Examples with Taxon dr.evolution.util.Taxon used on opensource projects

Example 21 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class TaxaEditorTableModel method removeLastRow.

// END: addEmptyRow
public void removeLastRow() {
    int lastIndex = taxaSet.getTaxonCount() - 1;
    Taxon taxon = taxaSet.getTaxon(lastIndex);
    taxaSet.removeTaxon(taxon);
    this.fireTableDataChanged();
}

Example 22 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class AlloppSpeciesNetworkModel method testExampleNetworkToMulLabTree.

/* *********************** TEST CODE **********************************/
/*
      * Test of conversion from network to mullab tree
      * 	 * 2011-05-07 It is called from testAlloppSpeciesNetworkModel.java.
      * I don't know how to put the code in there without
      * making lots public here.
      */
// grjtodo-oneday. should be possible to pass stuff in nmltTEST. Currently
// it just signals that this is indeed a test.
//AR - removing this as it creates a dependency to test.dr.* which is bad...
public String testExampleNetworkToMulLabTree(int testcase) {
    int ntaxa = apsp.numberOfSpecies();
    Taxon[] spp = new Taxon[ntaxa];
    for (int tx = 0; tx < ntaxa; ++tx) {
        spp[tx] = new Taxon(apsp.apspeciesName(tx));
    }
    // 1,2,3 (names b,c,d) are tets, 0,4 are dips (names a,e)
    double tetheight0 = 0.0;
    double tetheight1 = 0.0;
    double tetheight2 = 0.0;
    // case 1. one tettree with one foot in each diploid branch
    // case 2. one tettree with both feet in one diploid branch
    // case 3. one tettree with one joined
    // case 4. two tettrees, 2+1, first with one foot in each diploid
    // branch, second joined
    // case 5. three tettrees, 1+1+1, one of each type of feet, as in cases 1-3
    int ntettrees = 0;
    switch(testcase) {
        case 1:
        case 2:
        case 3:
            ntettrees = 1;
            break;
        case 4:
            ntettrees = 2;
            break;
        case 5:
            ntettrees = 3;
            break;
    }
    tettrees = new ArrayList<AlloppLeggedTree>(ntettrees);
    Taxon l0 = new Taxon("L0");
    Taxon l1 = new Taxon("L1");
    Taxon l2 = new Taxon("L2");
    Taxon r0 = new Taxon("R0");
    Taxon r1 = new Taxon("R1");
    Taxon r2 = new Taxon("R2");
    Taxon[] tets123 = { spp[1], spp[2], spp[3] };
    Taxon[] tets12 = { spp[1], spp[2] };
    Taxon[] tets1 = { spp[1] };
    Taxon[] tets2 = { spp[2] };
    Taxon[] tets3 = { spp[3] };
    Taxon[] dips = new Taxon[0];
    switch(testcase) {
        case 1:
            tettrees.add(new AlloppLeggedTree(tets123));
            tetheight0 = tettrees.get(0).getRootHeight();
            dips = new Taxon[] { spp[0], l0, r0, spp[4] };
            break;
        case 2:
            tettrees.add(new AlloppLeggedTree(tets123));
            tetheight0 = tettrees.get(0).getRootHeight();
            dips = new Taxon[] { spp[0], l0, r0, spp[4] };
            break;
        case 3:
            tettrees.add(new AlloppLeggedTree(tets123));
            tetheight0 = tettrees.get(0).getRootHeight();
            dips = new Taxon[] { spp[0], l0, r0, spp[4] };
            break;
        case 4:
            tettrees.add(new AlloppLeggedTree(tets12));
            tettrees.add(new AlloppLeggedTree(tets3));
            tetheight0 = tettrees.get(0).getRootHeight();
            tetheight1 = tettrees.get(1).getRootHeight();
            dips = new Taxon[] { spp[0], l0, r0, l1, r1, spp[4] };
            break;
        case 5:
            tettrees.add(new AlloppLeggedTree(tets1));
            tettrees.add(new AlloppLeggedTree(tets2));
            tettrees.add(new AlloppLeggedTree(tets3));
            tetheight0 = tettrees.get(0).getRootHeight();
            tetheight1 = tettrees.get(1).getRootHeight();
            tetheight2 = tettrees.get(2).getRootHeight();
            dips = new Taxon[] { spp[0], l0, r0, l1, r1, l2, r2, spp[4] };
            break;
    }
    assert dips.length >= 2;
    int ndhnodes = 2 * dips.length - 1;
    SimpleNode[] dhnodes = new SimpleNode[ndhnodes];
