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/**
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* Copyright (C) 2009 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.xper;
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import java.util.List;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.WorkingSet;
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import fr_jussieu_snv_lis.XPApp;
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import fr_jussieu_snv_lis.base.Base;
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import fr_jussieu_snv_lis.base.ControlerBase;
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import fr_jussieu_snv_lis.base.Group;
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import fr_jussieu_snv_lis.base.IBase;
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import fr_jussieu_snv_lis.base.IControlerBase;
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import fr_jussieu_snv_lis.base.Individual;
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import fr_jussieu_snv_lis.base.Mode;
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import fr_jussieu_snv_lis.base.Variable;
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import fr_jussieu_snv_lis.utils.Utils;
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/**
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* @author a.mueller
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* @date 12.04.2011
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*
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*/
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public class CdmXperBaseControler extends ControlerBase implements IControlerBase {
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private static final Logger logger = Logger.getLogger(CdmXperBaseControler.class);
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// private IBase base;
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private CdmXperAdapter cdmXperAdapter;
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public CdmXperBaseControler(BaseCdm base, CdmXperAdapter cdmXperAdapter) {
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super(base);
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this.cdmXperAdapter = cdmXperAdapter;
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// this.base = base;
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base.setBaseControler(this);
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}
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protected CdmXperAdapter getAdapter() {
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return cdmXperAdapter;
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}
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private WorkingSet getWorkingSet() {
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return cdmXperAdapter.getWorkingSet();
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}
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private FeatureTree getFeatureTree() {
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return getWorkingSet().getDescriptiveSystem();
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}
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public void loadFeatures() {
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this.cdmXperAdapter.loadFeatures();
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}
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//*********************** IControlerBase ********************************************/
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#createBase(java.lang.String, java.lang.String)
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*/
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@Override
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public void createBase(String path, String name) throws Exception {
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//TODO
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throw new RuntimeException("A new base can not be created in an external base controler");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#createBase(java.lang.String)
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*/
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@Override
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public void createBase(String name) throws Exception {
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//TODO
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throw new RuntimeException("A new base can not be opened in an external base controler");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#setBase(fr_jussieu_snv_lis.base.Base)
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*/
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@Override
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public void setBase(Base b) {
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logger.warn("Base is newly defined. This may lead to errors as controler base is a CdmXperBaseControler");
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this.base = b;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#getBase()
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*/
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@Override
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public IBase getBase() {
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return base;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#getBaseName()
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*/
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@Override
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public String getBaseName() {
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return base.getName();
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#closeBase()
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*/
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@Override
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public void closeBase() {
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logger.warn("closeBase Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#createNewGroup(java.lang.String)
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*/
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@Override
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public Group createNewGroup(String name) {
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logger.warn("createNewGroup Not yet implemented");
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return null;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addGroup(fr_jussieu_snv_lis.base.Group)
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*/
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@Override
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public boolean addGroup(Group group) {
