This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository jmodeltest.
commit d9247988673a082beab59909de066cb1fc32db0a Author: Andreas Tille <[email protected]> Date: Fri Jan 15 17:38:51 2016 +0100 Imported Upstream version 2.1.9+dfsg --- build.xml | 18 ++-- manual/manual.tex | 9 ++ .../darwin/jmodeltest/ApplicationOptions.java | 7 +- .../java/es/uvigo/darwin/jmodeltest/ModelTest.java | 48 ++++------ .../darwin/jmodeltest/ModelTestConfiguration.java | 6 +- .../jmodeltest/exception/InternalException.java | 2 +- .../darwin/jmodeltest/exe/PhymlSingleModel.java | 33 ++++--- .../es/uvigo/darwin/jmodeltest/exe/RunPhyml.java | 106 +++++++++++++++++++-- .../es/uvigo/darwin/jmodeltest/gui/FrameMain.java | 4 +- .../es/uvigo/darwin/jmodeltest/gui/XManager.java | 5 +- .../es/uvigo/darwin/jmodeltest/gui/icons/JMT24.gif | Bin .../es/uvigo/darwin/jmodeltest/gui/icons/JMT48.gif | Bin .../es/uvigo/darwin/jmodeltest/gui/icons/JMT96.gif | Bin .../uvigo/darwin/jmodeltest/gui/icons/Open16.gif | Bin .../uvigo/darwin/jmodeltest/gui/icons/Open24.gif | Bin .../uvigo/darwin/jmodeltest/io/HtmlReporter.java | 1 + .../darwin/jmodeltest/tree/TreeDistancesCache.java | 2 +- .../darwin/jmodeltest/utilities/Utilities.java | 33 +++++-- src/main/resources/CHANGELOG | 7 ++ src/main/resources/README | 2 +- src/main/resources/conf/jmodeltest.conf | 5 +- 21 files changed, 205 insertions(+), 83 deletions(-) diff --git a/build.xml b/build.xml index 9912efd..0052998 100644 --- a/build.xml +++ b/build.xml @@ -2,7 +2,8 @@ <project name="jModelTest" default="jar" basedir="."> <property name="src.dir" location="src/main/java" /> - <property name="bin.dir" location="build/classes" /> + <property name="build.base.dir" location="build" /> + <property name="build.dir" location="${build.base.dir}/classes" /> <property name="lib.dir" location="lib" /> <property name="dist.dir" location="dist" /> <property name="exe.dir" location="${dist.dir}/exe/phyml" /> @@ -28,26 +29,23 @@ </target> <target name="compile" description="Compile code"> - <mkdir dir="${bin.dir}" /> + <mkdir dir="${build.dir}" /> <mkdir dir="${lib.dir}" /> <property environment="env" /> <property name="java6.boot.classpath" value="${env.JAVA6_BOOTCLASSES}" /> - <javac srcdir="${src.dir}" destdir="${bin.dir}" includeAntRuntime="no" + <javac srcdir="${src.dir}" destdir="${build.dir}" includeAntRuntime="no" target="1.6" source="1.6" bootclasspath="${java5.boot.classpath}" classpathref="lib.path" debug="${compile.debug}"> <compilerarg value="-Xlint:all"/> </javac> - <copy todir="${bin.dir}/es"> - <fileset dir="${src.resources.dir}/es" includes="**/*.xml,**/*.properties,**/*.gif,**/*.ico" /> - </copy> - </target> <target name="jar" depends="compile" description="Build jar"> <mkdir dir="${dist.dir}" /> - <jar jarfile="${jarfile}" basedir="${bin.dir}" manifest="Manifest"> + <jar jarfile="${jarfile}" basedir="${build.dir}" manifest="Manifest"> + <fileset dir="${src.dir}" includes="**/*.xml,**/*.properties,**/*.gif,**/*.ico" /> <!-- Merge library jars into final jar file - <zipgroupfileset refid="lib.jars"/>--> + <zipgroupfileset refid="lib.jars"/>--> </jar> <mkdir dir="${dist.dir}/lib" /> <copy todir="${dist.dir}/lib"> @@ -70,7 +68,7 @@ </target> <target name="clean" description="Remove build and dist directories"> - <delete dir="${bin.dir}" /> + <delete dir="${build.base.dir}" /> <delete dir="${dist.dir}" /> <delete dir="${manual.dir}" includes="*.aux *.bbl *.out *.toc *.log *.blg *.dvi" /> </target> diff --git a/manual/manual.tex b/manual/manual.tex index 62bc31e..5adc82f 100644 --- a/manual/manual.tex +++ b/manual/manual.tex @@ -88,6 +88,15 @@ These programs are protected by their own license and conditions, and using jMod \begin{itemize} + \item 