    for (int n = 0; n < ndhnodes; n++) {
        dhnodes[n] = new SimpleNode();
        if (n < dips.length) {
            dhnodes[n].setTaxon(dips[n]);
        } else {
            dhnodes[n].setTaxon(new Taxon(""));
        }
    }
    int dhroot = -1;
    switch(testcase) {
        case 1:
            dhnodes[1].setHeight(tetheight0 + 1.0);
            dhnodes[2].setHeight(tetheight0 + 1.0);
            addSimpleNodeChildren(dhnodes[4], dhnodes[0], dhnodes[1], 1.0);
            addSimpleNodeChildren(dhnodes[5], dhnodes[2], dhnodes[3], 1.0);
            addSimpleNodeChildren(dhnodes[6], dhnodes[4], dhnodes[5], 1.0);
            dhroot = 6;
            break;
        case 2:
            dhnodes[1].setHeight(tetheight0 + 1.0);
            dhnodes[2].setHeight(tetheight0 + 1.0);
            addSimpleNodeChildren(dhnodes[4], dhnodes[0], dhnodes[1], 1.0);
            addSimpleNodeChildren(dhnodes[5], dhnodes[2], dhnodes[4], 1.0);
            addSimpleNodeChildren(dhnodes[6], dhnodes[3], dhnodes[5], 1.0);
            dhroot = 6;
            break;
        case 3:
            dhnodes[1].setHeight(tetheight0 + 1.0);
            dhnodes[2].setHeight(tetheight0 + 1.0);
            addSimpleNodeChildren(dhnodes[4], dhnodes[1], dhnodes[2], 1.0);
            addSimpleNodeChildren(dhnodes[5], dhnodes[0], dhnodes[4], 1.0);
            addSimpleNodeChildren(dhnodes[6], dhnodes[3], dhnodes[5], 1.0);
            dhroot = 6;
            break;
        case 4:
            dhnodes[1].setHeight(tetheight0 + 1.0);
            dhnodes[2].setHeight(tetheight0 + 1.0);
            dhnodes[3].setHeight(tetheight1 + 1.0);
            dhnodes[4].setHeight(tetheight1 + 1.0);
            addSimpleNodeChildren(dhnodes[6], dhnodes[0], dhnodes[1], 1.0);
            addSimpleNodeChildren(dhnodes[7], dhnodes[3], dhnodes[4], 1.0);
            addSimpleNodeChildren(dhnodes[8], dhnodes[6], dhnodes[7], 1.0);
            addSimpleNodeChildren(dhnodes[9], dhnodes[2], dhnodes[5], 1.0);
            addSimpleNodeChildren(dhnodes[10], dhnodes[8], dhnodes[9], 1.0);
            dhroot = 10;
            break;
        case 5:
            dhnodes[1].setHeight(tetheight0 + 1.0);
            dhnodes[2].setHeight(tetheight0 + 1.0);
            dhnodes[3].setHeight(tetheight1 + 1.0);
            dhnodes[4].setHeight(tetheight1 + 1.0);
            dhnodes[5].setHeight(tetheight2 + 1.0);
            dhnodes[6].setHeight(tetheight2 + 1.0);
            addSimpleNodeChildren(dhnodes[8], dhnodes[0], dhnodes[1], 1.0);
            addSimpleNodeChildren(dhnodes[9], dhnodes[5], dhnodes[6], 1.0);
            addSimpleNodeChildren(dhnodes[10], dhnodes[2], dhnodes[7], 1.0);
            addSimpleNodeChildren(dhnodes[11], dhnodes[3], dhnodes[8], 1.0);
            addSimpleNodeChildren(dhnodes[12], dhnodes[4], dhnodes[11], 1.0);
            addSimpleNodeChildren(dhnodes[13], dhnodes[9], dhnodes[12], 1.0);
            addSimpleNodeChildren(dhnodes[14], dhnodes[10], dhnodes[13], 1.0);
            dhroot = 14;
            break;
    }
    AlloppDiploidHistory adhist = new AlloppDiploidHistory(dhnodes, dhroot, tettrees, true, apsp);
    int ntippopparams = numberOfTipPopParameters();
    int nrootpopparams = numberOfRootPopParameters();
    int maxnhybpopparams = maxNumberOfHybPopParameters();
    Parameter testtippopvalues = new Parameter.Default(ntippopparams);
    Parameter testrootpopvalues = new Parameter.Default(nrootpopparams);
    double[] testhybpopvalues = new double[maxnhybpopparams];
    for (int pp = 0; pp < ntippopparams; pp++) {
        testtippopvalues.setParameterValue(pp, 1000 + pp);
    }
    for (int pp = 0; pp < nrootpopparams; pp++) {
        testrootpopvalues.setParameterValue(pp, 2000 + pp);
    }
    for (int pp = 0; pp < maxnhybpopparams; pp++) {
        testhybpopvalues[pp] = 3000 + pp;
    }
    AlloppMulLabTree testmullabtree = new AlloppMulLabTree(adhist, tettrees, apsp, testtippopvalues, testrootpopvalues, testhybpopvalues);
    System.out.println(testmullabtree.asText());
    String newick = testmullabtree.mullabTreeAsNewick();
    return newick;
}