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logger.warn("addGroup Not yet implemented");
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return false;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addGroupToBase(fr_jussieu_snv_lis.base.Group, fr_jussieu_snv_lis.base.IBase)
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*/
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@Override
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public boolean addGroupToBase(Group group, IBase b) {
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logger.warn("addGroupToBase Not yet implemented");
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return false;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addGroupAndVariablesToBase(fr_jussieu_snv_lis.base.Group, fr_jussieu_snv_lis.base.IBase)
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*/
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@Override
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public boolean addGroupAndVariablesToBase(Group group, IBase b) {
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logger.warn("addGroupAndVariablesToBase Not yet implemented");
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return false;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addGroupAt(int, fr_jussieu_snv_lis.base.Group)
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*/
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@Override
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public void addGroupAt(int i, Group g) {
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logger.warn("addGroupAt Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addGroupToBaseAt(fr_jussieu_snv_lis.base.Group, fr_jussieu_snv_lis.base.IBase, int)
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*/
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@Override
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public void addGroupToBaseAt(Group g, IBase b, int i) {
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logger.warn("addGroupToBaseAt Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#deleteGroupFromBase(fr_jussieu_snv_lis.base.Group, fr_jussieu_snv_lis.base.IBase)
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*/
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@Override
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public void deleteGroupFromBase(Group g, IBase b) {
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logger.warn("deleteGroupFromBase Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#deleteGroups(java.lang.Object[])
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*/
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@Override
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public void deleteGroups(Object[] tab) {
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logger.warn("deleteGroups Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#deleteGroup(fr_jussieu_snv_lis.base.Group)
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*/
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@Override
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public void deleteGroup(Group g) {
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logger.warn("deleteGroup Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#deleteGroupFromVariable(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Group)
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*/
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@Override
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public void deleteGroupFromVariable(Variable v, Group g) {
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logger.warn("deleteGroupFromVariable Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#deleteGroupFromVariables(java.lang.Object[], fr_jussieu_snv_lis.base.Group)
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*/
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@Override
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public void deleteGroupFromVariables(Object[] tab, Group g) {
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logger.warn("deleteGroupFromVariables Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#deleteAllGroups(fr_jussieu_snv_lis.base.IBase)
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*/
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@Override
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public void deleteAllGroups(IBase b) {
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logger.warn("deleteAllGroups Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#getGroupsNoBelongingToVariable(fr_jussieu_snv_lis.base.Variable)
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*/
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@Override
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public List<Group> getGroupsNoBelongingToVariable(Variable v) {
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logger.warn("getGroupsNoBelongingToVariable Not yet implemented");
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return null;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#getGroupsNoBelongingToVariables(java.lang.Object[])
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*/
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@Override
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public List<Group> getGroupsNoBelongingToVariables(Variable[] tab) {
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logger.warn("getGroupsNoBelongingToVariables Not yet implemented");
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return null;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#getGroupsBelongingToVariable(fr_jussieu_snv_lis.base.Variable)
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*/
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@Override
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public List<Group> getGroupsBelongingToVariable(Variable v) {
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logger.warn("getGroupsBelongingToVariable Not yet implemented");
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return null;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#getGroupsBelongingToVariables(java.lang.Object[])
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*/
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@Override
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public List<Group> getGroupsBelongingToVariables(Variable[] tab) {
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logger.warn("getGroupsBelongingToVariables Not yet implemented");
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return null;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#getAllGroups()
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*/
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@Override
