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Revision e3a4a3ff

Added by Andreas Müller almost 7 years ago

ref #6446 merge taxon name subclasses in TaxEditor

View differences:

eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/BulkEditorLineDisplay.java
24 24
import eu.etaxonomy.cdm.model.common.IAnnotatableEntity;
25 25
import eu.etaxonomy.cdm.model.common.ICdmBase;
26 26
import eu.etaxonomy.cdm.model.common.Marker;
27
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
27
import eu.etaxonomy.cdm.model.name.TaxonName;
28 28
import eu.etaxonomy.cdm.model.reference.Reference;
29 29
import eu.etaxonomy.taxeditor.annotatedlineeditor.EntityListener;
30 30
import eu.etaxonomy.taxeditor.annotatedlineeditor.ILineDisplayStrategy;
......
35 35
 *
36 36
 * @author p.ciardelli
37 37
 * @created 07.07.2009
38
 * @version 1.0
39 38
 */
40 39
public class BulkEditorLineDisplay implements ILineDisplayStrategy {
41 40

  
......
50 49
		this.editor = editor;
51 50
	}
52 51

  
53
	/* (non-Javadoc)
54
	 * @see eu.etaxonomy.taxeditor.bulkeditor.ILineDisplayStrategy#getIcon(java.lang.Object)
55
	 */
56 52
	/** {@inheritDoc} */
57 53
	@Override
58 54
    public Image getIcon(Object entity) {
59 55
		return null;
60 56
	}
61 57

  
62
	/* (non-Javadoc)
63
	 * @see eu.etaxonomy.taxeditor.bulkeditor.ILineDisplayStrategy#getIndent(java.lang.Object)
64
	 */
65 58
	/** {@inheritDoc} */
66 59
	@Override
67 60
    public int getIndent(Object entity) {
68 61
		return 0;
69 62
	}
70 63

  
71
	/* (non-Javadoc)
72
	 * @see eu.etaxonomy.taxeditor.bulkeditor.ILineDisplayStrategy#getText(java.lang.Object)
73
	 */
74 64
	/** {@inheritDoc} */
75 65
	@Override
76 66
    public String getText(Object entity) {
77 67
		return editor.getEditorInput().getText((ICdmBase) entity);
78 68
	}
79 69

  
80

  
81
	/* (non-Javadoc)
82
	 * @see eu.etaxonomy.taxeditor.annotatedlineeditor.ILineDisplayStrategy#getSupplementalText(java.lang.Object)
83
	 */
84 70
	/** {@inheritDoc} */
85 71
	@Override
86 72
    public String getSupplementalText(Object entity) {
......
111 97
		return supplementalText;
112 98
	}
113 99

  
114
	/* (non-Javadoc)
115
	 * @see eu.etaxonomy.taxeditor.bulkeditor.ILineDisplayStrategy#setText(java.lang.String, java.lang.Object)
116
	 */
117 100
	/** {@inheritDoc} */
118 101
	@Override
119 102
    public void setText(String text, Object entity) {
......
122 105
		}
123 106
	}
124 107

  
125
	/* (non-Javadoc)
126
	 * @see eu.etaxonomy.taxeditor.bulkeditor.ILineDisplayStrategy#getHoverText(java.lang.Object)
127
	 */
128 108
	/** {@inheritDoc} */
129 109
	@Override
130 110
    public String getHoverText(Object entity) {
......
155 135
		}).start();
156 136
	}
157 137

  
158
	/* (non-Javadoc)
159
	 * @see eu.etaxonomy.taxeditor.annotatedlineeditor.ILineDisplayStrategy#getEmptyText(java.lang.Object)
160
	 */
161 138
	/** {@inheritDoc} */
162 139
	@Override
163 140
    public String getEmptyCacheMessage(Object entity) {
164 141
		return entity.toString();
165 142
	}
166 143

  
167
	/* (non-Javadoc)
168
	 * @see eu.etaxonomy.taxeditor.annotatedlineeditor.ILineDisplayStrategy#isEntityCacheEmpty(java.lang.Object)
169
	 */
170 144
	/** {@inheritDoc} */
171 145
	@Override
172 146
    public boolean isEntityCacheEmpty(Object entity) {
......
174 148
			String text = ((Reference) entity).getTitleCache();
175 149
			return (text == null || text.equals(""));
176 150
		}
177
		if (entity instanceof TaxonNameBase) {
178
			String text = ((TaxonNameBase) entity).getTitleCache();
151
		if (entity instanceof TaxonName) {
152
			String text = ((TaxonName) entity).getTitleCache();
179 153
			return (text == null || text.equals(""));
180 154
		}
181 155
		if (entity instanceof AgentBase) {
......
185 159
		return false;
186 160
	}
187 161

  
188
	/* (non-Javadoc)
189
	 * @see eu.etaxonomy.taxeditor.annotatedlineeditor.ILineDisplayStrategy#addDisplayListener(java.lang.Object)
190
	 */
191 162
	/** {@inheritDoc} */
192 163
	@Override
193 164
    public void addDisplayListener(Object entity, EntityListener listener) {
eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/handler/DeleteHandler.java
20 20
import org.eclipse.core.runtime.Status;
21 21
import org.eclipse.jface.dialogs.MessageDialog;
22 22
import org.eclipse.jface.text.TextSelection;
23
import org.eclipse.jface.text.source.Annotation;
24 23
import org.eclipse.jface.viewers.IStructuredSelection;
25 24
import org.eclipse.ui.IEditorInput;
26 25
import org.eclipse.ui.IEditorPart;
......
43 42
import eu.etaxonomy.cdm.model.common.Group;
44 43
import eu.etaxonomy.cdm.model.common.User;
45 44
import eu.etaxonomy.cdm.model.media.Media;
46
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
45
import eu.etaxonomy.cdm.model.name.TaxonName;
47 46
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
48 47
import eu.etaxonomy.cdm.model.reference.Reference;
49 48
import eu.etaxonomy.cdm.model.taxon.Synonym;
......
96 95

  
97 96
			IStructuredSelection structuredSelection = (IStructuredSelection) selection;
98 97
			DeleteConfiguratorBase config = null;
99
			IEntityPersistenceService persistenceService = (IEntityPersistenceService) input;
98
			IEntityPersistenceService<?> persistenceService = (IEntityPersistenceService<?>) input;
100 99
			DeleteResult result = new DeleteResult();
101 100
			String errorMessage= "The object ";
102 101
			for(Object object : structuredSelection.toList()){
103 102
			    if (object instanceof CdmBase){
104 103
			        CdmBase base = (CdmBase)object;
105
			        LineAnnotation annotation = (LineAnnotation) model.getAnnotation(object);
104
			        LineAnnotation<?> annotation = (LineAnnotation<?>) model.getAnnotation(object);
106 105
			        if (base.getId() != 0){
107 106

  
108 107

  
......
119 118
                                    return null;
120 119
                                }
121 120
        						if (object != null){
122
        							result = service.isDeletable(((SpecimenOrObservationBase) object).getUuid(), config);
121
        							result = service.isDeletable(((SpecimenOrObservationBase<?>) object).getUuid(), config);
123 122
        							errorMessage = "The specimen or observation ";
124 123

