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(); }