Examples with Importer dr.evolution.io.Importer used on opensource projects

Example 6 with Importer

use of dr.evolution.io.Importer in project beast-mcmc by beast-dev.

the class Coevolve method readNexusFile.

/**
     * @param fileName
     * @throws java.io.IOException
     */
private Alignment readNexusFile(String fileName) throws java.io.IOException {
    Alignment alignment = null;
    TaxonList taxonList = null;
    try {
        FileReader reader = new FileReader(fileName);
        NexusImporter importer = new NexusImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusImporter.NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxonList != null) {
                        throw new NexusImporter.MissingBlockException("TAXA block already defined");
                    }
                    taxonList = importer.parseTaxaBlock();
                } else if (block == NexusImporter.DATA_BLOCK) {
                    // A data block doesn't need a taxon block before it
                    // but if one exists then it will use it.
                    alignment = importer.parseDataBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                // ignore tree block
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
    } catch (Importer.ImportException ime) {
        System.err.println("Error reading alignment: " + ime);
    }
    return alignment;
}

Example 7 with Importer

use of dr.evolution.io.Importer in project beast-mcmc by beast-dev.

the class Coevolve method readTreeFile.

/**
     * @param fileName
     * @throws java.io.IOException
     */
private Tree readTreeFile(String fileName) throws java.io.IOException {
    Alignment alignment = null;
    Tree[] trees = null;
    TaxonList taxonList = null;
    try {
        FileReader reader = new FileReader(fileName);
        NexusImporter importer = new NexusImporter(reader);
        boolean done = false;
        while (!done) {
            try {
                NexusImporter.NexusBlock block = importer.findNextBlock();
                if (block == NexusImporter.TAXA_BLOCK) {
                    if (taxonList != null) {
                        throw new NexusImporter.MissingBlockException("TAXA block already defined");
                    }
                    taxonList = importer.parseTaxaBlock();
                } else if (block == NexusImporter.DATA_BLOCK) {
                    // A data block doesn't need a taxon block before it
                    // but if one exists then it will use it.
                    alignment = importer.parseDataBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else if (block == NexusImporter.TREES_BLOCK) {
                    trees = importer.parseTreesBlock(taxonList);
                    if (taxonList == null) {
                        taxonList = alignment;
                    }
                } else {
                // Ignore the block..
                }
            } catch (EOFException ex) {
                done = true;
            }
        }
    } catch (Importer.ImportException ime) {
        System.err.println("Error reading alignment: " + ime);
    }
    return trees[0];
}

Example 8 with Importer

use of dr.evolution.io.Importer in project beast-mcmc by beast-dev.

the class TreeAnnotator method summarizeTrees.

private Tree summarizeTrees(int burnin, CladeSystem cladeSystem, String inputFileName) throws /*, boolean useSumCladeCredibility */
IOException {
    Tree bestTree = null;
    double bestScore = Double.NEGATIVE_INFINITY;
    progressStream.println("Analyzing " + totalTreesUsed + " trees...");
    progressStream.println("0              25             50             75            100");
    progressStream.println("|--------------|--------------|--------------|--------------|");
    int stepSize = totalTrees / 60;
    if (stepSize < 1)
        stepSize = 1;
    int counter = 0;
    int bestTreeNumber = 0;
    TreeImporter importer = new NexusImporter(new FileReader(inputFileName), true);
    try {
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (counter >= burnin) {
                double score = scoreTree(tree, cladeSystem);
                //                    progressStream.println(score);
                if (score > bestScore) {
                    bestTree = tree;
                    bestScore = score;
                    bestTreeNumber = counter + 1;
                }
            }
            if (counter > 0 && counter % stepSize == 0) {
                progressStream.print("*");
                progressStream.flush();
            }
            counter++;
        }
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
        return null;
    }
    progressStream.println();
    progressStream.println();
    progressStream.println("Best tree: " + bestTree.getId() + " (tree number " + bestTreeNumber + ")");
    //        if (useSumCladeCredibility) {
    //            progressStream.println("Highest Sum Clade Credibility: " + bestScore);
    //        } else {
    progressStream.println("Highest Log Clade Credibility: " + bestScore);
    return bestTree;
}

Example 9 with Importer

use of dr.evolution.io.Importer in project beast-mcmc by beast-dev.

the class TreeLengthFinder method report.

/**
     * Recursively analyzes trees files.
     *
     * @param name       the file to analyze (if this is a directory then the files within it are analyzed)
     * @param burnin     the burnin to use
     */
private void report(String name, int burnin) {
    double treeLength = 0.0;
    int count = 0;
    try {
        FileReader fileReader = new FileReader(new File(name));
        TreeImporter importer = new NexusImporter(fileReader);
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (count >= burnin) {
                treeLength += TreeLength.FACTORY.createStatistic().getSummaryStatistic(tree)[0];
            }
            count++;
        }
        treeLength /= (count - burnin);
        System.out.println(name + "\t" + burnin + "\t" + treeLength);
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
    } catch (IOException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
    }
}

Example 10 with Importer

use of dr.evolution.io.Importer in project beast-mcmc by beast-dev.

the class TaxaOriginTrait method main.

/*
    * Arguments:
    * 0: Trait name
    * 1: File name for list of taxaNames of interest
    * 2: File name for trees (output from BranchJumpPlotter)
    * 3: Output file name root
    * */
public static void main(String[] args) {
    try {
        BufferedReader taxonReader = new BufferedReader(new FileReader(args[1]));
        HashSet<String> tempTaxa = new HashSet<String>();
        String line;
        while ((line = taxonReader.readLine()) != null) {
            tempTaxa.add(line);
        }
        String[] taxa = tempTaxa.toArray(new String[tempTaxa.size()]);
        NexusImporter importer = new NexusImporter(new FileReader(args[2]));
        importer.setSuppressWarnings(true);
        ArrayList<FlexibleTree> tempTrees = new ArrayList<FlexibleTree>();
        int count = 0;
        while (importer.hasTree()) {
            if (count % 100 == 0) {
                System.out.println("Loaded " + count + " trees");
            }
            tempTrees.add((FlexibleTree) importer.importNextTree());
            count++;
        }
        FlexibleTree[] trees = tempTrees.toArray(new FlexibleTree[tempTrees.size()]);
        TaxaOriginTrait examiner = new TaxaOriginTrait(taxa, trees, args[0], args[3]);
        examiner.tabulateOrigins();
    } catch (IOException e) {
        System.out.println("Failed to read files");
    } catch (Importer.ImportException e) {
        System.out.println("Failed to import trees");
    }
}