/
MolDefs.pas
2111 lines (1977 loc) · 69.8 KB
/
MolDefs.pas
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unit MolDefs;
interface
uses Classes, SysUtils, {$IFNDEF FPC}Graphics,{$ENDIF} Dialogs;
const
Nucleotides = 'ACGT';
NucNames : array[1..4] of string = ('Adenine','Cytosine','Guanine','Thymine');
{ The amino acids are listed in alphabetical order by the 3 letter code }
AminoAcids = 'ARNDCQEGHILKMFPSTWYV';
AminoAcid3 : array[1..20] of string[3] = ('Ala','Arg','Asn','Asp','Cys',
'Gln','Glu','Gly','His','Ile','Leu','Lys','Met','Phe','Pro',
'Ser','Thr','Trp','Tyr','Val');
AANames : array[1..20] of string = ('Alanine','Arginine','Asparagine',
'Aspartic Acid','Cysteine','Glutamine','Glutamic Acid','Glycine',
'Histidine','Isoleucine','Leucine','Lysine','Methionine',
'Phenylalanine','Proline','Serine','Threonine','Tryptophan',
'Tyrosine','Valine');
DayhoffMat : array[1..20,1..20] of integer =
((9867,1,4,6,1,3,10,21,1,2,3,2,1,1,13,28,22,0,1,13),
(2,9913,1,0,1,9,0,1,8,2,1,37,1,1,5,11,2,2,0,2),
(9,1,9822,42,0,4,7,12,18,3,3,25,0,1,2,34,13,0,3,1),
(10,0,36,9859,0,5,56,11,3,1,0,6,0,0,1,7,4,0,0,1),
(3,1,0,0,9973,0,0,1,1,2,0,0,0,0,1,11,1,0,3,3),
(8,10,4,6,0,9876,35,3,20,1,6,12,2,0,8,4,3,0,0,2),
(17,0,6,53,0,27,9865,7,1,2,1,7,0,0,3,6,2,0,1,2),
(21,0,6,6,0,1,4,9935,0,0,1,2,0,1,2,16,2,0,0,3),
(2,10,21,4,1,23,2,1,9912,0,4,2,0,2,5,2,1,0,4,3),
(6,3,3,1,1,1,3,0,0,9872,22,4,5,8,1,2,11,0,1,57),
(4,1,1,0,0,3,1,1,1,9,9947,1,8,6,2,1,2,0,1,11),
(2,19,13,3,0,6,4,2,1,2,2,9926,4,0,2,7,8,0,0,1),
(6,4,0,0,0,4,1,1,0,12,45,20,9874,4,1,4,6,0,0,17),
(2,1,1,0,0,0,0,1,2,7,13,0,1,9946,1,3,1,1,21,1),
(22,4,2,1,1,6,3,3,3,0,3,3,0,0,9926,17,5,0,0,3),
(35,6,20,5,5,2,4,21,1,1,1,8,1,2,12,9840,32,1,1,2),
(32,1,9,3,1,2,2,3,1,7,3,11,2,1,4,38,9871,0,1,10),
(0,8,1,0,0,0,0,0,1,0,4,0,0,3,0,5,0,9976,2,0),
(2,0,4,0,3,0,1,0,4,1,2,1,0,28,0,2,2,1,9945,2),
(18,1,1,1,2,1,2,5,1,33,15,1,4,0,2,2,9,0,1,9901));
type
TDataTypes = (dtNucleotide, dtAminoAcid);
TNucModels = (nmJC, nmK2, nmEqInp, nmHKY, nmGenRes);
TAAModels = (amPoisson, amDayhoff);
TIndelDistType = (idtPoisson, idtPower);
TAAFreqs = array[1..20] of double;
TSqNucMat = array[1..4,1..4] of double;
TSqAAMat = array[1..20,1..20] of double;
TDoubleArray = array of array of double;
TIntArray = array of integer;
TDArray = array of double;
TIndelModel = class
private
fActive : boolean;
fDist : TIndelDistType;
fRate : double;
fSize : double;
fPower : double;
fSizeProb : TDArray;
function GetSizeProb(i : integer) : double;
function FromPowerDistribution(var seed : integer) : integer;
procedure InitPowerDistribution;
public
property IsActive : boolean read fActive;
property Dist : TIndelDistType read fDist;
property Rate : double read fRate;
property Size : double read fSize;
property Powre : double read fPower;
property SizeProb[i : integer] : double read GetSizeProb;
constructor Create;
destructor Destroy; override;
function NewIndel(var seed : integer) : integer;
procedure SetModel(NewType : TIndelDistType; NewRate,NewSize,NewPower : double);
end;
{-----Substitution Model Declarations-----}
TSubstitutionModel = class
private
fTotalRate : double;
fRate : double; // Substitution rate per site
fIsGamma : boolean; // Are we using a gamma distribution?
