public hierarchicalCluster(DistanceMeasure dMeasure, HierarchicalCInput hier, string dirName)
{
this.dMeasure = dMeasure;
this.linkageType = hier.linkageType;
this.dirName = dirName;
progressRead = 0;
hierOpt = hier;
}
public HashClusterDendrog(DCDFile dcd, HashCInput input, HierarchicalCInput dendrogOpt) : base(dcd, input)
{
this.dMeasure = dendrogOpt.distance;
this.linkageType = dendrogOpt.linkageType;
this.atoms = dendrogOpt.atoms;
this.jury1d = dendrogOpt.reference1DjuryH;
this.profileName = dendrogOpt.hammingProfile;
this.refJuryProfile = dendrogOpt.jury1DProfileH;
hier = dendrogOpt;
}
public FastDendrog(DistanceMeasure dMeasure, HierarchicalCInput input, string dirName)
{
this.dMeasure = dMeasure;
this.initNodesNum = input.numInitNodes;
this.linkage = input.linkageType;
this.useKMeans = input.ItMeans;
this.hConcensus = input.HConsensus;
this.kMeansIter = input.ItNum;
this.dirName = dirName;
this.input = input;
}
public FastDendrog(DistanceMeasure dMeasure,HierarchicalCInput input,string dirName)
{
this.dMeasure = dMeasure;
this.initNodesNum = input.numInitNodes;
this.linkage = input.linkageType;
this.useKMeans = input.ItMeans;
this.hConcensus = input.HConsensus;
this.kMeansIter = input.ItNum;
this.dirName = dirName;
this.input = input;
}
public HierarchicalCForm(HierarchicalCInput obj,ClusterAlgorithm alg,INPUTMODE mode,bool flag,List<string> profiles)
{
this.alg = alg;
objCopy = obj;
this.mode = mode;
InitializeComponent();
if (profiles != null)
{
button3.Visible = true;
profileFile = profiles[0];
}
else
button3.Visible = false;
userHash1.regularizationOff();
SizeHeight = this.Size.Height;
distanceControl1.refChanged = ReferanceCheckChanged;
//distanceControl1.FreezeCAtoms();
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
distanceControl1.HideAtoms = true;
foreach (var item in Enum.GetValues(typeof(AglomerativeType)))
comboBox1.Items.Add(Enum.GetName(typeof(AglomerativeType),item));
if (obj != null)
{
comboBox1.SelectedItem=Enum.GetName(typeof(AglomerativeType),obj.linkageType);
numericBox1.Text = obj.numInitNodes.ToString();
DBIndex.Value = (decimal)obj.indexDB;
threshold.Value = (decimal)obj.numberOfStruct;
maxRepeat.Value = (decimal)obj.repeatTime;
maxK.Value = (decimal)obj.maxK;
switch (alg)
{
case ClusterAlgorithm.FastHCluster:
AglomRadio.Checked = false;
FastHClusterRadio.Checked = true;
KmeansRadio.Checked = false;
userHash1.Visible = false;
radioButton3.Checked = false;
groupBox1.Visible = true;
if (radioButton1.Checked)
if (distanceControl1.reference)
jury1DSetup3.Visible = false;
else
jury1DSetup3.Visible = true;
this.Size = new Size(this.Size.Width, SizeHeight / 2 + SizeHeight / 4);
distanceControl1.reference = obj.reference1DjuryFast;
distanceControl1.referenceProfile = obj.consensusProfile;
userHash1.profRefFile = obj.jury1DProfileFast;
break;
case ClusterAlgorithm.HKmeans:
AglomRadio.Checked = false;
FastHClusterRadio.Checked = false;
KmeansRadio.Checked = true;
groupBox1.Visible = false;
radioButton3.Checked = false;
userHash1.Visible = false;
this.Size = new Size(this.Size.Width, SizeHeight / 2 + SizeHeight/3);
