Java Alignment.getSiteCount方法代码示例

import beast.evolution.alignment.Alignment; //导入方法依赖的package包/类
static public Integer[] guessSizes(Alignment alignment_) {
	Integer[] guessedSizes = new Integer[alignment_.getSiteCount()];
	for (int site = 0; site < alignment_.getSiteCount(); ++site) {
		guessedSizes[site] = 0;
		for (int i : alignment_.getPattern(alignment_.getPatternIndex(site))) {
			if (i >= guessedSizes[site]) {
				guessedSizes[site] = i + 1;
			}
		}
	}
	return guessedSizes;
}
 

import beast.evolution.alignment.Alignment; //导入方法依赖的package包/类
static public CompoundDataType datatype0() {
	Alignment alignment0 = alignment0();
	List<DataType> types = new ArrayList<DataType>();
	Integer[] sizes = new Integer[alignment0.getSiteCount()];
	DataType standard = new StandardData();
	for (int i = 0; i < alignment0.getSiteCount(); ++i) {
		types.add(standard);
		sizes[i] = 2;
	}
	return new CompoundDataType(types, sizes, sizes);
}
 

import beast.evolution.alignment.Alignment; //导入方法依赖的package包/类
String alignmentToString(Alignment data, int iTaxon) throws Exception {
        int[] states = new int[data.getSiteCount()];
        for (int i = 0; i < data.getSiteCount(); i++) {
            int iPattern = data.getPatternIndex(i);
            int[] sitePattern = data.getPattern(iPattern);
            states[i] = sitePattern[iTaxon];
        }

//        for (int i = 0; i < data.getPatternCount(); i++) {
//            int[] sitePattern = data.getPattern(i);
//            states[i] = sitePattern[iTaxon];
//        }
        return data.getDataType().state2string(states);
    }
 

import beast.evolution.alignment.Alignment; //导入方法依赖的package包/类
/** set up relative weights and parameter input **/
   private void setUpOperator() {
   	String weights = "";
   	List<RealParameter> parameters = operator.parameterInput.get();
   	parameters.clear();
   	double commonClockRate = -1;
   	boolean isAllClocksAreEqual = true;
	try {
    	for (int i = 0; i < doc.alignments.size(); i++) {
    		Alignment data = doc.alignments.get(i); 
    		int weight = data.getSiteCount();
    		BranchRateModel.Base clockModel = (BranchRateModel.Base) doc.clockModels.get(i);
    		RealParameter clockRate = clockModel.meanRateInput.get();
    		//clockRate.m_bIsEstimated.setValue(true, clockRate);
    		if (clockRate.isEstimatedInput.get()) {
    			if (commonClockRate < 0) {
    				commonClockRate = clockRate.valuesInput.get().get(0);
    			} else {
    				if (Math.abs(commonClockRate - clockRate.valuesInput.get().get(0)) > 1e-10) {
    					isAllClocksAreEqual = false;
    				}
    			}
   				weights += weight + " ";
    			parameters.add(clockRate);
    		}
    		//doc.autoSetClockRate = false;
    	}
    	if (!fixMeanRatesCheckBox.isSelected()) {
    		fixMeanRatesValidateLabel.setVisible(false);
    		return;
    	}
    	if (parameters.size() == 0) {
    		fixMeanRatesValidateLabel.setVisible(true);
    		fixMeanRatesValidateLabel.m_circleColor = Color.red;
    		fixMeanRatesValidateLabel.setToolTipText("The model is invalid: At least one clock rate should be estimated.");
    		return;
    	}