fGammaA : double; // gamma parameter
fInsertionModel : TIndelModel;
fDeletionModel : TIndelModel;
fAlpha : double; // transition rate
fBeta : double; // transversion rate
fAA : TAAFreqs; // Frequency of amino acids
GenResParams, // parameters for the general reversible model
NucTransMat : TSqNucMat;
// SiteRates : array of double;
RelRate : array[1..4] of double;
// AATransMat : TSqAAMat;
// function Dayhoff_Sub(t : double; var seed : integer; x : char) : char;
procedure CalcNucTransMat;
procedure SetupSiteRates(seq : string);
procedure SetRelRates;
function NewAminoAcid(x : char; var seed : integer) : char;
function NewNucleotide(x : char; var seed : integer) : char;
//function NewNucleotide2(CMat : TSqNucMat; x : char; var seed : integer) : char;
//function FindSite (var seed : integer): integer;
function FindSite (var seed : integer; seq : string): integer;
procedure AdjustTotalRate(site : integer; oldnuc,newnuc : char);
function GetTransRatio : double;
function GetKappa : double;
function GetAAf(i : integer) : double;
procedure PutAAf(i : integer; freq : double);
procedure SetPowerDistribution(P : TDArray; a,b : double);
public
DataType : TDataTypes; // Nucleotide or Amino Acid data?
NucModel : TNucModels; // Which nuclear model are we using?
AAModel : TAAModels; // Which amino acid model are we using?
fNuc : array[1..4] of double; // Frequency of nucleotides
GammaRates : array of extended;
//alpha2,beta2 : double;
property AAFreq[i : integer] : double read GetAAf write PutAAf;
property Alpha : double read fAlpha write fAlpha;
property Beta : double read fBeta write fBeta;
property Rate : double read fRate write fRate;
property IsGamma : boolean read fIsGamma;
property GammaA : double read fGammaA;
property Insertions : TIndelModel read fInsertionModel write fInsertionModel;
property Deletions : TIndelModel read fDeletionModel write fDeletionModel;
property TRatio : double read GetTransRatio; { transition/transversion ratio }
property kappa : double read GetKappa;
//procedure CalcPMat(var CMat : TSqNucMat; t : double);
constructor Create;
destructor Destroy; override;
function Simulate(expected : double; var realized,seed : integer; Sequence : string;
var InsSite,InsSize : TIntArray; IndList : TStringList) : string;
//function Simulate2(brlength : double; var seed : integer; Sequence : string) : string;
procedure SetupNucFreq(fa,fc,fg,ft : double);
procedure SetGenRes(pAC,pAG,pAT,pCG,pCT,pGT : double); // setup paramaters for general reversible model
procedure SetGamma(a : double; n : integer; var seed : integer);
procedure SetGammaDesc(a : double; n : integer; var seed : integer;
OldRates : array of extended);
procedure CopyGamma(a : double; OldRates : array of extended);
end;
{-----Gene Declarations-----}
TGene = class
public
Name,
Sequence : string;
Expected : double;
Observed,
Realized : integer;
SubstitutionModel : TSubstitutionModel;
constructor create;
end;
{-----Tree Declarations-----}
TNode = class
{ Add ability to include other characters are trait values }
public
Genes : TList;
Name : string;
BrLength : double;
Ancestor : TNode;
Descendents : TList;
constructor create;
destructor Destroy; override;
procedure AddChild(newchild : TNode);
procedure SetGeneNumber(n : integer);
end;
TDrawnNode = record
startx,endx,yp : integer;
LNode : TNode;
end;
TDrawRecs = array of TDrawnNode;
TSubRec = record
SNode : TNode;
SModel : TSubstitutionModel;
end;
TSubList = array of TSubRec;
{ Essential math functions }
FUNCTION gammln(xx: real): real;