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public List<Group> getAllGroups() {
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return base.getGroups();
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#findGroupByName(java.lang.String)
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*/
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@Override
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public Group findGroupByName(String n) {
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logger.warn("findGroupByName Not yet implemented");
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return null;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistanceGroup()
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*/
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@Override
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public boolean checkExistanceGroup() {
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logger.warn("checkExistanceGroup Not yet implemented");
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return false;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addGroupToVariableAt(fr_jussieu_snv_lis.base.Group, fr_jussieu_snv_lis.base.Variable, int)
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*/
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@Override
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public void addGroupToVariableAt(Group g, Variable v, int i) {
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logger.warn("addGroupToVariableAt Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addGroupToVariable(fr_jussieu_snv_lis.base.Group, fr_jussieu_snv_lis.base.Variable)
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*/
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@Override
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public void addGroupToVariable(Group g, Variable v) {
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logger.warn("addGroupToVariable Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addGroupToVariables(fr_jussieu_snv_lis.base.Group, java.lang.Object[])
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*/
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@Override
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public void addGroupToVariables(Group g, Object[] al) {
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logger.warn("addGroupToVariables Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addVariableToGroups(fr_jussieu_snv_lis.base.Variable, java.util.List)
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*/
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@Override
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public void addVariableToGroups(Variable v, List<Group> al) {
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logger.warn("addVariableToGroups Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistanceGroup(java.lang.String)
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*/
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@Override
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public boolean checkExistanceGroup(String s) {
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logger.warn("checkExistanceGroup Not yet implemented");
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return false;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistanceGroup(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Group)
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*/
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@Override
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public boolean checkExistanceGroup(Variable var, Group g) {
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logger.warn("checkExistanceGroup Not yet implemented");
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return false;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#findModeByName(java.lang.String, fr_jussieu_snv_lis.base.Variable)
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*/
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@Override
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public Mode findModeByName(String str, Variable var) {
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logger.warn("findModeByName Not yet implemented");
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return null;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addModeToVariable(fr_jussieu_snv_lis.base.Mode, fr_jussieu_snv_lis.base.Variable)
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*/
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@Override
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public boolean addModeToVariable(Mode m, Variable v) {
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return super.addModeToVariable(m, v);
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#addModeToVariableAt(fr_jussieu_snv_lis.base.Mode, fr_jussieu_snv_lis.base.Variable, int)
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*/
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@Override
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public void addModeToVariableAt(Mode m, Variable v, int i) {
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logger.warn("addModeToVariableAt Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#moveUpModeFromVariable(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Mode)
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*/
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@Override
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public void moveUpModeFromVariable(Variable v, Mode m) {
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logger.warn("moveUpModeFromVariable Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#moveDownModeFromVariable(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Mode)
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*/
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@Override
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public void moveDownModeFromVariable(Variable v, Mode m) {
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logger.warn("moveDownModeFromVariable Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#deleteModeFromVariable(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Mode)
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*/
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@Override
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public void deleteModeFromVariable(Variable v, Mode m) {
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logger.warn("deleteModeFromVariable Not yet implemented");
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#fusionModeFromvariable(fr_jussieu_snv_lis.base.Variable, java.lang.Object[])
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*/
