replaced jloda2 by jloda-core and jloda-fx

Author: dhuson

pom.xml

@@ -42,8 +42,13 @@
     <dependencies>
         <dependency>
             <groupId>org.husonlab</groupId>
-            <artifactId>jloda2</artifactId>
-            <version>2.0.0-SNAPSHOT</version>
+            <artifactId>jloda-core</artifactId>
+            <version>1.0.0-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+            <groupId>org.husonlab</groupId>
+            <artifactId>jloda-fx</artifactId>
+            <version>1.0.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>org.openjfx</groupId>
@@ -87,7 +92,11 @@
             <artifactId>core</artifactId>
             <version>3.5.3</version>
         </dependency>
-
+        <dependency>
+            <groupId>org.fxmisc.richtext</groupId>
+            <artifactId>richtextfx</artifactId>
+            <version>0.11.2</version>
+        </dependency>
         <!--
         <dependency>
                 <groupId>com.github.lejon</groupId>

src/main/java/module-info.java

@@ -1,9 +1,9 @@
 module splitstreesix {
-	requires transitive jloda2;
+	requires transitive jloda_core;
+	requires transitive jloda_fx;
 	requires transitive javafx.controls;
 	requires transitive javafx.graphics;
 	requires transitive javafx.fxml;
-	requires transitive javafx.swing;
 	requires javafx.base;
 
 	requires org.apache.commons.collections4;

src/main/java/splitstree6/algorithms/characters/characters2distances/HammingDistances.java

@@ -21,7 +21,7 @@
 
 import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.SimpleBooleanProperty;
-import jloda.fx.util.ProgramExecutorService;
+import jloda.util.ProgramExecutorService;
 import jloda.util.Single;
 import jloda.util.progress.ProgressListener;
 import splitstree6.algorithms.characters.characters2distances.utils.FixUndefinedDistances;

src/main/java/splitstree6/algorithms/distances/distances2splits/neighbornet/NeighborNetSplitWeights_MultiThreaded.java

@@ -1,8 +1,8 @@
 package splitstree6.algorithms.distances.distances2splits.neighbornet;
 
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.window.NotificationManager;
 import jloda.util.CanceledException;
+import jloda.util.ProgramExecutorService;
 import jloda.util.progress.ProgressListener;
 import splitstree6.splits.ASplit;
 

src/main/java/splitstree6/algorithms/genomes/genome2distances/Mash.java

@@ -20,7 +20,6 @@
 package splitstree6.algorithms.genomes.genome2distances;
 
 import javafx.beans.property.*;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.window.NotificationManager;
 import jloda.kmers.GenomeDistanceType;
 import jloda.kmers.mash.MashDistance;

src/main/java/splitstree6/algorithms/splits/splits2report/ShapleyValues.java

@@ -19,10 +19,10 @@
 
 package splitstree6.algorithms.splits.splits2report;
 
-import jloda.fx.util.ProgramExecutorService;
 import jloda.util.BitSetUtils;
 import jloda.util.ExecuteInParallel;
 import jloda.util.NumberUtils;
+import jloda.util.ProgramExecutorService;
 import jloda.util.progress.ProgressListener;
 import splitstree6.data.SplitsBlock;
 import splitstree6.data.TaxaBlock;

src/main/java/splitstree6/algorithms/splits/splits2splits/BootstrapSplits.java

@@ -20,8 +20,8 @@
 package splitstree6.algorithms.splits.splits2splits;
 
 import javafx.beans.property.*;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.util.Pair;
+import jloda.util.ProgramExecutorService;
 import jloda.util.Single;
 import jloda.util.progress.ProgressListener;
 import jloda.util.progress.ProgressSilent;

src/main/java/splitstree6/algorithms/trees/trees2distances/AverageDistances.java

@@ -19,9 +19,9 @@
 
 package splitstree6.algorithms.trees.trees2distances;
 
-import jloda.fx.util.ProgramExecutorService;
 import jloda.util.CanceledException;
 import jloda.util.NumberUtils;
+import jloda.util.ProgramExecutorService;
 import jloda.util.Single;
 import jloda.util.progress.ProgressListener;
 import jloda.util.progress.ProgressSilent;

src/main/java/splitstree6/algorithms/trees/trees2splits/AntiConsensusNetwork.java