  
125 124
        						}
......
134 133
        				        errorMessage = "The group ";
135 134
        				    }else if (object instanceof User){
136 135
        				        errorMessage = "The user ";
137
         				    } else if (object instanceof TaxonNameBase){
138
         				        TaxonNameBase name = HibernateProxyHelper.deproxy(object, TaxonNameBase.class);
136
         				    } else if (object instanceof TaxonName){
137
         				        TaxonName name = HibernateProxyHelper.deproxy(object, TaxonName.class);
139 138
         				        if (object != null){
140 139
         				            config = new NameDeletionConfigurator();
141 140

  
eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/input/BulkEditorInputType.java
24 24
import eu.etaxonomy.cdm.model.common.User;
25 25
import eu.etaxonomy.cdm.model.media.Media;
26 26
import eu.etaxonomy.cdm.model.name.NameRelationship;
27
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
27
import eu.etaxonomy.cdm.model.name.TaxonName;
28 28
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
29 29
import eu.etaxonomy.cdm.model.reference.Reference;
30 30
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
......
89 89
	public static BulkEditorInputType getByType(Class clazz) {
90 90
		if (Reference.class.isAssignableFrom(clazz)) {
91 91
			return REFERENCE;
92
		} else if (TaxonNameBase.class.isAssignableFrom(clazz)) {
92
		} else if (TaxonName.class.isAssignableFrom(clazz)) {
93 93
			return NAME;
94 94
		} else if (AgentBase.class.isAssignableFrom(clazz)) {
95 95
			return AGENT;
eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/input/NameEditorInput.java
17 17
import eu.etaxonomy.cdm.api.service.config.DeleteConfiguratorBase;
18 18
import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
19 19
import eu.etaxonomy.cdm.api.service.config.NameDeletionConfigurator;
20
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
20
import eu.etaxonomy.cdm.model.name.TaxonName;
21 21
import eu.etaxonomy.taxeditor.annotatedlineeditor.IEntityCreator;
22 22
import eu.etaxonomy.taxeditor.bulkeditor.IBulkEditorSortProvider;
23 23
import eu.etaxonomy.taxeditor.bulkeditor.input.entitycreator.NameCreator;
......
29 29
 *
30 30
 * @author p.ciardelli
31 31
 * @created 20.08.2009
32
 * @version 1.0
33 32
 */
34
public class NameEditorInput extends AbstractBulkEditorInput<TaxonNameBase> {
33
public class NameEditorInput extends AbstractBulkEditorInput<TaxonName> {
35 34

  
36
	/**
37
	 *
38
	 */
39 35
	private static final long serialVersionUID = -3085029575759626823L;
40 36
	private static NameEditorInput instance;
41 37

  
......
54 50
		return instance;
55 51
	}
56 52

  
57
	/* (non-Javadoc)
58
	 * @see org.eclipse.ui.IEditorInput#getName()
59
	 */
60 53
	/**
61 54
	 * <p>getName</p>
62 55
	 *
......
67 60
		return BulkEditorInputType.NAME.label;
68 61
	}
69 62

  
70
	/* (non-Javadoc)
71
	 * @see org.eclipse.ui.IEditorInput#getToolTipText()
72
	 */
73 63
	/**
74 64
	 * <p>getToolTipText</p>
75 65
	 *
......
114 104
	}
115 105
*/
116 106
	@Override
117
    public boolean delete(TaxonNameBase entity, DeleteConfiguratorBase config)  {
107
    public boolean delete(TaxonName entity, DeleteConfiguratorBase config)  {
118 108
		NameDeletionConfigurator nameConfig = null;
119 109
		if (config instanceof NameDeletionConfigurator){
120 110
			nameConfig = (NameDeletionConfigurator) config;
......
126 116
	
127 117
	/** {@inheritDoc} */
128 118
	@Override
129
    public TaxonNameBase save(TaxonNameBase entity) {
130
		TaxonNameBase mergedName = null;
119
    public TaxonName save(TaxonName entity) {
120
		TaxonName mergedName = null;
131 121
		mergedName =  CdmStore.getService(INameService.class).merge(entity, true).getMergedEntity();
132 122
	   	return mergedName;
133 123
		
134 124
	}
135 125

  
136
	/* (non-Javadoc)
137
	 * @see eu.etaxonomy.taxeditor.bulkeditor.input.AbstractBulkEditorInput#createEntityCreator()
138
	 */
139 126
	@Override
140
	protected IEntityCreator<TaxonNameBase> createEntityCreator() {
127
	protected IEntityCreator<TaxonName> createEntityCreator() {
141 128
		return new NameCreator();
142 129
	}
143 130

  
144
	/* (non-Javadoc)
145
	 * @see eu.etaxonomy.taxeditor.bulkeditor.input.AbstractBulkEditorInput#getSortProviders()
146
	 */
147 131
	@Override
148
	public List<IBulkEditorSortProvider<TaxonNameBase>> getSortProviders() {
149
		List<IBulkEditorSortProvider<TaxonNameBase>> sortProviders = super.getSortProviders();
132
	public List<IBulkEditorSortProvider<TaxonName>> getSortProviders() {
133
		List<IBulkEditorSortProvider<TaxonName>> sortProviders = super.getSortProviders();
150 134

  
151
		sortProviders.add(0, new IdentifiableEntitySortProvider<TaxonNameBase>());
135
		sortProviders.add(0, new IdentifiableEntitySortProvider<>());
152 136

  
153 137
		return sortProviders;
154 138
	}
155 139

  
156
	/* (non-Javadoc)
157
	 * @see eu.etaxonomy.taxeditor.bulkeditor.input.AbstractBulkEditorInput#getTypeText(java.lang.Object)
158
	 */
159 140
	@Override
160 141
	public String getTypeText(Object entity) {
161
		if((entity instanceof TaxonNameBase) && (((TaxonNameBase) entity).getNomenclaturalCode() != null)){
162
			return ((TaxonNameBase) entity).getNomenclaturalCode().getTitleCache();
142
		if((entity instanceof TaxonName) && (((TaxonName) entity).getNomenclaturalCode() != null)){
143
			return ((TaxonName) entity).getNomenclaturalCode().getTitleCache();
163 144
		}
164 145
		return super.getTypeText(entity);
165 146
	}
166 147

  
167
	/* (non-Javadoc)
168
	 * @see eu.etaxonomy.taxeditor.bulkeditor.input.AbstractBulkEditorInput#getText(eu.etaxonomy.cdm.model.common.ICdmBase)
169
	 */
170 148
	@Override
171
	public String getText(TaxonNameBase entity) {
149
	public String getText(TaxonName entity) {
172 150
		return (entity).getFullTitleCache();
173 151
	}
174 152

  
175
    /* (non-Javadoc)
176
     * @see eu.etaxonomy.taxeditor.editor.CdmEntitySessionInput#merge()
177
     */
178 153
    @Override
179 154
    public void merge() {
180 155

  
181 156
    }
182 157

  
183 158
	@Override
184
	protected TaxonNameBase loadEntity(UUID entityUuid) {
159
	protected TaxonName loadEntity(UUID entityUuid) {
185 160
		List<String> propertyPaths = Arrays.asList(new String[]{});
186 161
		return CdmStore.getService(INameService.class).load(entityUuid, getPropertyPaths());
187 162
	}
eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/input/entitycreator/NameCreator.java
15 15
import java.util.TreeMap;
16 16

  
17 17
import eu.etaxonomy.cdm.model.name.Rank;
18
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
18
import eu.etaxonomy.cdm.model.name.TaxonName;
19 19
import eu.etaxonomy.taxeditor.annotatedlineeditor.IEntityCreator;
20 20
import eu.etaxonomy.taxeditor.parser.ParseHandler;
21 21
import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
......
28 28
 * @created 07.07.2009
29 29
 * @version 1.0
30 30
 */
31
public class NameCreator implements IEntityCreator<TaxonNameBase> {
31
public class NameCreator implements IEntityCreator<TaxonName> {
32 32

  
33
	/* (non-Javadoc)
34
	 * @see eu.etaxonomy.taxeditor.bulkeditor.IEntityCreator#createEntity(java.lang.String)
35
	 */
36 33
	/** {@inheritDoc} */
37 34
    @Override
38
    public TaxonNameBase createEntity(String text) {
39
		TaxonNameBase name = PreferencesUtil.getPreferredNomenclaturalCode().getNewTaxonNameInstance(null);
35
    public TaxonName createEntity(String text) {
36
		TaxonName name = PreferencesUtil.getPreferredNomenclaturalCode().getNewTaxonNameInstance(null);
40 37
		name.setTitleCache(text, true);
41 38
		//name.setTitleCache(text);
42 39
		return name;
43 40
	}
44 41