FUNCTION ran3(VAR idum: integer): extended;
FUNCTION gasdev(VAR idum: integer): double;
FUNCTION poidev(xm: real; VAR idum: integer): real;
function rand(var seed : integer; lo,hi:integer):integer;
function NewGam(alpha : double; var seed : integer) : extended;
function NewGamma(alpha : double; var seed : integer) : extended;
PROCEDURE indexx(n: integer; VAR arrin: TDArray;
VAR indx: TIntArray);
{ Sequence functions }
function RandomNucSequence(n : integer; var seed : integer; ga,gc,gg,gt : double) : string;
function RandomAASequence(n : integer; var seed : integer; ExpAAF : TAAFreqs) : string;
procedure CalcNucF(seq : string; var fa,fc,fg,ft : double);
procedure CalcAAF(seq : string; var AAFreqs : TAAFreqs);
procedure CalcDDMatrix(seqs : TStringList; var DDMat : TDoubleArray);
function CountNonGapSites(seq : string) : integer;
function InsertGapIntoSequence(seq : string; ISites,ILengths : TIntArray) : string;
{ Tree functions }
procedure WriteTreePar(node : TNode; dat : byte; gene : integer; blformat : string; var parout : string);
procedure ReadTreePar(tree : string; var start : TNode);
procedure ReadTreeKumar(inname : string; var tree : TNode);
procedure ReadTreeNodal(inname : string; var Tree : TNode);
procedure ClearSequences(node : TNode);
function FindRootNode(node : TNode) : TNode;
function IsDescendent(a,d : TNode) : boolean;
function AreSiblings(n1,n2 : TNode) : boolean;
function AncestorToDescendentDistance(A,D : TNode) : double;
function DistanceonTree(n1,n2 : TNode) : double;
function CountTips(node : TNode) : integer;
procedure LadLeft(node : TNode);
procedure LadRight(node : TNode);
function MaxNodeTipLength(node : TNode) : double;
function MaxNodeName(node : TNode) : string;
{$IFNDEF FPC}
function DrawTree(canv : TCanvas; var cnt : integer; minx,maxx,miny,maxy : integer; tree : TNode;
scale : double; DoLabels,DoBrLen : boolean; lines : TDrawRecs) : integer;
{$ENDIF}
procedure SetSubMatrix(node : TNode; gene : integer; SM : TSubstitutionModel);
//procedure CalcExpectedChanges(node : TNode; gn,n : integer);
function WriteExpectedChanges(node : TNode; gene : integer; blformat,outp : string) : string;
function WriteObservedChanges(node : TNode; gene : integer; outp : string) : string;
function WriteRealizedChanges(node : TNode; gene : integer; outp : string) : string;
function LowDivergence(node : TNode) : boolean;
function LowAADiv(node : TNode) : boolean;
procedure SimulateOnTree(tree : TNode; var seed : integer; IndList : TStringList);
procedure WriteTipSequences(Tree : TNode; var OutP : TStringList);
procedure WriteTipSequencesGene(Tree : TNode; gn : integer; var OutP : TStringList);
procedure WriteTipNames(Tree : TNode; var outp : string; pref : string);
procedure GetTipNames(Tree : TNode; outp : TStringList; pref : string);
procedure CreateNodeList(Tree : TNode; NodeList : TList);
procedure OutputInternalNodes(Tree : TNode; NodeList : TStringList);
procedure OutputAllNodes(Tree : TNode; NodeList : TStringList);
procedure OutputNodeSequences(Tree : TNode; NodeList : TStringList; SeqList : TStringList);
procedure AddInsertionsToTree(Tree,Base : TNode; GeneN : integer;
InsSite,InsSize : TIntArray);
procedure GetTipNodes(Tree : TNode; NodeList : TList);
procedure GetModelList(Node : TNode; GeneN : integer; ModelList : TList);
procedure AddNewGammaRates(SubModel : TSubstitutionModel; ISites,ILengths : TIntArray);
procedure UpdateTreeGamma(TreeNode : TNode; GeneN : integer; ISites,ILengths : TIntArray);
function CalcExpected(SModel : TSubstitutionModel; nsites : integer;
