From a7501aba69130c72032597a806fdaeb0a3435a1c Mon Sep 17 00:00:00 2001 From: Daniel Date: Thu, 11 Apr 2024 17:15:17 +0200 Subject: [PATCH] purged CE --- .gitignore | 2 +- installer/splitstree6.install4j | 24 +++++++++---------- pom.xml | 8 +++---- .../dialog/AskToDiscardChanges.java | 3 ++- .../io/writers/view/GMLWriter.java | 4 ++-- src/main/java/splitstree6/main/Version.java | 2 +- src/main/resources/LICENSE.txt | 2 +- src/main/resources/NOTICE.txt | 2 +- .../dialog/importdialog/ImportDialog.fxml | 2 +- tools/bfilter-tool | 2 +- tools/genetree-viewer | 2 +- tools/genome-context | 2 +- tools/mash-sketches | 2 +- tools/workflow-export | 2 +- tools/workflow-run | 2 +- 15 files changed, 31 insertions(+), 30 deletions(-) diff --git a/.gitignore b/.gitignore index cde9b1e9..2f0517df 100644 --- 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 index 44b0708e..dc56d6c8 100644 --- a/installer/splitstree6.install4j +++ b/installer/splitstree6.install4j @@ -1,7 +1,7 @@ - - - + + + @@ -15,7 +15,7 @@ install4j* - + @@ -35,7 +35,7 @@ - + @@ -51,7 +51,7 @@ - + The SplitsTree App. @@ -60,7 +60,7 @@ - + @@ -74,9 +74,9 @@ - - - + + + @@ -1158,8 +1158,8 @@ return true; - - + + diff --git a/pom.xml b/pom.xml index fb8a38ea..bca2d930 100644 --- a/pom.xml +++ b/pom.xml @@ -24,10 +24,10 @@ 4.0.0 org.husonlab - SplitsTreeCE + SplitsTree 1.0.0-SNAPSHOT - SplitsTreeCE + SplitsTree UTF-8 @@ -131,7 +131,7 @@ ${main.class} - + org.codehaus.mojo license-maven-plugin @@ -145,7 +145,7 @@ - + org.apache.maven.plugins diff --git a/src/main/java/splitstree6/dialog/AskToDiscardChanges.java b/src/main/java/splitstree6/dialog/AskToDiscardChanges.java index c77acea2..0eef9212 100644 --- 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 index dfe85ef0..dcba3cfb 100644 --- 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 index 1a6129a8..f01435c0 100755 --- 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 index 00bb5cf8..5a4650e0 100644 --- 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 index c57d367a..30c20db8 100644 --- 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 index 36a0affc..0d575a69 100644 --- a/src/main/resources/splitstree6/dialog/importdialog/ImportDialog.fxml +++ b/src/main/resources/splitstree6/dialog/importdialog/ImportDialog.fxml @@ -48,7 +48,7 @@ -