package Obj; import java.io.*; import javax.swing.*; import java.util.*; public class SimObj implements Serializable { // // necessary data , important for each run of simulation // // data comes from project configuration // public ProjObj projInfo; private ProjObj projObj; private String simPath; // the path to the current simulation private String simFilePath; // mainparams file path private String extFilePath; // extraparams file path private boolean isNew = true; private String OUTFILE; private String simName; // the key paramter that could be changed during the runs private int MAXPOPS; // data in the main parameters panel public int BURNIN; public int NUMREPS; // // data in the computational model panel // public boolean FREQSCORR; // data related to FREQSCORR public boolean ONEFST; public float FPRIORMEAN; public float FPRIORSD; public boolean FQSETLAMBDA; public boolean FQINFERLAMBDA; public boolean INDIFQSETLAMBDA; public boolean INDIFQINFERLAMBDA; public boolean NOADMIX; // data related to NOADMIX public boolean USEDEFAULTADMBURNIN; public int ADMBURNIN; public boolean INFERALPHA; // data related to INFERALPHA public float ALPHA; public boolean POPALPHAS; public boolean UNIFPRIORALPHA; public float ALPHAMAX; public float ALPHAPROPSD; public float ALPHAPRIORA; public float ALPHAPRIORB; public boolean RECOMBINE; //data related to RECOMBINE public boolean SITEBYSITE; public float RSTART; public float RSTEP; public float RMAX; public float RMIN; public float RSTD; public boolean MARKOVPHASE; public boolean USEPOPINFO; // data related to USEPOPINFO public int GENSBACK; public float MIGRPRIOR; // for missing popinfo individuals, use which model public boolean POPNOADMIX; public boolean POPRECOMBINE; // // data in the additional parameters model panel // public boolean INFERLAMBDA; //data related to INFERLAMBDA public boolean POPSPECIFICLAMBDA; public float LAMBDA; public boolean COMPUTEPROB; public boolean ANCESTDIST; public boolean PRINTQ; public int NUMBOXES; public float ANCESTPINT; public boolean STARTPOPINFO; public int METROFREQ; public SimObj(ProjObj projObj){ this.projObj = projObj; } public String getConfig(){ String str = new String("#define OUTFILE "+ OUTFILE + "\n"); str += projObj.getConfig(); ///////////////////////////////////////////// // // // print the Running Length // // // ///////////////////////////////////////////// str += new String("#define MAXPOPS " + MAXPOPS +"\n"); str += new String("#define BURNIN " + BURNIN + "\n"); str += new String("#define NUMREPS " + NUMREPS + "\n\n"); ///////////////////////////////////////////// // // // print the ancestry model parameters // // // ///////////////////////////////////////////// if(USEPOPINFO){ str += new String("\n\n#define USEPOPINFO 1 \n"); if(!POPRECOMBINE){ str += new String("#define GENSBACK " + GENSBACK + "\n"); str += new String("#define MIGRPRIOR " + MIGRPRIOR + "\n"); } else{ str += new String("#define GENSBACK 0 \n"); str += new String("#define MIGRPRIOR 0 \n"); } // for individuals without popinfo data, the default model is if(POPRECOMBINE){ str += new String("\n#define LINKAGE 1 \n"); str += new String("#define NOADMIX 0 \n"); if(SITEBYSITE) str += new String("#define SITEBYSITE 1 \n"); else str += new String("#define SITEBYSITE 0 \n"); if(MARKOVPHASE) str += new String("#define MARKOVPHASE 1 \n"); else str += new String("#define MARKOVPHASE 0 \n"); str += new String("#define LOG10RSTART "+ RSTART +"\n"); str += new String("#define LOG10RMAX "+ RMAX +"\n"); str += new String("#define LOG10RMIN "+ RMIN +"\n"); str += new String("#define LOG10RPROPSD "+ RSTD +"\n"); if(USEDEFAULTADMBURNIN) str += new String("#define ADMBURNIN "+ BURNIN/2 +"\n"); else str += new String("#define ADMBURNIN "+ ADMBURNIN + "\n"); }else if(!POPNOADMIX){ str += new String("\n#define NOADMIX 0\n"); str += new String("\n#define LINKAGE 0\n"); if(INFERALPHA){ str += new String("#define INFERALPHA 1\n"); str += new String("#define ALPHA " + ALPHA + "\n"); if(POPALPHAS) str += new String("#define POPALPHAS 1 \n"); else str += new String("#define POPALPHAS 0 \n"); if(UNIFPRIORALPHA){ str += new String("#define UNIFPRIORALPHA 1 \n"); str += new String("#define ALPHAMAX " + ALPHAMAX + "\n"); str += new String("#define ALPHAPROPSD " + ALPHAPROPSD +"\n"); } else { str += new String("#define UNIFPRIORALPHA 0 \n"); str += new String("#define ALPHAPRIORA " + ALPHAPRIORA + "\n"); str += new String("#define ALPHAPRIORB " + ALPHAPRIORB + "\n"); } }else{ str += new String("#define INFERALPHA 0\n"); str += new String("#define ALPHA " + ALPHA + "\n"); } } else { str += new String("\n#define LINKAGE 0\n"); str += new String("#define NOADMIX 1\n"); str += new String("#define ADMBURNIN "+BURNIN/2 +" \n"); } } else if(RECOMBINE){ str += new String("\n#define LINKAGE 1 \n"); str += new String("#define NOADMIX 0 \n"); str += new String("#define USEPOPINFO 0 \n"); if(SITEBYSITE) str += new String("#define SITEBYSITE 1 \n"); else str += new String("#define SITEBYSITE 0 \n"); if(MARKOVPHASE) str += new String("#define MARKOVPHASE 1 \n"); else str += new String("#define MARKOVPHASE 0 \n"); str += new String("#define LOG10RSTART "+ RSTART +"\n"); str += new String("#define LOG10RMAX "+ RMAX +"\n"); str += new String("#define LOG10RMIN "+ RMIN +"\n"); str += new String("#define LOG10RPROPSD "+ RSTD +"\n"); if(USEDEFAULTADMBURNIN) str += new String("#define ADMBURNIN "+ BURNIN/2 +"\n"); else str += new String("#define ADMBURNIN "+ ADMBURNIN + "\n"); } else if (!NOADMIX) { str += new String("\n#define NOADMIX 0\n"); str += new String("#define LINKAGE 0\n"); str += new String("#define USEPOPINFO 0\n"); if(INFERALPHA){ str += new String("#define INFERALPHA 1\n"); str += new String("#define ALPHA " + ALPHA + "\n"); if(POPALPHAS) str += new String("#define POPALPHAS 1 \n"); else str += new String("#define POPALPHAS 0 \n"); if(UNIFPRIORALPHA){ str += new String("#define UNIFPRIORALPHA 1 \n"); str += new String("#define ALPHAMAX " + ALPHAMAX + "\n"); str += new String("#define ALPHAPROPSD " + ALPHAPROPSD +"\n"); } else { str += new String("#define UNIFPRIORALPHA 0 \n"); str += new String("#define ALPHAPRIORA " + ALPHAPRIORA + "\n"); str += new String("#define ALPHAPRIORB " + ALPHAPRIORB + "\n"); } }else{ str += new String("#define INFERALPHA 0\n"); str += new String("#define ALPHA " + ALPHA + "\n"); } } else { str += new String("\n#define LINKAGE 0\n"); str += new String("#define NOADMIX 1\n"); str += new