fr.profi.mzdb.db.model.params.AbstractParamTree Maven / Gradle / Ivy

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package fr.profi.mzdb.db.model.params;

import java.util.ArrayList;
import java.util.List;

import javax.xml.bind.annotation.XmlElement;

import fr.profi.mzdb.db.model.params.param.CVParam;
import fr.profi.mzdb.db.model.params.param.CVEntry;
import fr.profi.mzdb.db.model.params.param.UserParam;
import fr.profi.mzdb.db.model.params.param.UserText;

/**
 * @author David Bouyssie
 * 
 */
public abstract class AbstractParamTree { // implements IParamContainer

	/** The cv params. */
	protected List cvParams;

	/** The user params. */
	protected List userParams;

	/**
	 * The userText params: newly introduced for handling Thermo metadata in text field
	 */
	protected List userTexts;

	@XmlElement(name = "cvParam", type = CVParam.class, required = false)
	public List getCVParams() {
		if (this.cvParams == null)
			this.cvParams = new ArrayList();

		return cvParams;
	}

	// Marc: most of the object does not contain any UserParam,
	// so this is set to be non abstract to avoid to override it in subclasses
	// DBO: why ???
	@XmlElement(name = "userParam", type = UserParam.class, required = false)
	public List getUserParams() {
		if (this.userParams == null)
			this.userParams = new ArrayList();

		return this.userParams;
	}

	@XmlElement(name = "userText", type = UserText.class, required = false)
	public List getUserTexts() {
		if (this.userTexts == null)
			this.userTexts = new ArrayList();
		return this.userTexts;
	}
	
	public void setCvParams(List cvParams) {
		this.cvParams = cvParams;
	}

	public void setUserParams(List userParams) {
		this.userParams = userParams;
	}

	public void setUserTexts(List userTexts) {
		this.userTexts = userTexts;
	}

	public UserParam getUserParam(String name) {

		UserParam foundUP = null;
		for (UserParam up : this.getUserParams()) {
			if (up.getName().equals(name)) {
				foundUP = up;
				break;
			}
		}
		
		return foundUP;
	}

	public CVParam getCVParam(CVEntry cvEntry) {
		CVParam foundCV = null;
		for (CVParam cv : this.getCVParams()) {
			if (cv.getAccession().equals(cvEntry.getAccession()) ) {
				foundCV = cv;
				break;
			}
		}
		
		return foundCV;
	}

	public CVParam[] getCVParams(CVEntry[] cvEntries) {
		CVParam[] cvParams = new CVParam[cvEntries.length];
		
		int i = 0;
		for (CVEntry cvEntry : cvEntries) {
			cvParams[i] = this.getCVParam(cvEntry);
			i++;
		}
		
		return cvParams;
	}

}