15 Jan 2016 - Version 2.1.9 + + \begin{itemize} + \item Added automatic search for PhyML binary in /usr/bin + \item Removed non-ASCII characters + \item Disable logging if writing is not possible + \item Merge GUI images into jarfile + \end{itemize} + \item 20 Oct 2015 - Version 2.1.8 \begin{itemize} diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java b/src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java index f632b4e..c3e570d 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java @@ -169,7 +169,12 @@ public class ApplicationOptions implements Serializable { if (ModelTestConfiguration.isPhymlLogEnabled() && getInputFile() != null) { logFile = new File(ModelTestConfiguration.getLogDir() + File.separator + getInputFile().getName() + ".phyml." + executionName + ".log"); - } else { + if (!logFile.canWrite()) + { + logFile = null; + } + } + if (logFile == null) { logFile = File.createTempFile("jmodeltest-phyml", ".log"); logFile.deleteOnExit(); } diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java b/src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java index 20d4c2d..5393bf0 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java @@ -96,7 +96,7 @@ public class ModelTest { public static final double INFINITY = 9999; public static final int MAX_NUM_MODELS = 88; public static final int MAX_NAME = 60; - public static final String CURRENT_VERSION = "2.1.8 v20151020"; + public static final String CURRENT_VERSION = "2.1.9 v20160115"; public static final String programName = ("jModeltest"); public static final String URL = "http://code.google.com/p/jmodeltest2";; public static final String WIKI = "http://code.google.com/p/jmodeltest2/wiki/GettingStarted";; @@ -165,15 +165,7 @@ public class ModelTest { execMode = ExecMode.GUI; XManager.getInstance(); // Check binary - if (!ModelTestConfiguration.isGlobalPhymlBinary()) { - if (!RunPhyml.phymlBinary.exists()) { - Utilities - .printRed("ERROR: PhyML binary cannot be found: " + RunPhyml.phymlBinary.getAbsolutePath() + "\n"); - } else if (!RunPhyml.phymlBinary.canExecute()) { - Utilities - .printRed("ERROR: PhyML binary exists, but it cannot be executed: " + RunPhyml.phymlBinary.getAbsolutePath() + "\n"); - } - } + RunPhyml.checkBinary(); } else { System.err.println(""); System.err.println("ERROR: You are trying to run a GUI interface in a headless server."); @@ -189,17 +181,21 @@ public class ModelTest { execMode = ExecMode.CONSOLE; ParseArguments(); + if (MPJ_ME == 0) { + // print header information + printHeader(MAIN_CONSOLE); + + // print citation information + printCitation(MAIN_CONSOLE); + + // print notice information + printNotice(MAIN_CONSOLE); + } + // Check binary - if (!ModelTestConfiguration.isGlobalPhymlBinary()) { - if (!RunPhyml.phymlBinary.exists()) { - System.err.println(" "); - System.err.println("ERROR: PhyML binary cannot be found: " + RunPhyml.phymlBinary.getAbsolutePath()); - finalize(-1); - } else if (!RunPhyml.phymlBinary.canExecute()) { - System.err.println(" "); - System.err.println("ERROR: PhyML binary exists, but it cannot be executed: " + RunPhyml.phymlBinary.getAbsolutePath()); - finalize(-1); - } + if (!RunPhyml.checkBinary()) + { + finalize(-1); } options.createLogFile(); @@ -300,15 +296,6 @@ public class ModelTest { public void runCommandLine() { if (MPJ_ME == 0) { - // print header information - printHeader(MAIN_CONSOLE); - - // print citation information - printCitation(MAIN_CONSOLE); - - // print notice information - printNotice(MAIN_CONSOLE); - // print the command line MAIN_CONSOLE.println(" "); MAIN_CONSOLE.print("Arguments ="); @@ -1389,7 +1376,8 @@ public class ModelTest { stream.println("jModelTest " + CURRENT_VERSION); stream.println("Copyright (C) 