purged CE

husonlab · Apr 11, 2024 · a7501ab · a7501ab
1 parent ac27f37
commit a7501ab
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diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,7 @@ out/
 !**/src/test/**/out/
 
 .idea
-splitstreeCE.iml
+*.iml
 
 ### Eclipse ###
 .apt_generated

diff --git a/installer/splitstree6.install4j b/installer/splitstree6.install4j
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<install4j version="10.0.6" transformSequenceNumber="10">
-  <directoryPresets config="../target/SplitsTreeApp-1.0.0-SNAPSHOT.jar" />
-  <application name="SplitsTreeApp" applicationId="5610-7746-7010-9445" mediaDir="../../../builds" shortName="SplitsTreeApp" publisher="Daniel H. Huson and David Bryant" publisherWeb="https://www.splitstree.org" version="0.0.0_beta" allPathsRelative="true" macVolumeId="b8c0a1154e563a9a" javaMinVersion="16">
+<install4j version="10.0.7" transformSequenceNumber="10">
+  <directoryPresets config="../target/SplitsTree-1.0.0-SNAPSHOT.jar" />
+  <application name="SplitsTree" applicationId="5610-7746-7010-9445" mediaDir="../../../builds" shortName="SplitsTree" publisher="Daniel H. Huson and David Bryant" publisherWeb="http://splitstree.husonlab.org" version="6.0.0" allPathsRelative="true" macVolumeId="b8c0a1154e563a9a" javaMinVersion="16">
     <variables>
       <variable name="renderingVMOption" />
     </variables>
@@ -15,7 +15,7 @@
         <entry>install4j*</entry>
       </macSearchedJars>
     </codeSigning>
-    <jreBundles jdkProviderId="Liberica" release="20/20.0.2+10">
+    <jreBundles jdkProviderId="Liberica" release="22/22+37">
       <modules />
     </jreBundles>
   </application>
@@ -35,7 +35,7 @@
           <entry location="install4j-runtime-10.0.5.jar" />
         </exclude>
       </dirEntry>
-      <fileEntry mountPoint="1691242167" file="../target/SplitsTreeApp-1.0.0-SNAPSHOT.jar" />
+      <fileEntry mountPoint="1691242167" file="../target/SplitsTree-1.0.0-SNAPSHOT.jar" />
       <fileEntry mountPoint="1691243203" file="../target/dependency/install4j-runtime-10.0.5.jar" />
       <dirEntry mountPoint="1691242153" file="../examples" subDirectory="examples" />
       <fileEntry mountPoint="1691243205" file="../tools/genome-context" fileMode="755" overrideFileMode="true" />
@@ -51,7 +51,7 @@
       <fileEntry mountPoint="675425072" file="../src/main/resources/NOTICE.txt" />
     </entries>
     <components>
-      <component name="SplitsTreeApp" id="1691242194" changeable="false">
+      <component name="SplitsTree" id="1691242194" changeable="false">
         <description>The SplitsTree App.</description>
         <include>
           <entry location="jars" />
@@ -60,7 +60,7 @@
           <entry location="Licenses" />
           <entry location="LICENSE.txt" />
           <entry location="NOTICE.txt" />
-          <entry location="SplitsTreeApp" fileType="launcher" />
+          <entry location="SplitsTree" fileType="launcher" />
         </include>
       </component>
       <component name="Examples" id="1691243204">
@@ -74,9 +74,9 @@
     </components>
   </files>
   <launchers>
-    <launcher name="SplitsTreeApp" id="1691242142" menuName="SplitsTree App ">
-      <executable name="SplitsTreeApp" iconSet="true" redirectStdout="true" executableMode="gui" singleInstance="true" checkConsoleParameter="true" dpiAware="false">
-        <versionInfo include="true" fileDescription="SplitsTree app - analysis of phylogenetic trees and networks" legalCopyright="Copyright (C) 2024 ${compiler:sys.publisher}" internalName="SplitsTreeApp" />
+    <launcher name="SplitsTree" id="1691242142" menuName="SplitsTree ">
+      <executable name="SplitsTree" iconSet="true" redirectStdout="true" executableMode="gui" singleInstance="true" checkConsoleParameter="true" dpiAware="false">
+        <versionInfo include="true" fileDescription="SplitsTree App - analysis of phylogenetic trees and networks" legalCopyright="Copyright (C) 2024 ${compiler:sys.publisher}" internalName="SplitsTree" />
       </executable>
       <java mainClass="splitstreesix/splitstree6.main.SplitsTree6" mainMode="module" vmParameters="-server -Duser.language=en -Duser.region=US ${compiler:renderingVMOption}">
         <modulePath>
@@ -1158,8 +1158,8 @@ return true;</property>
         <variable name="renderingVMOption" value="-Dprism.forceGPU=true" />
       </variables>
     </unixInstaller>
-    <macosFolder name="Mac OS X Folder" id="1691242165" installDir="SplitsTreeApp" overridePrincipalLanguage="true" architecture="universal" compressDmg="true" signLaunchers="true" />
-    <windows name="Windows64bit" id="1691242288" installDir="SplitsTreeApp" overridePrincipalLanguage="true" architecture="64">
+    <macosFolder name="Mac OS X Folder" id="1691242165" installDir="SplitsTree" overridePrincipalLanguage="true" architecture="universal" compressDmg="true" signLaunchers="true" />
+    <windows name="Windows64bit" id="1691242288" installDir="SplitsTree" overridePrincipalLanguage="true" architecture="64">
       <overriddenPrincipalLanguage id="409" />
       <exclude>
         <entry location="tools" />