String("#define ADMBURNIN "+BURNIN/2 +" \n"); str += new String("#define USEPOPINFO 0\n"); } ///////////////////////////////////////////// // // // print the frequency model parameters // // // ///////////////////////////////////////////// if(INFERLAMBDA){ str += new String("\n\n#define INFERLAMBDA 1 \n"); str += new String("\n#define FREQSCORR 0\n"); if(POPSPECIFICLAMBDA) str += new String("#define POPSPECIFICLAMBDA 1 \n"); else str += new String("#define POPSPECIFICLAMBDA 0 \n"); str += new String("#define LAMBDA " + LAMBDA + "\n"); }else if(FREQSCORR){ str += new String("\n\n#define FREQSCORR 1 \n"); if(ONEFST) str += new String("#define ONEFST 1\n"); else str += new String("#define ONEFST 0\n"); str += new String("#define FPRIORMEAN " + FPRIORMEAN + "\n"); str += new String("#define FPRIORSD " + FPRIORSD + "\n"); if(FQINFERLAMBDA){ str += new String("\n\n#define INFERLAMBDA 1 \n"); if(POPSPECIFICLAMBDA) str += new String("#define POPSPECIFICLAMBDA 1 \n"); else str += new String("#define POPSPECIFICLAMBDA 0 \n"); str += new String("#define LAMBDA " + LAMBDA + "\n"); }else if(FQSETLAMBDA){ str += new String("\n\n#define INFERLAMBDA 0 \n"); str += new String("#define LAMBDA "+ LAMBDA + "\n"); } }else { str += new String("\n#define FREQSCORR 0\n"); if(INDIFQINFERLAMBDA){ str += new String("\n\n#define INFERLAMBDA 1 \n"); if(POPSPECIFICLAMBDA) str += new String("#define POPSPECIFICLAMBDA 1 \n"); else str += new String("#define POPSPECIFICLAMBDA 0 \n"); str += new String("#define LAMBDA " + LAMBDA + "\n"); }else if(INDIFQSETLAMBDA) str += new String("#define LAMBDA "+ LAMBDA + "\n"); } ///////////////////////////////////////////// // // // print additonal computation parameters // // // ///////////////////////////////////////////// if(COMPUTEPROB) str += new String("#define COMPUTEPROB 1 \n"); else str += new String("#define COMPUTEPROB 0 \n"); if(ANCESTDIST){ str += new String("#define ANCESTDIST 1 \n"); str += new String("#define NUMBOXES " + NUMBOXES + "\n"); str += new String("#define ANCESTPINT " + ANCESTPINT + "\n"); }else { str += new String("#define ANCESTDIST 0 \n"); } if(STARTPOPINFO) str += new String("#define STARTATPOPINFO 1 \n"); else str += new String("#define STARTATPOPINFO 0 \n"); str += new String("#define METROFREQ " + METROFREQ + "\n\n\n"); str += new String("#define UPDATEFREQ 1 \n"); if(PRINTQ){ str += new String("#define PRINTQHAT 1\n"); } return str; } public String printSimInfo(){ String str = new String(""); str+="\n"; str += " ==================== Parameter Set: "+getSimName()+ " ==================== \n\n\n"; str += " Running Length \n\n"; str += " Length of Burnin Period: " + BURNIN + "\n"; str += " Number of MCMC Reps after Burnin: "+ NUMREPS + "\n\n\n"; str += " Ancestry Model Info \n\n"; if(USEPOPINFO){ str += " Use Prior Population Information to Assist Clustering \n"; if(!POPRECOMBINE){ str += " * GENSBACK = " + GENSBACK + "\n"; str += " * MIGRPRIOR = " + MIGRPRIOR +"\n"; } str += " * For Individuals without population information data, use \n"; // for individuals without popinfo data, the default model is if(POPRECOMBINE){ str += " LinkageModel \n"; if(SITEBYSITE) str += " ** Print site-by-site information \n"; if(MARKOVPHASE) str += " ** The