2011 D. Darriba, G.L. Taboada, R. Doallo and D. Posada"); stream.println("This program comes with ABSOLUTELY NO WARRANTY"); - stream.println("This is free software, and you are welcome to redistribute it under certain conditions"); + stream.println("This is free software, and you are welcome to redistribute it under certain"); + stream.println("conditions"); stream.println(" "); stream.println("Notice: This program may contain errors. Please inspect results carefully."); stream.println(" "); diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestConfiguration.java b/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestConfiguration.java index ac88975..a9b4a66 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestConfiguration.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestConfiguration.java @@ -114,9 +114,9 @@ public abstract class ModelTestConfiguration { } if (!existsKey(LOG_DIR)) { - APPLICATION_PROPERTIES.setProperty(HTML_LOG, "disabled"); - APPLICATION_PROPERTIES.setProperty(PHYML_LOG, "disabled"); - APPLICATION_PROPERTIES.setProperty(CKP_LOG, "disabled"); + disableHtmlLog(); + disablePhymlLog(); + disableCkpLog(); } } catch (IOException e) { diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/exception/InternalException.java b/src/main/java/es/uvigo/darwin/jmodeltest/exception/InternalException.java index cef9583..8e9e91d 100755 --- a/src/main/java/es/uvigo/darwin/jmodeltest/exception/InternalException.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/exception/InternalException.java @@ -20,7 +20,7 @@ package es.uvigo.darwin.jmodeltest.exception; /** * The Class ProtTestInternalException. * - * @author Diego Darriba López + * @author Diego Darriba */ public class InternalException extends RuntimeException { diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/exe/PhymlSingleModel.java b/src/main/java/es/uvigo/darwin/jmodeltest/exe/PhymlSingleModel.java index 610afc4..a1db6df 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/exe/PhymlSingleModel.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/exe/PhymlSingleModel.java @@ -23,12 +23,9 @@ import java.io.FileOutputStream; import java.io.PrintWriter; import java.util.Observable; -import javax.sql.rowset.spi.SyncResolver; - import pal.tree.TreeParseException; import es.uvigo.darwin.jmodeltest.ApplicationOptions; import es.uvigo.darwin.jmodeltest.ModelTest; -import es.uvigo.darwin.jmodeltest.ModelTestConfiguration; import es.uvigo.darwin.jmodeltest.io.TextInputStream; import es.uvigo.darwin.jmodeltest.model.Model; import es.uvigo.darwin.jmodeltest.observer.ProgressInfo; @@ -64,9 +61,9 @@ public class PhymlSingleModel extends Observable implements Runnable { this.ignoreGaps = ignoreGaps; this.phymlStatFileName = options.getAlignmentFile().getAbsolutePath() - + RunPhyml.PHYML_STATS_SUFFIX + model.getName() + ".txt"; + + RunPhyml.PHYML_STATS_SUFFIX + model.getName(); this.phymlTreeFileName = options.getAlignmentFile().getAbsolutePath() - + RunPhyml.PHYML_TREE_SUFFIX + model.getName() + ".txt"; + + RunPhyml.PHYML_TREE_SUFFIX + model.getName(); } public PhymlSingleModel(Model model, int index, boolean justGetJCTree, @@ -217,8 +214,9 @@ public class PhymlSingleModel extends Observable implements Runnable { private void executeCommandLine() { String[] executable = new String[1]; + boolean printLog = options.getLogFile() != null; try { - if (!ModelTestConfiguration.isGlobalPhymlBinary()) { + if (!RunPhyml.isPhymlGlobal()) { if (!RunPhyml.phymlBinary.exists()) { notifyObservers( ProgressInfo.ERROR_BINARY_NOEXISTS, index, model, RunPhyml.phymlBinary.getAbsolutePath()); @@ -246,12 +244,16 @@ public class PhymlSingleModel extends Observable implements Runnable { // any output? FileOutputStream