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@Override
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public Mode fusionModeFromvariable(Variable var, Object[] tab) {
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logger.warn("fusionModeFromvariable Not yet implemented");
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return null;
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}
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/* (non-Javadoc)
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* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistanceMode(fr_jussieu_snv_lis.base.Variable, java.lang.String)
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*/
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@Override
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public boolean checkExistanceMode(Variable v, String s) {
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logger.warn("checkExistanceMode only implemented as super");
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return super.checkExistanceMode(v, s);
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|
}
|
414
|
|
415
|
/* (non-Javadoc)
|
416
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistanceMode(fr_jussieu_snv_lis.base.Individual, fr_jussieu_snv_lis.base.Variable, java.lang.String)
|
417
|
*/
|
418
|
@Override
|
419
|
public boolean checkExistanceMode(Individual ind, Variable var, String s) {
|
420
|
logger.warn("checkExistanceMode Not yet implemented");
|
421
|
return false;
|
422
|
}
|
423
|
|
424
|
/* (non-Javadoc)
|
425
|
* @see fr_jussieu_snv_lis.base.IControlerBase#matchModes(fr_jussieu_snv_lis.base.Individual, fr_jussieu_snv_lis.base.Variable, java.util.List, int)
|
426
|
*/
|
427
|
@Override
|
428
|
public boolean matchModes(Individual ind, Variable var, List<Mode> modes, int operator) {
|
429
|
logger.warn("matchModes Not yet implemented");
|
430
|
return false;
|
431
|
}
|
432
|
|
433
|
/* (non-Javadoc)
|
434
|
* @see fr_jussieu_snv_lis.base.IControlerBase#matchNumValue(fr_jussieu_snv_lis.base.Individual, fr_jussieu_snv_lis.base.Variable, java.lang.Double)
|
435
|
*/
|
436
|
@Override
|
437
|
public boolean matchNumValue(Individual ind, Variable var, Double value) {
|
438
|
logger.info("matchNumValue implemented by using super");
|
439
|
return super.matchNumValue(ind, var, value);
|
440
|
}
|
441
|
|
442
|
/* (non-Javadoc)
|
443
|
* @see fr_jussieu_snv_lis.base.IControlerBase#createNewMode(fr_jussieu_snv_lis.base.Variable, java.lang.String)
|
444
|
*/
|
445
|
@Override
|
446
|
public Mode createNewMode(Variable va, String name) {
|
447
|
Mode newMode = new Mode(name);
|
448
|
|
449
|
boolean hasChanged = addModeToVariable(newMode, va); // Add the new Mode to the list of Mode of the Variable
|
450
|
|
451
|
if (hasChanged){
|
452
|
XPApp.baseChanged = true;
|
453
|
}
|
454
|
Feature feature = getAdapter().getFeature(va);
|
455
|
getAdapter().saveNewState(newMode, feature);
|
456
|
return newMode;
|
457
|
}
|
458
|
|
459
|
/* (non-Javadoc)
|
460
|
* @see fr_jussieu_snv_lis.base.IControlerBase#controlModeExVariable(boolean, fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Mode)
|
461
|
*/
|
462
|
@Override
|
463
|
public void controlModeExVariable(boolean selected, Variable v, Mode modeException) {
|
464
|
logger.warn("controlModeExVariable Not yet implemented");
|
465
|
|
466
|
}
|
467
|
|
468
|
/* (non-Javadoc)
|
469
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteModeExFromVariable(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Mode)
|
470
|
*/
|
471
|
@Override
|
472
|
public void deleteModeExFromVariable(Variable v, Mode m) {
|
473
|
logger.warn("deleteModeExFromVariable Not yet implemented");
|
474
|
|
475
|
}
|
476
|
|
477
|
/* (non-Javadoc)
|
478
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistIndividual()
|
479
|
*/
|
480
|
@Override
|
481
|
public boolean checkExistIndividual() {
|
482
|
logger.warn("checkExistIndividual Not yet implemented");
|
483
|
return false;
|
484
|
}
|
485
|
|
486
|
/* (non-Javadoc)
|
487
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteIndividualFromBase(fr_jussieu_snv_lis.base.Individual, fr_jussieu_snv_lis.base.IBase)
|
488
|
*/
|
489
|
@Override
|
490
|
public void deleteIndividualFromBase(Individual ind, IBase b) {
|
491
|
logger.warn("deleteIndividualFromBase Not yet implemented");
|
492
|
|
493
|
}
|
494
|
|
495
|
/* (non-Javadoc)
|
496
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteIndividual(fr_jussieu_snv_lis.base.Individual)
|
497
|
*/
|
498
|
@Override
|
499
|
public void deleteIndividual(Individual ind) {
|
500
|
throw new RuntimeException("delete individual not supported by CDM version");
|
501
|
|
502
|
}
|
503
|
|
504
|
/* (non-Javadoc)
|
505
|
* @see fr_jussieu_snv_lis.base.IControlerBase#addIndividual(fr_jussieu_snv_lis.base.Individual)
|
506
|
*/
|
507
|
@Override
|
508
|
public void addIndividual(Individual ind) {
|
509
|
super.addIndividual(ind);
|
510
|
}
|
511
|
|
512
|
/* (non-Javadoc)
|
513
|
* @see fr_jussieu_snv_lis.base.IControlerBase#addIndividualToBaseAt(fr_jussieu_snv_lis.base.Individual, fr_jussieu_snv_lis.base.IBase, int)
|
514
|
*/
|
515
|
@Override
|
516
|
public void addIndividualToBaseAt(Individual ind, IBase b, int i) {
|
517
|
logger.warn("addIndividualToBaseAt Not yet implemented");
|
518
|
|
519
|
}
|
520
|
|
521
|
/* (non-Javadoc)
|
522
|
* @see fr_jussieu_snv_lis.base.IControlerBase#findIndividualByName(java.lang.String)
|
523
|
*/
|
524
|
@Override
|
525
|
public Individual findIndividualByName(String ind) {
|
526
|
return super.findIndividualByName(ind);
|
527
|
}
|
528
|
|
529
|
/* (non-Javadoc)
|
530
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistanceOneIndividual(java.lang.String)
|
531
|
*/
|
532
|
@Override
|
533
|
public boolean checkExistanceOneIndividual(String s) {
|
534
|
logger.warn("checkExistanceOneIndividual Not yet implemented");
|
535
|
return false;
|
536
|
}
|
537
|
|
538
|
/* (non-Javadoc)
|
539
|
* @see fr_jussieu_snv_lis.base.IControlerBase#createNewIndividual(java.lang.String)
|
540
|
*/
|
541
|
@Override
|
542
|
public Individual createNewIndividual(String name) {
|
543
|
logger.warn("createNewIndividual Not yet implemented");
|
544
|
return null;
|
545
|
}
|
546
|
|
547
|
/* (non-Javadoc)
|
548
|
* @see fr_jussieu_snv_lis.base.IControlerBase#copyIndividual(fr_jussieu_snv_lis.base.Individual, java.lang.String)
|
549
|
*/
|
550
|
@Override
|
551
|
public Individual copyIndividual(Individual indtocopy, String name) {
|
552
|
logger.warn("copyIndividual Not yet implemented");
|
553
|
return null;
|
554
|
}
|
555
|
|
556
|
/* (non-Javadoc)
|
557
|
* @see fr_jussieu_snv_lis.base.IControlerBase#copyVariable(fr_jussieu_snv_lis.base.Variable, java.lang.String)
|
558
|
*/
|
559
|
@Override
|
560
|
public Variable copyVariable(Variable vartocopy, String name) {
|
561
|
logger.warn("copyVariable Not yet implemented");
