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Java MesquiteString.setValue方法代碼示例

本文整理匯總了Java中mesquite.lib.MesquiteString.setValue方法的典型用法代碼示例。如果您正苦於以下問題：Java MesquiteString.setValue方法的具體用法？Java MesquiteString.setValue怎麽用？Java MesquiteString.setValue使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類mesquite.lib.MesquiteString的用法示例。


在下文中一共展示了MesquiteString.setValue方法的8個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Java代碼示例。

示例1: processInfoFile

import mesquite.lib.MesquiteString; //導入方法依賴的package包/類
public static void processInfoFile(String infoFilePath, MesquiteString fullName, MesquiteString voucherCode){
	String s = MesquiteFile.getFileContentsAsString(infoFilePath); 
	Document doc = XMLUtil.getDocumentFromString(s);
	if (doc == null) {  // must be old format
		fullName.setValue(s);
	} else {
		Element rootElement = doc.getRootElement();
		Element chromaseqElement = rootElement.element("chromaseq");
		if (chromaseqElement != null) {
			String versionString = chromaseqElement.attributeValue("version");
			int versionInXml = MesquiteInteger.fromString(versionString);
			if (versionInXml==infoFileVersion) {
				Element processedFolderElement = chromaseqElement.element("processedFolder");
				Element sampleElement = processedFolderElement.element("sample");
				String name = sampleElement.attributeValue("fullName");
				if (fullName!=null) fullName.setValue(name);
				String voucher = sampleElement.attributeValue("voucherCode");
				if (voucherCode!=null) voucherCode.setValue(voucher);
			}

		}
	}

}
開發者ID:MesquiteProject，項目名稱:Chromaseq，代碼行數:25，代碼來源:ChromaseqInfoFile.java

示例2: calculateNumber

import mesquite.lib.MesquiteString; //導入方法依賴的package包/類
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString){
	if (result==null)
		return;
	result.setToUnassigned();
	Taxa taxa = taxon.getTaxa();
	int it = taxon.getIndex();
	clearResultAndLastResult(result);
	int count = 0;
	for (int im = 0; im < getProject().getNumberCharMatrices(taxa); im++){
		CharacterData data = getProject().getCharacterMatrix(taxa, im);
		if (data.hasDataForTaxon(it)){
			count++;
		}
	}
	result.setValue(count);

	if (resultString!=null){
			resultString.setValue(result.toString());
	}
	saveLastResult(result);
	saveLastResultString(resultString);
}
開發者ID:MesquiteProject，項目名稱:Chromaseq，代碼行數:23，代碼來源:NumMatricesWithDataForTaxon.java

示例3: getTerminals

import mesquite.lib.MesquiteString; //導入方法依賴的package包/類
public static int getTerminals(Element element, String[] names, boolean[] leaves, boolean[] hasChildren, MesquiteString termName, MesquiteInteger c) {
	boolean isNode = isNode(element);
	boolean isName = "Name".equalsIgnoreCase(element.getName());
	List children = element.content();
	Iterator iterator = children.iterator();
	int terms = 0;
	while (iterator.hasNext()) {
		Object o = iterator.next();
		if (isName){
			if (o instanceof CDATA) {
				termName.setValue(((CDATA)o).getText());
			}
		}
		else if (o instanceof Element) {
			Element e = (Element)o;
			if (isContinuable(e))
				terms += getTerminals((Element) o, names, leaves,hasChildren, termName, c);
		}
	}
	if (isNode && terms == 0) {

		names[c.getValue()] =  new String(termName.getValue()); //element.getAttributeValue("NAME");
		if (isLeaf(element))
			leaves[c.getValue()] = true;
		else
			leaves[c.getValue()] = false;
		if (hasChildren(element))
			hasChildren[c.getValue()] = true;
		else
			hasChildren[c.getValue()] = false;
		c.increment();
		return 1;
	}
	else 
		return terms;