BrLength,ga,gc,gg,gt : double) : double;
procedure CalcJCParameter(rate : double; var alpha : double);
procedure CalcK2Parameters(rate,transratio : double; var alpha,beta : double);
procedure CalcEqInpParameters(rate,fa,fc,fg,ft : double; var alpha : double);
procedure CalcHKYParameters(rate,transratio,fa,fc,fg,ft : double; var alpha,beta : double);
procedure CalcGenResParameters(rate,fa,fc,fg,ft : double; var Pac,Pag,Pat,Pcg,Pct,Pgt : double);
{ Random # generator variables }
var
Ran3Inext,Ran3Inextp: integer;
Ran3Ma: array[1..55] of extended;
PoidevOldm,PoidevSq,PoidevAlxm,PoidevG: extended;
GamNa,GamNd,GamNc : double;
GasdevIset: integer;
GasdevGset: extended;
implementation
Uses Math;
{---------------From Numerical Recipes---------------}
FUNCTION gammln(xx: real): real;
CONST
stp = 2.50662827465;
VAR
x,tmp,ser: double;
BEGIN
x := xx-1.0;
tmp := x+5.5;
tmp := (x+0.5)*ln(tmp)-tmp;
ser := 1.0+76.18009173/(x+1.0)-86.50532033/(x+2.0)+24.01409822/(x+3.0)
-1.231739516/(x+4.0)+0.120858003e-2/(x+5.0)-0.536382e-5/(x+6.0);
gammln := tmp+ln(stp*ser)
END;
PROCEDURE indexx(n: integer; VAR arrin: TDArray; VAR indx: TIntArray);
LABEL 99;
VAR
l,j,ir,indxt,i: integer;
q: real;
BEGIN
FOR j := 1 TO n DO
indx[j] := j;
IF n = 1 THEN GOTO 99;
l := (n DIV 2) + 1;
ir := n;
WHILE true DO BEGIN
IF l > 1 THEN BEGIN
l := l-1;
indxt := indx[l];
q := arrin[indxt]
END
ELSE BEGIN
indxt := indx[ir];
q := arrin[indxt];
indx[ir] := indx[1];
ir := ir-1;
IF ir = 1 THEN BEGIN
indx[1] := indxt;
GOTO 99
END
END;
i := l;
j := l+l;
WHILE j <= ir DO BEGIN
IF j < ir THEN
IF arrin[indx[j]] < arrin[indx[j+1]] THEN j := j+1;
IF q < arrin[indx[j]] THEN BEGIN
indx[i] := indx[j];
i := j;
j := j+j
END
ELSE
j := ir+1
END;
indx[i] := indxt
END;
99:
END;
{----------Random Number Generator----------}
FUNCTION ran3(VAR idum: integer): extended;
CONST
mbig = 4.0e6;
mseed = 1618033.0;
mz = 0.0;
fac = 2.5e-7;
VAR
i,ii,k: integer;
mj,mk: extended;
BEGIN
IF idum < 0 THEN BEGIN
mj := mseed+idum;
IF mj >= 0.0 THEN
mj := mj-mbig*trunc(mj/mbig)
ELSE
mj := mbig-abs(mj)+mbig*trunc(abs(mj)/mbig);
Ran3Ma[55] := mj;
mk := 1;
FOR i := 1 TO 54 DO BEGIN
ii := 21*i MOD 55;
Ran3Ma[ii] := mk;
mk := mj-mk;
IF mk < mz THEN mk := mk+mbig;
mj := Ran3Ma[ii]
END;
FOR k := 1 TO 4 DO BEGIN
FOR i := 1 TO 55 DO BEGIN
Ran3Ma[i] := Ran3Ma[i]-Ran3Ma[1+((i+30) MOD 55)];
IF Ran3Ma[i] < mz THEN Ran3Ma[i] := Ran3Ma[i]+mbig
END
END;
Ran3Inext := 0;
Ran3Inextp := 31;
idum := 1
END;
Ran3Inext := Ran3Inext+1;
IF Ran3Inext = 56 THEN
Ran3Inext := 1;
Ran3Inextp := Ran3Inextp+1;
IF Ran3Inextp = 56 THEN Ran3Inextp := 1;
mj := Ran3Ma[Ran3Inext]
-Ran3Ma[Ran3Inextp];
IF mj < mz THEN mj := mj+mbig;
Ran3Ma[Ran3Inext] := mj;
ran3 := mj*fac
END;
{----------Random Numbers from Normal Distribution----------}
FUNCTION gasdev(VAR idum: integer): double;
VAR
fac,r,v1,v2: double;
BEGIN
IF GasdevIset = 0 THEN BEGIN
REPEAT
v1 := 2.0*ran3(idum)-1.0;
v2 := 2.0*ran3(idum)-1.0;
r := sqr(v1)+sqr(v2);
UNTIL (r < 1.0) AND (r > 0.0);
fac := sqrt(-2.0*ln(r)/r);
GasdevGset := v1*fac;
gasdev := v2*fac;
GasdevIset := 1
END
ELSE BEGIN
GasdevIset := 0;
gasdev := GasdevGset;
END
END;
{----------Random Numbers from Poisson Distribution----------}
FUNCTION poidev(xm: real; VAR idum: integer): real;
CONST
pi = 3.141592654;
VAR
em,t,y: real;
BEGIN
IF xm < 12.0 THEN BEGIN
IF xm <> PoidevOldm THEN BEGIN
PoidevOldm := xm;
PoidevG := exp(-xm)
END;
em := -1;
t := 1.0;
REPEAT
em := em+1.0;
t := t*ran3(idum);
UNTIL t <= PoidevG
END
ELSE BEGIN
IF xm <> PoidevOldm THEN BEGIN
PoidevOldm := xm;
