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/**
* Title: ProAlign<p>
* Description: <p>
* Copyright: Copyright (c) Ari Loytynoja<p>
* License: GNU GENERAL PUBLIC LICENSE<p>
* @see http://www.gnu.org/copyleft/gpl.html
* Company: ULB<p>
* @author Ari Loytynoja
* @version 1.0
*/
package proalign;
import java.util.HashMap;
public class ParameterEstimates {
String[][] pairs;
HashMap seqs;
PwAlignment pwa;
ParameterEstimates(ResultWindow rw,SetParameters sp) {
this.seqs = rw.seqs;
PwSubstitutionMatrix psm = new PwSubstitutionMatrix();
String pwAlphabet;
int[][] pwSubst;
int gOpen, gExt;
if(ProAlign.isDna){
pwAlphabet = psm.dnaAlphabet;
pwSubst = psm.swdna;
gOpen = -1*rw.pa.pwDnaOpen;
gExt = -1*rw.pa.pwDnaExt;
} else {
pwAlphabet = psm.protAlphabet;
if(rw.pa.pwProtMatrix.equals("pam60")) {
pwSubst = psm.pam60;
} else if(rw.pa.pwProtMatrix.equals("pam160")) {
pwSubst = psm.pam160;
} else if(rw.pa.pwProtMatrix.equals("pam250")) {
pwSubst = psm.pam250;
} else {
pwSubst = psm.pam120;
}
gOpen = -1*rw.pa.pwProtOpen;
gExt = -1*rw.pa.pwProtExt;
}
pwa = new PwAlignment(pwSubst,gOpen,gExt,pwAlphabet,ProAlign.isDna);
pairs = rw.root.getTerminalPairNames();
this.estimate();
sp.textDelta.setText((""+ProAlign.modelDelta+" ").substring(0,5));
sp.textEpsil.setText((""+ProAlign.modelEpsilon+" ").substring(0,5));
}
ParameterEstimates(RunCommandLine rcl) {
ProAlign.log("ParameterEstimates");
AlignmentNode root = rcl.root;
seqs = rcl.pa.seqs;
pwa = rcl.pwa;
pairs = root.getTerminalPairNames();
this.estimate();
}
void estimate() {
double gapFreq = 0d;
double sumDelta = 0d;
double sumEpsilon = 0d;
for(int i=0; i<pairs.length; i++) {
String s0 = (String)seqs.get(pairs[i][0]);
String s1 = (String)seqs.get(pairs[i][1]);
String[] revSeq = pwa.revAligned(s0,s1);
int all = 0;
int ms = 0; // match sum
int mn = 1; // match numebr
int ml = 0; // match length
int gs = 0;
int gn = 1;
int gl = 0;
double mm = 5d; // match mean
double mg = 5d;
boolean isM = false;
for(int k=0; k<revSeq[0].length(); k++) {
if(k==0) {
if(revSeq[0].charAt(k)=='-' || revSeq[1].charAt(k)=='-') {
gn++;
} else {
mn++;
}
}
if(revSeq[0].charAt(k)=='-' || revSeq[1].charAt(k)=='-') {
gs++;
gl++;
if(isM) {
if(k>0) {
if(mn>1) {
mm = ((double)mm*(mn-1)+ml)/mn;
} else {
mm = (mm+ml)/2;
}
ml=0;
gn++;
}
isM = false;
}
} else {
ms++;
ml++;
if(!isM) {
if(k>0) {
if(gn>1) {
mg = ((double)mg*(gn-1)+gl)/gn;
} else {
mg = (mg+gl)/2;
}
gl=0;
mn++;
}
isM = true;
}
}
if(k+1==revSeq[0].length()) {
if(isM) {
if(mn>1) {
mm = ((double)mm*(mn-1)+ml)/mn;
} else {
mm = ml;
}
} else {
if(gn>1) {
mg = ((double)mg*(gn-1)+gl)/gn;
} else {
mg = gl;
}
}
}
all++;
}
gapFreq += (double)gs/(2*all);
sumDelta += mm;
sumEpsilon += mg;
}
gapFreq /= pairs.length;
sumDelta /= pairs.length;
sumEpsilon /= pairs.length;
if(ProAlign.estimateDelta) {
ProAlign.modelDelta = 0.5d/(sumDelta+1);
ProAlign.log.println(" HMM delta estimate: "+ProAlign.modelDelta);
// System.out.println("modelDelta: "+ProAlign.modelDelta);
}
if(ProAlign.estimateEpsilon) {
ProAlign.modelEpsilon = (1d-1d/(sumEpsilon+1));
ProAlign.log.println(" HMM epsilon estimate: "+ProAlign.modelEpsilon);
// System.out.println("modelEpsilon: "+ProAlign.modelEpsilon);
}
if(ProAlign.estimateGapFreq) {
ProAlign.gapFreq = gapFreq;
ProAlign.log.println(" gap frequency estimate: "+ProAlign.gapFreq);
// System.out.println("gapFreq: "+ProAlign.gapFreq);
}
if(ProAlign.estimateGapProb) {
if(ProAlign.isDna) {
ProAlign.gapProb = gapFreq/4d;
} else {
ProAlign.gapProb = gapFreq/20d;
}
ProAlign.log.println(" gap probability estimate: "+ProAlign.gapProb);
// System.out.println("gapProb: "+ProAlign.gapProb);
}
}
}
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