-package jalview.ext.archaeopteryx;
-
-import jalview.analysis.TreeBuilder;
-import jalview.datamodel.SequenceI;
-import jalview.ext.forester.DataConversions;
-import jalview.ext.forester.ForesterMatrix;
-import jalview.ext.treeviewer.ExternalTreeBuilderI;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.forester.evoinference.matrix.distance.DistanceMatrix;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.NodeData;
-import org.forester.phylogeny.data.Sequence;
-
-/**
- * Class for converting trees made in Jalview (through TreeBuilder) to trees
- * compatible with Forester (Phylogeny objects).
- *
- * Note that this currently demands a 1:1 relationship between tree nodes and
- * the sequences used for generating them.
- *
- * @author kjvanderheide
- *
- */
-public class AptxTreeBuilder
- implements ExternalTreeBuilderI<Phylogeny, PhylogenyNode>
-{
- protected final SequenceI[] sequences;
-
- protected final DistanceMatrix distances;
-
- protected final TreeBuilder jalviewTree;
-
- public String treeTitle;
-
- private final Phylogeny aptxTree;
-
- private PhylogenyNode rootNode;
-
- private final Map<SequenceI, PhylogenyNode> alignmentWithNodes;
-
- private final Map<PhylogenyNode, SequenceI> nodesWithAlignment;
-
- public AptxTreeBuilder(final TreeBuilder calculatedTree)
- {
- jalviewTree = calculatedTree;
- sequences = jalviewTree.getSequences();
- distances = ForesterMatrix.convertJalviewToForester(
- jalviewTree.getDistances(), sequences);
-
- aptxTree = new Phylogeny();
- rootNode = new PhylogenyNode();
-
- int amountOfSequences = distances.getSize();
- alignmentWithNodes = new HashMap<>(amountOfSequences);
- nodesWithAlignment = new HashMap<>(amountOfSequences);
-
-
- }
-
- @Override
- public Phylogeny buildTree(final PhylogenyNode treeRoot)
- {
-
- if (treeRoot != null)
- {
- rootNode = treeRoot;
- }
-
- buildTree();
-
- return aptxTree;
-
- }
-
-
- @Override
- public Phylogeny buildTree()
- {
-
- for (SequenceI sequence : sequences)
- {
- Sequence seq = DataConversions
- .createForesterSequence(sequence, true);
- PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
-
- NodeData nodeData = sequenceNode.getNodeData();
- nodeData.setSequence(seq);
-
- MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
- sequenceNode, sequence);
- MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
- sequence, sequenceNode);
- rootNode.addAsChild(sequenceNode);
- }
-
-
- aptxTree.setRoot(rootNode);
-
- treeTitle = generateTreeName();
- aptxTree.setName(treeTitle);
-
- return aptxTree;
-
- }
-
- @Override
- public Map<SequenceI, PhylogenyNode> getAlignmentBoundNodes()
- {
- return alignmentWithNodes;
- }
-
- @Override
- public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
- {
- return nodesWithAlignment;
- }
-
- private Phylogeny clusterNodes()
- {
- return aptxTree;
-
- }
- /**
- * Formats a localised title for the tree panel, like
- * <p>
- * Neighbour Joining Using BLOSUM62
- * <p>
- * For a tree loaded from file, just uses the file name
- *
- * @return
- */
- @Override
- public String generateTreeName() // Move this and add selection region to the
- // title when applicable
- {
- if (treeTitle != null) // will currently never happen, loaded tree file will
- // take a different path
- {
- return treeTitle;
- }
- else
- {
- /*
- * i18n description of Neighbour Joining or Average Distance method
- */
- String treecalcnm = MessageManager
- .getString("label.tree_calc_" + jalviewTree.getClass()
- .getSimpleName().substring(0, 2).toLowerCase());
- /*
- * short score model name (long description can be too long)
- */
- String smn = jalviewTree.getScoreModel().getName();
-
- /*
- * put them together as <method> Using <model>
- */
- final String ttl = MessageManager
- .formatMessage("label.treecalc_title", treecalcnm, smn);
- return ttl;
- }
- }
-
-
-}
+// package jalview.ext.archaeopteryx;
+//
+// import jalview.analysis.TreeBuilder;
+// import jalview.datamodel.SequenceI;
+// import jalview.ext.forester.ForesterMatrix;
+// import jalview.ext.treeviewer.TreeBuilderI;
+// import jalview.ext.treeviewer.TreeI;
+// import jalview.ext.treeviewer.TreeNodeI;
+// import jalview.util.MappingUtils;
+// import jalview.util.MessageManager;
+//
+// import java.util.HashMap;
+// import java.util.Map;
+//
+// import org.forester.evoinference.matrix.distance.DistanceMatrix;
+// import org.forester.phylogeny.Phylogeny;
+// import org.forester.phylogeny.PhylogenyNode;
+//
+/// **
+// * Class for converting trees made in Jalview (through TreeBuilder) to trees
+// * compatible with Forester (Phylogeny objects).
