1 package jalview.ext.archaeopteryx;
3 import jalview.analysis.TreeBuilder;
4 import jalview.datamodel.SequenceI;
5 import jalview.ext.forester.ForesterMatrix;
6 import jalview.ext.treeviewer.TreeBuilderI;
7 import jalview.ext.treeviewer.TreeI;
8 import jalview.ext.treeviewer.TreeNodeI;
9 import jalview.util.MappingUtils;
10 import jalview.util.MessageManager;
12 import java.util.HashMap;
15 import org.forester.evoinference.matrix.distance.DistanceMatrix;
16 import org.forester.phylogeny.Phylogeny;
17 import org.forester.phylogeny.PhylogenyNode;
20 * Class for converting trees made in Jalview (through TreeBuilder) to trees
21 * compatible with Forester (Phylogeny objects).
23 * Note that this currently demands a 1:1 relationship between tree nodes and
24 * the sequences used for generating them.
26 * @author kjvanderheide
29 public class AptxTreeBuilder
30 implements TreeBuilderI
32 protected final SequenceI[] sequences;
34 protected final DistanceMatrix distances;
36 protected final TreeBuilder jalviewTree;
38 public String treeTitle;
40 private final TreeI aptxTree;
42 private TreeNodeI rootNode;
44 private final Map<SequenceI, TreeNodeI> alignmentWithNodes;
46 private final Map<TreeNodeI, SequenceI> nodesWithAlignment;
48 public AptxTreeBuilder(final TreeBuilder calculatedTree)
50 jalviewTree = calculatedTree;
51 sequences = jalviewTree.getSequences();
52 distances = ForesterMatrix.convertJalviewToForester(
53 jalviewTree.getDistances(), sequences);
55 aptxTree = new Tree(new Phylogeny());
56 rootNode = TreeNode.getUniqueWrapper(new PhylogenyNode());
58 int amountOfSequences = distances.getSize();
59 alignmentWithNodes = new HashMap<>(amountOfSequences);
60 nodesWithAlignment = new HashMap<>(amountOfSequences);
66 public TreeI buildTree(final TreeNodeI treeRoot)
82 public TreeI buildTree()
85 for (SequenceI sequence : sequences)
88 TreeNodeI sequenceNode = TreeNode
90 new PhylogenyNode(sequence.getName()));
92 sequenceNode.setSequence(sequence);
94 MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
95 sequenceNode, sequence);
96 MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
97 sequence, sequenceNode);
98 rootNode.addAsChild(sequenceNode);
102 aptxTree.setRoot(rootNode);
104 treeTitle = generateTreeName();
105 aptxTree.setTreeName(treeTitle);
112 public Map<SequenceI, TreeNodeI> getAlignmentBoundNodes()
114 return alignmentWithNodes;
118 public Map<TreeNodeI, SequenceI> getNodesBoundAlignment()
120 return nodesWithAlignment;
125 * Formats a localised title for the tree panel, like
127 * Neighbour Joining Using BLOSUM62
129 * For a tree loaded from file, just uses the file name
134 public String generateTreeName() // Move this and add selection region to the
135 // title when applicable
137 if (treeTitle != null) // will currently never happen, loaded tree file will
138 // take a different path
145 * i18n description of Neighbour Joining or Average Distance method
147 String treecalcnm = MessageManager
148 .getString("label.tree_calc_" + jalviewTree.getClass()
149 .getSimpleName().substring(0, 2).toLowerCase());
151 * short score model name (long description can be too long)
153 String smn = jalviewTree.getScoreModel().getName();
156 * put them together as <method> Using <model>
158 final String ttl = MessageManager
159 .formatMessage("label.treecalc_title", treecalcnm, smn);