//Command Handler
public void ExecuteCommand(CommandConsole c, ReturnArgs retArgs, string[] swtchs, List<string> outputFeed)
{
ArgClass existRef = null;
if (this._argName != "")
{
// existRef = (from ArgClass r in c._argRefs
// where (r is Reference) && r.FullName == this.FullName
// select r).ToList<ArgClass>();
existRef = c.GetReference(this);
}
var existClass = (from ArgClass r in c._argRefs
where !(r is Reference) && r.FullName == "" + this.Prefix
select r).FirstOrDefault();
bool hasParenths = this._suffix != null && this._suffix[this._suffix.Length - 1] == ')', stdOut = false, stdEx = false;
bool hasFunction = false;
if (this.ArgName != null)
hasFunction = this.Parent._funcs.ContainsKey(this.ArgName);
List<ArgClass> refChain = new List<ArgClass> { this };
if (this._dotHierarchy.Length > 1)
refChain = existClass.GetReferenceChain(this._dotHierarchy, this._dotHierarchy[this._dotHierarchy.Length - 1]);
//ArgClass rf, fnc;
//this.GetObjectFunction(this, refChain, out rf, out fnc);
//if (hasFunction && (rf == null || fnc == null))
// return;
Reference er = null;
if (existRef != null && existRef is Reference)
er = (Reference)existRef;
if (hasParenths)
{
////////////////////
if (existRef == null && !hasFunction)
{
bool? cnstrct = this.AttemptConstruct(c, er, retArgs, swtchs, outputFeed);
if (cnstrct.HasValue && cnstrct.Value)
{
if (existRef == null)
{
c.AddReference(this);
outputFeed.Add("'" + this.FullName + "' was constructed.");
return;
}
}
else
{
//if (!cnstrct.HasValue)
outputFeed.Add("'" + this.FullName + "' was unable to be constructed.");
return;
}
}
//////////////////////////
bool? b = null;
if (!hasFunction)
b = this.ExecuteCall(c, er, retArgs, swtchs, outputFeed);
else
b = this._parRef._funcs[this._argName](c, this, retArgs, swtchs, outputFeed);
stdEx = b.HasValue && b.Value;
if (!stdEx)
return;
}
//Handle no class
if (existClass == null)
return;
if (!stdEx && this._argName == null)
{
outputFeed.Add("'" + this.FullName + "' is a type.");
return;
}
//Handleno reference
if (!stdEx && (existClass == null || existRef == null))
{
if (!hasFunction)
outputFeed.Add("'" + this.FullName + "' is null.");
else
outputFeed.Add("'" + this.FullName + "' must be called with ().");
return;
}
else if (!stdEx)
stdOut = true;
//Standard output from object
if (stdOut || stdEx)
{
if (stdOut)
{
var o = this.StandardOutput;
if (o != null && o != "")
outputFeed.Add(o);
else
outputFeed.Add("'" + this.FullName + "' is instantiated.");
}
if (stdEx)
outputFeed.Add("'" + this.FullName + "' was called.");
return;
}
return;
}
public virtual bool? AttemptConstruct(CommandConsole c, Reference existRef, ReturnArgs retArgs, string[] sws, List<string> outputFeed)
{
return false;
}
//Functions
public override bool? ExecuteCall(CommandConsole c, Reference existRef, ReturnArgs retArgs, string[] swtchs, List<string> outputFeed)
{
return false;
}
//Functions
public virtual bool? ExecuteCall(CommandConsole c, Reference existRef, ReturnArgs retArgs, string[] swtchs, List<string> outputFeed)
{
outputFeed.Add("'" + this.FullName + "' was called.");
return false;
}
public Reference HandleCommand(CommandConsole c, ReturnArgs args, string req, List<string> outputFeed)
{
if (req == null || c == null || req.Length == 0)
return null;
//Vars
string[] dotArgs;
string argName = null, suffix = null, dblprfx = null;
int sindent = 0, pindent = 0;
//Get Prefix
//var prfxArg = (from LineArgumentHandler la in c._argTypes
// where la.Prefix == req[0]
// select la).FirstOrDefault();
if (this._prefix.HasValue && this._prefix.Value != req[0])
return null;
if (this._prefix.HasValue)
pindent++;
//Get Double prefix
if (req.Length > 2)
{
dblprfx = ArgClass.GetDoublePrefix(req.Substring(pindent, 2));
if (dblprfx != null)
pindent += 2;
}
//Suffix
if (req.Length >= pindent + 2)
{
int ind1 = req.IndexOf(@"(");
if (ind1 != -1)
{
int ind2 = req.IndexOf(@")", ind1);
if (ind1 != -1 && ind2 != -1)
suffix = ArgClass.GetSuffix(req.Substring(ind1, (ind2 - ind1) + 1));
}
}