    	IntegerParameter weightParameter = new IntegerParameter(weights);
		weightParameter.setID("weightparameter");
		weightParameter.isEstimatedInput.setValue(false, weightParameter);
    	operator.parameterWeightsInput.setValue(weightParameter, operator);
    	if (!isAllClocksAreEqual) {
    		fixMeanRatesValidateLabel.setVisible(true);
    		fixMeanRatesValidateLabel.m_circleColor = Color.orange;
    		fixMeanRatesValidateLabel.setToolTipText("Not all clocks are equal. Are you sure this is what you want?");
    	} else if (parameters.size() == 1) {
    		fixMeanRatesValidateLabel.setVisible(true);
    		fixMeanRatesValidateLabel.m_circleColor = Color.orange;
    		fixMeanRatesValidateLabel.setToolTipText("At least 2 clock models should have their rate estimated");
    	} else if (parameters.size() < doc.alignments.size()) {
    		fixMeanRatesValidateLabel.setVisible(true);
    		fixMeanRatesValidateLabel.m_circleColor = Color.orange;
    		fixMeanRatesValidateLabel.setToolTipText("Not all partitions have their rate estimated");
    	} else {
    		fixMeanRatesValidateLabel.setVisible(false);
    	}
		repaint();
   		//doc.autoSetClockRate = true;
	} catch (Exception e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
	}
}
 

import beast.evolution.alignment.Alignment; //导入方法依赖的package包/类
public void initAndValidate() {
    super.initAndValidate();
    alignments = alignmentsInput.get();
    substModels = substModelsInput.get();
    if(alignments.size() != substModels.size()){
        throw new RuntimeException("The number of assignments ("+alignments.size()+") " +
                "does not match up with the the number of models ("+substModels.size()+").");
    }

    ratePointers = ratePointersInput.get();
    rateList = rateListInput.get();
     dpValRate =  dpValRateInput.get();

    int rateCount = rateList.getDimension();

    int alignmentCount = alignments.size();


    siteModelMatrix = (HashMap<Integer, QuietSiteModel>[]) new HashMap[alignmentCount];
    storedSiteModelMatrix = (HashMap<Integer, QuietSiteModel>[]) new HashMap[alignmentCount];

    siteModelCount = (HashMap<Integer,Integer>[]) new HashMap[alignmentCount];
    storedSiteModelCount = (HashMap<Integer,Integer>[]) new HashMap[alignmentCount];

    int totalSiteCount = ratePointers.getDimension();
    siteModelMap = new int[totalSiteCount];
    storedSiteModelMap = new int[totalSiteCount];

    alignmentRef = new int[totalSiteCount];
    int k = 0;
    for(int i = 0; i < alignmentCount; i++){
        siteModelMatrix[i] =  new HashMap<Integer,QuietSiteModel>();
        siteModelCount[i] = new HashMap<Integer, Integer>();

        Alignment alignment = alignments.get(i);
        int siteCount = alignment.getSiteCount();
        ArrayList<Integer> rateIndices = new ArrayList<Integer>();

        for(int j = 0; j < siteCount; j++){
            alignmentRef[k] = i;
            //System.out.println("site: "+k+" "+alignmentRef[k]);
            siteModelMap[k] = ratePointers.getParameter(k).getIDNumber();
            int rateIndex = rateList.indexOf(ratePointers.getParameter(k));
            if(!rateIndices.contains(rateIndex)){
                rateIndices.add(rateIndex);
            }
            if(siteModelCount[i].containsKey(siteModelMap[k])){
                siteModelCount[i].put(siteModelMap[k], siteModelCount[i].get(siteModelMap[k]) + 1);

            }else{
                siteModelCount[i].put(siteModelMap[k],1);
            }
            //System.out.println(i+" "+siteModelCount[i].get(siteModelMap[k]));
            k++;

        }


        for(int j = 0; j < rateCount; j++){
            if(rateIndices.contains(j)){
                QuietRealParameter muParameter = rateList.getParameter(j);
                QuietSiteModel siteModel = new QuietSiteModel(substModels.get(i),muParameter);
                siteModelMatrix[i].put(muParameter.getIDNumber(),siteModel);
                siteModels.add(siteModel);


            }
        }

    }




}