eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/name/TypeDesignationSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AbstractDeterminationEventDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AbstractEventDetailElement.java -text
-eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AmplificationDetailElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AmplificationCloningDetailElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AmplificationCloningDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AmplificationGeneralDetailElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AmplificationGeneralDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AmplificationPrimerDetailElement.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/AmplificationPrimerDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/ArtworkGeneralDetailElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/ArtworkGeneralDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/CollectingAreasDetailSection.java -text
private String getCauseRecursively(Throwable t) {
if(t == null){
- return null;
+ return "";
}
if(t.getCause() != null){
import eu.etaxonomy.taxeditor.ui.section.name.ProtologueSection;
import eu.etaxonomy.taxeditor.ui.section.name.SpecimenTypeDesignationElement;
import eu.etaxonomy.taxeditor.ui.section.name.TypeDesignationSection;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationCloningDetailElement;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationCloningDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationGeneralDetailElement;
import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationGeneralDetailSection;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationPrimerDetailElement;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationPrimerDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.ArtworkGeneralDetailElement;
import eu.etaxonomy.taxeditor.ui.section.occurrence.ArtworkGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.CollectingAreasDetailSection;
* @return a {@link eu.etaxonomy.taxeditor.ui.element.CheckboxElement}
* object.
*/
- public CheckboxElement createCheckbox(ICdmFormElement parentElement, String label, boolean initialState, int style) {
+ public CheckboxElement createCheckbox(ICdmFormElement parentElement, String label, Boolean initialState, int style) {
+ if(initialState==null){
+ initialState = Boolean.FALSE;
+ }
CheckboxElement element = new CheckboxElement(this, parentElement, label, initialState, style | orientation);
adapt(element);
parentElement.addElement(element);
return section;
}
+ public AmplificationPrimerDetailSection createAmplificationPrimerDetailSection(ConversationHolder conversation, ICdmFormElement parentElement, ISelectionProvider selectionProvider, int style){
+ AmplificationPrimerDetailSection section = new AmplificationPrimerDetailSection(this, conversation, parentElement, selectionProvider, style);
+ addAndAdaptSection(parentElement, section);
+ return section;
+ }
+
+ public AmplificationCloningDetailSection createAmplificationCloningDetailSection(ConversationHolder conversation, ICdmFormElement parentElement, ISelectionProvider selectionProvider, int style){
+ AmplificationCloningDetailSection section = new AmplificationCloningDetailSection(this, conversation, parentElement, selectionProvider, style);
+ addAndAdaptSection(parentElement, section);
+ return section;
+ }
+
public SpecimenScanGeneralDetailSection createSpecimenScanGeneralDetailSection(ConversationHolder conversation, ICdmFormElement parentElement, ISelectionProvider selectionProvider, int style){
SpecimenScanGeneralDetailSection section = new SpecimenScanGeneralDetailSection(this, conversation, parentElement, selectionProvider, style);
addAndAdaptSection(parentElement, section);
return element;
}
+ public AmplificationPrimerDetailElement createAmplificationPrimerDetailElement(ICdmFormElement parentElement){
+ AmplificationPrimerDetailElement element = new AmplificationPrimerDetailElement(this, parentElement);
+ addAndAdaptElement(parentElement, element);
+ return element;
+ }
+
+ public AmplificationCloningDetailElement createAmplificationCloningDetailElement(ICdmFormElement parentElement){
+ AmplificationCloningDetailElement element = new AmplificationCloningDetailElement(this, parentElement);
+ addAndAdaptElement(parentElement, element);
+ return element;
+ }
+
public SpecimenScanGeneralDetailElement createSpecimenScanGeneralDetailElement(ICdmFormElement parentElement){
SpecimenScanGeneralDetailElement element = new SpecimenScanGeneralDetailElement(this, parentElement);
addAndAdaptElement(parentElement, element);
--- /dev/null
+// $Id$
+/**
+* Copyright (C) 2014 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+package eu.etaxonomy.taxeditor.ui.section.occurrence;
+
+import eu.etaxonomy.cdm.model.agent.AgentBase;
+import eu.etaxonomy.cdm.model.common.DefinedTerm;
+import eu.etaxonomy.cdm.model.molecular.Amplification;
+import eu.etaxonomy.cdm.model.molecular.Cloning;
+import eu.etaxonomy.taxeditor.ui.campanula.compatibility.ICdmFormElement;
+import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