@@ -20,7 +20,6 @@
 package splitstree6.algorithms.trees.trees2splits;
 
 import javafx.beans.property.*;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.window.NotificationManager;
 import jloda.graph.Edge;
 import jloda.graph.Graph;

src/main/java/splitstree6/algorithms/trees/trees2splits/ConsensusSplits.java

@@ -20,7 +20,6 @@
 package splitstree6.algorithms.trees.trees2splits;
 
 import javafx.beans.property.*;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.window.NotificationManager;
 import jloda.util.*;
 import jloda.util.progress.ProgressListener;

src/main/java/splitstree6/algorithms/trees/trees2trees/BootstrapTree.java

@@ -20,15 +20,11 @@
 package splitstree6.algorithms.trees.trees2trees;
 
 import javafx.beans.property.*;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.graph.Edge;
 import jloda.graph.EdgeArray;
 import jloda.graph.Node;
 import jloda.phylo.PhyloTree;
-import jloda.util.BitSetUtils;
-import jloda.util.NumberUtils;
-import jloda.util.Single;
-import jloda.util.StringUtils;
+import jloda.util.*;
 import jloda.util.progress.ProgressListener;
 import jloda.util.progress.ProgressSilent;
 import splitstree6.algorithms.splits.splits2splits.BootstrapSplits;

src/main/java/splitstree6/algorithms/trees/trees2trees/RerootOrReorderTrees.java

@@ -24,7 +24,6 @@
 import javafx.beans.WeakInvalidationListener;
 import javafx.beans.property.ObjectProperty;
 import javafx.beans.property.SimpleObjectProperty;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.window.NotificationManager;
 import jloda.graph.Edge;
 import jloda.graph.Node;

src/main/java/splitstree6/dialog/analyzegenomes/AccessReferenceDatabase.java

@@ -20,7 +20,6 @@
 package splitstree6.dialog.analyzegenomes;
 
 import javafx.collections.ObservableList;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.window.NotificationManager;
 import jloda.graph.Node;
 import jloda.graph.NodeIntArray;

src/main/java/splitstree6/dialog/analyzegenomes/AnalyzeGenomesDialog.java

@@ -26,8 +26,8 @@
 import javafx.scene.Scene;
 import javafx.stage.Stage;
 import jloda.fx.util.ExtendedFXMLLoader;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.util.ProgramProperties;
+import jloda.util.ProgramExecutorService;
 import splitstree6.main.Version;
 
 import java.util.Map;

src/main/java/splitstree6/dialog/analyzegenomes/AnalyzeGenomesPresenter.java

@@ -35,13 +35,11 @@
 import javafx.stage.FileChooser;
 import javafx.stage.Stage;
 import jloda.fx.control.RichTextLabel;
+import jloda.fx.util.ProgramProperties;
 import jloda.fx.util.*;
 import jloda.fx.window.NotificationManager;
 import jloda.seq.FastAFileIterator;
-import jloda.util.FileUtils;
-import jloda.util.IFastAIterator;
-import jloda.util.NumberUtils;
-import jloda.util.StringUtils;
+import jloda.util.*;
 
 import java.io.File;
 import java.io.IOException;

src/main/java/splitstree6/io/FileLoader.java

@@ -20,10 +20,10 @@
 package splitstree6.io;
 
 import javafx.application.Platform;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.util.RecentFilesManager;
 import jloda.fx.window.MainWindowManager;
 import jloda.fx.window.NotificationManager;
+import jloda.util.ProgramExecutorService;
 import splitstree6.dialog.importdialog.ImportDialog;
 import splitstree6.io.nexus.workflow.WorkflowNexusInput;
 import splitstree6.io.readers.ImportManager;

src/main/java/splitstree6/layout/splits/SplitNetworkLayout.java

@@ -37,6 +37,7 @@
 import jloda.fx.selection.SetSelectionModel;
 import jloda.fx.util.DraggableUtils;
 import jloda.fx.util.GeometryUtilsFX;
+import jloda.fx.util.Icebergs;
 import jloda.fx.window.NotificationManager;
 import jloda.graph.Node;
 import jloda.graph.NodeArray;
@@ -56,7 +57,6 @@
 import splitstree6.layout.tree.LayoutUtils;
 import splitstree6.layout.tree.RadialLabelLayout;
 import splitstree6.splits.Compatibility;
-import splitstree6.view.utils.Icebergs;
 