}
開發者ID:MesquiteProject，項目名稱:MesquiteArchive，代碼行數:38，代碼來源:ToLUtil.java

示例4: getTerminals

import mesquite.lib.MesquiteString; //導入方法依賴的package包/類
public static int getTerminals(Element element, String[] names, boolean[] leaves, boolean[] hasChildren, MesquiteString termName, MesquiteInteger c) {
	boolean isNode = isNode(element);
	boolean isName = "Name".equalsIgnoreCase(element.getName());
	List children = element.getContent();
	Iterator iterator = children.iterator();
	int terms = 0;
	while (iterator.hasNext()) {
		Object o = iterator.next();
		if (isName){
			if (o instanceof CDATA) {
				termName.setValue(((CDATA)o).getText());
			}
		}
		else if (o instanceof Element) {
			Element e = (Element)o;
			if (isContinuable(e))
				terms += getTerminals((Element) o, names, leaves,hasChildren, termName, c);
		}
	}
	if (isNode && terms == 0) {

		names[c.getValue()] =  new String(termName.getValue()); //element.getAttributeValue("NAME");
		if (isLeaf(element))
			leaves[c.getValue()] = true;
		else
			leaves[c.getValue()] = false;
		if (hasChildren(element))
			hasChildren[c.getValue()] = true;
		else
			hasChildren[c.getValue()] = false;
		c.increment();
		return 1;
	}
	else 
		return terms;

}
開發者ID:MesquiteProject，項目名稱:MesquiteArchive，代碼行數:38，代碼來源:ToLUtil.java

示例5: calculateNumber

import mesquite.lib.MesquiteString; //導入方法依賴的package包/類
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString){
	if (result==null)
		return;
	result.setToUnassigned();
	clearResultAndLastResult(result);
	Taxa taxa = taxon.getTaxa();
	int it = taxa.whichTaxonNumber(taxon);
	if (taxa != currentTaxa || observedStates == null ) {
		observedStates = matrixSourceTask.getCurrentMatrix(taxa);
		currentTaxa = taxa;
	}
	if (observedStates==null)
		return;
	DNAData data = (DNAData)observedStates.getParentData();

	result.setValue(0);
	if (data!=null) {
		AceFile ace = AceFile.getAceFile(this, data, it);
		if (ace!=null)
			result.setValue(ace.getNumReads());
	}




	if (resultString!=null)
		resultString.setValue("Number of reads "+ observedStates.getName()  + ": " + result.toString());
	saveLastResult(result);
	saveLastResultString(resultString);
}
開發者ID:MesquiteProject，項目名稱:Chromaseq，代碼行數:31，代碼來源:NumberOfReads.java

示例6: calculateNumber

import mesquite.lib.MesquiteString; //導入方法依賴的package包/類
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString){
	if (result==null)
		return;
	clearResultAndLastResult(result);
	Taxa taxa = taxon.getTaxa();
	int it = taxa.whichTaxonNumber(taxon);
	if (taxa != currentTaxa || observedStates == null ) {
		observedStates = matrixSourceTask.getCurrentMatrix(taxa);
		currentTaxa = taxa;
	}
	if (observedStates==null)
		return;
	DNAData data = (DNAData)observedStates.getParentData();
	CharInclusionSet inclusion = null;
	if (data !=null)
		inclusion = (CharInclusionSet)data.getCurrentSpecsSet(CharInclusionSet.class);
	int numChars = observedStates.getNumChars();
	int charExc = 0;
	int tot = 0;
	int count = 0;
	double value = 0.0;
	if (numChars != 0) {
		for (int ic = 0; ic<data.getNumChars(); ic++) {
			if (inclusion == null || inclusion.isBitOn(ic)){
				long s = data.getState(ic,it);
				if (!CategoricalState.isUnassigned(s) && !CategoricalState.isInapplicable(s)) {
						if (s == A || s == T || s == AT) //monomorphic A or T or A&T or uncertain A or T
							tot++;
						else if (s == C || s == G || s == CG) { //monomorphic C or G or C&G or uncertain C or G
							tot++;
							count++;
						}
					
				}
			} else
				charExc++;
		}
		if (tot == 0)
			value = 0;
		else
			value = ((double)count)/tot;
		result.setValue(value);
	}	
	String exs = "";
	if (charExc > 0)
		exs = " (" + Integer.toString(charExc) + " characters excluded)";

	
	if (resultString!=null)
		resultString.setValue("Proportion of CG in taxon "+ observedStates.getName() + exs + ": " + result.toString());
	saveLastResult(result);
	saveLastResultString(resultString);
}
開發者ID:MesquiteProject，項目名稱:MesquiteArchive，代碼行數:54，代碼來源:CGBiasOfTaxon.java