|
562
|
return null;
|
563
|
}
|
564
|
|
565
|
/* (non-Javadoc)
|
566
|
* @see fr_jussieu_snv_lis.base.IControlerBase#mergeVariables(java.lang.Object[], java.lang.String)
|
567
|
*/
|
568
|
@Override
|
569
|
public Variable mergeVariables(Object[] tab, String name) {
|
570
|
logger.warn("mergeVariables Not yet implemented");
|
571
|
return null;
|
572
|
}
|
573
|
|
574
|
/* (non-Javadoc)
|
575
|
* @see fr_jussieu_snv_lis.base.IControlerBase#mergeIndividuals(java.lang.Object[], java.lang.String)
|
576
|
*/
|
577
|
@Override
|
578
|
public Individual mergeIndividuals(Object[] tab, String name) {
|
579
|
logger.warn("mergeIndividuals Not yet implemented");
|
580
|
return null;
|
581
|
}
|
582
|
|
583
|
/* (non-Javadoc)
|
584
|
* @see fr_jussieu_snv_lis.base.IControlerBase#controlModeIndVar(boolean, fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Individual, fr_jussieu_snv_lis.base.Mode)
|
585
|
*/
|
586
|
@Override
|
587
|
public void controlModeIndVar(boolean selected, Variable v, Individual i, Mode m) {
|
588
|
this.cdmXperAdapter.controlModeIndVar(selected, v, i, m);
|
589
|
super.controlModeIndVar(selected, v, i, m);
|
590
|
}
|
591
|
|
592
|
/* (non-Javadoc)
|
593
|
* @see fr_jussieu_snv_lis.base.IControlerBase#controlModeIndVarRec(boolean, fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Individual, fr_jussieu_snv_lis.base.Mode)
|
594
|
*/
|
595
|
@Override
|
596
|
public void controlModeIndVarRec(boolean selected, Variable v, Individual i, Mode m) {
|
597
|
logger.warn("controlModeIndVarRec Not yet implemented");
|
598
|
}
|
599
|
|
600
|
@Override
|
601
|
public void controlNumValue(Individual ind, Variable var, Double min,
|
602
|
Double max, Double mean, Double sd, Double umethLower,
|
603
|
Double umethUpper, Integer nSample) {
|
604
|
this.cdmXperAdapter.controlModeIndVar(ind, var, min, max, mean, sd,
|
605
|
umethLower, umethUpper, nSample);
|
606
|
super.controlNumValue(ind, var, min, max, mean, sd, umethLower, umethUpper,
|
607
|
nSample);
|
608
|
}
|
609
|
|
610
|
/* (non-Javadoc)
|
611
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkBadDescription(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Individual)
|
612
|
*/
|
613
|
@Override
|
614
|
public void checkBadDescription(Variable var, Individual ind) {
|
615
|
logger.warn("checkBadDescription Not yet implemented");
|
616
|
|
617
|
}
|
618
|
|
619
|
/* (non-Javadoc)
|
620
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkingUnknown(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Individual)
|
621
|
*/
|
622
|
@Override
|
623
|
public boolean checkingUnknown(Variable var, Individual ind) {
|
624
|
return super.checkingUnknown(var, ind);
|
625
|
}
|
626
|
|
627
|
/* (non-Javadoc)
|
628
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkUnknown(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Individual, boolean, boolean)
|
629
|
*/
|
630
|
@Override
|
631
|
public void checkUnknown(Variable var, Individual ind, boolean value, boolean withDaughters) {
|
632
|
this.cdmXperAdapter.checkUnknown(var, ind, value, withDaughters);
|
633
|
super.checkUnknown(var, ind, value, withDaughters);
|
634
|
}
|
635
|
|
636
|
/* (non-Javadoc)
|
637
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkUnknown(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Individual[], boolean, boolean)
|
638
|
*/
|
639
|
@Override
|
640
|
public void checkUnknown(Variable var, Individual[] tab, boolean b, boolean withDaughters) {
|
641
|
super.checkUnknown(var, tab, b, withDaughters); //super calls check unknown for each individual
|
642
|
}
|
643
|
|
644
|
/* (non-Javadoc)
|
645
|
* @see fr_jussieu_snv_lis.base.IControlerBase#buildIndividualsBitSetMatrix()
|
646
|
*/
|
647
|
@Override
|
648
|
public void buildIndividualsBitSetMatrix() {
|
649
|
logger.warn("buildIndividualsBitSetMatrix Not yet implemented");
|
650
|
|
651
|
}
|
652
|
|
653
|
/* (non-Javadoc)
|
654
|
* @see fr_jussieu_snv_lis.base.IControlerBase#buildIndividualsIntegerBitMatrix()
|
655
|
*/
|
656
|
@Override
|
657
|
public void buildIndividualsIntegerBitMatrix() {
|
658
|
logger.warn("buildIndividualsIntegerBitMatrix Not yet implemented");
|
659
|
|
660
|
}
|
661
|
|
662
|
/* (non-Javadoc)
|
663
|
* @see fr_jussieu_snv_lis.base.IControlerBase#addVariable(fr_jussieu_snv_lis.base.Variable)
|
664
|
*/
|
665
|
@Override
|
666
|
public boolean addVariable(Variable variable) {
|
667
|
logger.warn("addVariable Not yet implemented");
|
668
|
return false;
|
669
|
}
|
670
|
|
671
|
/* (non-Javadoc)
|
672
|
* @see fr_jussieu_snv_lis.base.IControlerBase#addVariableToBase(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.IBase)
|
673
|
*/
|
674
|
@Override
|
675
|
public void addVariableToBase(Variable variable, IBase b) {
|
676
|
logger.warn("addVariableToBase Not yet implemented");
|
677
|
|
678
|
}
|
679
|
|
680
|
/* (non-Javadoc)
|
681
|
* @see fr_jussieu_snv_lis.base.IControlerBase#addMother(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Variable)
|
682
|
*/
|
683
|
@Override
|
684
|
public boolean addMother(Variable current, Variable mother) {
|
685
|
logger.warn("addMother Not yet implemented");
|
686
|
return false;
|
687
|
}
|
688
|
|
689
|
/* (non-Javadoc)
|
690
|
* @see fr_jussieu_snv_lis.base.IControlerBase#removeMother(fr_jussieu_snv_lis.base.Variable)
|
691
|
*/
|
692
|
@Override
|
693
|
public void removeMother(Variable current) {
|
694
|
logger.warn("removeMother Not yet implemented");
|
695
|
|
696
|
}
|
697
|
|
698
|
/* (non-Javadoc)
|
699
|
* @see fr_jussieu_snv_lis.base.IControlerBase#changeMother(fr_jussieu_snv_lis.base.Variable, fr_jussieu_snv_lis.base.Variable)
|
700
|
*/
|
701
|
@Override
|
702
|
public void changeMother(Variable current, Variable newMother) {
|
703
|
//from super
|
704
|
super.removeMother(current);
|
705
|
super.addMother(current, newMother);
|
706
|
|
707
|
getAdapter().moveFeature(current, newMother);
|
708
|
}
|
709
|
|
710
|
/* (non-Javadoc)
|
711
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistVariable()
|
712
|
*/
|
713
|
@Override
|
714
|
public boolean checkExistVariable() {
|
715
|
logger.warn("checkExistVariable Not yet implemented");
|
716
|
return false;
|
717
|
}
|
718
|
|
719
|
/* (non-Javadoc)
|
720
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistVariable(fr_jussieu_snv_lis.base.Variable)
|
721
|
*/
|
722
|
@Override
|
723
|
public boolean checkExistVariable(Variable v) {
|
724
|
logger.warn("checkExistVariable Not yet implemented");
|
725
|
return false;
|
726
|
}
|
727
|
|
728
|
/* (non-Javadoc)
|
729
|
* @see fr_jussieu_snv_lis.base.IControlerBase#findVariableByName(java.lang.String)
|
730
|
*/
|
731
|
@Override
|
732
|
public Variable findVariableByName(String str) {
|
733
|
logger.warn("findVariableByName implemented as super");
|
734
|
return super.findVariableByName(str);
|
735
|
}
|
736
|
|
737
|
/**
|
738
|
* Returns the variable with variable.uuid equal to uuid.
