public PDBFiles()
{
Settings set = new Settings();
set.Load();
mode = set.mode;
}
//Flag true only CA will be readed
public MolData(string fileName,PDBMODE flag,INPUTMODE mode,CHAIN_MODE chainFlag=CHAIN_MODE.SINGLE)
{
using (StreamReader rr = new StreamReader(fileName)) {
switch (mode)
{
case INPUTMODE.PROTEIN:
mol = new Molecule( flag,chainFlag);
break;
case INPUTMODE.RNA:
mol = new MoleculeRNA(flag);
break;
}
bool res = mol.ReadMolecule(rr);
if (!res)
return;
if (mol.Chains.Count == 0)
{
ErrorBase.AddErrors("Error in reading file: " + fileName + "\nCannot find residues, file will not be considered!");
rr.Close();
return;
}
molLength = mol.Chains[0].chainSequence.Length;
}
//CenterMol();
}
public Aglomerative(HierarchicalCInput obj, ClusterAlgorithm alg, INPUTMODE mode, bool flag, List <string> profiles)
{
InitializeComponent();
Settings set = new Settings();
set.Load();
switch (set.mode)
{
case INPUTMODE.RNA:
distanceControl1.HideAtoms = true;
break;
case INPUTMODE.USER_DEFINED:
distanceControl1.HideRmsdLike = true;
break;
}
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);
distanceControl1.reference = obj.reference1DjuryH;
distanceControl1.referenceProfile = obj.jury1DProfileH;
distanceControl1.distDef = obj.distance;
distanceControl1.CAtoms = obj.atoms;
distanceControl1.profileName = obj.hammingProfile;
}
}
//Flag true only CA will be readed
public MolData(string fileName, PDBMODE flag, INPUTMODE mode, CHAIN_MODE chainFlag = CHAIN_MODE.SINGLE)
{
using (StreamReader rr = new StreamReader(fileName)) {
switch (mode)
{
case INPUTMODE.PROTEIN:
mol = new Molecule(flag, chainFlag);
break;
case INPUTMODE.RNA:
mol = new MoleculeRNA(flag);
break;
}
bool res = mol.ReadMolecule(rr);
if (!res)
{
return;
}
if (mol.Chains.Count == 0)
{
ErrorBase.AddErrors("Error in reading file: " + fileName + "\nCannot find residues, file will not be considered!");
rr.Close();
return;
}
molLength = mol.Chains[0].chainSequence.Length;
}
//CenterMol();
}
public uQlustTreeAdvanced(Options obj, ClusterAlgorithm alg, INPUTMODE mode, bool flag, List <string> profiles)
{
InitializeComponent();
if (profiles != null)
{
button3.Visible = true;
profileFile = profiles[0];
}
else
{
button3.Visible = false;
}
Settings set = new Settings();
set.Load();
switch (set.mode)
{
case INPUTMODE.RNA:
distanceControl1.HideAtoms = true;
break;
case INPUTMODE.USER_DEFINED:
distanceControl1.HideRmsdLike = true;
break;
}
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.hierarchical.linkageType);
relevantC.Value = obj.hash.relClusters;
percentData.Value = obj.hash.perData;
distanceControl1.reference = obj.hierarchical.reference1DjuryH;
distanceControl1.referenceProfile = obj.hash.profileName;
distanceControl1.distDef = obj.hierarchical.distance;
distanceControl1.CAtoms = obj.hierarchical.atoms;
distanceControl1.profileName = obj.hierarchical.hammingProfile;
jury1DSetup1.profileName = obj.hash.profileName;
if (obj.hash.jury)
{
radioButton1.Checked = true;
radioButton2.Checked = false;
}
else
{
radioButton1.Checked = false;
radioButton2.Checked = true;
}
}
}
public bool CheckAccessibility(profileNode profile, INPUTMODE type)
{
Type t = Type.GetType(internalList[profile]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
if (c.destination.Contains(type))
{
return(true);
}
return(false);
}
public KMeansForm(KmeansInput obj, bool flag, INPUTMODE inputmode, List <string> profiles = null)
{
InitializeComponent();
this.inputmode = inputmode;