  
45
	/* (non-Javadoc)
46
	 * @see eu.etaxonomy.taxeditor.annotatedlineeditor.IEntityCreator#createEntity(java.lang.Class, java.lang.String)
47
	 */
48 42
	/** {@inheritDoc} */
49 43
    @Override
50
    public TaxonNameBase createEntity(Object key, String text) {
44
    public TaxonName createEntity(Object key, String text) {
51 45
		return ParseHandler.parseName(text, (Rank) key);
52 46
	}
53 47

  
54
	/* (non-Javadoc)
55
	 * @see eu.etaxonomy.taxeditor.annotatedlineeditor.IEntityCreator#getClassLabelPairs()
56
	 */
57 48
	/**
58 49
	 * <p>getKeyLabelPairs</p>
59 50
	 *
eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/input/entitycreator/TaxonCreator.java
6 6
import eu.etaxonomy.cdm.model.agent.Person;
7 7
import eu.etaxonomy.cdm.model.agent.Team;
8 8
import eu.etaxonomy.cdm.model.name.Rank;
9
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
9
import eu.etaxonomy.cdm.model.name.TaxonName;
10 10
import eu.etaxonomy.cdm.model.taxon.Synonym;
11 11
import eu.etaxonomy.cdm.model.taxon.Taxon;
12 12
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
eu.etaxonomy.taxeditor.bulkeditor/src/main/java/eu/etaxonomy/taxeditor/bulkeditor/referencingobjects/ReferencingObjectsView.java
70 70
import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
71 71
import eu.etaxonomy.cdm.model.media.Media;
72 72
import eu.etaxonomy.cdm.model.molecular.Sequence;
73
import eu.etaxonomy.cdm.model.name.NonViralName;
73
import eu.etaxonomy.cdm.model.name.TaxonName;
74 74
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
75 75
import eu.etaxonomy.cdm.model.reference.Reference;
76 76
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
......
278 278
        try {
279 279
        	if (objectClass.getSuperclass().equals(TeamOrPersonBase.class) ){
280 280
	        	referencedObject = CdmStore.getService(IAgentService.class).load(entity);
281
        	} else if (objectClass.getSuperclass().equals(NonViralName.class)){
281
        	} else if (objectClass.getSuperclass().equals(TaxonName.class)){
282 282
        		referencedObject = CdmStore.getService(INameService.class).load(entity);
283 283
        	} else if (objectClass.getSuperclass().equals(TaxonBase.class)){
284 284
        		referencedObject = CdmStore.getService(ITaxonService.class).load(entity);
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/MultiPageTaxonEditor.java
29 29
import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
30 30
import eu.etaxonomy.cdm.api.conversation.IConversationEnabled;
31 31
import eu.etaxonomy.cdm.model.common.CdmBase;
32
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
32
import eu.etaxonomy.cdm.model.name.TaxonName;
33 33
import eu.etaxonomy.cdm.model.taxon.Taxon;
34 34
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
35 35
import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap;
......
299 299
    protected void setPartName() {
300 300

  
301 301
        String partName = null;
302
        TaxonNameBase<?, ?> name = getTaxon().getName();
302
        TaxonName name = getTaxon().getName();
303 303

  
304 304
        if (name != null) {
305 305
            partName = name.getTitleCache();
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/MultiPageTaxonEditorDataChangeBehaviour.java
13 13

  
14 14
import org.apache.log4j.Logger;
15 15

  
16
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
16
import eu.etaxonomy.cdm.model.name.TaxonName;
17 17
import eu.etaxonomy.cdm.model.taxon.Synonym;
18 18
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
19 19
import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeEvent;
......
96 96
		for(CdmDataChangeEvent event : events){
97 97
			
98 98
			// update editor title
99
			if(event.getEntity() instanceof TaxonNameBase){
99
			if(event.getEntity() instanceof TaxonName){
100 100
				if(input.getTaxon().getName().equals(event.getEntity())){
101 101
					// set the name of the editor window
102 102
					source.setPartName();
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/OpenEditorConfiguration.java
9 9

  
10 10
package eu.etaxonomy.taxeditor.editor;
11 11

  
12
import eu.etaxonomy.cdm.model.name.NonViralName;
12
import eu.etaxonomy.cdm.model.name.INonViralName;
13 13
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
14 14

  
15 15
/**
......
17 17
 *
18 18
 * @author n.hoffmann
19 19
 * @created Sep 27, 2010
20
 * @version 1.0
21 20
 */
22 21
public class OpenEditorConfiguration {
23 22
	
24 23
	private TaxonNode parentNode;
25 24
	
26
	private NonViralName nonViralName;
25
	private INonViralName nonViralName;
27 26
	
28 27
	private boolean openInEditor;
29 28
	
......
70 69
	 *
71 70
	 * @return the nonViralName
72 71
	 */
73
	public NonViralName getNonViralName() {
72
	public INonViralName getNonViralName() {
74 73
		return nonViralName;
75 74
	}
76 75

  
......
79 78
	 *
80 79
	 * @param nonViralName the nonViralName to set
81 80
	 */
82
	public void setNonViralName(NonViralName nonViralName) {
81
	public void setNonViralName(INonViralName nonViralName) {
83 82
		this.nonViralName = nonViralName;
84 83
	}
85 84

  
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/TaxonEditorInput.java
28 28
import eu.etaxonomy.cdm.api.service.ITaxonNodeService;
29 29
import eu.etaxonomy.cdm.api.service.ITaxonService;
30 30
import eu.etaxonomy.cdm.model.common.CdmBase;
31
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
31
import eu.etaxonomy.cdm.model.name.TaxonName;
32 32
import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
33 33
import eu.etaxonomy.cdm.model.taxon.Synonym;
34 34
import eu.etaxonomy.cdm.model.taxon.Taxon;
......
154 154
    private void initForParentTaxonNode(UUID parentNodeUuid){
155 155

  
156 156

  
157
        TaxonNameBase<?, ?> name = PreferencesUtil.getPreferredNomenclaturalCode().getNewTaxonNameInstance(null);
157
        TaxonName name = PreferencesUtil.getPreferredNomenclaturalCode().getNewTaxonNameInstance(null);
158 158
        ITaxonTreeNode parentNode = CdmStore.getService(IClassificationService.class).getTreeNodeByUuid(parentNodeUuid);
159 159

  
160 160
        Taxon newTaxon = Taxon.NewInstance(name, parentNode.getReference());
......
273 273
        if(getTaxon() == null){
274 274
            return null;
275 275
        }
276
        TaxonNameBase<?, ?> name = getTaxon().getName();
276
        TaxonName name = getTaxon().getName();
277 277
        if (name == null || name.getTitleCache() == null) {
278 278
            return Messages.TaxonEditorInput_NEW_TAXON;
279 279
        } else {
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java
49 49
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
50 50
import eu.etaxonomy.cdm.model.name.INonViralName;
51 51
import eu.etaxonomy.cdm.model.name.NameRelationship;
52
import eu.etaxonomy.cdm.model.name.NonViralName;
53
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
52
import eu.etaxonomy.cdm.model.name.TaxonName;
54 53
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
55 54
import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
56 55
import eu.etaxonomy.taxeditor.editor.CdmDataTransfer;
......
178 177
				// parse the text
179 178
				String text = nameViewer.getTextWidget().getText();
180 179