logFile = new FileOutputStream( options.getLogFile(), true); - StreamGobbler outputGobbler = new StreamGobbler( + StreamGobbler outputGobbler = null; + + if (printLog) + outputGobbler = new StreamGobbler( proc.getInputStream(), "PHYML", logFile, ModelTest.getPhymlConsole()); // kick them off errorGobbler.start(); - outputGobbler.start(); + if (printLog) + outputGobbler.start(); // any error??? int exitVal = proc.waitFor(); @@ -280,7 +282,7 @@ public class PhymlSingleModel extends Observable implements Runnable { if (ModelTest.getPhymlConsole() != null) { synchronized (ModelTest.getPhymlConsole()) { ModelTest.getPhymlConsole().println(" "); - ModelTest.getPhymlConsole().println("Command line used for process "+ outputGobbler.getRunId() +":"); + ModelTest.getPhymlConsole().println("Command line used for process "+ errorGobbler.getRunId() +":"); ModelTest.getPhymlConsole().println(" " + RunPhyml.phymlBinary.getAbsolutePath() + " " + uCommand); ModelTest.getPhymlConsole().println(" "); @@ -288,7 +290,6 @@ public class PhymlSingleModel extends Observable implements Runnable { ModelTest.getPhymlConsole().close(); } } - } catch (InterruptedException e) { notifyObservers(ProgressInfo.INTERRUPTED, index, model, null); interrupted = true; @@ -314,11 +315,13 @@ public class PhymlSingleModel extends Observable implements Runnable { boolean showParsing = false; - // Get model likelihood - // TextInputStream phymlLkFile = new TextInputStream(phymlLkFileName); - // currentModel.lnL = (-1.0) * phymlLkFile.readFloat(); - // phymlLkFile.close(); - + File f = new File(phymlStatFileName); + if (!f.exists()) + { + phymlStatFileName += ".txt"; + phymlTreeFileName += ".txt"; + } + // Get model likelihood and parameter estimates try { TextInputStream phymlStatFile = new TextInputStream( diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhyml.java b/src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhyml.java index 52d43b7..809ef57 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhyml.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/exe/RunPhyml.java @@ -17,7 +17,11 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ package es.uvigo.darwin.jmodeltest.exe; +import java.io.BufferedReader; import java.io.File; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; @@ -60,7 +64,8 @@ public abstract class RunPhyml extends Observable implements Observer { protected Model[] models; protected Model gtrModel = null; - public static final String PHYML_VERSION = "3.0"; + public static final String[] COMPATIBLE_VERSIONS = {"20130103", "20131022", "20141009", "20141029", "20150501"}; + public static String PHYML_VERSION = "3.0"; public static String PHYML_TREE_SUFFIX = "_phyml_tree_"; public static String PHYML_STATS_SUFFIX = "_phyml_stats_"; @@ -68,16 +73,93 @@ public abstract class RunPhyml extends Observable implements Observer { public static File phymlBinary; public static String phymlBinaryStr; private static String CURRENT_DIRECTORY = ModelTestConfiguration.PATH; - private static boolean PHYML_GLOBAL = false; + private static boolean PHYML_GLOBAL = ModelTestConfiguration.isGlobalPhymlBinary(); public static String PHYML_PATH = CURRENT_DIRECTORY + "exe/phyml/"; - + private static boolean compatiblePhyml = false; protected Observer progress; + public static boolean isCompatible() { + return compatiblePhyml; + } + + public static boolean checkBinary() { + boolean canExecute = false; + if (!ModelTestConfiguration.isGlobalPhymlBinary()) { + if (!RunPhyml.phymlBinary.exists()) { + Utilities + .printRed("ERROR: PhyML binary cannot be found: " + RunPhyml.phymlBinary.getAbsolutePath() + "\n"); + } else if (!RunPhyml.phymlBinary.canExecute()) { + Utilities + .printRed("ERROR: PhyML binary exists, but it cannot be executed: " + RunPhyml.phymlBinary.getAbsolutePath() + "\n"); + } else if (!RunPhyml.isCompatible()){ + Utilities + .printRed("WARNING: PhyML binary is not in the list of compatibility: \n"); + Utilities + .printRed(RunPhyml.phymlBinary.getAbsolutePath() + " v" + RunPhyml.PHYML_VERSION +"\n"); + Utilities.printRed("Compatible versions: "); + for (int i=0; i<RunPhyml.COMPATIBLE_VERSIONS.length; i++) + Utilities.printBlue(RunPhyml.COMPATIBLE_VERSIONS[i] + " "); + Utilities.printBlue("\n"); + Utilities + .printRed("jModelTest will try to continue execution anyway, but it might fail.\n"); + canExecute = true; + } else { + Utilities + .printBlue("PhyML binary: " + RunPhyml.phymlBinary.getAbsolutePath() + " v" + RunPhyml.PHYML_VERSION + "\n"); + canExecute = true; + } + } + return canExecute; + } + private static boolean checkPhymlCompatibility(String binary) { + boolean binaryFound = false; + if (Utilities.findCurrentOS() != Utilities.OS_LINUX) + return false; + // get process and execute command line + String cmd[] = {binary, "--version"}; + Runtime rt = Runtime.getRuntime(); + Process proc; + try { + proc = rt.exec(cmd, null, null); + InputStream stdin = proc.getInputStream(); + InputStreamReader isr = new InputStreamReader(stdin); + BufferedReader br = new BufferedReader(isr); + + String line = null; + while ( (line = br.readLine()) != null) { + if (line.toLowerCase().contains("phyml version")) { + String[] linesplit = line.trim().replace(".", "").split(" "); + String version = linesplit[linesplit.length - 1]; + PHYML_VERSION = version; + if (Arrays.asList(COMPATIBLE_VERSIONS).contains(version)) { + compatiblePhyml = true; + } else { + compatiblePhyml = false; + } + binaryFound = true; + } + } + br.close(); + isr.close(); + stdin.close(); + proc.destroy(); + } catch (IOException e) { + return false; + } + return binaryFound; + } + + public static boolean isPhymlGlobal() { + return PHYML_GLOBAL; + } + static { if (PHYML_GLOBAL) { PHYML_PATH = ""; + phymlBinaryStr = "phyml"; } else { + /* check the local paths */ String path = ModelTestConfiguration.getExeDir(); if (!path.startsWith(File.separator)) { PHYML_PATH = CURRENT_DIRECTORY + File.separator + path; @@ -87,18 +169,26 @@ public abstract class RunPhyml extends Observable implements Observer { if (!PHYML_PATH.endsWith(File.separator)) { PHYML_PATH += File.separator; } - } - if (PHYML_GLOBAL) { - phymlBinaryStr = "phyml"; - } else { phymlBinary = new File(PHYML_PATH + "phyml"); if (phymlBinary.exists() && phymlBinary.canExecute()) { phymlBinaryStr = phymlBinary.getAbsolutePath(); + compatiblePhyml = true; } else { phymlBinaryStr = PHYML_PATH + Utilities.getBinaryVersion(); } - /* Check if binary exists */ + /* Check if binary exists and is compatible */ phymlBinary = new File(phymlBinaryStr); + if (!checkPhymlCompatibility(phymlBinaryStr)) { + /* Check for system wide PhyML */ + if (!(phymlBinary.exists() && phymlBinary.canExecute())) + { + if(checkPhymlCompatibility("/usr/bin/phyml")) { + PHYML_PATH = "/usr/bin"; + phymlBinary = new File(PHYML_PATH + "/phyml"); + phymlBinaryStr = phymlBinary.getAbsolutePath(); + } + } + } } } public RunPhyml(Observer progress, ApplicationOptions options, diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/gui/FrameMain.java b/src/main/java/es/uvigo/darwin/jmodeltest/gui/FrameMain.java index da1fbcd..107e5ad 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/gui/FrameMain.