(cmd);833			is = new BufferedReader(new InputStreamReader(p.getErrorStream()));834			String line;835			int errLine = -1;836			Pattern pattern = Pattern.compile("":\\d+:"");837			while ((line = is.readLine()) != null) {838				log.append(line);839				Matcher matcher = pattern.matcher(line);840				if (matcher.find()) {841					errLine = Integer.valueOf(842							line.substring(matcher.start() + 1, matcher.end() - 1))843							.intValue();844					if (line.matches(""(?i).*unrecognized escape sequence"")) {845						log.append(Messages.getString(""Util.use.double.backslash""));846					}847					break;848				}849			}850			is.close();851			p.waitFor();852			if (errLine != -1) {853				throw new ExecException(Messages.getString(""Util.exec.failed"")854						+ "": "" + cmd, errLine);855			}856			if (p.exitValue() != 0) {857				throw new ExecException(Messages.getString(""Util.exec.failed"")858						+ ""("" + p.exitValue() + ""): "" + cmd);859			}860		} catch (IOException e) {861			close(is);862			throw new ExecException(e);863		} catch (InterruptedException e) {864			close(is);865			throw new ExecException(e);866		}867	}868 869	public static void close(final InputStream o) {870		if (o != null) {871			try {872				o.close();873			} catch (IOException e) {874				System.err.println(e); // XXX log875			}876		}877	}878 879	public static void close(final OutputStream o) {880		if (o != null) {881			try {882				o.close();883			} catch (IOException e) {884				System.err.println(e); // XXX log885			}886		}887	}888 889	public static void close(final Reader o) {890		if (o != null) {891			try {892				o.close();893			} catch (IOException e) {894				System.err.println(e); // XXX log895			}896		}897	}898 899	public static void close(final Writer o) {900		if (o != null) {901			try {902				o.close();903			} catch (IOException e) {904				System.err.println(e); // XXX log905			}906		}907	}908 909	public static boolean delete(File f) {910		return (f != null) ? f.delete() : false;911	}912}913","Java"
914"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/Log.java",".java","3125","106","/*915	Launch4j (http://launch4j.sourceforge.net/)916	Cross-platform Java application wrapper for creating Windows native executables.917 918	Copyright (c) 2004, 2007 Grzegorz Kowal919 920	All rights reserved.921 922	Redistribution and use in source and binary forms, with or without modification,923	are permitted provided that the following conditions are met:924 925	    * Redistributions of source code must retain the above copyright notice,926	      this list of conditions and the following disclaimer.927	    * Redistributions in binary form must reproduce the above copyright notice,928	      this list of conditions and the following disclaimer in the documentation929	      and/or other materials provided with the distribution.930	    * Neither the name of the Launch4j nor the names of its contributors931	      may be used to endorse or promote products derived from this software without932	      specific prior written permission.933 934	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS935	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT936	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR937	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR938	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,939	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,940	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR941	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF942	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING943	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS944	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.945*/946 947/*948 * Created on May 12, 2005949 */950package net.sf.launch4j;951 952import javax.swing.JTextArea;953import javax.swing.SwingUtilities;954 955/**956 * @author Copyright (C) 2005 Grzegorz Kowal957 */958public abstract class Log {959	private static final Log _consoleLog = new ConsoleLog();960	private static final Log _antLog = new AntLog();961 962	public abstract void clear();963	public abstract void append(String line);964 965	public static Log getConsoleLog() {966		return _consoleLog;967	}968	969	public static Log getAntLog() {970		return _antLog;971	}972 973	public static Log getSwingLog(JTextArea textArea) {974		return new SwingLog(textArea);975	}976}977 978class ConsoleLog extends Log {979	public void clear() {980		System.out.println(""\n"");981	}982 983	public void append(String line) {984		System.out.println(""launch4j: "" + line);985	}986}987 988class AntLog extends Log {989	public void clear() {990		System.out.println(""\n"");991	}992 993	public void append(String line) {994		System.out.println(line);995	}996}997 998class SwingLog extends Log {999	private final JTextArea _textArea;1000 1001	public SwingLog(JTextArea textArea) {1002		_textArea = textArea;1003	}1004 1005	public void clear() {1006		SwingUtilities.invokeLater(new Runnable() {1007			public void run() {1008				_textArea.setText("""");1009		}});1010	}1011 1012	public void append(final String line) {1013		SwingUtilities.invokeLater(new Runnable() {1014			public void run() {1015				_textArea.append(line + ""\n"");1016		}});1017	}1018}1019","Java"
1020"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/BuilderException.java",".java","2038","53","/*1021	Launch4j (http://launch4j.sourceforge.net/)1022	Cross-platform Java application wrapper for creating Windows native executables.1023 1024	Copyright (c) 2004, 2007 Grzegorz Kowal1025 1026	All rights reserved.1027 1028	Redistribution and use in source and binary forms, with or without modification,1029	are permitted provided that the following conditions are met:1030 1031	    * Redistributions of source code must retain the above copyright notice,1032	      this list of conditions and the following disclaimer.1033	    * Redistributions in binary form must reproduce the above copyright notice,1034	      this list of conditions and the following disclaimer in the documentation1035	      and/or other materials provided with the distribution.1036	    * Neither the name of the Launch4j nor the names of its contributors1037	      may be used to endorse or