  
181
				TaxonNameBase<?,?> name = (TaxonNameBase<?,?>)parseHandler.parse(text);
180
				TaxonName name = (TaxonName)parseHandler.parse(text);
182 181
				getTaxonBase().setName(name);
183 182
				getTaxonBase().setTitleCache((getTaxonBase().generateTitle()));
184 183

  
......
244 243
	 *
245 244
	 */
246 245
	private void showNameRelations() {
247
		TaxonNameBase<?, ?> name = getName();
246
		TaxonName name = getName();
248 247
		if (name == null) {
249 248
			return;
250 249
		}
......
259 258
		}
260 259
		// for (NameRelationship nameRelation : nameRelations) {
261 260
		// String typeLabel = null;
262
		// TaxonNameBase<?, ?> relatedName = null;
261
		// TaxonName relatedName = null;
263 262
		//
264 263
		// if (name.equals(nameRelation.getFromName())) {
265 264
		// typeLabel = labelProvider.getNameRelationTypeLabel(
......
382 381
	 */
383 382
	protected void handleSplitText(String text) {
384 383
		// Create a synonym in a new homotypic group using text as name
385
		TaxonNameBase synonymName = ParseHandler
386
				.parseReferencedName(text, null);
384
		TaxonName synonymName = TaxonName.castAndDeproxy(
385
				ParseHandler.parseReferencedName(text, null));
387 386

  
388 387
		EditorUtil.executeOperation(new CreateSynonymInNewGroupOperation(
389 388
				Messages.AbstractGroupedContainer_NEW_HETERO_SYNONYM, getEditor().getUndoContext(),
......
451 450
	 * @return
452 451
	 */
453 452
	private boolean isFreetextEditingAllowed() {
454
		NonViralName name = (NonViralName) HibernateProxyHelper
453
		INonViralName name = (INonViralName) HibernateProxyHelper
455 454
				.deproxy(getName());
456 455
		boolean enableFreetext = true;
457 456

  
......
486 485
	}
487 486

  
488 487
	private boolean isNameParsable() {
489
		TaxonNameBase name = getName();
488
		TaxonName name = getName();
490 489

  
491 490
		boolean isParsable = true;
492 491
		isParsable &= CdmUtils.isEmpty(name.getAppendedPhrase()); // taxonFieldsEmpty();
493 492

  
494
		if (name instanceof NonViralName) {
495
			NonViralName nonViralName = (NonViralName) name;
496
			isParsable &= !nonViralName.isProtectedAuthorshipCache();
497
			isParsable &= !nonViralName.isProtectedNameCache();
498
		}
493
		isParsable &= !name.isProtectedAuthorshipCache();
494
		isParsable &= !name.isProtectedNameCache();
499 495

  
500 496
		return isParsable;
501 497
	}
......
529 525
	 *
530 526
	 * @return a {@link eu.etaxonomy.cdm.model.name.TaxonNameBase} object.
531 527
	 */
532
	public TaxonNameBase getName() {
528
	public TaxonName getName() {
533 529
		return HibernateProxyHelper.deproxy(getTaxonBase()
534 530
				.getName());
535 531
	}
......
549 545
			// @Override
550 546
			// protected IStatus run(IProgressMonitor monitor) {
551 547
			//
552
			final TaxonNameBase<?,?> name = (TaxonNameBase<?,?>)parseHandler
548
			final TaxonName name = (TaxonName)parseHandler
553 549
					.parseAndResolveDuplicates(unparsedNameString);
554 550
			//
555 551
			// Display.getDefault().asyncExec(new Runnable(){
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/SynonymContainer.java
17 17
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
18 18
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
19 19
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
20
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
20
import eu.etaxonomy.cdm.model.name.TaxonName;
21 21
import eu.etaxonomy.cdm.model.taxon.Synonym;
22 22
import eu.etaxonomy.taxeditor.editor.EditorUtil;
23 23
import eu.etaxonomy.taxeditor.editor.l10n.Messages;
......
70 70
	}
71 71
	
72 72
	protected void updateIcon(){
73
		TaxonNameBase name = getName();
73
		TaxonName name = getName();
74 74
		
75 75
		if(! name.getStatus().isEmpty()){
76 76
			
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/ChangeSynonymToAcceptedTaxonHandler.java
27 27
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
28 28
import eu.etaxonomy.cdm.model.common.CdmBase;
29 29
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
30
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
30
import eu.etaxonomy.cdm.model.name.TaxonName;
31 31
import eu.etaxonomy.cdm.model.taxon.Synonym;
32 32
import eu.etaxonomy.cdm.model.taxon.Taxon;
33 33
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
......
47 47
 *
48 48
 * @author n.hoffmann
49 49
 * @created 21.04.2009
50
 * @version 1.0
51 50
 */
52 51
public class ChangeSynonymToAcceptedTaxonHandler extends AbstractHandler implements IPostOperationEnabled {
53 52
	private static final Logger logger = Logger
......
85 84

  
86 85
		TaxonNode parentNode = (TaxonNode) HibernateProxyHelper.deproxy(((TaxonEditorInput) input).getTaxonNode().getParent());
87 86

  
88
		List<UUID> excludeTaxa = new ArrayList<UUID>();
87
		List<UUID> excludeTaxa = new ArrayList<>();
89 88
		//excludeTaxa.add(taxon.getUuid());//there are some cases where the accepted taxon should be the parent of the new created accepted taxon
90 89

  
91 90
		TaxonNode newParentNode = TaxonNodeSelectionDialog.select(HandlerUtil.getActiveShell(event), editor.getConversationHolder(), Messages.ChangeSynonymToAcceptedTaxonHandler_SELECT_PARENT, null, null, ((TaxonEditorInput) input).getTaxonNode().getClassification());
......
96 95
			// TODO get synonyms from homotypical group and add them as homotypic synonyms to new accepted taxon
97 96
			// apply confirmation dialog
98 97
			HomotypicalGroup group = synonym.getHomotypicGroup();
99
			Set<TaxonNameBase> namesInGroup = group.getTypifiedNames();
98
			Set<TaxonName> namesInGroup = group.getTypifiedNames();
100 99
			// FIXME with this implementation we can not create a taxonNode that is a direct child of the classification node
101 100
			AbstractPostOperation operation = new ChangeSynonymToAcceptedTaxonOperation(Messages.ChangeSynonymToAcceptedTaxonHandler_CHANGE_SYN_TO_ACC_TAXON, EditorUtil.getUndoContext(),
102 101
					taxon, newParentNode, synonym, namesInGroup, this, editor, (ICdmEntitySessionEnabled)editor.getEditorInput()); //$NON-NLS-1$
......
107 106
		return null;
108 107
	}
109 108

  
110
	/* (non-Javadoc)
111
	 * @see eu.etaxonomy.taxeditor.operations.IPostOperationEnabled#postOperation(eu.etaxonomy.cdm.model.common.CdmBase)
112
	 */
113 109
	/** {@inheritDoc} */
114 110
	@Override
115 111
    public boolean postOperation(CdmBase objectAffectedByOperation) {
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/CreateHeterotypicSynonymHandler.java
16 16
import org.eclipse.core.commands.IHandler;
17 17
import org.eclipse.core.commands.common.NotDefinedException;
18 18

  
19
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
19
import eu.etaxonomy.cdm.model.name.TaxonName;
20 20
import eu.etaxonomy.taxeditor.editor.EditorUtil;
21 21
import eu.etaxonomy.taxeditor.editor.Page;
22 22
import eu.etaxonomy.taxeditor.editor.name.TaxonNameEditor;
......
29 29
 *
30 30
 * @author n.hoffmann
31 31
 * @created 06.02.2009
32
 * @version 1.0
33 32
 */
34 33
public class CreateHeterotypicSynonymHandler extends AbstractHandler implements
35 34
		IHandler {
36 35
	private static final Logger logger = Logger
37 36
			.getLogger(CreateHeterotypicSynonymHandler.class);
38 37