|
739
|
* Returns <code>null</code> if no such variable exists or
|
740
|
* if <code>uuid == null</code>
|
741
|
* @param uuid
|
742
|
* @return
|
743
|
*/
|
744
|
public Variable findVariableByUuid(UUID uuid) {
|
745
|
if (uuid == null){
|
746
|
return null;
|
747
|
}
|
748
|
//TODO improve performance by storing variables also in a
|
749
|
//hashmap
|
750
|
for (Variable var : base.getVariables()) {
|
751
|
if (uuid.equals(var.getUuid())) {
|
752
|
return var;
|
753
|
}
|
754
|
}
|
755
|
return null;
|
756
|
}
|
757
|
|
758
|
/* (non-Javadoc)
|
759
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkExistanceOneVariable(java.lang.String)
|
760
|
*/
|
761
|
@Override
|
762
|
public boolean checkExistanceOneVariable(String s) {
|
763
|
logger.info("checkExistanceOneVariable implemented as super");
|
764
|
return super.checkExistanceOneVariable(s);
|
765
|
}
|
766
|
|
767
|
/* (non-Javadoc)
|
768
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkCommunModeName(fr_jussieu_snv_lis.base.Variable[])
|
769
|
*/
|
770
|
@Override
|
771
|
public boolean checkCommunModeName(Variable[] tab) {
|
772
|
logger.warn("checkCommunModeName Not yet implemented");
|
773
|
return false;
|
774
|
}
|
775
|
|
776
|
/* (non-Javadoc)
|
777
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkNumericalType(fr_jussieu_snv_lis.base.Variable[])
|
778
|
*/
|
779
|
@Override
|
780
|
public boolean checkNumericalType(Variable[] tab) {
|
781
|
logger.warn("checkNumericalType Not yet implemented");
|
782
|
return false;
|
783
|
}
|
784
|
|
785
|
/* (non-Javadoc)
|
786
|
* @see fr_jussieu_snv_lis.base.IControlerBase#checkStateNumber(fr_jussieu_snv_lis.base.Variable[])
|
787
|
*/
|
788
|
@Override
|
789
|
public boolean checkStateNumber(Variable[] tab) {
|
790
|
logger.warn("checkStateNumber Not yet implemented");
|
791
|
return false;
|
792
|
}
|
793
|
|
794
|
/* (non-Javadoc)
|
795
|
* @see fr_jussieu_snv_lis.base.IControlerBase#createNewVariable(java.lang.String)
|
796
|
*/
|
797
|
@Override
|
798
|
public Variable createNewCategoricalVariable(String name) {
|
799
|
Variable newVariable = new Variable(name);
|
800
|
newVariable.setType(Utils.catType);
|
801
|
newVariable.setUuid(UUID.randomUUID());
|
802
|
|
803
|
// By default, a new Variable has two Modes
|
804
|
//TODO Do we really need to add new modes immediately? SDD data sometimes do not have to states
|
805
|
// Mode mode1 = new Mode(XPApp.messages.getString("mode") + " 1");
|
806
|
// Mode mode2 = new Mode(XPApp.messages.getString("mode") + " 2");
|
807
|
// newVariable.addMode(mode1);
|
808
|
// newVariable.addMode(mode2);
|
809
|
|
810
|
base.addVariable(newVariable); // add the new Variable to the List of Variable of the Base
|
811
|
//TODO needed
|
812
|
XPApp.baseChanged = true;
|
813
|
|
814
|
this.cdmXperAdapter.createNewVariable(newVariable);
|
815
|
|
816
|
return newVariable;
|
817
|
}
|
818
|
|
819
|
/* (non-Javadoc)
|
820
|
* @see fr_jussieu_snv_lis.base.IControlerBase#createNewVariableNumOrEnum(java.lang.String, java.lang.String)
|
821
|
*/
|
822
|
@Override
|
823
|
public Variable createNewVariableNumOrEnum(String name, String type) {
|
824
|
Variable newVariable = new Variable(name);
|
825
|
newVariable.setType(type);
|
826
|
newVariable.setUuid(UUID.randomUUID());
|
827
|
|
828
|
base.addVariable(newVariable); // add the new Variable to the List of Variable of the Base
|
829
|
//TODO needed
|
830
|
XPApp.baseChanged = true;
|
831
|
|
832
|
this.cdmXperAdapter.createNewVariable(newVariable);
|
833
|
|
834
|
return newVariable;
|
835
|
|
836
|
}
|
837
|
|
838
|
/* (non-Javadoc)
|
839
|
* @see fr_jussieu_snv_lis.base.IControlerBase#addNewVariableAndItsModesToMatrix(fr_jussieu_snv_lis.base.Variable)
|
840
|
*/
|
841
|
@Override
|
842
|
public void addNewVariableAndItsModesToMatrix(Variable newVariable) {
|
843
|
logger.warn("addNewVariableAndItsModesToMatrix still needs to add 'unknown data' as a value for the feature");
|
844
|
super.addNewVariableAndItsModesToMatrix(newVariable);
|
845
|
}
|
846
|
|
847
|
/* (non-Javadoc)
|
848
|
* @see fr_jussieu_snv_lis.base.IControlerBase#addNewVariableNumAndItsModesToMatrix(fr_jussieu_snv_lis.base.Variable)
|
849
|
*/
|
850
|
@Override
|
851
|
public void addNewVariableNumAndItsModesToMatrix(Variable newVariable) {
|
852
|
logger.warn("addNewVariableNumAndItsModesToMatrix Not yet implemented");