phase info follows a Markov model"; str += " ** LOG10(RSTART) = "+ RSTART +"\n"; str += " ** LOG10(RMAX) = "+ RMAX +"\n"; str += " ** LOG10(RMIN) = "+ RMIN +"\n"; str += " ** LOG10(RPROPSD) = "+ RSTD +"\n"; if(USEDEFAULTADMBURNIN) str += " ** Admixture burnin length: "+ BURNIN/2 +"\n"; else str += " ** Admixture burnin length: "+ ADMBURNIN +"\n"; }else if(!POPNOADMIX){ str += " Admixture Model \n"; if(INFERALPHA){ str += " ** Infer Alpha\n"; str += " ** Initial Value of ALPHA (Dirichlet Parameter for Degree of Admixture): " + ALPHA + "\n"; if(POPALPHAS) str += " ** Use Individual Alpha for Each Population\n"; else str += " ** Use Same Alpha for all Populations\n"; if(UNIFPRIORALPHA){ str += " ** Use a Uniform Prior for Alpha\n"; str += " *** Maximum Value for Alpha: " + ALPHAMAX + "\n"; str += " *** SD of Proposal for Updating Alpha: " + ALPHAPROPSD +"\n"; } else { str += " ** Use a Gamma Prior for Alpha \n"; str += " *** A: " + ALPHAPRIORA + "\n"; str += " *** B: " + ALPHAPRIORB + "\n"; } }else{ str += " ** Use Constant Alpha Value\n"; str += " ** Value of Alpha (Dirichlet Parameter for Defree of Admixture): " + ALPHA + "\n"; } } else { str += " No Admixture Model \n\n"; } } else if(RECOMBINE){ str += " Use Linkage Model \n"; if(SITEBYSITE) str += " * Print site-by-site information \n"; if(MARKOVPHASE) str += " * The phase info follows a Markov model \n"; str += " * LOG10(RSTART) = "+ RSTART +"\n"; str += " * LOG10(RMAX) = "+ RMAX +"\n"; str += " * LOG10(RMIN) = "+ RMIN +"\n"; str += " * LOG10(RPROPSD) = "+ RSTD +"\n"; if(USEDEFAULTADMBURNIN) str += " * Admixture burnin length: "+ BURNIN/2 +"\n"; else str += " * Admixture burnin length: "+ ADMBURNIN +"\n"; } else if (!NOADMIX) { str += " Use Admixture Model \n"; if(INFERALPHA){ str += " * Infer Alpha\n"; str += " * Initial Value of ALPHA (Dirichlet Parameter for Degree of Admixture): " + ALPHA + "\n"; if(POPALPHAS) str += " * Use Individual Alpha for Each Population\n"; else str += " * Use Same Alpha for all Populations\n"; if(UNIFPRIORALPHA){ str += " * Use a Uniform Prior for Alpha\n"; str += " ** Maximum Value for Alpha: " + ALPHAMAX + "\n"; str += " ** SD of Proposal for Updating Alpha: " + ALPHAPROPSD +"\n"; } else { str += " * Use a Gamma Prior for Alpha \n"; str += " ** A: " + ALPHAPRIORA + "\n"; str += " ** B: " + ALPHAPRIORB + "\n"; } }else{ str += " * Use Constant Alpha Value\n"; str += " * Value of Alpha (Dirichlet Parameter for Defree of Admixture): " + ALPHA + "\n"; } } else { str += " Use No Admixture Model \n\n"; } str += "\n\n"; str += " Frequency Model Info \n\n"; if(INFERLAMBDA){ str += " Infer Lambda (Allele Frequencies Parameter) \n"; if(POPSPECIFICLAMBDA) str += " * Infer a Separate Lambda for each Population\n"; else str += " * Use a Uniform Lambda for All Population\n"; str += " * Initial Value of Lambda: " + LAMBDA + "\n"; }else if(FREQSCORR){ str += " Allele Frequencies are Correlated among Pops\n"; if(ONEFST) str += " * Assume Same Value of Fst for All Subpopulations\n"; else str += " * Assume Different Values of Fst for Different Subpopulations\n"; str += " * Prior Mean of Fst for Pops: " + FPRIORMEAN + "\n"; str += " * Prior SD of Fst for Pops: " + FPRIORSD + "\n"; if(FQINFERLAMBDA){ str += " * Infer LAMBDA \n"; if(POPSPECIFICLAMBDA) str += " ** Infer a Separate Lambda for each Population\n"; else str += " ** Use a Uniform Lambda for All Population\n"; str += " ** Initial Value of Lambda: " + LAMBDA + "\n"; }else if(FQSETLAMBDA){ str += " * Use Constant Lambda (Allele Frequencies Parameter) \n"; str += " * Value of Lambda: " + LAMBDA + "\n"; } }else { str += " Allele Frequencies are Independent among Pops\n"; if(INDIFQINFERLAMBDA){ str += " * Infer LAMBDA \n"; if(POPSPECIFICLAMBDA) str += " ** Infer a Separate Lambda for each Population\n"; else str += " ** Use a Uniform Lambda for All Population\n"; str += " ** Initial Value of Lambda: " + LAMBDA + "\n"; } else if(INDIFQSETLAMBDA){ str += " * Use Constant Lambda (Allele Frequencies Parameter) \n"; str += " * Value of Lambda: " + LAMBDA + "\n"; } } str += "\n\n"; str += " Advanced Options \n\n"; if(COMPUTEPROB) str += " Estimate the Probability of the Data Under the Model \n"; if(ANCESTDIST){ str += " Collect Data About the Distribution of Ancestry Coefficients Q for each Individual\n"; str += " * Distribution of Q values is Stored as a Histogram with " + NUMBOXES + " Boxes\n"; str += " * Size of the Displayed Probability Interval on Q: " + ANCESTPINT + "\n"; } if(PRINTQ) str += " Print Q-hat\n"; if(STARTPOPINFO) str += " Initialize at POPINFO \n"; str += " Frequency of Metropolis update for Q: " + METROFREQ + "\n\n\n"; return str; } // the result name public String getRstName(){ File f = new File(OUTFILE); return f.getName(); } public boolean isNew(){ return isNew; } public boolean createSimSpace(){ String projPath = projObj.getWorkingPath(); while(true){ simName = JOptionPane.showInputDialog("Please name the new parameter set "); if(simName == null) return false; StringTokenizer st = new StringTokenizer(simName); if(!st.hasMoreTokens()) continue; if(projObj.checkSimName(simName)) break; else JOptionPane.showMessageDialog(null, "The parameter set with name "+simName +" already exists ", "Structure", JOptionPane.ERROR_MESSAGE); } File simDir = new File(projPath,simName); simDir.mkdirs(); simPath = simDir.getAbsolutePath(); File resultDir = new File(simPath,"Results"); if(!resultDir.exists()) resultDir.mkdirs(); File plotDir = new File(simPath,"PlotData"); if(!plotDir.exists()) plotDir.mkdirs(); isNew = false; return true; } public String getSimName(){ return simName; } public String getSimPath(){ return simPath; } // reset simpath every time simObj is loaded public void setSimPath(String path){ simPath = path; } public boolean setOutFile(String filename){ File resultDir = new File(simPath,"Results"); String testname = filename+"_f"; File targetFile = new File(resultDir.getAbsolutePath(),testname); if(targetFile.exists()) return false; OUTFILE = (new File(resultDir.getAbsolutePath(),filename)).getAbsolutePath(); return true; } public void setMAXPOPS(int K){ MAXPOPS = K; } public int getMAXPOPS(){ return MAXPOPS; } public void writeParamFile(){ File paramFile = new File(simPath,"mainparams"); PrintStream out = OpenOutputFile(paramFile); out.println(getConfig()); simFilePath = paramFile.getAbsolutePath(); // create an empty extraparam file File extraFile = new File(simPath,"extraparams"); PrintStream exout = OpenOutputFile(extraFile); exout.println(" "); extFilePath = extraFile.getAbsolutePath(); } public void writeSimFile(){ String simFileName = ".sim" ; // structure project file File f= new File (simPath, simFileName); try { ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream(f)); oos.writeObject(this); oos.close(); }catch( IOException e){ } } static public SimObj loadSimObj(File f){ try{ ObjectInputStream ois = new ObjectInputStream(new FileInputStream(f)); SimObj sim = (SimObj)ois.readObject(); ois.close(); File dir = new File(f.getParent()); sim.setSimPath(dir.getAbsolutePath()); return sim; }catch (IOException e){ JOptionPane.showMessageDialog(null, "Simulation data corrupted", "Error", JOptionPane.ERROR_MESSAGE); System.err.println(e); return null; }catch (ClassNotFoundException cnfe){ JOptionPane.showMessageDialog(null, "Simulation data corrupted", "Error", JOptionPane.ERROR_MESSAGE); return null; } } public String getParamFile(){ return simFilePath; } public String getExtraFile(){ return extFilePath; } private static PrintStream OpenOutputFile(File file){ PrintStream out; try { // try to open output file as well... out = new PrintStream(new FileOutputStream(file)); } catch (FileNotFoundException e) { System.err.println("**Error: unable to open output file."); out = null; }//try-catch catch (SecurityException e) { System.err.println("**Error: no permission to write output file."); out = null; }//try-catch catch (IOException e) { System.err.println("**Error: unknown error opening output file."); out = null; }//try-catch return out; } public boolean equals(SimObj obj){ return ( BURNIN == obj.BURNIN && NUMREPS == obj.NUMREPS && FREQSCORR == obj.FREQSCORR && ONEFST == obj.ONEFST && FPRIORMEAN == obj.FPRIORMEAN && FPRIORSD == obj.FPRIORSD && NOADMIX == obj.NOADMIX && ADMBURNIN == obj.ADMBURNIN && INFERALPHA == obj.INFERALPHA && ALPHA == obj.ALPHA && POPALPHAS == obj.POPALPHAS && UNIFPRIORALPHA == obj.UNIFPRIORALPHA && ALPHAMAX == obj.ALPHAMAX && ALPHAPROPSD == obj.ALPHAPROPSD && ALPHAPRIORA == obj.ALPHAPRIORA && ALPHAPRIORB == obj.ALPHAPRIORB && RECOMBINE == obj.RECOMBINE && SITEBYSITE == obj.SITEBYSITE && RSTART == obj.RSTART&& RMAX == obj.RMAX&& RMIN == obj.RMIN&& RSTD == obj.RSTD&& USEPOPINFO == obj.USEPOPINFO && GENSBACK == obj.GENSBACK && MIGRPRIOR == obj.MIGRPRIOR && INFERLAMBDA == obj.INFERLAMBDA && POPSPECIFICLAMBDA == obj.POPSPECIFICLAMBDA && LAMBDA == obj.LAMBDA && COMPUTEPROB == obj.COMPUTEPROB && ANCESTDIST == obj.ANCESTDIST && NUMBOXES == obj.NUMBOXES && ANCESTPINT == obj.ANCESTPINT && STARTPOPINFO == obj.STARTPOPINFO && METROFREQ == obj.METROFREQ && INDIFQSETLAMBDA == obj.INDIFQSETLAMBDA && INDIFQINFERLAMBDA == obj.INDIFQINFERLAMBDA && FQSETLAMBDA == obj.FQSETLAMBDA && FQINFERLAMBDA == obj.FQINFERLAMBDA && USEDEFAULTADMBURNIN == obj.USEDEFAULTADMBURNIN&& POPNOADMIX == obj.POPNOADMIX && POPRECOMBINE == obj.POPRECOMBINE && PRINTQ == obj.PRINTQ ); } public void setProjObj(ProjObj proj){ this.projObj = proj; } public ProjObj getProjObj(){ return projObj; } private void writeObject(ObjectOutputStream out) throws IOException { out.defaultWriteObject(); } private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException{ in.defaultReadObject(); } }