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/gui/FrameMain.java @@ -537,7 +537,7 @@ public class FrameMain extends JModelTestFrame { // getContentPane().setLayout(null); getContentPane().setLayout(new BorderLayout()); setTitle("jModelTest " + ModelTest.CURRENT_VERSION); - setSize(new java.awt.Dimension(630, 695)); + setSize(new java.awt.Dimension(780, 695)); setResizable(true); // event handling @@ -1142,7 +1142,7 @@ public class FrameMain extends JModelTestFrame { private void menuAboutCreditsActionPerformed(java.awt.event.ActionEvent e) { try { String credits = "Likelihood calculations with Phyml by Stephane Guindon et al.\n"; - credits += "Alignment conversion with ALTER by Daniel Glez-Peña et al.\n"; + credits += "Alignment conversion with ALTER by Daniel Glez-Pena et al.\n"; credits += "Phylogenetic trees management with PAL: Phylogenetic Analysis Library by A. Drummond and K. Strimmer\n"; credits += "Table utilities by Philip Milne\n"; credits += "BrowserLauncher by Eric Albert and Jeff Chapman\n"; diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/gui/XManager.java b/src/main/java/es/uvigo/darwin/jmodeltest/gui/XManager.java index 8bef0e7..66f496e 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/gui/XManager.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/gui/XManager.java @@ -59,6 +59,7 @@ public class XManager { public static final Point MAIN_LOCATION = new Point(281, 80); + public static SimpleAttributeSet blueText; public static SimpleAttributeSet redText; public static SimpleAttributeSet blackText; @@ -82,9 +83,11 @@ public class XManager { FONT_STATUS = new Font("Dialog", 0, 9); FONT_TABULAR = new java.awt.Font("Verdana", 0, 12); - redText = new SimpleAttributeSet(); blackText = new SimpleAttributeSet(); + redText = new SimpleAttributeSet(); + blueText = new SimpleAttributeSet(); + StyleConstants.setForeground(blueText, Color.blue); StyleConstants.setForeground(redText, Color.red); StyleConstants.setForeground(blackText, Color.black); } diff --git a/src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/JMT24.gif b/src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/JMT24.gif similarity index 100% rename from src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/JMT24.gif rename to src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/JMT24.gif diff --git a/src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/JMT48.gif b/src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/JMT48.gif similarity index 100% rename from src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/JMT48.gif rename to src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/JMT48.gif diff --git a/src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/JMT96.gif b/src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/JMT96.gif similarity index 100% rename from src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/JMT96.gif rename to src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/JMT96.gif diff --git a/src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/Open16.gif b/src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/Open16.gif similarity index 100% rename from src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/Open16.gif rename to src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/Open16.gif diff --git a/src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/Open24.gif b/src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/Open24.gif similarity index 100% rename from src/main/resources/es/uvigo/darwin/jmodeltest/gui/icons/Open24.gif rename to src/main/java/es/uvigo/darwin/jmodeltest/gui/icons/Open24.gif diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/io/HtmlReporter.java b/src/main/java/es/uvigo/darwin/jmodeltest/io/HtmlReporter.java index c7a16a4..0e4137e 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/io/HtmlReporter.