|
853
|
}
|
854
|
|
855
|
/* (non-Javadoc)
|
856
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteVariableFromMatrix(fr_jussieu_snv_lis.base.Variable)
|
857
|
*/
|
858
|
@Override
|
859
|
public void deleteVariableFromMatrix(Variable variable) {
|
860
|
logger.warn("deleteVariableFromMatrix Not yet implemented");
|
861
|
}
|
862
|
|
863
|
/* (non-Javadoc)
|
864
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteVariable(fr_jussieu_snv_lis.base.Variable)
|
865
|
*/
|
866
|
@Override
|
867
|
public void deleteVariable(Variable va) {
|
868
|
logger.warn("deleteVariable Not yet implemented");
|
869
|
}
|
870
|
|
871
|
/* (non-Javadoc)
|
872
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteVariableAndAllDaughters(fr_jussieu_snv_lis.base.Variable)
|
873
|
*/
|
874
|
@Override
|
875
|
public void deleteVariableAndAllDaughters(Variable v) {
|
876
|
logger.warn("deleteVariableAndAllDaughters Not yet implemented");
|
877
|
}
|
878
|
|
879
|
/* (non-Javadoc)
|
880
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteVariablesAndAllDaughters(fr_jussieu_snv_lis.base.Variable[])
|
881
|
*/
|
882
|
@Override
|
883
|
public void deleteVariablesAndAllDaughters(Variable[] tab) {
|
884
|
logger.warn("deleteVariablesAndAllDaughters Not yet implemented");
|
885
|
}
|
886
|
|
887
|
/* (non-Javadoc)
|
888
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteVariableWithoutDaughters(fr_jussieu_snv_lis.base.Variable)
|
889
|
*/
|
890
|
@Override
|
891
|
public void deleteVariableWithoutDaughters(Variable v) {
|
892
|
logger.warn("deleteVariableWithoutDaughters Not yet implemented");
|
893
|
|
894
|
}
|
895
|
|
896
|
/* (non-Javadoc)
|
897
|
* @see fr_jussieu_snv_lis.base.IControlerBase#deleteVariablesWithoutDaughters(fr_jussieu_snv_lis.base.Variable[])
|
898
|
*/
|
899
|
@Override
|
900
|
public void deleteVariablesWithoutDaughters(Variable[] tab) {
|
901
|
logger.warn("deleteVariablesWithoutDaughters Not yet implemented");
|
902
|
}
|
903
|
|
904
|
/* (non-Javadoc)
|
905
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getVariableDescendant(java.util.List, fr_jussieu_snv_lis.base.Variable)
|
906
|
*/
|
907
|
@Override
|
908
|
public List<Variable> getVariableDescendant(List<Variable> listDescendant, Variable v) {
|
909
|
logger.warn("getVariableDescendant Not yet implemented");
|
910
|
return null;
|
911
|
}
|
912
|
|
913
|
/* (non-Javadoc)
|
914
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getVariableDaughters(fr_jussieu_snv_lis.base.Variable)
|
915
|
*/
|
916
|
@Override
|
917
|
public List<Variable> getVariableDaughters(Variable v) {
|
918
|
return super.getVariableDaughters(v);
|
919
|
}
|
920
|
|
921
|
/* (non-Javadoc)
|
922
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getVariablesWithoutMother()
|
923
|
*/
|
924
|
@Override
|
925
|
public List<Variable> getVariablesWithoutMother() {
|
926
|
return super.getVariablesWithoutMother();
|
927
|
}
|
928
|
|
929
|
/* (non-Javadoc)
|
930
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getVariablesWithoutMother(java.util.List)
|
931
|
*/
|
932
|
@Override
|
933
|
public List<Variable> getVariablesWithoutMother(List<Variable> variables) {
|
934
|
return super.getVariablesWithoutMother(variables);
|
935
|
}
|
936
|
|
937
|
/* (non-Javadoc)
|
938
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getVariablesWithoutDaughter(java.util.List)
|
939
|
*/
|
940
|
@Override
|
941
|
public List<Variable> getVariablesWithoutDaughter(List<Variable> variables) {
|
942
|
logger.warn("getVariablesWithoutDaughter Not yet implemented");
|
943
|
return null;
|
944
|
}
|
945
|
|
946
|
/* (non-Javadoc)
|
947
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getListVariable()
|
948
|
*/
|
949
|
@Override
|
950
|
public List<Variable> getListVariable() {
|
951
|
List<Variable> result = base.getVariables();
|
952
|
// List<FeatureNode> rootChildren = getFeatureTree().getRootChildren();
|
953
|
// List<Variable> result = cdmXperAdapter.adaptFeatureListToVariableList(-1, rootChildren);
|
954
|
return result; //base.getVariables();
|
955
|
}
|
956
|
|
957
|
/* (non-Javadoc)
|
958
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getVariablesByGroup(java.util.List, fr_jussieu_snv_lis.base.Group)
|
959
|
*/
|
960
|
@Override
|
961
|
public List<Variable> getVariablesByGroup(List<Variable> variables, Group group) {