示例7: getTerminalsWithAuthors

import mesquite.lib.MesquiteString; //導入方法依賴的package包/類
public static int getTerminalsWithAuthors(Element element, String[] names, String[] authors, boolean[] leaves, boolean[] hasChildren, MesquiteString termName,MesquiteString authorName, MesquiteInteger c) {
	boolean isNode = isNode(element);
	boolean isName = "Name".equalsIgnoreCase(element.getName());
	boolean isAuthor = "Authority".equalsIgnoreCase(element.getName());
	List children = element.content();
	Iterator iterator = children.iterator();
	int terms = 0;
	while (iterator.hasNext()) {
		Object o = iterator.next();
		if (isName){
			if (o instanceof CDATA) {
				termName.setValue(((CDATA)o).getText());
			}
		}
		else if (isAuthor){
			if (o instanceof CDATA) {
				authorName.setValue(((CDATA)o).getText());
			}
		}
		else if (o instanceof Element) {
			Element e = (Element)o;
			if (isContinuable(e))
				terms += getTerminals((Element) o, names, leaves,hasChildren, termName, c);
		}
	}
	if (isNode && terms == 0) {

		names[c.getValue()] =  new String(termName.getValue()); //element.getAttributeValue("NAME");
		authors[c.getValue()] =  new String(authorName.getValue()); //element.getAttributeValue("NAME");
		if (isLeaf(element))
			leaves[c.getValue()] = true;
		else
			leaves[c.getValue()] = false;
		if (hasChildren(element))
			hasChildren[c.getValue()] = true;
		else
			hasChildren[c.getValue()] = false;
		c.increment();
		return 1;
	}
	else 
		return terms;

}
開發者ID:MesquiteProject，項目名稱:MesquiteArchive，代碼行數:45，代碼來源:ToLUtil.java

示例8: calculateNumber

import mesquite.lib.MesquiteString; //導入方法依賴的package包/類
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString){
	if (result==null)
		return;
	clearResultAndLastResult(result);
	Taxa taxa = taxon.getTaxa();
	int it = taxa.whichTaxonNumber(taxon);
	if (taxa != currentTaxa || observedStates == null ) {
		observedStates = matrixSourceTask.getCurrentMatrix(taxa);
		currentTaxa = taxa;
	}
	if (observedStates==null)
		return;
	DNAData data = (DNAData)observedStates.getParentData();
	CharInclusionSet inclusion = null;
	if (data !=null)
		inclusion = (CharInclusionSet)data.getCurrentSpecsSet(CharInclusionSet.class);
	int numChars = observedStates.getNumChars();
	int charExc = 0;
	int tot = 0;
	int count = 0;
	double value = 0.0;
	if (numChars != 0) {
		for (int ic = 0; ic<data.getNumChars(); ic++) {
			if (inclusion == null || inclusion.isBitOn(ic)){
				long s = data.getState(ic,it);
				if (!CategoricalState.isUnassigned(s) && !CategoricalState.isInapplicable(s)) {
						if (s == A || s == T || s == AT) //monomorphic A or T or A&T or uncertain A or T
							tot++;
						else if (s == C || s == G || s == CG) { //monomorphic C or G or C&G or uncertain C or G
							tot++;
							count++;
						}
					
				}
			} else
				charExc++;
		}
		if (tot == 0)
			value = MesquiteDouble.unassigned; //changed from 0,  26 jan '14
		else
			value = ((double)count)/tot;
		result.setValue(value);
	}	
	String exs = "";
	if (charExc > 0)
		exs = " (" + Integer.toString(charExc) + " characters excluded)";

	
	if (resultString!=null)
		resultString.setValue("Proportion of CG in taxon "+ observedStates.getName() + exs + ": " + result.toString());
	saveLastResult(result);
	saveLastResultString(resultString);
}
開發者ID:MesquiteProject，項目名稱:MesquiteCore，代碼行數:54，代碼來源:CGBiasOfTaxon.java


注：本文中的mesquite.lib.MesquiteString.setValue方法示例由純淨天空整理自Github/MSDocs等開源代碼及文檔管理平台，相關代碼片段篩選自各路編程大神貢獻的開源項目，源碼版權歸原作者所有，傳播和使用請參考對應項目的License；未經允許，請勿轉載。