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/io/HtmlReporter.java @@ -625,6 +625,7 @@ public abstract class HtmlReporter { } } + @SuppressWarnings("resource") public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeDistancesCache.java b/src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeDistancesCache.java index a4b3a9b..d28e567 100755 --- a/src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeDistancesCache.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/tree/TreeDistancesCache.java @@ -28,7 +28,7 @@ import pal.tree.Tree; * * This cache support both euclidean and RF distances. * - * @author Diego Darriba López + * @author Diego Darriba * * @since 3.0 */ diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java b/src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java index 5e510e4..64fc3f1 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java @@ -31,6 +31,7 @@ import java.util.Locale; import java.util.StringTokenizer; import javax.swing.text.Document; +import javax.swing.text.SimpleAttributeSet; import pal.alignment.Alignment; import es.uvigo.darwin.jmodeltest.ModelTest; @@ -263,21 +264,37 @@ public final class Utilities { } } - /** - * printRed - * - * Prints to the main console text in red - */ - - public static void printRed(String text) { + private static void printColor(String text, SimpleAttributeSet color) { if (ModelTest.buildGUI) { try { Document doc = XManager.getInstance().getPane().getDocument(); - doc.insertString(doc.getLength(), text, XManager.redText); + doc.insertString(doc.getLength(), text, color); } catch (javax.swing.text.BadLocationException e) { + System.err.println("Bad Location Exception"); } + } else { + System.out.print(text); } } + + /** + * printRed + * + * Prints to the main console text in red + */ + public static void printRed(String text) { + printColor(text, XManager.redText); + } + + /** + * printBlue + * + * Prints to the main console text in blue + */ + + public static void printBlue(String text) { + printColor(text, XManager.blueText); + } /****************** * RoundDoubleTo ************************** diff --git a/src/main/resources/CHANGELOG b/src/main/resources/CHANGELOG index a16c616..a2d38d3 100644 --- a/src/main/resources/CHANGELOG +++ b/src/main/resources/CHANGELOG @@ -1,3 +1,10 @@ +15 Jan 2016 Version 2.1.9 Revision 20160115 + + * Added automatic search for PhyML binary in /usr/bin + * Removed non-ASCII characters + * Disable logging if writing is not possible + * Merge GUI images into jarfile + 20 Oct 2015 Version 2.1.8 Revision 20151020 * Removed ReadSeq dependency diff --git a/src/main/resources/README b/src/main/resources/README index b2c18ff..1d4fd02 100644 --- a/src/main/resources/README +++ b/src/main/resources/README @@ -1,5 +1,5 @@ ----------------------------------------------------------------------------- -jModelTest 2.1.8 Readme - Oct/20/2015 +jModelTest 2.1.9 Readme - Jan/15/2016 Diego Darriba ([email protected]) Guillermo L. Taboada ([email protected]) diff --git a/src/main/resources/conf/jmodeltest.conf b/src/main/resources/conf/jmodeltest.conf index d55ee37..8368c7d 100644 --- a/src/main/resources/conf/jmodeltest.conf +++ b/src/main/resources/conf/jmodeltest.conf @@ -39,9 +39,10 @@ log-dir = log # # # Environment variables in curly brackets can be used # # e.g., ${HOME} or ${PHYML_HOME} # +# # ########################################################## global-phyml-exe = false -exe-dir = exe/phyml +exe-dir = exe/phyml ########################################################## # # @@ -58,4 +59,4 @@ exe-dir = exe/phyml ########################################################## gamma-threads = 4 inv-threads = 2 -uniform-threads = 1 +uniform-threads = 1 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/jmodeltest.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