PoidevSq := sqrt(2.0*xm);
PoidevAlxm := ln(xm);
PoidevG := xm*PoidevAlxm
-gammln(xm+1.0)
END;
REPEAT
REPEAT
y := pi*ran3(idum);
y := sin(y)/cos(y);
em := PoidevSq*y+xm;
UNTIL em >= 0.0;
em := trunc(em);
t := 0.9*(1.0+sqr(y))*exp(em*PoidevAlxm-gammln(em+1.0)-PoidevG);
UNTIL ran3(idum) <= t
END;
poidev := em
END;
{------------------------------}
function NewGam(alpha : double; var seed : integer) : extended;
var
v,x,u : extended;
done : boolean;
begin
if (alpha <> GamNa) then begin
GamNd := alpha - 1.0 / 3.0;
GamNc := 1.0 / sqrt(9.0 * GamNd);
end;
done := false;
repeat
repeat
x := GasDev(Seed);
v := 1.0 + GamNc * x;
until (v > 0.0);
//v := v*v*v;
v := IntPower(v,3);
u := ran3(seed);
if (u < 1.0-0.0331*(sqr(x)*sqr(x))) or
(log10(u) < 0.5*sqr(x)+GamNd*(1.0-v+log10(v))) then done := true;
until done;
result := GamNd * v;
end;
function NewGamma(alpha : double; var seed : integer) : extended;
begin
if (alpha <= 0.0) then result := sqrt(-1)
else if (alpha < 1.0) then
result := NewGam(1.0+alpha,seed) * power(ran3(seed),1.0/alpha)
else if (alpha > 1.0) then result := NewGam(alpha,seed)
else result := -log10(ran3(seed));
end;
{-----------Uniform Random Integer Between lo and hi----------}
function rand(var seed : integer; lo,hi:integer):integer;
begin
rand := trunc(ran3(seed) * (hi - lo + 1)) + lo;
end;
{----------Insertion/Deletion Models----------}
constructor TIndelModel.Create;
begin
inherited Create;
fActive := false;
fRate := 10;
fSize := 4;
fPower := 1;
fSizeProb := nil;
fDist := idtPoisson;
end;
destructor TIndelModel.Destroy;
begin
fSizeProb := nil;
end;
function TIndelModel.GetSizeProb(i : integer) : double;
begin
if (i > 0) and (i <= length(fSizeProb)) then
result := fSizeProb[i-1]
else result := 0.0;
end;
function TIndelModel.NewIndel(var seed : integer) : integer;
begin
case fDist of
idtPoisson : result := round(PoiDev(Size-1.0,seed)) + 1;
idtPower : result := FromPowerDistribution(seed);
else result := 1;
end;
end;
function TIndelModel.FromPowerDistribution(var seed : integer) : integer;
var
p,s : double;
i,m : integer;
begin
m := length(fSizeProb);
p := ran3(seed);
i := 1;
s := SizeProb[i];
while (p > s) and (i < m) do begin
inc(i);
s := s + SizeProb[i];
end;
result := i;
end;
procedure TIndelModel.SetModel(NewType : TIndelDistType;
NewRate,NewSize,NewPower : double);
begin
fActive := true;
fDist := NewType;
fRate := NewRate;
fSize := NewSize;
fPower := NewPower;
if (fDist = idtPower) then InitPowerDistribution;
end;
procedure TIndelModel.InitPowerDistribution;
var
m,i: Integer;
s : double;
begin
// currently the length of 100 is a temporary value that should be replaced
// by a variable
m := 100;
SetLength(fSizeProb,m);
s := 0.0;
for i := 0 to m - 1 do begin
fSizeProb[i] := fRate * power(i+1,fPower);
s := s + fSizeProb[i];
end;
for i := 0 to m - 1 do fSizeProb[i] := fSizeProb[i] / s;
end;
{----------Substitution Model----------}
constructor TSubstitutionModel.Create;
begin
inherited create;
// SiteRates := nil;
GammaRates := nil;
{ defaults }
DataType := dtNucleotide;
NucModel := nmJC;
fIsGamma := false;
fInsertionModel := TIndelModel.Create;
fDeletionModel := TIndelModel.Create;
end;
destructor TSubstitutionModel.Destroy;
begin
// SiteRates := nil;
GammaRates := nil;
fInsertionModel.Free;
fDeletionModel.Free;
inherited destroy;
end;
function TSubstitutionModel.Simulate(expected : double; var realized,seed : integer;
Sequence : string; var InsSite,InsSize : TIntArray; IndList : TStringList) : string;
var
r,i,j,o,l,ss : integer;
oldn : char;