|
962
|
logger.warn("getVariablesByGroup Not yet implemented");
|
963
|
return null;
|
964
|
}
|
965
|
|
966
|
/* (non-Javadoc)
|
967
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getVariablesWithoutGroup(java.util.List)
|
968
|
*/
|
969
|
@Override
|
970
|
public List<Variable> getVariablesWithoutGroup(List<Variable> variables) {
|
971
|
logger.warn("getVariablesWithoutGroup only implemented as super");
|
972
|
return super.getVariablesWithoutGroup(variables);
|
973
|
}
|
974
|
|
975
|
|
976
|
/* (non-Javadoc)
|
977
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getCurrentVar()
|
978
|
*/
|
979
|
@Override
|
980
|
public Variable getCurrentVar() {
|
981
|
return super.getCurrentVar();
|
982
|
}
|
983
|
|
984
|
/* (non-Javadoc)
|
985
|
* @see fr_jussieu_snv_lis.base.IControlerBase#setCurrentVar(fr_jussieu_snv_lis.base.Variable)
|
986
|
*/
|
987
|
@Override
|
988
|
public void setCurrentVar(Variable var) {
|
989
|
super.setCurrentVar(var);
|
990
|
}
|
991
|
|
992
|
/* (non-Javadoc)
|
993
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getCurrentInd()
|
994
|
*/
|
995
|
@Override
|
996
|
public Individual getCurrentInd() {
|
997
|
return super.getCurrentInd();
|
998
|
}
|
999
|
|
1000
|
/* (non-Javadoc)
|
1001
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getCurrentIndArray()
|
1002
|
*/
|
1003
|
@Override
|
1004
|
public Individual[] getCurrentIndArray() {
|
1005
|
return super.getCurrentIndArray();
|
1006
|
}
|
1007
|
|
1008
|
/* (non-Javadoc)
|
1009
|
* @see fr_jussieu_snv_lis.base.IControlerBase#setCurrentInd(fr_jussieu_snv_lis.base.Individual)
|
1010
|
*/
|
1011
|
@Override
|
1012
|
public void setCurrentInd(Individual ind) {
|
1013
|
super.setCurrentInd(ind);
|
1014
|
}
|
1015
|
|
1016
|
/* (non-Javadoc)
|
1017
|
* @see fr_jussieu_snv_lis.base.IControlerBase#setCurrentIndArray(fr_jussieu_snv_lis.base.Individual[])
|
1018
|
*/
|
1019
|
@Override
|
1020
|
public void setCurrentIndArray(Individual[] tab) {
|
1021
|
super.setCurrentIndArray(tab);
|
1022
|
}
|
1023
|
|
1024
|
/* (non-Javadoc)
|
1025
|
* @see fr_jussieu_snv_lis.base.IControlerBase#setCurrentIndArray(java.lang.Object[])
|
1026
|
*/
|
1027
|
@Override
|
1028
|
public void setCurrentIndArray(Object[] tab) {
|
1029
|
super.setCurrentIndArray(tab);
|
1030
|
}
|
1031
|
|
1032
|
|
1033
|
@Override
|
1034
|
public boolean isAllowIndividualEditing() {
|
1035
|
//editing of individuals is not allowed in CDM mode
|
1036
|
return false;
|
1037
|
}
|
1038
|
|
1039
|
/* (non-Javadoc)
|
1040
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getSortedIndividuals()
|
1041
|
*/
|
1042
|
@Override
|
1043
|
public List<Individual> getSortedIndividuals() {
|
1044
|
logger.warn("getSortedIndividuals Not yet implemented");
|
1045
|
return null;
|
1046
|
}
|
1047
|
|
1048
|
/* (non-Javadoc)
|
1049
|
* @see fr_jussieu_snv_lis.base.IControlerBase#getSortedGroups()
|
1050
|
*/
|
1051
|
@Override
|
1052
|
public List<Group> getSortedGroups() {
|
1053
|
logger.warn("getSortedGroups Not yet implemented");
|
1054
|
return null;
|
1055
|
}
|
1056
|
|
1057
|
/* (non-Javadoc)
|
1058
|
* @see fr_jussieu_snv_lis.base.IControlerBase#moveIndividualTo(int, fr_jussieu_snv_lis.base.Individual)
|
1059
|
*/
|
1060
|
@Override
|
1061
|
public void moveIndividualTo(int i, Individual ind) {
|
1062
|
logger.warn("moveIndividualTo Not yet implemented");
|
1063
|
|
1064
|
}
|
1065
|
|
1066
|
/* (non-Javadoc)
|
1067
|
* @see fr_jussieu_snv_lis.base.IControlerBase#moveVariableTo(int, fr_jussieu_snv_lis.base.Variable)
|
1068
|
*/
|
1069
|
@Override
|
1070
|
public void moveVariableTo(int i, Variable v) {
|
1071
|
logger.warn("moveVariableTo Not yet implemented");
|
1072
|
}
|
1073
|
|
1074
|
/* (non-Javadoc)
|
1075
|
* @see fr_jussieu_snv_lis.base.IControlerBase#moveVariablesTo(int, java.util.List)
|
1076
|
*/
|
1077
|
@Override
|
1078
|
public void moveVariablesTo(int i, List<Variable> a) {
|
1079
|
logger.warn("moveVariablesTo Not yet implemented");
|
1080
|
}
|
1081
|
|
1082
|
/* (non-Javadoc)
|
1083
|
* @see fr_jussieu_snv_lis.base.IControlerBase#moveGroupTo(int, fr_jussieu_snv_lis.base.Group)
|
1084
|
*/
|
1085
|
@Override
|
1086
|
public void moveGroupTo(int i, Group g) {
|
1087
|
logger.warn("moveGroupTo Not yet implemented");
|
1088
|
}
|
1089
|
|
1090
|
|
1091
|
}
|