if (suffix != null)
sindent += suffix.Length;
//Get next invalid char, if same as indented, then
int invChar = ArgClass.GetInvalidCharIndex(pindent, req, ".", true);
if (invChar == pindent && invChar < req.Length - sindent)
return null;
//Get Dot Hiearchy and final argument
string ss = req.Substring(pindent, req.Length - sindent - pindent), ss2 = null;
if (this._prefix.HasValue)
ss2 = this._prefix.Value + "." + ss;
dotArgs = ss2.Split(new char[] { '.' }, StringSplitOptions.RemoveEmptyEntries);
if (dotArgs.Length > 1)
argName = dotArgs[dotArgs.Length - 1];
if (argName != null)
{
int i = ArgClass.GetInvalidCharIndex(argName);
if (i != -1)
{
outputFeed.Add("'" + argName[i] + "' is an invalid character.");
return null;
}
}
ArgClass par = this;
if (argName != null && argName != "")
{
var ch1 = this.GetReferenceChain(dotArgs, dotArgs[dotArgs.Length - 2]);
if (ch1 == null)
{
outputFeed.Add("'" + ss + "' is null or invalid.");
return null;
}
var ch2 = ch1[ch1.Count - 1];
par = ch2;
}
//Get boolean states
//bool refsObj =
return this.CreateNewReference(par, dotArgs, argName, dblprfx, suffix);
}
public override bool? AttemptConstruct(CommandConsole c, Reference r, CommandConsole.ReturnArgs retArgs, string[] sws, List<string> outputFeed)
{
var a = (string)null;
if (sws.Length > 0)
for (int i = 0; i < AlphabetTypes.Length; i++)
if (sws.Contains<string>(AlphabetTypes[i]))
{
a = Alphabets[i];
break;
}
bool hasFile = false;
bool? longOutput = false;
var hasFileType = -1;
var s = "";
if (sws.Contains<string>("show"))
longOutput = true;
else if (sws.Contains<string>("hide"))
longOutput = null;
if (this._conParams.Length > 0)
s = this._conParams[0];
var p = c.WorkingDirectory + "\\" + s;
if (this._conParams != null && this._conParams.Length > 0)
{
if (File.Exists(p))
{
hasFile = true;
for (int i = 0; i < ValidFileTypes.Length; i++)
if (ValidFileTypes[i] == s.Substring(s.Length - ValidFileTypes[i].Length, ValidFileTypes[i].Length))
{
hasFileType = i;
break;
}
}
}
if (hasFileType != -1)
{
var f = Management.GetTextFromFile(p);
List<string> fasta = new List<string>(), seqs = new List<string>(), o = new List<string>();
if (ValidFileTypes[hasFileType] == "fasta" || ValidFileTypes[hasFileType] == "txt")
{
bool startFound = false, endStartFound = false;
for (int i = 0; i < f.Length; i++)
{
//f[i] = f[i].Replace(@", ", "; ");
//f[i] = f[i].Replace(@",", "-");
if (f[i].Contains(">"))
{
endStartFound = false;
fasta.Add(f[i].Trim());
seqs.Add("");
o.Add(f[i].Trim());
startFound = true;
if (true || f[i].Contains("]") || sws.Contains<string>("literal"))
endStartFound = true;
continue;
}
if (startFound & !endStartFound)
{
if (!f[i].Contains("]"))
{
fasta[fasta.Count - 1] += f[i].Trim();
continue;
}
else
{
var ind = f[i].IndexOf("]");
fasta[fasta.Count - 1] += f[i].Substring(0, ind).Trim();
seqs[seqs.Count - 1] += f[i].Substring(ind, f[i].Length - ind).Trim();
endStartFound = true;
continue;
}
}
if (endStartFound)
{
if (!f[i].Contains(">"))
{
seqs[seqs.Count - 1] += f[i].Trim();
continue;
}
else
{
i--;
startFound = false;
continue;
}
}
/*
while (i < f.Length && !f[i].Contains(">"))
{
var addStr = (string)null;
if (a != null)
addStr = StateSequence.RemoveInvalidAlphas(f[i], a);
else
addStr = f[i];
seqs[seqs.Count - 1] += addStr;
i++;
}
o.Add(seqs[seqs.Count - 1]);
i--;
*/
/*
if ((i + 2) % 2 == 0)
fasta.Add(f[i]);
else
seqs.Add(f[i]);
//outputFeed.Add(f[i]);*/
}
}
else if (ValidFileTypes[hasFileType] == "txt2")
{
for (int i = 0; i < f.Length; i++)
{
fasta.Add("");
seqs.Add(f[i]);
//outputFeed.Add(f[i]);
}
}
this._allFasta = fasta;
this._allSeqs = seqs;
List<string> t = null;
if (a != null)
{
t = new List<string>();
for (int i = 0; i < a.Length; i++)
t.Add("" + a[i]);
}
this._myAlpha.AddMessageSamples(this._allSeqs, t);
this._myAlpha.UpdateInfo();
var rs = "";
if (fasta.Count > 0)
rs += fasta.Count + " fasta lines";
if (fasta.Count > 0 && seqs.Count > 0)
rs += " and ";
if (seqs.Count > 0)
rs += seqs.Count + " sequence lines";
if (rs.Length > 0)
