Move newtreeannotator to treeannotator (the default)

src/dr/app/tools/newtreeannotator/AnnotationAction.java → src/dr/app/tools/treeannotator/AnnotationAction.java

@@ -25,17 +25,14 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.tree.MutableTree;
 import dr.evolution.tree.NodeRef;
 import dr.evolution.tree.Tree;
-import dr.evolution.util.TaxonList;
 import dr.geo.contouring.ContourMaker;
 import dr.geo.contouring.ContourPath;
 import dr.geo.contouring.ContourWithSynder;
-import dr.inference.trace.TraceCorrelation;
-import dr.inference.trace.TraceType;
 import dr.stats.DiscreteStatistics;
 import dr.util.HeapSort;
 

src/dr/app/tools/newtreeannotator/BEASTTreesImporter.java → src/dr/app/tools/treeannotator/BEASTTreesImporter.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.io.Importer;
 import dr.evolution.io.TreeImporter;

src/dr/app/tools/newtreeannotator/BiClade.java → src/dr/app/tools/treeannotator/BiClade.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.util.Taxon;
 import dr.util.Pair;

src/dr/app/tools/newtreeannotator/CAHeights.java → src/dr/app/tools/treeannotator/CAHeights.java

@@ -1,12 +1,35 @@
-package dr.app.tools.newtreeannotator;
+/*
+ * CAHeights.java
+ *
+ * Copyright © 2002-2024 the BEAST Development Team
+ * http://beast.community/about
+ *
+ * This file is part of BEAST.
+ * See the NOTICE file distributed with this work for additional
+ * information regarding copyright ownership and licensing.
+ *
+ * BEAST is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ *  BEAST is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with BEAST; if not, write to the
+ * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ * Boston, MA  02110-1301  USA
+ *
+ */
+
+package dr.app.tools.treeannotator;
 
 import dr.evolution.io.Importer;
-import dr.evolution.io.NexusImporter;
 import dr.evolution.tree.MutableTree;
-import dr.evolution.tree.NodeRef;
-import dr.evolution.tree.Tree;
 
-import java.io.FileReader;
 import java.io.IOException;
 import java.util.BitSet;
 

src/dr/app/tools/newtreeannotator/Clade.java → src/dr/app/tools/treeannotator/Clade.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.util.Taxon;
 

src/dr/app/tools/newtreeannotator/CladeAction.java → src/dr/app/tools/treeannotator/CladeAction.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.tree.NodeRef;
 import dr.evolution.tree.Tree;

src/dr/app/tools/newtreeannotator/CladeSystem.java → src/dr/app/tools/treeannotator/CladeSystem.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.tree.NodeRef;
 import dr.evolution.tree.Tree;

src/dr/app/tools/newtreeannotator/CollectionAction.java → src/dr/app/tools/treeannotator/CollectionAction.java

@@ -25,14 +25,13 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.tree.NodeRef;
 import dr.evolution.tree.Tree;
 
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.Iterator;
 import java.util.Set;
 
 class CollectionAction implements CladeAction {

src/dr/app/tools/newtreeannotator/FastClade.java → src/dr/app/tools/treeannotator/FastClade.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.util.Taxon;
 import dr.util.Pair;

src/dr/app/tools/newtreeannotator/HIPSTRTreeBuilder.java → src/dr/app/tools/treeannotator/HIPSTRTreeBuilder.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.evolution.tree.*;
 import dr.evolution.util.Taxon;

src/dr/app/tools/newtreeannotator/RunLengthBitSet.java → src/dr/app/tools/treeannotator/RunLengthBitSet.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import java.util.Arrays;
 import java.util.BitSet;

src/dr/app/tools/newtreeannotator/TreeAnnotator.java → src/dr/app/tools/treeannotator/TreeAnnotator.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.app.beast.BeastVersion;
 import dr.app.tools.BaseTreeTool;

src/dr/app/tools/newtreeannotator/TreeAnnotatorDialog.java → src/dr/app/tools/treeannotator/TreeAnnotatorDialog.java

@@ -25,7 +25,7 @@
  *
  */
 
-package dr.app.tools.newtreeannotator;
+package dr.app.tools.treeannotator;
 
 import dr.app.gui.FileDrop;
 import dr.app.gui.components.RealNumberField;