e : double;
tempseq,inseq : string;
begin
InsSite := nil; InsSize := nil;
{ Setup transition matrix }
SetRelRates;
case DataType of
dtNucleotide : begin
case NucModel of
nmJC : begin
for i := 1 to 4 do fNuc[i] := 0.25;
beta := alpha;
end;
nmK2 : for i := 1 to 4 do fNuc[i] := 0.25;
nmEqInp : beta := alpha;
end;
CalcNucTransMat;
end;
end;
SetupSiteRates(sequence);
Realized := round(PoiDev(Expected,seed));
for i := 1 to Realized do begin
r := FindSite(seed,Sequence);
oldn := Sequence[r];
case DataType of
dtNucleotide : Sequence[r] := NewNucleotide(Sequence[r],seed);
dtAminoAcid : case AAModel of
amPoisson : Sequence[r] := NewAminoAcid(Sequence[r],seed);
// amDayhoff : Sequence[r] := Dayhoff_Sub(seed,Sequence[i]);
end;
end;
if (DataType = dtNucleotide) then
case NucModel of
nmEqInp,nmHKY,nmGenRes : AdjustTotalRate(r,oldn,Sequence[r]);
end;
end;
// deletion events
if Deletions.IsActive then begin
e := Realized / Deletions.Rate;
o := round(PoiDev(e,seed));
for i := 1 to o do begin
r := rand(seed,1,length(Sequence));
l := Deletions.NewIndel(seed);
for j:= 1 to l do begin
if (r <= length(Sequence)) then begin
while (Sequence[r] = '-') and (r < length(Sequence)) do inc(r);
Sequence[r] := '-';
end;
end;
IndList.Add(IntToStr(l));
end;
end;
// insertion events
if Insertions.IsActive then begin
e := Realized / Insertions.Rate;
o := round(PoiDev(e,seed));
for i := 1 to o do begin
repeat
r := rand(seed,1,length(Sequence));
until (Sequence[r] <> '-');
l := Insertions.NewIndel(seed);
SetLength(InsSite,length(InsSite)+1);
SetLength(InsSize,length(InsSize)+1);
j := length(InsSite) - 1;
InsSite[j] := r;
InsSize[j] := l;
inseq := RandomNucSequence(l,seed,FNuc[1],FNuc[2],FNuc[3],FNuc[4]);
tempseq := Sequence;
if (r < length(Sequence)) then begin
Sequence := Copy(tempseq,1,r) + inseq + Copy(tempseq,r+1,length(tempseq));
if fIsGamma then begin
j := length(GammaRates);
//SetLength(GammaRates,j + l);
SetLength(GammaRates,length(Sequence));
//for ss := j + l - 1 downto r + l - 1 do GammaRates[ss] := GammaRates[ss - l];
for ss := length(Sequence) - 1 downto r + l - 1 do GammaRates[ss] := GammaRates[ss - l];
for ss := r to r + l - 1 do GammaRates[ss] := NewGamma(GammaA,seed);
end;
end else begin
Sequence := tempseq + inseq;
if fIsGamma then begin
j := length(GammaRates);
//SetLength(GammaRates,j + l);
//for ss := j to j + l - 1 do GammaRates[ss] := NewGamma(GammaA,seed);
SetLength(GammaRates,length(Sequence));
for ss := j to length(Sequence) - 1 do GammaRates[ss] := NewGamma(GammaA,seed);
end;
end;
IndList.Add(IntToStr(l));
end;
end;
result := Sequence;
end;
procedure TSubstitutionModel.SetRelRates;
var
i,j : integer;
begin
if (DataType = dtNucleotide) then
case NucModel of
nmJC,nmK2 : for i := 1 to 4 do relrate[i] := 1.0;
nmEqInp : for i := 1 to 4 do
relrate[i] := alpha * (1.0 - fNuc[i]);
nmHKY : begin
relrate[1] := beta * (fNuc[2] + fNuc[4]) + alpha * fNuc[3];
relrate[2] := beta * (fNuc[1] + fNuc[3]) + alpha * fNuc[4];
relrate[3] := beta * (fNuc[2] + fNuc[4]) + alpha * fNuc[1];
relrate[4] := beta * (fNuc[1] + fNuc[3]) + alpha * fNuc[2];
end;
nmGenRes : for i := 1 to 4 do begin
relrate[i] := 0.0;
for j := 1 to 4 do
if (i <> j) then
relrate[i] := relrate[i] + GenResParams[i,j] * fNuc[j];
end;
end;
end;
procedure TSubstitutionModel.SetupSiteRates(seq : string);
var
i,n : integer;
NCnt : array[1..4] of integer;
begin
n := length(seq);
fTotalRate := 0.0;
if IsGamma then begin
for i := 0 to n - 1 do
if (seq[i+1] <> '-') then
fTotalRate := fTotalRate + GammaRates[i] * relrate[Pos(seq[i+1],Nucleotides)];
