edu.rit.compbio.phyl

Class Results

java.lang.Object

edu.rit.compbio.phyl.Results

public class Results
extends java.lang.Object

Class Results provides a method for reporting the results of a maximum parsimony phylogenetic tree construction program. The results are stored in files in a specified directory. The following files are created:

• "index.html" has all the results. Open this file in a web browser to view the results.

• "tree_001.png", "tree_002.png", and so on have pictures of the phylogenetic trees. Each tip node is labeled with a DNA sequence name. Each interior node is labeled with the number of state changes at that node.

• "sequences.phy" has a copy of the input DNA sequences in interleaved PHYLIP format.

• "trees.txt" has all the phylogenetic trees, one per line, in Newick Standard format.

Method Summary

Modifier and Type	Method and Description
static void	report(java.io.File directory, java.lang.String programName, java.lang.String hostName, int K, java.io.File infile, DnaSequenceList originalSeqList, DnaSequenceList sortedSeqList, int initialBound, int treeStoreLimit, MaximumParsimonyResults results, long t1, long t2, long t3) Report the results of a maximum parsimony phylogenetic tree construction program.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

report

public static void report(java.io.File directory,
                          java.lang.String programName,
                          java.lang.String hostName,
                          int K,
                          java.io.File infile,
                          DnaSequenceList originalSeqList,
                          DnaSequenceList sortedSeqList,
                          int initialBound,
                          int treeStoreLimit,
                          MaximumParsimonyResults results,
                          long t1,
                          long t2,
                          long t3)
                   throws java.io.IOException

Report the results of a maximum parsimony phylogenetic tree construction program.

Parameters:

directory - Directory in which to store the files. If the directory does not exist, it is created.

programName - Name of the program.

hostName - Name of the host computer, or null if none.

K - Number of parallel threads, or 0 if none.

infile - Input file.

originalSeqList - List of DNA sequences read from the input file, in the order in which the sequences appeared in the input file.

sortedSeqList - List of DNA sequences read from the input file, in the order in which the sequences were added to the phylogenetic trees during the search.

initialBound - Initial bound for branch-and-bound search, or 0 if no initial bound.

treeStoreLimit - Maximum number of trees to store.

results - Maximum parsimony results object containing results of the search.

t1 - System clock snapshot at beginning.

t2 - System clock snapshot after preprocessing.

t3 - System clock snapshot after computation.

Throws:

java.io.IOException - Thrown if an I/O error occurred.