rs += " were loaded into object '" + this.FullName + "'.";
else
{
outputFeed.Add("No sequence data was found in the requested file.");
return false;
}
if (longOutput != null && ((!longOutput.Value && o.Count < 350) || longOutput.Value))
outputFeed.AddRange(o);
outputFeed.AddRange(new string[] { "", rs });
return true;
}
else if (hasFile)
{
outputFeed.Add("'" + this._conParams[0] + "' is an invalid file type");
return false;
}
outputFeed.Add("Invalid parameters");
return false;
}
//Override Functions
public override bool? ExecuteCall(CommandConsole c, Reference existRef, CommandConsole.ReturnArgs retArgs, string[] swtchs, List<string> outputFeed)
{
if (this._argName == null)
return this.Parent.ExecuteCall(c, existRef, retArgs, swtchs, outputFeed);
return false;
}
public SeqRef(CommandConsole.ArgClass par, string[] dotHierarchy, string name, string dblprfx, string sfx)
: base(par, dotHierarchy, name, dblprfx, sfx)
{
}
public override bool? ExecuteCall(CommandConsole c, Reference existRef, CommandConsole.ReturnArgs retArgs, string[] swtchs, List<string> outputFeed)
{
return base.ExecuteCall(c, existRef, retArgs, swtchs, outputFeed);
}
public override Reference CreateNewReference(CommandConsole.ArgClass par, string[] dotHierarchy, string name, string dblprfx, string sfx)
{
return new SeqRef(par, dotHierarchy, name, dblprfx, sfx);
}
public static bool? ToCSV(CommandConsole c, Reference existRef, CommandConsole.ReturnArgs retArgs, string[] swtchs, List<string> outputFeed)
{
var sr = (SeqRef)existRef.Parent;
var n = sr.ArgName;
if (n == null || n == "")
{
outputFeed.Add("parameter required: file name");
return false;
}
n += ".csv";
var ss = new List<string[]>();
for (int i = 0; i < sr.AllFasta.Count; i++)
{
var s = new string[] { sr.AllFasta[i], sr.AllSeqs[i] };
ss.Add(s);
}
try
{
Management.WriteTextToCSVFile(c.WorkingDirectory + @"\" + n, ss.ToArray<string[]>(), false);
}
catch (Exception e)
{
outputFeed.Add("unable to write csv file.");
return false;
}
var o = Management.GetTextFromFile(c.WorkingDirectory + @"\" + n);
return true;
}
public static bool? FuncStats(CommandConsole c, Reference existRef, CommandConsole.ReturnArgs retArgs, string[] swtchs, List<string> outputFeed)
{
SeqRef sr = null;
if (existRef.Parent is SeqRef)
{
sr = (SeqRef)existRef.Parent;
//outputFeed.AddRange(((SeqRef)existRef.Parent).OutputText);
}
var a = sr.MyAlphabet;
var infos = a.MyInfo;
var allStates = new List<string>();
for (int i = 0; i < infos.Length; i++)
{
var infoI = infos[i];
infoI.UpdateInfo();
for (int j = 0; j < infoI.States.Count; j++)
allStates.Add(infoI.States[j]);
}
var allProbs = new List<List<double>>();
for (int i = 0; i < infos.Length; i++)
{
allProbs.Add(new List<double>());
for (int j = 0; j < allStates.Count; j++)
{
var queryState = allStates[j];
if (queryState.Length == infos[i].StateLength)
{
var tind = infos[i].States.IndexOf(queryState);
if (tind != -1)
allProbs[i].Add(infos[i].StateProbabilities[tind]);
}
}
}
var r = new List<string>();
var max = 0;
for (int i = 0; i < allProbs.Count; i++)
{
max = Math.Max(allProbs[i].Count, max);
}
for (int i = 0; i < allStates.Count; i++)
{
for (int j = 0; j < infos.Length; j++)
{
if (r.Count <= i)
r.Add(allStates[i]);
var curState = allStates[i];
var curInfo = infos[j];
if (curInfo.StateLength == curState.Length)
{
var tind = infos[j].States.IndexOf(curState);
r[i] += ("\t\t" + curInfo.StateProbabilities[tind].ToString("E5").PadRight(16));
}
else
r[i] += ("\t\t-").PadRight(16);
continue;
}
}
var ts = 0;
/*
for (int i = 0; i < allProbs.Count; i++)
{
for (int j = 0; j < max; j++)
{
if (r.Count <= j)
r.Add(allStates[j]);
var s = "";
if (j >= allProbs[i].Count)
s = " - ";
else
{
s = ("" + Math.Round(allProbs[i][j], 4));
if (s.Contains('.'))
s = s.Substring(1, s.Length - 2);
}
r[j] += ("\t\t" + s.PadRight(16));
}
}*/
r.Insert(0, "State");
for (int i = 0; i < infos.Length; i++)
r[0] += "\t\tProbability(n=" + infos[i].StateLength + ")";
outputFeed.AddRange(r);
return true;
}