  
39
	/* (non-Javadoc)
40
	 * @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent)
41
	 */
42 38
	/** {@inheritDoc} */
43 39
	public Object execute(ExecutionEvent event) throws ExecutionException {
44 40
		TaxonNameEditor editor = (TaxonNameEditor) EditorUtil.getActiveEditorPage(
45 41
				Page.NAME);
46 42
		
47
		TaxonNameBase newSynonymName = ParseHandler.createEmptyName();
43
		TaxonName newSynonymName = ParseHandler.createEmptyName();
48 44
		
49
		AbstractPostOperation operation;
45
		AbstractPostOperation<?> operation;
50 46
		try {
51 47
			operation = new CreateSynonymInNewGroupOperation(event.getCommand().getName(), 
52 48
					editor.getUndoContext(), editor.getTaxon(), newSynonymName, editor);
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/CreateHomotypicSynonymHandler.java
16 16
import org.eclipse.core.commands.common.NotDefinedException;
17 17

  
18 18
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
19
import eu.etaxonomy.cdm.model.name.INonViralName;
20
import eu.etaxonomy.cdm.model.name.NonViralName;
21
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
19
import eu.etaxonomy.cdm.model.name.TaxonName;
22 20
import eu.etaxonomy.cdm.model.taxon.Taxon;
23 21
import eu.etaxonomy.taxeditor.editor.EditorUtil;
24 22
import eu.etaxonomy.taxeditor.editor.Page;
......
33 31
 *
34 32
 * @author n.hoffmann
35 33
 * @created 06.02.2009
36
 * @version 1.0
37 34
 */
38 35
public class CreateHomotypicSynonymHandler extends AbstractHandler implements
39 36
		IHandler {
40 37

  
41
	/* (non-Javadoc)
42
	 * @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent)
43
	 */
44 38
	/** {@inheritDoc} */
45 39
	@Override
46 40
    public Object execute(ExecutionEvent event) throws ExecutionException {
......
48 42
				Page.NAME);
49 43
		Taxon taxon = editor.getTaxon();
50 44
		HomotypicalGroup group = taxon.getHomotypicGroup();
51
		TaxonNameBase<?,?> newSynonymName = ParseHandler.createEmptyName();
45
		TaxonName newSynonymName = ParseHandler.createEmptyName();
52 46

  
53
		AbstractPostOperation operation;
47
		AbstractPostOperation<?> operation;
54 48
		try {
55 49
			operation = new CreateSynonymInExistingHomotypicalGroupOperation(event.getCommand().getName(),
56 50
					editor.getUndoContext(), taxon, group, newSynonymName, editor);
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/CreateMisapplicationHandler.java
15 15
import org.eclipse.core.commands.ExecutionException;
16 16
import org.eclipse.core.commands.common.NotDefinedException;
17 17

  
18
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
18
import eu.etaxonomy.cdm.model.name.TaxonName;
19 19
import eu.etaxonomy.cdm.model.taxon.Taxon;
20 20
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
21 21
import eu.etaxonomy.taxeditor.editor.EditorUtil;
......
30 30
 *
31 31
 * @author n.hoffmann
32 32
 * @created 16.04.2009
33
 * @version 1.0
34 33
 */
35 34
public class CreateMisapplicationHandler extends AbstractHandler {
36 35
	private static final Logger logger = Logger
37 36
			.getLogger(CreateMisapplicationHandler.class);
38 37

  
39
	/* (non-Javadoc)
40
	 * @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent)
41
	 */
42 38
	/** {@inheritDoc} */
43 39
	public Object execute(ExecutionEvent event) throws ExecutionException {
44 40
		TaxonNameEditor editor = (TaxonNameEditor) EditorUtil.getActiveEditorPage(
45 41
				Page.NAME);
46 42
		
47 43

  
48
		TaxonNameBase conceptName = ParseHandler.createEmptyName();
44
		TaxonName conceptName = ParseHandler.createEmptyName();
49 45
		Taxon concept = Taxon.NewInstance(conceptName, null);
50 46
		
51 47
		TaxonRelationshipType type = TaxonRelationshipType.MISAPPLIED_NAME_FOR();
52 48
		
53
		AbstractPostOperation operation;
49
		AbstractPostOperation<?> operation;
54 50
		try {
55 51
			operation = new CreateConceptRelationOperation(event.getCommand().getName(), 
56 52
					editor.getUndoContext(), editor.getTaxon(), concept, type, editor);
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/handler/CreateSynonymInHomotypicalGroupHandler.java
20 20
import org.eclipse.ui.handlers.HandlerUtil;
21 21

  
22 22
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
23
import eu.etaxonomy.cdm.model.name.INonViralName;
24
import eu.etaxonomy.cdm.model.name.NonViralName;
25
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
23
import eu.etaxonomy.cdm.model.name.TaxonName;
26 24
import eu.etaxonomy.cdm.model.taxon.Synonym;
27 25
import eu.etaxonomy.taxeditor.editor.EditorUtil;
28 26
import eu.etaxonomy.taxeditor.editor.Page;
......
64 62

  
65 63
		HomotypicalGroup group = synonym.getHomotypicGroup();
66 64

  
67
		TaxonNameBase<?,?> newSynonymName = ParseHandler.createEmptyName();
65
		TaxonName newSynonymName = ParseHandler.createEmptyName();
68 66

  
69
		AbstractPostOperation operation;
67
		AbstractPostOperation<?> operation;
70 68

  
71 69
		try {
72 70
			operation = new CreateSynonymInExistingHomotypicalGroupOperation(event.getCommand().getName(), editor.getUndoContext(),
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/ChangeConceptToSynonymOperation.java
20 20
import eu.etaxonomy.cdm.api.service.ITaxonService;
21 21
import eu.etaxonomy.cdm.api.service.exception.DataChangeNoRollbackException;
22 22
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
23
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
23
import eu.etaxonomy.cdm.model.name.TaxonName;
24 24
import eu.etaxonomy.cdm.model.taxon.Synonym;
25 25
import eu.etaxonomy.cdm.model.taxon.Taxon;
26 26
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
......
87 87
			throws ExecutionException {
88 88

  
89 89
		// Create new synonym using concept name
90
		TaxonNameBase<?, ?> synonymName = concept.getName();
90
		TaxonName synonymName = concept.getName();
91 91
		Synonym synonym = null;
92 92
		try {
93 93
			synonym =
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/ChangeHomotypicGroupOperation.java
17 17

  
18 18
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
19 19
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
20
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
20
import eu.etaxonomy.cdm.model.name.TaxonName;
21 21
import eu.etaxonomy.cdm.model.taxon.Synonym;
22 22
import eu.etaxonomy.cdm.model.taxon.SynonymType;
23 23
import eu.etaxonomy.cdm.model.taxon.Taxon;
......
75 75
			throws ExecutionException {
76 76

  
77 77
    	// Get synonym name
78
		TaxonNameBase<?, ?> synonymName = synonym.getName();
78
		TaxonName synonymName = synonym.getName();
79 79
		monitor.worked(20);
80 80

  
81 81
		// TODO pass in homotypical group's taxon in case we are dragging from one editor to another
......
117 117
			throws ExecutionException {
118 118

  
119 119
		// Get synonym name
120
		TaxonNameBase<?, ?> synonymName = this.synonym.getName();
120
		TaxonName synonymName = this.synonym.getName();
121 121
		if(synonymName == null){
122 122
			// TODO
123 123
		}
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/ChangeHomotypicalGroupBasionymOperation.java
19 19

