diff --git a/src/dr/app/tools/newtreeannotator/AnnotationAction.java b/src/dr/app/tools/treeannotator/AnnotationAction.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/AnnotationAction.java rename to src/dr/app/tools/treeannotator/AnnotationAction.java index d802ee68e6..e6b70c412e 100644 --- a/src/dr/app/tools/newtreeannotator/AnnotationAction.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/BEASTTreesImporter.java b/src/dr/app/tools/treeannotator/BEASTTreesImporter.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/BEASTTreesImporter.java rename to src/dr/app/tools/treeannotator/BEASTTreesImporter.java index 25bd1406b0..55d0f41103 100644 --- a/src/dr/app/tools/newtreeannotator/BEASTTreesImporter.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/BiClade.java b/src/dr/app/tools/treeannotator/BiClade.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/BiClade.java rename to src/dr/app/tools/treeannotator/BiClade.java index ae2933f8c2..0690433ad2 100644 --- a/src/dr/app/tools/newtreeannotator/BiClade.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/CAHeights.java b/src/dr/app/tools/treeannotator/CAHeights.java similarity index 79% rename from src/dr/app/tools/newtreeannotator/CAHeights.java rename to src/dr/app/tools/treeannotator/CAHeights.java index 6b928ca828..799f18b379 100644 --- a/src/dr/app/tools/newtreeannotator/CAHeights.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/Clade.java b/src/dr/app/tools/treeannotator/Clade.java similarity index 97% rename from src/dr/app/tools/newtreeannotator/Clade.java rename to src/dr/app/tools/treeannotator/Clade.java index e2281e2796..be44d3c9b7 100644 --- a/src/dr/app/tools/newtreeannotator/Clade.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/CladeAction.java b/src/dr/app/tools/treeannotator/CladeAction.java similarity index 96% rename from src/dr/app/tools/newtreeannotator/CladeAction.java rename to src/dr/app/tools/treeannotator/CladeAction.java index be5eacc0d5..80d619701f 100644 --- a/src/dr/app/tools/newtreeannotator/CladeAction.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/CladeSystem.java b/src/dr/app/tools/treeannotator/CladeSystem.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/CladeSystem.java rename to src/dr/app/tools/treeannotator/CladeSystem.java index be6833f3a8..22b8eddd30 100644 --- a/src/dr/app/tools/newtreeannotator/CladeSystem.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/CollectionAction.java b/src/dr/app/tools/treeannotator/CollectionAction.java similarity index 97% rename from src/dr/app/tools/newtreeannotator/CollectionAction.java rename to src/dr/app/tools/treeannotator/CollectionAction.java index 3ee40df9a9..e5ba911b2c 100644 --- a/src/dr/app/tools/newtreeannotator/CollectionAction.java +++ b/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 { diff --git a/src/dr/app/tools/newtreeannotator/FastClade.java b/src/dr/app/tools/treeannotator/FastClade.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/FastClade.java rename to src/dr/app/tools/treeannotator/FastClade.java index 5aaec01ff9..3330d37ca4 100644 --- a/src/dr/app/tools/newtreeannotator/FastClade.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/HIPSTRTreeBuilder.java b/src/dr/app/tools/treeannotator/HIPSTRTreeBuilder.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/HIPSTRTreeBuilder.java rename to src/dr/app/tools/treeannotator/HIPSTRTreeBuilder.java index cf5fa54198..cfe6a37b9a 100644 --- a/src/dr/app/tools/newtreeannotator/HIPSTRTreeBuilder.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/RunLengthBitSet.java b/src/dr/app/tools/treeannotator/RunLengthBitSet.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/RunLengthBitSet.java rename to src/dr/app/tools/treeannotator/RunLengthBitSet.java index b0501a527b..912a567646 100644 --- a/src/dr/app/tools/newtreeannotator/RunLengthBitSet.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/TreeAnnotator.java b/src/dr/app/tools/treeannotator/TreeAnnotator.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/TreeAnnotator.java rename to src/dr/app/tools/treeannotator/TreeAnnotator.java index 0e8dcb22c7..c1bde428ec 100644 --- a/src/dr/app/tools/newtreeannotator/TreeAnnotator.java +++ b/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; diff --git a/src/dr/app/tools/newtreeannotator/TreeAnnotatorDialog.java b/src/dr/app/tools/treeannotator/TreeAnnotatorDialog.java similarity index 99% rename from src/dr/app/tools/newtreeannotator/TreeAnnotatorDialog.java rename to src/dr/app/tools/treeannotator/TreeAnnotatorDialog.java index 45abe5d5d2..6ee177a5bc 100644 --- a/src/dr/app/tools/newtreeannotator/TreeAnnotatorDialog.java +++ b/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;