update version nr CompEvol/beast2#1095 and clean up code #6

CompEvol · Mar 20, 2023 · a215adc · a215adc
1 parent 9ae1a0e
commit a215adc
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Showing 6 changed files with 16 additions and 6 deletions.
diff --git a/build.xml b/build.xml
@@ -100,6 +100,7 @@
 		<!-- Compile the java code from ${srcFX} into ${buildFX} /bin -->
 		<javac srcdir="${srcFX}" destdir="${buildFX}" classpathref="classpath" 
 		       fork="true"
+			   encoding="UTF-8"
 		       memoryinitialsize="256m"
 		       memorymaximumsize="1024m"
 			   >

diff --git a/fxtemplates/Standard.xml b/fxtemplates/Standard.xml
@@ -19,7 +19,11 @@
         inputLabelMap='beast.base.inference.MCMC.operator=Operators,
 	        beast.base.inference.MCMC.logger=Loggers,
 			beast.base.evolution.sitemodel.SiteModel.mutationRate =Substitution Rate,
-			beast.base.evolution.speciation.YuleModel.birthDiffRate=Birth Rate'
+			beast.base.evolution.speciation.YuleModel.birthDiffRate=Birth Rate,
+			beast.base.evolution.branchratemodel.UCRelaxedClockModel.clock.rate=Mean clock rate,
+			beast.base.evolution.branchratemodel.StrictClockModel.clock.rate=Mean clock rate,
+			beast.base.evolution.branchratemodel.RandomLocalClockModel.clock.rate=Mean clock rate
+			'
         inlinePlugins ='beast.base.inference.MCMC.distribution,
             beast.base.evolution.sitemodel.SiteModel.substModel,
             beast.base.evolution.tree.coalescent.ExponentialGrowth,

diff --git a/src/beastfx/app/beauti/ThemeProvider.java b/src/beastfx/app/beauti/ThemeProvider.java
@@ -70,9 +70,13 @@ private static void initThemeMap() {
 	abstract public String getThemeName();
 
 
+	static public boolean clear = true;
 	static public boolean loadStyleSheet(Scene scene, String themeFile) {
 		try {
-			scene.getStylesheets().clear();
+			if (clear) {
+				scene.getStylesheets().clear();
+				clear = false;
+			}
 			URL url = ThemeProvider.class.getResource(themeFile);
 			String css = url.toExternalForm();
 			scene.getStylesheets().add(css);
@@ -99,6 +103,7 @@ static public boolean loadStyleSheet(Scene scene) {
 	 * @return true if stylesheet was successfully loaded
 	 */
 	abstract public boolean loadMyStyleSheet(Scene scene);
+
 
 
 

diff --git a/src/beastfx/app/tools/Application.java b/src/beastfx/app/tools/Application.java
@@ -111,7 +111,7 @@ public Application(beast.base.inference.Runnable analyser, String title, int pre
 	}
 
 	public Application(beast.base.inference.Runnable analyser, String[] suppressedInputs, String title, String[] args) throws Exception {
-		this(analyser, null, title, prefDialogWidth, prefDialogHeight, args);
+		this(analyser, suppressedInputs, title, prefDialogWidth, prefDialogHeight, args);
 	}
 
 	public Application(beast.base.inference.Runnable analyser, String[] suppressedInputs, String title, int prefDialogWidth, int prefDialogHeight, String[] args) throws Exception {

diff --git a/src/beastfx/app/util/FXUtils.java b/src/beastfx/app/util/FXUtils.java
@@ -90,7 +90,7 @@ public static File[] getFile(String message, boolean isLoadNotSave, File default
 		if (extensions != null) {
 			for (String extension : extensions) {
 				if (extension.equals("")) {
-					extension = "*.*";
+					extension = "*";
 				}
 				fileChooser.getExtensionFilters().add(
 						new FileChooser.ExtensionFilter(extension, "*."+extension)

diff --git a/version.xml b/version.xml
@@ -1,5 +1,5 @@
-<package name='BEAST.app' version='2.7.3'>
-	<depends on='BEAST.base' atleast='2.7.3' atmost="2.7.9"/>
+<package name='BEAST.app' version='2.7.4'>
+	<depends on='BEAST.base' atleast='2.7.4' atmost="2.7.9"/>
 
 			<service type="beastfx.app.beauti.ThemeProvider">
 				<provider classname="beastfx.app.beauti.theme.Default"/>