本文整理汇总了Java中beast.core.Logger类的典型用法代码示例。如果您正苦于以下问题：Java Logger类的具体用法？Java Logger怎么用？Java Logger使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
Logger类属于beast.core包，在下文中一共展示了Logger类的11个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: testScaleWithInt
import beast.core.Logger; //导入依赖的package包/类
@Test
public void testScaleWithInt() throws Exception {
Randomizer.setSeed(1);
XMLParser parser = new XMLParser();
beast.core.Runnable runnable = parser.parseFile(
new File("test/epiinf/xmltests/ScaleWithIntTest.xml"));
Logger.FILE_MODE = Logger.LogFileMode.overwrite;
runnable.run();
List<Expectation> expectations = new ArrayList<>();
expectations.add(new Expectation("x1", 0.5, 0.01));
expectations.add(new Expectation("y1", 0.5, 0.01));
expectations.add(new Expectation("y2", 0.5, 0.01));
expectations.add(new Expectation("y3", 0.5, 0.01));
expectations.add(new Expectation("n", 50.0, 1.0));
LogAnalyser logAnalyser = new LogAnalyser("ScaleWithIntTest.log", expectations);
try {
for (Expectation expectation : expectations) {
assertTrue(expectation.isValid());
assertTrue(expectation.isPassed());
}
} catch (Exception e) {
throw e;
} finally {
Files.deleteIfExists(Paths.get("ScaleWithIntTest.xml.state"));
Files.deleteIfExists(Paths.get("ScaleWithIntTest.log"));
}
}
开发者ID:tgvaughan，项目名称:EpiInf，代码行数:33，代码来源:OperatorTests.java
示例2: createDistribution
import beast.core.Logger; //导入依赖的package包/类
@Override
public List<Distribution> createDistribution(BeautiDoc doc) {
MRCAPrior prior = new MRCAPrior();
try {
List<Tree> trees = new ArrayList<>();
getDoc().scrubAll(true, false);
State state = (State) doc.pluginmap.get("state");
for (StateNode node : state.stateNodeInput.get()) {
if (node instanceof Tree) { // && ((Tree) node).m_initial.get() != null) {
trees.add((Tree) node);
}
}
int treeIndex = 0;
if (trees.size() > 1) {
String[] treeIDs = new String[trees.size()];
for (int j = 0; j < treeIDs.length; j++) {
treeIDs[j] = trees.get(j).getID();
}
treeIndex = JOptionPane.showOptionDialog(null, "Select a tree", "MRCA selector",
JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null,
treeIDs, trees.get(0));
}
if (treeIndex < 0) {
return null;
}
prior.treeInput.setValue(trees.get(treeIndex), prior);
TaxonSet taxonSet = new TaxonSet();
TaxonSetDialog dlg = new TaxonSetDialog(taxonSet, getTaxonCandidates(prior), doc);
if (!dlg.showDialog() || dlg.taxonSet.getID() == null || dlg.taxonSet.getID().trim().equals("")) {
return null;
}
taxonSet = dlg.taxonSet;
if (taxonSet.taxonsetInput.get().size() == 0) {
JOptionPane.showMessageDialog(doc.beauti, "At least one taxon should be included in the taxon set",
"Error specifying taxon set", JOptionPane.ERROR_MESSAGE);
return null;
}
int i = 1;
String id = taxonSet.getID();
while (doc.pluginmap.containsKey(taxonSet.getID()) && doc.pluginmap.get(taxonSet.getID()) != taxonSet) {
taxonSet.setID(id + i);
i++;
}
BEASTObjectPanel.addPluginToMap(taxonSet, doc);
prior.taxonsetInput.setValue(taxonSet, prior);
prior.setID(taxonSet.getID() + ".prior");
// this sets up the type
prior.distInput.setValue(new OneOnX(), prior);
// this removes the parametric distribution
prior.distInput.setValue(null, prior);
Logger logger = (Logger) doc.pluginmap.get("tracelog");
logger.loggersInput.setValue(prior, logger);
} catch (Exception e) {
// TODO: handle exception
}
List<Distribution> selectedPlugins = new ArrayList<>();
selectedPlugins.add(prior);
g_collapsedIDs.add(prior.getID());
return selectedPlugins;
}
开发者ID:CompEvol，项目名称:beast2，代码行数:64，代码来源:PriorListInputEditor.java
示例3: analyse
import beast.core.Logger; //导入依赖的package包/类
public void analyse(int index_XML) throws Exception {
// for (int i = 0; i < xmls.length; i++) {
// if (giveExpectations(i).size() > 0) {
Randomizer.setSeed(SEED);
Logger.FILE_MODE = Logger.LogFileMode.overwrite;
long beagleFlags = BeagleFlag.PROCESSOR_CPU.getMask() | BeagleFlag.VECTOR_SSE.getMask();
System.setProperty("beagle.preferred.flags", Long.toString(beagleFlags));
String fileName = dirName + xmls[index_XML];
System.out.println("Processing " + fileName);
XMLParser parser = new XMLParser();
beast.core.Runnable runable = parser.parseFile(new File(fileName));
runable.setStateFile("tmp.state", false);
// runable.setInputValue("preBurnin", 0);
// runable.setInputValue("chainLength", 1000);
runable.run();
String logFile = logDir + testFile + (useSeed ? SEED : "") + ".log";
System.out.println("\nAnalysing log " + logFile);
LogAnalyser logAnalyser = new LogAnalyser(logFile, giveExpectations(index_XML)); // burnIn = 0.1 * maxState
for (Expectation expectation : logAnalyser.m_pExpectations.get()) {