Example 23 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class MulSpeciesBindings method apspeciesId2speciesindiv.

// grj
public SpeciesIndivPair apspeciesId2speciesindiv(String apspId) {
    int sp = -1;
    int iv = -1;
    for (int s = 0; s < apspecies.length; s++) {
        for (int i = 0; i < apspecies[s].individuals.length; i++) {
            for (int t = 0; t < apspecies[s].individuals[i].taxa.length; t++) {
                Taxon taxon = apspecies[s].individuals[i].taxa[t];
                if (taxon.getId().compareTo(apspId) == 0) {
                    sp = s;
                    iv = i;
                }
            }
        }
    }
    assert sp != -1;
    SpeciesIndivPair x = new SpeciesIndivPair(sp, iv);
    return x;
}

Example 24 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class MulSpeciesBindings method collectCoalInfo.

// jh + grj
/**
     * Collect coalescence information for sub-tree rooted at 'node'.
     *
     * @param tree
     * @param node
     * @param loc  Place node data in loc, sub-tree info before that.
     * @param info array to fill
     * @return location of next available location
     */
private int collectCoalInfo(Tree tree, NodeRef node, GeneTreeInfo.SequenceAssignment[] seqassigns, int loc, CoalInfo[] info) {
    info[loc] = new CoalInfo(tree.getNodeHeight(node), tree.getChildCount(node));
    int newLoc = loc - 1;
    for (int i = 0; i < 2; i++) {
        NodeRef child = tree.getChild(node, i);
        info[loc].sinfo[i] = new FixedBitSet(nSpSeqs());
        if (tree.isExternal(child)) {
            Taxon taxon = tree.getNodeTaxon(child);
            int ti = taxon2index.get(taxon);
            int spseq = spsq[seqassigns[ti].spIndex][seqassigns[ti].seqIndex];
            info[loc].sinfo[i].set(spseq);
            assert tree.getNodeHeight(child) == 0;
        } else {
            final int used = collectCoalInfo(tree, child, seqassigns, newLoc, info);
            for (int j = 0; j < info[newLoc].sinfo.length; ++j) {
                info[loc].sinfo[i].union(info[newLoc].sinfo[j]);
            }
            newLoc = used;
        }
    }
    return newLoc;
}

Example 25 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class DriftedTraitsLogger method computeMaxHeight.

private void computeMaxHeight(Tree tree) {
    if (maxHeight < 0) {
        int m = tree.getTaxonCount();
        for (int i = 0; i < m; i++) {
            Taxon taxon = tree.getTaxon(i);
            double height = taxon.getHeight();
            if (height > maxHeight) {
                maxHeight = height;
            }
        }
    }
}