 import java.io.IOException;
 import java.util.ArrayList;

src/main/java/splitstree6/layout/tree/LabeledEdgeShape.java

@@ -23,8 +23,8 @@
 import javafx.scene.Node;
 import javafx.scene.shape.Shape;
 import jloda.fx.control.RichTextLabel;
+import jloda.fx.util.Icebergs;
 import jloda.fx.util.MouseDragToTranslate;
-import splitstree6.view.utils.Icebergs;
 
 import java.util.ArrayList;
 

src/main/java/splitstree6/layout/tree/LabeledNodeShape.java

@@ -23,7 +23,7 @@
 import javafx.scene.Node;
 import javafx.scene.shape.Shape;
 import jloda.fx.control.RichTextLabel;
-import splitstree6.view.utils.Icebergs;
+import jloda.fx.util.Icebergs;
 
 import java.util.ArrayList;
 

src/main/java/splitstree6/main/SplitsTree6.java

@@ -24,7 +24,6 @@
 import javafx.geometry.Point2D;
 import javafx.stage.Stage;
 import jloda.fx.util.ArgsOptions;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.util.ProgramProperties;
 import jloda.fx.util.ResourceManagerFX;
 import jloda.fx.window.MainWindowManager;
@@ -34,6 +33,7 @@
 import jloda.phylo.PhyloTree;
 import jloda.util.Basic;
 import jloda.util.CanceledException;
+import jloda.util.ProgramExecutorService;
 import jloda.util.UsageException;
 import splitstree6.io.FileLoader;
 import splitstree6.window.MainWindow;

src/main/java/splitstree6/qr/QRViewUtils.java

@@ -35,8 +35,8 @@
 import javafx.scene.paint.Color;
 import jloda.fx.util.BasicFX;
 import jloda.fx.util.DraggableLabel;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.util.Basic;
+import jloda.util.ProgramExecutorService;
 import jloda.util.StringUtils;
 import splitstree6.main.SplitsTree6;
 import splitstree6.utils.ClipboardUtils;

src/main/java/splitstree6/tools/ComputeMashSketches.java

@@ -20,7 +20,6 @@
 package splitstree6.tools;
 
 import jloda.fx.util.ArgsOptions;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.kmers.mash.MashSketch;
 import jloda.thirdparty.HexUtils;
 import jloda.util.*;

src/main/java/splitstree6/tools/ExportWorkflow.java

@@ -23,14 +23,10 @@
 import javafx.application.Platform;
 import javafx.stage.Stage;
 import jloda.fx.util.ArgsOptions;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.util.ProgramProperties;
 import jloda.fx.util.ResourceManagerFX;
 import jloda.fx.window.NotificationManager;
-import jloda.util.Basic;
-import jloda.util.FileUtils;
-import jloda.util.IteratorUtils;
-import jloda.util.PeakMemoryUsageMonitor;
+import jloda.util.*;
 import jloda.util.progress.ProgressPercentage;
 import splitstree6.cite.ExtractMethodsText;
 import splitstree6.io.nexus.workflow.WorkflowNexusInput;

src/main/java/splitstree6/tools/GenomeContext.java

@@ -20,7 +20,6 @@
 package splitstree6.tools;
 
 import jloda.fx.util.ArgsOptions;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.kmers.mash.MashDistance;
 import jloda.seq.FastAFileIterator;
 import jloda.util.*;

src/main/java/splitstree6/tools/RunWorkflow.java

@@ -24,7 +24,6 @@
 import javafx.beans.value.ChangeListener;
 import javafx.stage.Stage;
 import jloda.fx.util.ArgsOptions;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.util.ProgramProperties;
 import jloda.fx.util.ResourceManagerFX;
 import jloda.fx.window.NotificationManager;

src/main/java/splitstree6/utils/Stabilizer.java

@@ -1,11 +1,11 @@
 package splitstree6.utils;
 
