void RunHTree(string name, string dirName, string alignmentFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashCluster hCluster;
if (dcd != null)
{
hCluster = new HashCluster(dcd, opt.hash);
}
else
if (alignmentFile != null)
{
hCluster = new HashCluster("", alignmentFile, opt.hash);
}
else
{
hCluster = new HashCluster(dirName, null, opt.hash);
}
HTree h = new HTree(dirName, alignmentFile, hCluster);
beginJob(currentProcessName, h.ToString(), dirName, "HAMMING");
progressDic.Add(name, h);
hCluster.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
ClusterOutput output = new ClusterOutput();
output = h.RunHTree();
UpdateOutput(name, dirName, alignmentFile, output, "NONE", cpuPart1, cpuPart2, h);
}
private void RunHashDendrog(string name, string dirName, string alignmentFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashCluster hk = null;
if (dcd != null)
{
hk = new HashCluster(dcd, opt.hash);
}
else
if (alignmentFile != null)
{
hk = new HashCluster("", alignmentFile, opt.hash);
}
else
{
hk = new HashCluster(dirName, null, opt.hash);
}
progressDic.Add(name, hk);
hk.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
ClusterOutput output;
output = hk.RunHashDendrog();
UpdateOutput(name, dirName, alignmentFile, output, "NONE", cpuPart1, cpuPart2, hk);
}
private void RunHashCluster(string name, string dirName, string alignmentFile = null, DCDFile dcd = null)
{
DateTime cpuPart1 = DateTime.Now;
HashCluster hk = null;
if (dcd != null)
{
hk = new HashCluster(dcd, opt.hash);
}
else
if (alignmentFile != null)
{
hk = new HashCluster("", alignmentFile, opt.hash);
}
else
{
hk = new HashCluster(dirName, null, opt.hash);
}
progressDic.Add(name, hk);
if (beginJob != null)
{
beginJob(currentProcessName, hk.ToString(), dirName, "HAMMING");
}
hk.InitHashCluster();
DateTime cpuPart2 = DateTime.Now;
ClusterOutput output;
output = hk.RunHashCluster();
UpdateOutput(name, dirName, alignmentFile, output, "HAMMING", cpuPart1, cpuPart2, hk);
}
public HTree(Alignment _al, HashCluster hCl)
{
al = _al;
stateAlign = al.GetStateAlign();
hCluster = hCl;
}
public HTree(string dirName, string alignFile, HashCluster hCl)
{
this.dirName = dirName;
this.alignmentFile = alignFile;
hCluster = hCl;
}