promote products derived from this software without1038	      specific prior written permission.1039 1040	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS1041	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT1042	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR1043	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR1044	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,1045	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,1046	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR1047	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF1048	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING1049	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS1050	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.1051*/1052 1053/*1054 * Created on May 13, 20051055 */1056package net.sf.launch4j;1057 1058/**1059 * @author Copyright (C) 2005 Grzegorz Kowal1060 */1061public class BuilderException extends Exception {1062	public BuilderException() {}1063 1064	public BuilderException(Throwable t) {1065		super(t);1066	}1067	1068	public BuilderException(String msg) {1069		super(msg);1070	}1071}1072","Java"
1073"Bio foundation model","phylogeography/SPREADv1","release/tools/launch4j/src/net/sf/launch4j/RcBuilder.java",".java","11072","341","/*1074	Launch4j (http://launch4j.sourceforge.net/)1075	Cross-platform Java application wrapper for creating Windows native executables.1076 1077	Copyright (c) 2004, 2007 Grzegorz Kowal1078 1079	All rights reserved.1080 1081	Redistribution and use in source and binary forms, with or without modification,1082	are permitted provided that the following conditions are met:1083 1084	    * Redistributions of source code must retain the above copyright notice,1085	      this list of conditions and the following disclaimer.1086	    * Redistributions in binary form must reproduce the above copyright notice,1087	      this list of conditions and the following disclaimer in the documentation1088	      and/or other materials provided with the distribution.1089	    * Neither the name of the Launch4j nor the names of its contributors1090	      may be used to endorse or promote products derived from this software without1091	      specific prior written permission.1092 1093	THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS1094	""AS IS"" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT1095	LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR1096	A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR1097	CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,1098	EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,1099	PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR1100	PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF1101	LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING1102	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS1103	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.1104*/1105 1106/*1107 * Created on 2005-04-241108 */1109package net.sf.launch4j;1110 1111import java.io.BufferedWriter;1112import java.io.File;1113import java.io.FileWriter;1114import java.io.IOException;1115import java.util.List;1116 1117import net.sf.launch4j.config.Config;1118import net.sf.launch4j.config.ConfigPersister;1119import net.sf.launch4j.config.Jre;1120import net.sf.launch4j.config.Msg;1121import net.sf.launch4j.config.Splash;1122import net.sf.launch4j.config.VersionInfo;1123 1124/**1125 * @author Copyright (C) 2005 Grzegorz Kowal1126 */1127public class RcBuilder {1128 1129	// winnt.h1130	public static final int LANG_NEUTRAL = 0;1131	public static final int SUBLANG_NEUTRAL	= 0;1132	public static final int SUBLANG_DEFAULT	= 1;1133	public static final int SUBLANG_SYS_DEFAULT	= 2;1134 1135	// MANIFEST1136	public static final int MANIFEST = 1;1137 1138	// ICON1139	public static final int APP_ICON = 1;1140 1141	// BITMAP1142	public static final int SPLASH_BITMAP = 1;1143 1144	// RCDATA1145	public static final int JRE_PATH = 1;1146	public static final int JAVA_MIN_VER = 2;1147	public static final int JAVA_MAX_VER = 3;1148	public static final int SHOW_SPLASH = 4;1149	public static final int SPLASH_WAITS_FOR_WINDOW = 5;1150	public static final int SPLASH_TIMEOUT = 6;1151	public static final int SPLASH_TIMEOUT_ERR = 7;1152	public static final int CHDIR = 8;1153	public static final int SET_PROC_NAME = 9;1154	public static final int ERR_TITLE = 10;1155	public static final int GUI_HEADER_STAYS_ALIVE = 11;1156	public static final int JVM_OPTIONS = 12;1157	public static final int CMD_LINE = 13;1158	public static final int JAR = 14;1159	public static final int MAIN_CLASS = 15;1160	public static final int CLASSPATH = 16;1161	public static final int WRAPPER = 17;1162	public static final int JDK_PREFERENCE = 18;1163	public static final int ENV_VARIABLES = 19;1164	public static final int PRIORITY_CLASS = 20;1165	public static final int	DOWNLOAD_URL = 	21;1166	public static final int SUPPORT_URL = 22;1167	public static final int MUTEX_NAME = 23;1168	public static final int INSTANCE_WINDOW_TITLE = 24;1169	public static final int INITIAL_HEAP_SIZE = 25;1170	public static final int INITIAL_HEAP_PERCENT = 26;1171	public static final int MAX_HEAP_SIZE = 27;1172	public static final int MAX_HEAP_PERCENT = 28;1173	1174	public static final int STARTUP_ERR = 101;1175	public static final int BUNDLED_JRE_ERR = 102;1176	public static final int JRE_VERSION_ERR = 103;1177	public static final int LAUNCHER_ERR = 104;1178	public static final int INSTANCE_ALREADY_EXISTS_MSG = 105;1179	1180	private final StringBuffer _sb = new StringBuffer();1181 1182	public String getContent() {1183		return _sb.toString();1184	}1185 1186	public String getLine(int line) {1187		return _sb.toString().split(""\n"")[line - 1];1188	}1189 1190	public File build(Config c) throws IOException {1191		_sb.append(""LANGUAGE "");1192		_sb.append(LANG_NEUTRAL);1193		_sb.append("", "");1194		_sb.append(SUBLANG_DEFAULT);1195		_sb.append('\n');1196		addVersionInfo(c.getVersionInfo());1197		addJre(c.getJre());1198		addManifest(MANIFEST, c.getManifest());1199		addIcon(APP_ICON, c.getIcon());1200		addText(ERR_TITLE, c.getErrTitle());

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