Assert.assertTrue(xmls[index_XML] + ": Expected " + expectation.traceName.get() + " delta mean: "
+ expectation.expValue.get() + " - " + expectation.getTraceStatistics().getMean()
+ " <= delta stdErr: 2*(" + expectation.getStdError() + " + "
+ expectation.getTraceStatistics().getStdErrorOfMean() + ")", expectation.isPassed());
if (checkESS)
Assert.assertTrue(xmls[index_XML] + ": has very low effective sample sizes (ESS) "
+ expectation.getTraceStatistics().getESS(), expectation.isValid());
}
System.out.println("\nSucceed " + fileName);
System.out.println("\n***************************************\n");
// }
// }
}
开发者ID:CompEvol，项目名称:beast2，代码行数:41，代码来源:TestFramework.java
示例4: assertTraceLogEqual
import beast.core.Logger; //导入依赖的package包/类
void assertTraceLogEqual(String... ids) {
System.err.println("assertTraceLogEqual");
Logger logger = (Logger) doc.pluginmap.get("tracelog");
List<BEASTObject> logs = logger.loggersInput.get();
asserListsEqual(logs, ids);
}
开发者ID:CompEvol，项目名称:beast2，代码行数:7，代码来源:BeautiBase.java
示例5: testFileLog
import beast.core.Logger; //导入依赖的package包/类
@Test
public void testFileLog() throws Exception {
logger = new Logger();
logger.initByName("fileName", "beast.log", "log", new RealParameter(new Double[]{0.3, 0.7}));
File f_log = new File(logger.fileNameInput.get());
if (f_log.exists()) {
boolean log_deleted = f_log.delete();
System.out.println("Delete log : " + f_log.getAbsolutePath() + " for testFileLog.");
}
logger.init();
assertTrue("beast.log created successfully", f_log.exists());
// rI >= 0
int rI = new Random().nextInt(10000000);
logger.log(-1);
logger.log(rI);
logger.close();
//TODO cannot get "closing" status from PrintStream
// assertNull("m_out is beast.log after close", logger.getM_out());
BufferedReader in = new BufferedReader(new FileReader(f_log));
// column names
String line = in.readLine();
// 1st sample
String sample1 = in.readLine();
String[] sp = sample1.split("\t", -1);
assertFalse("check beast.log -1 not logged", sp[0].equals("-1"));
assertEquals("check beast.log 1st sample", Integer.toString(rI), sp[0]);
}
开发者ID:CompEvol，项目名称:beast2，代码行数:32，代码来源:LoggerTest.java
示例6: testScreenLog
import beast.core.Logger; //导入依赖的package包/类
@Test
public void testScreenLog() throws Exception {
logger = new Logger();
logger.initByName("fileName", "", "log", new RealParameter(new Double[]{0.3, 0.7}));
logger.init();
assertTrue("m_out is System.out", logger.getM_out() == System.out);
logger.log(1);
//TODO cannot extract content
// close all file, except stdout
logger.close();
assertTrue("m_out is still System.out after close", logger.getM_out() == System.out);
}
开发者ID:CompEvol，项目名称:beast2，代码行数:16，代码来源:LoggerTest.java
示例7: testGeomRandomWalk
import beast.core.Logger; //导入依赖的package包/类
@Test
public void testGeomRandomWalk() throws Exception {
Randomizer.setSeed(1);
XMLParser parser = new XMLParser();
beast.core.Runnable runnable = parser.parseFile(
new File("test/epiinf/xmltests/GeomRandomWalkTest.xml"));
Logger.FILE_MODE = Logger.LogFileMode.overwrite;
runnable.run();
List<Expectation> expectations = new ArrayList<>();
expectations.add(new Expectation("n", 50.0, 1.0));
LogAnalyser logAnalyser = new LogAnalyser("GeomRandomWalkTest.log", expectations);
try {
for (Expectation expectation : expectations) {
assertTrue(expectation.isValid());
assertTrue(expectation.isPassed());
}
} catch (Exception e) {
throw e;
} finally {
Files.deleteIfExists(Paths.get("GeomRandomWalkTest.xml.state"));
Files.deleteIfExists(Paths.get("GeomRandomWalkTest.log"));
}
}
开发者ID:tgvaughan，项目名称:EpiInf，代码行数:29，代码来源:OperatorTests.java
示例8: baseType
import beast.core.Logger; //导入依赖的package包/类
@Override
public Class<?> baseType() {
return Logger.class;
}
开发者ID:CompEvol，项目名称:beast2，代码行数:5，代码来源:LoggerListInputEditor.java
示例9: addSingleItem
import beast.core.Logger; //导入依赖的package包/类
@Override
protected void addSingleItem(BEASTInterface beastObject) {
currentLogger = (Logger) beastObject;
super.addSingleItem(beastObject);
}
开发者ID:CompEvol，项目名称:beast2，代码行数:6，代码来源:LoggerListInputEditor.java
示例10: traceLogAsString
import beast.core.Logger; //导入依赖的package包/类
String traceLogAsString() {
Logger logger = (Logger) doc.pluginmap.get("tracelog");
List<BEASTObject> logs = logger.loggersInput.get();
return "assertTraceLogEqual" + pluginListAsString(logs);
}
开发者ID:CompEvol，项目名称:beast2，代码行数:6，代码来源:BeautiBase.java
示例11: setUp
import beast.core.Logger; //导入依赖的package包/类
@Before
public void setUp() throws Exception {
logger = new Logger();
}
开发者ID:CompEvol，项目名称:beast2，代码行数:5，代码来源:LoggerTest.java
注：本文中的beast.core.Logger类示例整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
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