distanceControl1.reference = obj.reference1DjuryKmeans;
distanceControl1.referenceProfile = obj.jury1DProfileKmeans;
break;
case ClusterAlgorithm.uQlustTree:
userHash1.Visible = true;
AglomRadio.Checked = false;
FastHClusterRadio.Checked = false;
KmeansRadio.Checked = false;
groupBox1.Visible = false;
radioButton3.Checked = true;
this.Size = new Size(this.Size.Width, SizeHeight);
distanceControl1.reference = obj.reference1DjuryH;
distanceControl1.referenceProfile = obj.jury1DProfileH;
break;
default://Aglomerative
AglomRadio.Checked = true;
FastHClusterRadio.Checked = false;
KmeansRadio.Checked = false;
groupBox1.Visible = false;
userHash1.Visible = false;
radioButton3.Checked = false;
distanceControl1.reference = obj.reference1DjuryAglom;
distanceControl1.referenceProfile = obj.jury1DProfileAglom;
break;
}
distanceControl1.distDef = obj.distance;
distanceControl1.CAtoms = obj.atoms;
distanceControl1.profileName = obj.hammingProfile;
jury1DSetup3.profileName = obj.consensusProfile;
checkBox2.Checked = obj.ItMeans;
numericUpDown1.Value = obj.ItNum;
if (obj.HConsensus)
{
radioButton1.Checked = false;
radioButton2.Checked = true;
}
else
{
radioButton1.Checked = true;
radioButton2.Checked = false;
}
if (flag)
{
distanceControl1.FreezDist();
// distanceControl1.distDef = DistanceMeasures.HAMMING;
}
// distanceControl1.CAtoms = PDB.PDBMODE.ONLY_CA;
userHash1.SetHash(obj.hash);
}
}
private void SetOptions()
{
userHash1.UpdateMode();
localOpt = new HierarchicalCInput();
localOpt.linkageType = (AglomerativeType) Enum.Parse(typeof(AglomerativeType), comboBox1.SelectedItem.ToString());
localOpt.numInitNodes = Convert.ToInt32(numericBox1.Text);
localOpt.indexDB = (float)DBIndex.Value;
localOpt.numberOfStruct = (int)threshold.Value;
localOpt.repeatTime = (int)maxRepeat.Value;
localOpt.maxK = (int)maxK.Value;
if (AglomRadio.Checked)
{
alg = ClusterAlgorithm.HierarchicalCluster;
localOpt.reference1DjuryAglom = distanceControl1.reference;
localOpt.jury1DProfileAglom= distanceControl1.referenceProfile;
}
else
if (FastHClusterRadio.Checked)
{
alg = ClusterAlgorithm.FastHCluster;
localOpt.reference1DjuryFast = distanceControl1.reference;
localOpt.consensusProfile = distanceControl1.referenceProfile;
if (distanceControl1.reference)
{
localOpt.jury1DProfileFast = distanceControl1.referenceProfile;
}
}
else
if (KmeansRadio.Checked)
{
alg = ClusterAlgorithm.HKmeans;
localOpt.reference1DjuryKmeans = distanceControl1.reference;
localOpt.jury1DProfileKmeans = distanceControl1.referenceProfile;
}
else
{
alg = ClusterAlgorithm.uQlustTree;
localOpt.reference1DjuryH = distanceControl1.reference;
localOpt.jury1DProfileH = distanceControl1.referenceProfile;
}
localOpt.distance = distanceControl1.distDef;
localOpt.atoms = distanceControl1.CAtoms;
localOpt.hammingProfile = distanceControl1.profileName;
//localOpt.usedJuryForRef = distanceControl1.reference;
localOpt.consensusProfile = jury1DSetup3.profileName;
localOpt.ItMeans = checkBox2.Checked;
if (radioButton1.Checked)
localOpt.HConsensus = false;
else
localOpt.HConsensus = true ;
localOpt.ItNum = (int)numericUpDown1.Value;
localOpt.hash = userHash1.GetHash();
}