diff --git a/pom.xml b/pom.xml
@@ -24,10 +24,10 @@
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>org.husonlab</groupId>
-    <artifactId>SplitsTreeCE</artifactId>
+    <artifactId>SplitsTree</artifactId>
     <version>1.0.0-SNAPSHOT</version>
 
-    <name>SplitsTreeCE</name>
+    <name>SplitsTree</name>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -131,7 +131,7 @@
                     <mainClass>${main.class}</mainClass>
                 </configuration>
             </plugin>
-            <!-->
+
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>license-maven-plugin</artifactId>
@@ -145,7 +145,7 @@
                     </execution>
                 </executions>
             </plugin>
-            </!-->
+
             <!-->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>

diff --git a/src/main/java/splitstree6/dialog/AskToDiscardChanges.java b/src/main/java/splitstree6/dialog/AskToDiscardChanges.java
@@ -24,6 +24,7 @@
 import javafx.scene.control.ButtonType;
 import javafx.stage.Modality;
 import javafx.stage.Stage;
+import splitstree6.main.Version;
 
 /**
  * ask whether to discard changes
@@ -42,7 +43,7 @@ public static boolean apply(Stage stage, String message) {
 		alert.initModality(Modality.APPLICATION_MODAL);
 		alert.initOwner(stage);
 
-		alert.setTitle("Confirm " + message + " of Changes - SplitsTreeCE");
+		alert.setTitle("Confirm " + message + " of Changes - " + Version.NAME);
 		alert.setHeaderText("There are unsaved changes.");
 		alert.setContentText(message + " existing changes?");
 

diff --git a/src/main/java/splitstree6/io/writers/view/GMLWriter.java b/src/main/java/splitstree6/io/writers/view/GMLWriter.java
@@ -64,7 +64,7 @@ else if (view instanceof SplitsView splitsView) {
 					case "weight" -> StringUtils.removeTrailingZerosAfterDot("%.8f", graph.getWeight(e));
 					default -> null;
 				};
-				var comment = "Exported from SplitsTreeCE: %,d nodes, %,d edges, %,d splits".formatted(graph.getNumberOfNodes(), graph.getNumberOfEdges(), splitsView.getSplitsBlock().getNsplits());
+				var comment = "Exported from SplitsTree: %,d nodes, %,d edges, %,d splits".formatted(graph.getNumberOfNodes(), graph.getNumberOfEdges(), splitsView.getSplitsBlock().getNsplits());
 				var graphLabel = (graph.getName() != null ? graph.getName() : splitsView.getName());
 				GraphGML.writeGML(graph, comment, graphLabel, false, 1, w,
 						labelNodes, labelNodeValue, labelEdges, labelEdgeValue);
@@ -88,7 +88,7 @@ else if (view instanceof SplitsView splitsView) {
 					case "sites" -> networkView.getNetworkBlock().getEdgeData(e).get("sites");
 					default -> null;
 				};
-				var comment = "Exported from SplitsTreeCE: %,d nodes, %,d edges,".formatted(graph.getNumberOfNodes(), graph.getNumberOfEdges());
+				var comment = "Exported from SplitsTree: %,d nodes, %,d edges,".formatted(graph.getNumberOfNodes(), graph.getNumberOfEdges());
 				var graphLabel = (graph.getName() != null ? graph.getName() : networkView.getName());
 				GraphGML.writeGML(graph, comment, graphLabel, false, 1, w,
 						labelNodes, labelNodeValue, labelEdges, labelEdgeValue);

diff --git a/src/main/java/splitstree6/main/Version.java b/src/main/java/splitstree6/main/Version.java
@@ -25,7 +25,7 @@
  */
 public class Version {
 	static public final String NAME = "SplitsTree App";
-	static public final String SHORT_DESCRIPTION = "SplitsTree App (version 6.3.3, built 11 Apr 2024)";
+	static public final String SHORT_DESCRIPTION = "SplitsTree App (version 6.3.4, built 11 Apr 2024)";
 	static public final String VERSION = "6.0.0";
 