  
20 20
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
21 21
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
22
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
22
import eu.etaxonomy.cdm.model.name.TaxonName;
23 23
import eu.etaxonomy.cdm.model.taxon.Taxon;
24 24
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
25 25
import eu.etaxonomy.taxeditor.operation.AbstractPostTaxonOperation;
......
30 30
 *
31 31
 * @author p.ciardelli
32 32
 * @created 15.01.2009
33
 * @version 1.0
34 33
 */
35 34
public class ChangeHomotypicalGroupBasionymOperation extends
36 35
		AbstractPostTaxonOperation {
36
	
37 37
	private final TaxonBase taxonBase;
38 38

  
39 39
	/**
......
52 52
		this.taxonBase = taxonBase;
53 53
	}
54 54

  
55
	/* (non-Javadoc)
56
	 * @see org.eclipse.core.commands.operations.AbstractOperation#execute(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
57
	 */
58 55
	/** {@inheritDoc} */
59 56
	@Override
60 57
	public IStatus execute(IProgressMonitor monitor, IAdaptable info)
61 58
			throws ExecutionException {
62 59

  
63
		TaxonNameBase<?, ?> name = taxonBase.getName();
60
		TaxonName name = taxonBase.getName();
64 61

  
65 62
		monitor.worked(20);
66
		name = HibernateProxyHelper.deproxy(name, TaxonNameBase.class);
63
		name = HibernateProxyHelper.deproxy(name);
67 64
		HomotypicalGroup group = HibernateProxyHelper.deproxy(name.getHomotypicalGroup(), HomotypicalGroup.class);
68
        TaxonNameBase oldBasionym = name.getBasionym();
65
        TaxonName oldBasionym = name.getBasionym();
69 66

  
70 67
		name.setAsGroupsBasionym();
71 68

  
72 69
		monitor.worked(40);
73
		oldBasionym = HibernateProxyHelper.deproxy(oldBasionym, TaxonNameBase.class);
70
		oldBasionym = HibernateProxyHelper.deproxy(oldBasionym);
74 71
		if (oldBasionym != null){
75 72
			Set<TaxonBase> taxonBases = oldBasionym.getTaxonBases();
76 73
			if (!taxonBases.isEmpty()){
......
82 79
		return postExecute(taxonBase);
83 80
	}
84 81

  
85
	/* (non-Javadoc)
86
	 * @see org.eclipse.core.commands.operations.AbstractOperation#redo(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
87
	 */
88 82
	/** {@inheritDoc} */
89 83
	@Override
90 84
	public IStatus redo(IProgressMonitor monitor, IAdaptable info)
......
92 86
		return execute(monitor, info);
93 87
	}
94 88

  
95
	/* (non-Javadoc)
96
	 * @see org.eclipse.core.commands.operations.AbstractOperation#undo(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
97
	 */
98 89
	/** {@inheritDoc} */
99 90
	@Override
100 91
	public IStatus undo(IProgressMonitor monitor, IAdaptable info)
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/ChangeSynonymToAcceptedTaxonOperation.java
21 21
import eu.etaxonomy.cdm.api.service.ITaxonService;
22 22
import eu.etaxonomy.cdm.api.service.UpdateResult;
23 23
import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;
24
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
24
import eu.etaxonomy.cdm.model.name.TaxonName;
25 25
import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
26 26
import eu.etaxonomy.cdm.model.taxon.Synonym;
27 27
import eu.etaxonomy.cdm.model.taxon.Taxon;
......
38 38
 *
39 39
 * @author n.hoffmann
40 40
 * @created 16.01.2009
41
 * @version 1.0
42 41
 */
43 42
public class ChangeSynonymToAcceptedTaxonOperation extends AbstractPersistentPostOperation {
44 43

  
45
	private Taxon newTaxon;
46 44
	private final Synonym synonym;
47 45
	private final ITaxonTreeNode parentNode;
48 46

  
49 47
	private TaxonNode newNode;
50 48

  
51
	//private final Set<TaxonNameBase> namesInHomotypicGroup;
49
	//private final Set<TaxonName> namesInHomotypicGroup;
52 50

  
53 51
	/**
54 52
	 * <p>Constructor for ChangeSynonymToAcceptedTaxonOperation.</p>
......
67 65
			Taxon taxon,
68 66
			ITaxonTreeNode parentNode,
69 67
			Synonym synonym,
70
			Set<TaxonNameBase> namesInHomotypicalGroup,
68
			Set<TaxonName> namesInHomotypicalGroup,
71 69
			IPostOperationEnabled postOperationEnabled,
72 70
			IConversationEnabled conversationEnabled,
73 71
			ICdmEntitySessionEnabled cdmEntitySessionEnabled) {
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/CreateNameRelationOperation.java
16 16
import org.eclipse.core.runtime.IStatus;
17 17

  
18 18
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
19
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
19
import eu.etaxonomy.cdm.model.name.TaxonName;
20 20
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
21 21
import eu.etaxonomy.taxeditor.operation.AbstractPostTaxonOperation;
22 22
import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;
......
26 26
 *
27 27
 * @author n.hoffmann
28 28
 * @created Mar 30, 2010
29
 * @version 1.0
30 29
 */
31 30
public class CreateNameRelationOperation extends AbstractPostTaxonOperation {
32 31

  
33 32
	private TaxonBase taxonBase;
34
	private TaxonNameBase relatedName;
33
	private TaxonName relatedName;
35 34
	private NameRelationshipType type;
36 35

  
37 36
	/**
......
44 43
	 * @param type a {@link eu.etaxonomy.cdm.model.name.NameRelationshipType} object.
45 44
	 * @param postOperationEnabled a {@link eu.etaxonomy.taxeditor.operation.IPostOperationEnabled} object.
46 45
	 */
47
	public CreateNameRelationOperation(String label, IUndoContext undoContext, TaxonBase taxonBase, TaxonNameBase relatedName, NameRelationshipType type, IPostOperationEnabled postOperationEnabled) {
46
	public CreateNameRelationOperation(String label, IUndoContext undoContext, TaxonBase taxonBase, TaxonName relatedName, NameRelationshipType type, IPostOperationEnabled postOperationEnabled) {
48 47
		super(label, undoContext, postOperationEnabled);
49 48
		this.taxonBase = taxonBase;
50 49
		this.relatedName = relatedName;
51 50
		this.type = type;
52 51
	}
53 52
	
54
	/* (non-Javadoc)
55
	 * @see org.eclipse.core.commands.operations.AbstractOperation#execute(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
56
	 */
57 53
	/** {@inheritDoc} */
58 54
	@Override
59 55
	public IStatus execute(IProgressMonitor monitor, IAdaptable info)
60 56
			throws ExecutionException {
61 57
		
62
		TaxonNameBase fromName = taxonBase.getName();
58
		TaxonName fromName = taxonBase.getName();
63 59
		
64 60
		fromName.addRelationshipToName(relatedName, type, null);
65 61
		
66 62
		return postExecute(taxonBase);
67 63
	}
68 64

  
69
	/* (non-Javadoc)
70
	 * @see org.eclipse.core.commands.operations.AbstractOperation#redo(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
71
	 */
72 65
	/** {@inheritDoc} */
73 66
	@Override
74 67
	public IStatus redo(IProgressMonitor monitor, IAdaptable info)
......
76 69
		return execute(monitor, info);
77 70
	}
78 71

  
79
	/* (non-Javadoc)
80
	 * @see org.eclipse.core.commands.operations.AbstractOperation#undo(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
81
	 */
82 72
	/** {@inheritDoc} */
83 73
	@Override
84 74
	public IStatus undo(IProgressMonitor monitor, IAdaptable info)
85 75
			throws ExecutionException {
86
		TaxonNameBase fromName = taxonBase.getName();
76
		TaxonName fromName = taxonBase.getName();
87 77
		
88 78
		fromName.removeRelationToTaxonName(relatedName);
89 79
		
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/CreateSynonymInExistingHomotypicalGroupOperation.java
17 17