+// *
+// * Note that this currently demands a 1:1 relationship between tree nodes and
+// * the sequences used for generating them.
+// *
+// * @author kjvanderheide
+// *
+// */
+// public class AptxTreeBuilder
+// implements TreeBuilderI
+// {
+// protected final SequenceI[] sequences;
+//
+// protected final DistanceMatrix distances;
+//
+// protected final TreeBuilder jalviewTree;
+//
+// public String treeTitle;
+//
+// private final TreeI aptxTree;
+//
+// private TreeNodeI rootNode;
+//
+// private final Map<SequenceI, TreeNodeI> alignmentWithNodes;
+//
+// private final Map<TreeNodeI, SequenceI> nodesWithAlignment;
+//
+// public AptxTreeBuilder(final TreeBuilder calculatedTree)
+// {
+// jalviewTree = calculatedTree;
+// sequences = jalviewTree.getSequences();
+// distances = ForesterMatrix.convertJalviewToForester(
+// jalviewTree.getDistances(), sequences);
+//
+// aptxTree = new Tree(new Phylogeny());
+// rootNode = TreeNode.getUniqueWrapper(new PhylogenyNode());
+//
+// int amountOfSequences = distances.getSize();
+// alignmentWithNodes = new HashMap<>(amountOfSequences);
+// nodesWithAlignment = new HashMap<>(amountOfSequences);
+//
+//
+// }
+//
+// @Override
+// public TreeI buildTree(final TreeNodeI treeRoot)
+// {
+//
+// if (treeRoot != null)
+// {
+// rootNode = treeRoot;
+// }
+//
+// buildTree();
+//
+// return aptxTree;
+//
+// }
+//
+//
+// @Override
+// public TreeI buildTree()
+// {
+//
+// for (SequenceI sequence : sequences)
+// {
+//
+// TreeNodeI sequenceNode = TreeNode
+// .getUniqueWrapper(
+// new PhylogenyNode(sequence.getName()));
+//
+// sequenceNode.setSequence(sequence);
+//
+// MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
+// sequenceNode, sequence);
+// MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
+// sequence, sequenceNode);
+// rootNode.addAsChild(sequenceNode);
+// }
+//
+//
+// aptxTree.setRoot(rootNode);
+//
+// treeTitle = generateTreeName();
+// aptxTree.setTreeName(treeTitle);
+//
+// return aptxTree;
+//
+// }
+//
+// @Override
+// public Map<SequenceI, TreeNodeI> getAlignmentBoundNodes()
+// {
+// return alignmentWithNodes;
+// }
+//
+// @Override
+// public Map<TreeNodeI, SequenceI> getNodesBoundAlignment()
+// {
+// return nodesWithAlignment;
+// }
+//
+//
+// /**
+// * Formats a localised title for the tree panel, like
+// * <p>
+// * Neighbour Joining Using BLOSUM62
+// * <p>
+// * For a tree loaded from file, just uses the file name
+// *
+// * @return
+// */
+// @Override
+// public String generateTreeName() // Move this and add selection region to the
+// // title when applicable
+// {
+// if (treeTitle != null) // will currently never happen, loaded tree file will
+// // take a different path
+// {
+// return treeTitle;
+// }
+// else
+// {
+// /*
+// * i18n description of Neighbour Joining or Average Distance method
+// */
+// String treecalcnm = MessageManager
+// .getString("label.tree_calc_" + jalviewTree.getClass()
+// .getSimpleName().substring(0, 2).toLowerCase());
+// /*
+// * short score model name (long description can be too long)
+// */
+// String smn = jalviewTree.getScoreModel().getName();
+//
+// /*
+// * put them together as <method> Using <model>
+// */
+// final String ttl = MessageManager
+// .formatMessage("label.treecalc_title", treecalcnm, smn);
+// return ttl;
+// }
+// }
+//
+//
+//
+//
+// }
git://source.jalview.org / jalview.git / blobdiff