if (profiles != null)
{
button3.Visible = true;
profileFile = profiles[0];
}
else
{
button3.Visible = false;
}
distanceControl1.changedProfile = juryChanged;
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
{
distanceControl1.HideAtoms = true;
}
jury1DSetup1.profileNameChanged = juryChanged;
if (flag)
{
distanceControl1.FreezDist();
}
if (obj != null)
{
kmeansMaxK.Value = (decimal)obj.maxK;
if (obj.kMeans_init == Initialization.Jury1D)
{
juryRadio.Checked = true;
randomRadio.Checked = false;
}
else
{
juryRadio.Checked = false;
randomRadio.Checked = true;
}
distanceControl1.distDef = obj.kDistance;
distanceControl1.CAtoms = obj.kAtoms;
distanceControl1.profileName = obj.hammingProfile;
jury1DSetup1.profileName = obj.jury1DProfile;
numericUpDown1.Value = obj.maxIter;
distanceControl1.reference = obj.reference1Djury;
distanceControl1.referenceProfile = obj.jury1DProfile;
}
}
public KMeansForm(KmeansInput obj, bool flag,INPUTMODE inputmode,List<string> profiles=null)
{
InitializeComponent();
this.inputmode = inputmode;
if (profiles != null)
{
button3.Visible = true;
profileFile = profiles[0];
}
else
button3.Visible = false;
distanceControl1.changedProfile = juryChanged;
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
distanceControl1.HideAtoms = true;
jury1DSetup1.profileNameChanged = juryChanged;
if (flag)
distanceControl1.FreezDist();
if (obj != null)
{
kmeansMaxK.Value = (decimal)obj.maxK;
if (obj.kMeans_init == Initialization.Jury1D)
{
juryRadio.Checked = true;
randomRadio.Checked = false;
}
else
{
juryRadio.Checked = false;
randomRadio.Checked = true;
}
distanceControl1.distDef = obj.kDistance;
distanceControl1.CAtoms = obj.kAtoms;
distanceControl1.profileName = obj.hammingProfile;
jury1DSetup1.profileName = obj.jury1DProfile;
numericUpDown1.Value = obj.maxIter;
distanceControl1.reference = obj.reference1Djury;
distanceControl1.referenceProfile = obj.jury1DProfile;
}
}
public HashClusterForm(HashCInput input, INPUTMODE mode, List <string> profilesF = null)
{
InitializeComponent();
this.mode = mode;
if (profilesF != null)
{
profileFile = profilesF[0];
button3.Visible = true;
}
else
{
button3.Visible = false;
}
checkBox1.Checked = input.regular;
numericUpDown2.Value = input.wSize;
numericUpDown3.Value = input.regThreshold;
radioButton3.Checked = input.combine;
jury1DSetup1.profileName = input.profileName;
relevantC.Value = input.relClusters;
percentData.Value = input.perData;
radioButton4.Checked = input.fcolumns;
switch (input.selectionMethod)
{
case COL_SELECTION.ENTROPY:
comboBox1.SelectedIndex = 1;
break;
case COL_SELECTION.META_COL:
comboBox1.SelectedIndex = 0;
break;
}
if (input.jury)
{
radioButton1.Checked = true;
radioButton2.Checked = false;
}
else
{
radioButton1.Checked = false;
radioButton2.Checked = true;
}
}
public HashClusterForm(HashCInput input,INPUTMODE mode,List<string> profilesF=null)
{
InitializeComponent();
this.mode = mode;
if (profilesF != null)
{
profileFile = profilesF[0];
button3.Visible = true;
}
else
button3.Visible = false;
checkBox1.Checked = input.regular;
numericUpDown2.Value = input.wSize;
numericUpDown3.Value = input.regThreshold;
radioButton3.Checked = input.combine;
jury1DSetup1.profileName = input.profileName;
jury1DSetup2.profileName = input.profileNameReg;
relevantC.Value = input.relClusters;
percentData.Value = input.perData;
radioButton4.Checked = input.fcolumns;
switch (input.selectionMethod)
{
case COL_SELECTION.ENTROPY:
comboBox1.SelectedIndex = 1;
break;
case COL_SELECTION.META_COL:
comboBox1.SelectedIndex = 0;
break;
}
if (input.jury)
{
radioButton1.Checked = true;
radioButton2.Checked = false;
}
else
{
radioButton1.Checked = false;
radioButton2.Checked = true;
}
}
public RankingCForm(RankingCInput obj,ClusterAlgorithm alg,bool flag,INPUTMODE inputMode,List<string> profFiles=null)
{
this.alg = alg;
this.inputMode = inputMode;
InitializeComponent();
if (profFiles != null)
{
profileFile = profFiles[0];
button3.Visible = true;
}
else
button3.Visible = false;
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
distanceControl1.HideAtoms = true;
if (flag)
{
distanceControl1.FreezDist();
sift.Enabled = false;
if (sift.Checked)
{
jury1d.Checked = true;
}
}
switch(alg)
{
case ClusterAlgorithm.Jury1D:
jury1d.Checked = true;
jury3d.Checked = false;
sift.Checked = false;
break;
case ClusterAlgorithm.Jury3D:
jury1d.Checked = false;
jury3d.Checked = true;
sift.Checked = false;
break;
case ClusterAlgorithm.Sift:
jury1d.Checked = false;
jury3d.Checked = false;
sift.Checked = true;
break;
default:
jury1d.Checked = true;
jury3d.Checked = false;
sift.Checked = false;
break;
}
if (obj != null)
{
distanceControl1.distDef = obj.oDistance;
distanceControl1.CAtoms = obj.oAtoms;
distanceControl1.profileName = obj.hammingProfile;
jury1DSetup1.profileName = obj.juryProfile;
distanceControl1.referenceProfile = obj.referenceProfile;
distanceControl1.reference = obj.reference1Djury;
}
if(jury1d.Checked)
distanceControl1.Enabled = false;
}
public PDBFiles()
{
Settings set = new Settings();
set.Load();
mode = set.mode;
}
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);
}
}
public RankingCForm(RankingCInput obj, ClusterAlgorithm alg, bool flag, INPUTMODE inputMode, List <string> profFiles = null)
{
this.alg = alg;
this.inputMode = inputMode;
InitializeComponent();
if (profFiles != null)
{
profileFile = profFiles[0];
button3.Visible = true;
}
else
{
button3.Visible = false;
}
Settings set = new Settings();
set.Load();
if (set.mode == INPUTMODE.RNA)
{
distanceControl1.HideAtoms = true;
}
if (flag)
{
distanceControl1.FreezDist();
sift.Enabled = false;
if (sift.Checked)
{
jury1d.Checked = true;
}
}
switch (alg)
{
case ClusterAlgorithm.Jury1D:
jury1d.Checked = true;
jury3d.Checked = false;
sift.Checked = false;
break;
case ClusterAlgorithm.Jury3D:
jury1d.Checked = false;
jury3d.Checked = true;
sift.Checked = false;
break;
case ClusterAlgorithm.Sift:
jury1d.Checked = false;
jury3d.Checked = false;
sift.Checked = true;
break;
default:
jury1d.Checked = true;
jury3d.Checked = false;
sift.Checked = false;
break;
}
if (obj != null)
{
distanceControl1.distDef = obj.oDistance;
distanceControl1.CAtoms = obj.oAtoms;
distanceControl1.profileName = obj.hammingProfile;
jury1DSetup1.profileName = obj.juryProfile;
distanceControl1.referenceProfile = obj.referenceProfile;
distanceControl1.reference = obj.reference1Djury;
}
if (jury1d.Checked)
{
distanceControl1.Enabled = false;
}
}
public HierarchicalCForm(Options opt, ClusterAlgorithm alg, INPUTMODE mode, bool flag, List <string> profiles)
{
HierarchicalCInput obj = opt.hierarchical;
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(opt.hash);
}
}
public bool CheckAccessibility(profileNode profile,INPUTMODE type)
{
Type t = Type.GetType(internalList[profile]);
InternalProfileBase c = Activator.CreateInstance(t) as InternalProfileBase;
if (c.destination.Contains(type))
return true;
return false;
}