-import jloda.fx.util.ProgramExecutorService;
 import jloda.graph.algorithms.PQTree;
 import jloda.phylo.PhyloTree;
 import jloda.util.BitSetUtils;
 import jloda.util.ExecuteInParallel;
 import jloda.util.IteratorUtils;
+import jloda.util.ProgramExecutorService;
 import splitstree6.splits.TreesUtils;
 
 import java.util.*;

src/main/java/splitstree6/view/network/NetworkPane.java

@@ -34,9 +34,13 @@
 import javafx.scene.layout.StackPane;
 import jloda.fx.control.RichTextLabel;
 import jloda.fx.selection.SelectionModel;
-import jloda.fx.util.*;
+import jloda.fx.util.AService;
+import jloda.fx.util.BasicFX;
+import jloda.fx.util.GeometryUtilsFX;
+import jloda.fx.util.RunAfterAWhile;
 import jloda.graph.Edge;
 import jloda.graph.Node;
+import jloda.util.ProgramExecutorService;
 import splitstree6.data.NetworkBlock;
 import splitstree6.data.TaxaBlock;
 import splitstree6.data.parts.Taxon;

src/main/java/splitstree6/view/splits/viewer/SplitNetworkPane.java

@@ -36,8 +36,8 @@
 import jloda.fx.util.AService;
 import jloda.fx.util.BasicFX;
 import jloda.fx.util.GeometryUtilsFX;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.graph.Node;
+import jloda.util.ProgramExecutorService;
 import splitstree6.data.SplitsBlock;
 import splitstree6.data.TaxaBlock;
 import splitstree6.data.parts.Taxon;

src/main/java/splitstree6/view/splits/viewer/SplitsViewPresenter.java

@@ -38,12 +38,8 @@
 import jloda.fx.label.EditLabelDialog;
 import jloda.fx.undo.UndoManager;
 import jloda.fx.util.BasicFX;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.fx.util.RunAfterAWhile;
-import jloda.util.BitSetUtils;
-import jloda.util.IteratorUtils;
-import jloda.util.Single;
-import jloda.util.StringUtils;
+import jloda.util.*;
 import splitstree6.algorithms.utils.CharactersUtilities;
 import splitstree6.data.CharactersBlock;
 import splitstree6.data.SplitsBlock;

src/main/java/splitstree6/view/trees/densitree/DensiTreeDrawer.java

@@ -59,7 +59,6 @@
 import splitstree6.main.SplitsTree6;
 import splitstree6.splits.TreesUtils;
 import splitstree6.view.trees.InteractionSetup;
-import splitstree6.view.utils.Icebergs;
 import splitstree6.window.MainWindow;
 
 import java.util.*;

src/main/java/splitstree6/view/trees/treepages/TreePane.java

@@ -36,10 +36,10 @@
 import jloda.fx.selection.SetSelectionModel;
 import jloda.fx.util.AService;
 import jloda.fx.util.BasicFX;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.graph.Edge;
 import jloda.phylo.PhyloTree;
 import jloda.phylo.algorithms.RootedNetworkProperties;
+import jloda.util.ProgramExecutorService;
 import jloda.util.StringUtils;
 import splitstree6.data.TaxaBlock;
 import splitstree6.data.parts.Taxon;

src/main/java/splitstree6/xtra/alts/AltsNonBinary.java

@@ -20,11 +20,11 @@
 package splitstree6.xtra.alts;
 
 import jloda.fx.util.ArgsOptions;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.graph.Node;
 import jloda.phylo.NewickIO;
 import jloda.phylo.PhyloTree;
 import jloda.util.Pair;
+import jloda.util.ProgramExecutorService;
 import jloda.util.UsageException;
 import jloda.util.progress.ProgressListener;
 import jloda.util.progress.ProgressPercentage;

src/main/java/splitstree6/xtra/kernelize/RunKernelize.java

@@ -20,12 +20,12 @@
 package splitstree6.xtra.kernelize;
 
 import jloda.fx.util.ArgsOptions;
-import jloda.fx.util.ProgramExecutorService;
 import jloda.phylo.NewickIO;
 import jloda.phylo.PhyloTree;
 import jloda.phylo.algorithms.ClusterPoppingAlgorithm;
 import jloda.util.BitSetUtils;
 import jloda.util.FileUtils;
+import jloda.util.ProgramExecutorService;
 import jloda.util.UsageException;
 import jloda.util.progress.ProgressListener;
 import jloda.util.progress.ProgressPercentage;