1 package jalview.ext.archaeopteryx;
3 import jalview.analysis.TreeBuilder;
4 import jalview.datamodel.SequenceI;
5 import jalview.ext.forester.ForesterConversions;
6 import jalview.ext.forester.ForesterMatrix;
7 import jalview.util.MessageManager;
9 import java.util.HashMap;
12 import org.forester.evoinference.matrix.distance.DistanceMatrix;
13 import org.forester.phylogeny.Phylogeny;
14 import org.forester.phylogeny.PhylogenyNode;
15 import org.forester.phylogeny.data.NodeData;
16 import org.forester.phylogeny.data.Sequence;
19 * Class for converting trees made in Jalview (through TreeBuilder) to trees
20 * compatible with Forester (Phylogeny objects).
22 * Note that this currently demands a 1:1 relationship between tree nodes and
23 * the sequences used for generating them.
25 * @author kjvanderheide
28 public class ArchaeopteryxTreeConverter
30 protected final SequenceI[] sequences;
32 protected final DistanceMatrix distances;
34 protected final TreeBuilder jalviewTree;
36 public String treeTitle;
38 private final Phylogeny aptxTree;
40 private PhylogenyNode rootNode;
42 private final Map<SequenceI, PhylogenyNode> alignmentBoundNodes;
44 private final Map<PhylogenyNode, SequenceI> nodesBoundAlignment;
46 public ArchaeopteryxTreeConverter(final TreeBuilder calculatedTree)
48 jalviewTree = calculatedTree;
49 sequences = jalviewTree.getSequences();
50 distances = ForesterMatrix.convertJalviewToForester(
51 jalviewTree.getDistances(), sequences);
52 aptxTree = new Phylogeny();
53 rootNode = new PhylogenyNode();
54 alignmentBoundNodes = new HashMap<>(distances.getSize());
55 nodesBoundAlignment = new HashMap<>(distances.getSize());
60 public Phylogeny buildAptxTree(final PhylogenyNode treeRoot)
75 public Phylogeny buildAptxTree()
78 for (SequenceI sequence : sequences)
80 Sequence seq = ForesterConversions
81 .createForesterSequence(sequence, true);
82 PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
83 NodeData nodeData = sequenceNode.getNodeData();
84 nodeData.setSequence(seq);
86 nodesBoundAlignment.put(sequenceNode, sequence);
87 alignmentBoundNodes.put(sequence, sequenceNode);
88 rootNode.addAsChild(sequenceNode);
92 aptxTree.setRoot(rootNode);
94 treeTitle = generateTreeName();
95 aptxTree.setName(treeTitle);
101 public Map<SequenceI, PhylogenyNode> getAlignmentBoundNodes()
103 return alignmentBoundNodes;
106 public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
108 return nodesBoundAlignment;
111 private Phylogeny clusterNodes()
117 * Formats a localised title for the tree panel, like
119 * Neighbour Joining Using BLOSUM62
121 * For a tree loaded from file, just uses the file name
125 public String generateTreeName() // Move this and add selection region to the
126 // title when applicable
128 if (treeTitle != null) // will currently never happen, loaded tree file will
129 // take a different path
136 * i18n description of Neighbour Joining or Average Distance method
138 String treecalcnm = MessageManager
139 .getString("label.tree_calc_" + jalviewTree.getClass()
140 .getSimpleName().substring(0, 2).toLowerCase());
142 * short score model name (long description can be too long)
144 String smn = jalviewTree.getScoreModel().getName();
147 * put them together as <method> Using <model>
149 final String ttl = MessageManager
150 .formatMessage("label.treecalc_title", treecalcnm, smn);