end else begin
case DataType of
dtNucleotide : case NucModel of
nmJc,nmK2 : fTotalRate := CountNonGapSites(seq);
else begin
{ count curent frequencies }
for i := 1 to 4 do NCnt[i] := 0;
for i := 1 to n do
if (seq[i] <> '-') then
inc(Ncnt[Pos(Seq[i],Nucleotides)]);
for i := 1 to 4 do fTotalRate := fTotalRate + NCnt[i] * RelRate[i];
end;
end;
dtAminoAcid : fTotalRate := n;
end;
end;
end;
procedure TSubstitutionModel.AdjustTotalRate(site : integer; oldnuc,newnuc : char);
var
gam : double;
begin
// Relase 1.0.3 fixed bug where the following line had GammaRates[site]
// rather than GammaRates[site-1]
if IsGamma then gam := GammaRates[site-1]
else gam := 1.0;
fTotalRate := fTotalRate - gam *
(relrate[Pos(oldnuc,Nucleotides)] - relrate[Pos(newnuc,Nucleotides)]);
end;
{procedure TSubstitutionModel.CalcPMat(var CMat : TSqNucMat; t : double);
var
bigP : array[1..4] of double;
kap,
u,w,x,y,z,p,bP,min4beta : double;
i,j : integer;
begin
bigP[1] := fNuc[1] + fNuc[3];
bigP[2] := fNuc[2] + fNuc[4];
bigP[3] := fNuc[1] + fNuc[3];
bigP[4] := fNuc[2] + fNuc[4];
min4beta := -4.0 * beta2;
//min4beta := -4.0;
kap := alpha2 / beta2;
for i := 1 to 4 do begin
for j := 1 to 4 do begin
bP := bigP[j];
p := fNuc[j];
u := (1.0 / bP) - 1.0;
w := min4beta * (1.0 + bP * (kap - 1.0));
x := exp(min4beta * t);
y := exp(w * t);
z := (bP - p) / bP;
if (i = j) then
CMat[i,j] := p + p * u * x + z * y
else if ((i = 1) and (j = 3)) or ((i = 3) and (j = 1)) or
((i = 2) and (j = 4)) or ((i = 4) and (j = 2)) then
CMat[i,j] := p + p * u * x - (p / bP) * y
else CMat[i,j] := p * (1.0 - x);
end;
end;
end;}
{function TSubstitutionModel.NewNucleotide2(CMat : TSqNucMat; x : char; var seed : integer) : char;
var
i : integer;
s,P : double;
begin
P := ran3(seed);
i := 0; s := 0.0;
repeat
inc(i);
s := s + CMat[Pos(x,Nucleotides),i];
until (P <= s) or (i = 4);
result := Nucleotides[i];
end;}
{function TSubstitutionModel.Simulate2(brlength : double; var seed : integer;
Sequence : string) : string;
var
i : integer;
r : double;
ChMat : TSqNucMat;
begin
for i := 1 to length(Sequence) do begin
//if IsGamma then r := SiteRates[i] else
r := 1.0;
CalcPMat(ChMat,brlength*r);
Sequence[i] := NewNucleotide2(ChMat,Sequence[i],seed);
end;
result := Sequence;
end;}
function TSubstitutionModel.GetTransRatio : double;
begin
case NucModel of
nmJC,nmEqInp : result := 0.5;
nmHKY,nmK2 : result := alpha / (2.0 * beta);
else result := 0.5;
end;
end;
function TSubstitutionModel.GetKappa : double;
begin
case NucModel of
nmJC,nmEqInp : result := 1.0;
nmHKY,nmK2 : result := alpha / beta;
else result := 1.0;
end;
end;
procedure TSubstitutionModel.SetupNucFreq(fa,fc,fg,ft : double);
begin
FNuc[1] := fa; FNuc[2] := fc; FNuc[3] := fg; FNuc[4] := ft;
end;
function TSubstitutionModel.GetAAf(i : integer) : double;
begin
result := fAA[i];
end;
procedure TSubstitutionModel.PutAAf(i : integer; freq : double);
begin
fAA[i] := freq;
end;
procedure TSubstitutionModel.CopyGamma(a : double; OldRates : array of extended);
var
i : integer;
begin
FIsGamma := true;
FGammaA := a;
SetLength(GammaRates,length(OldRates));
for i := 0 to length(OldRates) - 1 do GammaRates[i] := OldRates[i];
end;
procedure TSubstitutionModel.SetGamma(a : double; n : integer; var seed : integer);
var
i : integer;
begin
FIsGamma := true;
FGammaA := a;
SetLength(GammaRates,n);
{ calculate a gamma value for each site }
for i := 0 to n - 1 do GammaRates[i] := NewGamma(GammaA,seed);
end;
procedure TSubstitutionModel.SetGammaDesc(a : double; n : integer; var seed : integer;