  
18 18
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
19 19
import eu.etaxonomy.cdm.model.name.INonViralName;
20
import eu.etaxonomy.cdm.model.name.NonViralName;
21
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
20
import eu.etaxonomy.cdm.model.name.TaxonName;
22 21
import eu.etaxonomy.cdm.model.taxon.Synonym;
23 22
import eu.etaxonomy.cdm.model.taxon.Taxon;
24 23
import eu.etaxonomy.taxeditor.operation.AbstractPostTaxonOperation;
......
34 33
		AbstractPostTaxonOperation {
35 34

  
36 35
	private final HomotypicalGroup group;
37
	private final TaxonNameBase<?,?> newSynonymName;
36
	private final TaxonName newSynonymName;
38 37

  
39 38
	private Synonym synonym;
40 39

  
......
50 49
	 */
51 50
	public CreateSynonymInExistingHomotypicalGroupOperation(String label,
52 51
			IUndoContext undoContext, Taxon taxon, HomotypicalGroup group, 
53
			TaxonNameBase<?,?> newSynonymName, IPostOperationEnabled postOperationEnabled) {
52
			TaxonName newSynonymName, IPostOperationEnabled postOperationEnabled) {
54 53
		super(label, undoContext, taxon, postOperationEnabled);
55 54
		this.group = group;
56 55
		this.newSynonymName = newSynonymName;
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/CreateSynonymInNewGroupOperation.java
17 17

  
18 18
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
19 19
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
20
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
20
import eu.etaxonomy.cdm.model.name.TaxonName;
21 21
import eu.etaxonomy.cdm.model.taxon.Synonym;
22 22
import eu.etaxonomy.cdm.model.taxon.Taxon;
23 23
import eu.etaxonomy.taxeditor.operation.AbstractPostTaxonOperation;
......
36 36
 */
37 37
public class CreateSynonymInNewGroupOperation extends AbstractPostTaxonOperation {
38 38

  
39
	private final TaxonNameBase newSynonymName;
39
	private final TaxonName newSynonymName;
40 40
	private Synonym newSynonym;
41 41

  
42 42
	/**
......
49 49
	 * @param postOperationEnabled a {@link eu.etaxonomy.taxeditor.operation.IPostOperationEnabled} object.
50 50
	 */
51 51
	public CreateSynonymInNewGroupOperation(String label,
52
			IUndoContext undoContext, Taxon taxon, TaxonNameBase newSynonymName, IPostOperationEnabled postOperationEnabled) {
52
			IUndoContext undoContext, Taxon taxon, TaxonName newSynonymName, IPostOperationEnabled postOperationEnabled) {
53 53
		super(label, undoContext, taxon, postOperationEnabled);
54 54

  
55 55
		this.newSynonymName = newSynonymName;
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/DeleteNameRelationOperation.java
16 16
import org.eclipse.core.runtime.IStatus;
17 17

  
18 18
import eu.etaxonomy.cdm.model.name.NameRelationship;
19
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
19
import eu.etaxonomy.cdm.model.name.TaxonName;
20 20
import eu.etaxonomy.taxeditor.operation.AbstractPostTaxonOperation;
21 21
import eu.etaxonomy.taxeditor.operation.IPostOperationEnabled;
22 22

  
......
25 25
 *
26 26
 * @author n.hoffmann
27 27
 * @created Mar 30, 2010
28
 * @version 1.0
29 28
 */
30 29
public class DeleteNameRelationOperation extends AbstractPostTaxonOperation {
31 30

  
......
45 44
		this.nameRelationship = nameRelationship;
46 45
	}
47 46
	
48
	/* (non-Javadoc)
49
	 * @see org.eclipse.core.commands.operations.AbstractOperation#execute(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
50
	 */
51 47
	/** {@inheritDoc} */
52 48
	@Override
53 49
	public IStatus execute(IProgressMonitor monitor, IAdaptable info)
54 50
			throws ExecutionException {
55 51
		
56
		TaxonNameBase fromName = nameRelationship.getFromName();
52
		TaxonName fromName = nameRelationship.getFromName();
57 53
		
58 54
		fromName.removeRelationToTaxonName(nameRelationship.getToName());
59 55
		
60 56
		return postExecute(null);
61 57
	}
62 58

  
63
	/* (non-Javadoc)
64
	 * @see org.eclipse.core.commands.operations.AbstractOperation#redo(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
65
	 */
66 59
	/** {@inheritDoc} */
67 60
	@Override
68 61
	public IStatus redo(IProgressMonitor monitor, IAdaptable info)
......
70 63
		return execute(monitor, info);
71 64
	}
72 65

  
73
	/* (non-Javadoc)
74
	 * @see org.eclipse.core.commands.operations.AbstractOperation#undo(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
75
	 */
76 66
	/** {@inheritDoc} */
77 67
	@Override
78 68
	public IStatus undo(IProgressMonitor monitor, IAdaptable info)
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/MoveSynonymToAnotherAcceptedTaxonOperation.java
13 13
import eu.etaxonomy.cdm.api.service.ITaxonService;
14 14
import eu.etaxonomy.cdm.api.service.UpdateResult;
15 15
import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;
16
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
16
import eu.etaxonomy.cdm.model.name.TaxonName;
17 17
import eu.etaxonomy.cdm.model.taxon.Synonym;
18 18
import eu.etaxonomy.cdm.model.taxon.Taxon;
19 19
import eu.etaxonomy.taxeditor.editor.EditorUtil;
......
63 63
			throws ExecutionException {
64 64

  
65 65
    	// Get synonym name
66
		TaxonNameBase<?, ?> synonymName = synonym.getName();
66
		TaxonName synonymName = synonym.getName();
67 67
		monitor.worked(20);
68 68

  
69 69
		// Switch groups
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/operation/RemoveHomotypicalGroupBasionymOperation.java
15 15
import org.eclipse.core.runtime.IProgressMonitor;
16 16
import org.eclipse.core.runtime.IStatus;
17 17

  
18
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
18
import eu.etaxonomy.cdm.model.name.TaxonName;
19 19
import eu.etaxonomy.cdm.model.taxon.Taxon;
20 20
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
21 21
import eu.etaxonomy.taxeditor.operation.AbstractPostTaxonOperation;
......
26 26
 *
27 27
 * @author p.ciardelli
28 28
 * @created 15.01.2009
29
 * @version 1.0
30 29
 */
31 30
public class RemoveHomotypicalGroupBasionymOperation extends
32 31
		AbstractPostTaxonOperation {
......
49 48
		this.taxonBase = taxonBase;
50 49
	}
51 50

  
52
	/* (non-Javadoc)
53
	 * @see org.eclipse.core.commands.operations.AbstractOperation#execute(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
54
	 */
55 51
	/** {@inheritDoc} */
56 52
	@Override
57 53
	public IStatus execute(IProgressMonitor monitor, IAdaptable info)
58 54
			throws ExecutionException {
59 55
		
60
		TaxonNameBase<?, ?> name = taxonBase.getName();
56
		TaxonName name = taxonBase.getName();
61 57
		monitor.worked(20);
62 58

  
63 59
		name.removeAsGroupsBasionym();
......
66 62
		return postExecute(taxonBase);
67 63
	}
68 64

  
69
	/* (non-Javadoc)
70
	 * @see org.eclipse.core.commands.operations.AbstractOperation#redo(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
71
	 */
72 65
	/** {@inheritDoc} */
73 66
	@Override
74 67
	public IStatus redo(IProgressMonitor monitor, IAdaptable info)
......
76 69
		return execute(monitor, info);
77 70
	}
78 71