 }
diff --git a/src/main/resources/LICENSE.txt b/src/main/resources/LICENSE.txt
@@ -1,4 +1,4 @@
-SplitsTreeCE https://github.com/husonlab/splitstree6
+SplitsTree https://github.com/husonlab/splitstree6
 
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007

diff --git a/src/main/resources/NOTICE.txt b/src/main/resources/NOTICE.txt
@@ -1,2 +1,2 @@
-SplitsTreeCE - Phylogenetic trees and networks - https://github.com/husonlab/splitstree6
+SplitsTree - Phylogenetic trees and networks - https://github.com/husonlab/splitstree6
 Daniel Huson and David Bryant, since 2020
diff --git a/src/main/resources/splitstree6/dialog/importdialog/ImportDialog.fxml b/src/main/resources/splitstree6/dialog/importdialog/ImportDialog.fxml
@@ -48,7 +48,7 @@
         </HBox>
     </bottom>
     <top>
-        <Label text="Import data into SplitsTreeCE" BorderPane.alignment="CENTER">
+        <Label text="Import data into SplitsTree" BorderPane.alignment="CENTER">
             <BorderPane.margin>
                 <Insets bottom="5.0" left="5.0" right="5.0" top="5.0"/>
             </BorderPane.margin>

diff --git a/tools/bfilter-tool b/tools/bfilter-tool
@@ -29,7 +29,7 @@ jars2_dir="$bin_dir/../jars2"
 jre_dir=${installer:sys.preferredJre}
 
 java=$jre_dir/bin/java
-vmOptions=$(grep "^-" "$bin_dir/../SplitsTreeCE.vmoptions")
+vmOptions=$(grep "^-" "$bin_dir/../SplitsTree.vmoptions")
 modulepath="$jars_dir:$jars2_dir"
 
 java_flags="-server -Duser.language=en -Duser.region=US $vmOptions"

diff --git a/tools/genetree-viewer b/tools/genetree-viewer
@@ -30,7 +30,7 @@ jars2_dir="$bin_dir/../jars2"
 jre_dir=${installer:sys.preferredJre}
 
 java=$jre_dir/bin/java
-vmOptions=$(grep "^-" $bin_dir/../SplitsTreeCE.vmoptions)
+vmOptions=$(grep "^-" $bin_dir/../SplitsTree.vmoptions)
 modulepath="$jars_dir:$jars2_dir"
 
 java_flags="-server -Duser.language=en -Duser.region=US $vmOptions"

diff --git a/tools/genome-context b/tools/genome-context
@@ -30,7 +30,7 @@ jars2_dir="$bin_dir/../jars2"
 jre_dir=${installer:sys.preferredJre}
 
 java=$jre_dir/bin/java
-vmOptions=$(grep "^-" $bin_dir/../SplitsTreeCE.vmoptions)
+vmOptions=$(grep "^-" $bin_dir/../SplitsTree.vmoptions)
 modulepath="$jars_dir:$jars2_dir"
 
 java_flags="-server -Duser.language=en -Duser.region=US $vmOptions"

diff --git a/tools/mash-sketches b/tools/mash-sketches
@@ -30,7 +30,7 @@ jars2_dir="$bin_dir/../jars2"
 jre_dir=${installer:sys.preferredJre}
 
 java=$jre_dir/bin/java
-vmOptions=$(grep "^-" $bin_dir/../SplitsTreeCE.vmoptions)
+vmOptions=$(grep "^-" $bin_dir/../SplitsTree.vmoptions)
 modulepath="$jars_dir:$jars2_dir"
 
 java_flags="-server -Duser.language=en -Duser.region=US $vmOptions"

diff --git a/tools/workflow-export b/tools/workflow-export
@@ -31,7 +31,7 @@ jars2_dir="$bin_dir/../jars2"
 jre_dir=${installer:sys.preferredJre}
 
 java=$jre_dir/bin/java
-vmOptions=$(grep "^-" $bin_dir/../SplitsTreeCE.vmoptions)
+vmOptions=$(grep "^-" $bin_dir/../SplitsTree.vmoptions)
 modulepath="$jars_dir:$jars2_dir"
 
 java_flags="-server -Duser.language=en -Duser.region=US $vmOptions"

diff --git a/tools/workflow-run b/tools/workflow-run
@@ -30,7 +30,7 @@ jars2_dir="$bin_dir/../jars2"
 jre_dir=${installer:sys.preferredJre}
 
 java=$jre_dir/bin/java
-vmOptions=$(grep "^-" $bin_dir/../SplitsTreeCE.vmoptions)
+vmOptions=$(grep "^-" $bin_dir/../SplitsTree.vmoptions)
 modulepath="$jars_dir:$jars2_dir"
 
 java_flags="-server -Duser.language=en -Duser.region=US $vmOptions"