OldRates : array of extended);
var
i : integer;
tempold,temprates : TDArray;
newind,oldind : TIntArray;
begin
FIsGamma := true;
FGammaA := a;
SetLength(temprates,n+1);
SetLength(tempold,n+1);
SetLength(newind,n+1);
SetLength(oldind,n+1);
{ calculate a gamma value for each site }
for i := 1 to n do begin
temprates[i] := NewGamma(GammaA,seed);
tempold[i] := Oldrates[i-1];
end;
indexx(n,temprates,newind);
indexx(n,tempold,oldind);
// similarly placed rates go in same spot
SetLength(GammaRates,n);
for i := 1 to n do begin
GammaRates[oldind[i]-1] := temprates[newind[i]];
end;
tempold := nil; temprates := nil;
newind := nil; oldind := nil;
end;
procedure TSubstitutionModel.SetPowerDistribution(P : TDArray; a,b : double);
var
i: Integer;
s : double;
begin
// currently the length of 100 is a temporary value that should be replaced
// by a variable
SetLength(P,101);
s := 0.0;
for i := 1 to 100 do begin
P[i] := a * power(i,b);
s := s + P[i];
end;
for i := 1 to 100 do P[i] := P[i] / s;
end;
procedure TSubstitutionModel.SetGenRes(pAC,pAG,pAT,pCG,pCT,pGT : double);
var
i : integer;
begin
for i := 1 to 4 do GenResParams[i,i] := 0.0;
GenResParams[1,2] := pAC; GenResParams[2,1] := pAC;
GenResParams[1,3] := pAG; GenResParams[3,1] := pAG;
GenResParams[1,4] := pAT; GenResParams[4,1] := pAT;
GenResParams[2,3] := pCG; GenResParams[3,2] := pCG;
GenResParams[2,4] := pCT; GenResParams[4,2] := pCT;
GenResParams[3,4] := pGT; GenResParams[4,3] := pGT;
end;
function TSubstitutionModel.FindSite(var seed : integer; seq : string) : integer;
var
i : integer;
runtot,P : extended;
begin
//try
repeat
P := ran3(seed) * fTotalRate;
i := 0; runtot := 0.0;
repeat
inc(i);
if (seq[i] <> '-') then begin
if IsGamma then
runtot := runtot + GammaRates[i-1] * relrate[Pos(seq[i],Nucleotides)]
else runtot := runtot + relrate[Pos(seq[i],Nucleotides)];
end;
until (P <= runtot) or (i = length(Seq));
result := i;
until (seq[i] <> '-');
//except on EMathError do begin end; //DoOver := true;
//end;
end;
procedure TSubstitutionModel.CalcNucTransMat;
var
i,j : integer;
total : double;
begin
for i := 1 to 4 do begin
total := 0.0;
case NucModel of
nmK2 : total := alpha + 2.0 * beta;
nmEqInp : for j := 1 to 4 do if (j <> i) then
total := total + alpha * fNuc[j];
nmHKY : for j := 1 to 4 do if (j <> i) then
if ((i = 1) and (j = 3)) or ((i = 3) and (j = 1)) or
((i = 2) and (j = 4)) or ((i = 4) and (j = 2)) then
total := total + alpha * fNuc[j]
else total := total + beta * fNuc[j];
nmGenRes : for j := 1 to 4 do if (j <> i) then
total := total + GenResParams[i,j] * fNuc[j];
end;
for j := 1 to 4 do begin
if (i = j) then NucTransMat[i,j] := 0.0
else case NucModel of
nmJC : NucTransMat[i,j] := 1.0 / 3.0;
nmK2 : if ((i = 1) and (j = 3)) or ((i = 3) and (j = 1)) or
((i = 2) and (j = 4)) or ((i = 4) and (j = 2)) then
NucTransMat[i,j] := alpha / total
else NucTransMat[i,j] := beta / total;
nmEqInp : NucTransMat[i,j] := (alpha * fNuc[j]) / total;
nmHKY : if ((i = 1) and (j = 3)) or ((i = 3) and (j = 1)) or
((i = 2) and (j = 4)) or ((i = 4) and (j = 2)) then
NucTransMat[i,j] := (alpha * fNuc[j]) / total
else NucTransMat[i,j] := (beta * fNuc[j]) / total;
nmGenRes : NucTransMat[i,j] := (GenResParams[i,j] * fNuc[j]) / total;
end;
end;
end;
end;
function TSubstitutionModel.NewAminoAcid(x : char; var seed : integer) : char;
var
r : integer;
begin
repeat
r := rand(seed,1,20);
until (r <> pos(x,AminoAcids));
result := AminoAcids[r];
end;
function TSubstitutionModel.NewNucleotide(x : char; var seed : integer) : char;
var
i : integer;
s,P : double;