  
79
	/* (non-Javadoc)
80
	 * @see org.eclipse.core.commands.operations.AbstractOperation#undo(org.eclipse.core.runtime.IProgressMonitor, org.eclipse.core.runtime.IAdaptable)
81
	 */
82 72
	/** {@inheritDoc} */
83 73
	@Override
84 74
	public IStatus undo(IProgressMonitor monitor, IAdaptable info)
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/checklist/ChecklistLabelProvider.java
36 36
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
37 37
import eu.etaxonomy.cdm.model.description.Distribution;
38 38
import eu.etaxonomy.cdm.model.description.TaxonDescription;
39
import eu.etaxonomy.cdm.model.name.NonViralName;
39
import eu.etaxonomy.cdm.model.name.TaxonName;
40 40
import eu.etaxonomy.cdm.model.taxon.Taxon;
41
import eu.etaxonomy.taxeditor.model.MessagingUtils;
42 41
import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
43 42
import eu.etaxonomy.taxeditor.store.CdmStore;
44 43

  
......
46 45
 *
47 46
 * @author a.oppermann
48 47
 * @created 30.04.2014
49
 * @version 1.0
50 48
 */
51 49
public class ChecklistLabelProvider extends LabelProvider implements ITableLabelProvider {
52 50

  
......
81 79
        return null;
82 80
    }
83 81

  
84
    /*
85
     * (non-Javadoc)
86
     *
87
     * @see
88
     * org.eclipse.jface.viewers.ITableLabelProvider#getColumnText(java.lang
89
     * .Object, int)
90
     */
91 82
    /** {@inheritDoc} */
92 83
	@Override
93 84
    public String getColumnText(Object element, int columnIndex) {
......
97 88

  
98 89
       // List<TaxonDescription> listTaxonDescriptions = descriptionService.listTaxonDescriptions(taxon, null, null, null, null, null, DESC_INIT_STRATEGY);;
99 90
        Set<TaxonDescription> listTaxonDescriptions = taxon.getDescriptions();
100
        NonViralName<?> nonViralName = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
91
        TaxonName nonViralName = HibernateProxyHelper.deproxy(taxon.getName());
101 92

  
102 93
        switch (columnIndex) {
103 94
        case 0:
......
199 190
    }
200 191

  
201 192
    public SortedSet<DefinedTermBase> getTermsOrderedByLabels(List<DefinedTermBase> listTerm,Language language){
202
        TermLanguageComparator comp = new TermLanguageComparator();
193
        TermLanguageComparator<?> comp = new TermLanguageComparator<>();
203 194
        comp.setCompareLanguage(language);
204
        SortedSet result = new TreeSet(comp);
195
        SortedSet<DefinedTermBase> result = new TreeSet(comp);
205 196
        if(listTerm != null){
206 197
            result.addAll(listTerm);
207 198
        }
......
221 212
     * @return
222 213
     */
223 214
    public SortedSet<DefinedTermBase> getTermsOrderedByIdInVocabulary(List<DefinedTermBase> namedAreas) {
224
        TermIdInVocabularyComparator comp = new TermIdInVocabularyComparator();
215
        TermIdInVocabularyComparator<?> comp = new TermIdInVocabularyComparator<>();
225 216

  
226
        SortedSet result = new TreeSet(comp);
217
        SortedSet<DefinedTermBase> result = new TreeSet(comp);
227 218
        if(namedAreas != null){
228 219
            result.addAll(namedAreas);
229 220
        }
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/checklist/filter/ChecklistEditorFilter.java
4 4
import org.eclipse.jface.viewers.ViewerFilter;
5 5

  
6 6
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
7
import eu.etaxonomy.cdm.model.name.NonViralName;
8
import eu.etaxonomy.cdm.model.reference.Reference;
7
import eu.etaxonomy.cdm.model.name.TaxonName;
9 8
import eu.etaxonomy.cdm.model.taxon.Taxon;
10 9

  
11 10
public class ChecklistEditorFilter extends ViewerFilter {
......
26 25
            return true;
27 26
        }
28 27
        Taxon taxon = (Taxon) element;
29
        NonViralName<?> nonVirlaName = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
28
        TaxonName nonVirlaName = HibernateProxyHelper.deproxy(taxon.getName());
30 29
      //  Reference reference = HibernateProxyHelper.deproxy(nonVirlaName.getNomenclaturalReference(), Reference.class);
31 30
      //  String rank = taxon.getName().getRank().toString();
32 31
        //TaxonName
eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/name/operation/ChangeConceptToSynonymOperationTest.java
18 18

  
19 19
import eu.etaxonomy.cdm.model.common.ICdmBase;
20 20
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
21
import eu.etaxonomy.cdm.model.name.NonViralName;
22
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
21
import eu.etaxonomy.cdm.model.name.INonViralName;
22
import eu.etaxonomy.cdm.model.name.TaxonName;
23 23
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
24 24
import eu.etaxonomy.cdm.model.taxon.Synonym;
25 25
import eu.etaxonomy.cdm.model.taxon.Taxon;
eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/name/operation/ChangeHomotypicGroupOperationTest.java
18 18

  
19 19
import eu.etaxonomy.cdm.model.common.ICdmBase;
20 20
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
21
import eu.etaxonomy.cdm.model.name.NonViralName;
22
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
21
import eu.etaxonomy.cdm.model.name.INonViralName;
22
import eu.etaxonomy.cdm.model.name.TaxonName;
23 23
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
24 24
import eu.etaxonomy.cdm.model.taxon.Synonym;
25 25
import eu.etaxonomy.cdm.model.taxon.Taxon;
eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/name/operation/ChangeSynonymToConceptOperationTest.java
16 16
import org.junit.Test;
17 17

  
18 18
import eu.etaxonomy.cdm.model.common.ICdmBase;
19
import eu.etaxonomy.cdm.model.name.NonViralName;
20
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
19
import eu.etaxonomy.cdm.model.name.INonViralName;
20
import eu.etaxonomy.cdm.model.name.TaxonName;
21 21
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
22 22
import eu.etaxonomy.cdm.model.taxon.Synonym;
23 23
import eu.etaxonomy.cdm.model.taxon.SynonymType;
eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/name/operation/ChangeSynonymToMisapplicationOperationTest.java
16 16
import org.junit.Test;
17 17

  
18 18
import eu.etaxonomy.cdm.model.common.ICdmBase;
19
import eu.etaxonomy.cdm.model.name.NonViralName;
20
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
19
import eu.etaxonomy.cdm.model.name.INonViralName;
20
import eu.etaxonomy.cdm.model.name.TaxonName;
21 21
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
22 22
import eu.etaxonomy.cdm.model.taxon.Synonym;
23 23
import eu.etaxonomy.cdm.model.taxon.SynonymType;
eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/name/operation/CreateSynonymInExisitingHomotypicalGroupOperationTest.java
15 15
import org.junit.Test;
16 16

  
17 17
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
18
import eu.etaxonomy.cdm.model.name.NonViralName;
19
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
18
import eu.etaxonomy.cdm.model.name.INonViralName;
19
import eu.etaxonomy.cdm.model.name.TaxonName;
20 20
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
21 21
import eu.etaxonomy.cdm.model.taxon.SynonymType;
22 22
import eu.etaxonomy.cdm.model.taxon.Taxon;
......
28 28
 */
29 29
public class CreateSynonymInExisitingHomotypicalGroupOperationTest extends AbstractTaxeditorOperationTestBase {
30 30

  
31
	private NonViralName<?> newSynonymName;
31
	private TaxonName newSynonymName;
32 32

  
33 33
	private HomotypicalGroup homotypicalGroup;
34 34

  
35 35

  
36
	private NonViralName<?> taxonName;
36
	private TaxonName taxonName;
37 37

  
38 38
	/**
39 39
	 * @throws java.lang.Exception
eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/name/operation/CreateSynonymInNewGroupOperationTest.java
14 14
import org.junit.BeforeClass;
15 15
import org.junit.Test;
16 16

  
17
import eu.etaxonomy.cdm.model.name.NonViralName;
18
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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