+import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
+import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
+import eu.etaxonomy.taxeditor.ui.element.TimePeriodElement;
+import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
+import eu.etaxonomy.taxeditor.ui.selection.EntitySelectionElement;
+
+/**
+ * @author pplitzner
+ * @date 15.01.2014
+ *
+ */
+public class AmplificationCloningDetailElement extends AbstractCdmDetailElement<Amplification> {
+ private TextWithLabelElement textCloningStrain;
+ private TimePeriodElement dateCloning;
+ private EntitySelectionElement<AgentBase> selectionCloningStaff;
+ private TermComboElement<DefinedTerm> comboCloningMaterialOrMethod;
+
+
+ /**
+ * @param formFactory
+ * @param formElement
+ */
+ public AmplificationCloningDetailElement(CdmFormFactory formFactory, ICdmFormElement formElement) {
+ super(formFactory, formElement);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#createControls
+ * (eu.etaxonomy.taxeditor.forms.ICdmFormElement, java.lang.Object, int)
+ */
+ @Override
+ protected void createControls(ICdmFormElement formElement, Amplification entity, int style) {
+ Cloning cloning = entity.getCloning();
+ textCloningStrain = formFactory.createTextWithLabelElement(formElement, "Cloning Strain", cloning==null?"":cloning.getStrain(), style);
+ dateCloning = formFactory.createTimePeriodElement(formElement, "Cloning Date", cloning==null?null:cloning.getTimeperiod(), style);
+ selectionCloningStaff = formFactory.createSelectionElement(AgentBase.class, getConversationHolder(), formElement, "Cloning Staff", cloning==null?null:cloning.getActor(), EntitySelectionElement.ALL, style);
+ comboCloningMaterialOrMethod = formFactory.createTermComboElement(DefinedTerm.class, formElement, "Cloning Mat. & Meth.", cloning==null?null:cloning.getDefinedMaterialOrMethod(), style);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#handleEvent(java
+ * .lang.Object)
+ */
+ @Override
+ public void handleEvent(Object eventSource) {
+ if(eventSource==textCloningStrain || eventSource==dateCloning|| eventSource==selectionCloningStaff || eventSource==comboCloningMaterialOrMethod){
+ Cloning cloning = getEntity().getCloning();
+ if(cloning==null){
+ cloning = Cloning.NewInstance();
+ getEntity().setCloning(cloning);
+ }
+ if(eventSource==textCloningStrain){
+ cloning.setStrain(textCloningStrain.getText());
+ }
+ else if(eventSource==dateCloning){
+ cloning.setTimeperiod(dateCloning.getTimePeriod());
+ }
+ else if(eventSource==selectionCloningStaff){
+ cloning.setActor(selectionCloningStaff.getSelection());
+ }
+ else if(eventSource==comboCloningMaterialOrMethod){
+ cloning.setDefinedMaterialOrMethod(comboCloningMaterialOrMethod.getSelection());
+ }
+ }
+ }
+
+}
--- /dev/null
+// $Id$
+/**
+* Copyright (C) 2014 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+package eu.etaxonomy.taxeditor.ui.section.occurrence;
+
+import org.eclipse.jface.viewers.ISelectionProvider;
+
+import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
+import eu.etaxonomy.cdm.model.molecular.Amplification;
+import eu.etaxonomy.taxeditor.ui.campanula.compatibility.ICdmFormElement;
+import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
+import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
+import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailSection;
+
+/**
+ * @author pplitzner
+ * @date 15.01.2014
+ *
+ */
+public class AmplificationCloningDetailSection extends AbstractCdmDetailSection<Amplification> {
+
+ /**
+ * @param formFactory
+ * @param conversation
+ * @param parentElement
+ * @param selectionProvider
+ * @param style
+ */
+ public AmplificationCloningDetailSection(CdmFormFactory formFactory,
+ ConversationHolder conversation, ICdmFormElement parentElement,
+ ISelectionProvider selectionProvider, int style) {
+ super(formFactory, conversation, parentElement, selectionProvider, style);
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.section.AbstractCdmDetailSection#getHeading()
+ */
+ @Override
+ public String getHeading() {
+ return "Cloning";
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailSection#createCdmDetailElement(eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailSection, int)
+ */
+ @Override
+ protected AbstractCdmDetailElement<Amplification> createCdmDetailElement(AbstractCdmDetailSection<Amplification> parentElement, int style) {
+ return formFactory.createAmplificationCloningDetailElement(parentElement);
+ }
+
+}
+++ /dev/null
-// $Id$
-/**
- * Copyright (C) 2007 EDIT
- * European Distributed Institute of Taxonomy
- * http://www.e-taxonomy.eu
- *
- * The contents of this file are subject to the Mozilla Public License Version 1.1
- * See LICENSE.TXT at the top of this package for the full license terms.
- */
-
-package eu.etaxonomy.taxeditor.ui.section.occurrence;
-
-import org.eclipse.swt.events.SelectionListener;
-
-import eu.etaxonomy.cdm.model.common.DefinedTerm;
-import eu.etaxonomy.cdm.model.molecular.Amplification;
-import eu.etaxonomy.taxeditor.ui.campanula.compatibility.ICdmFormElement;
-import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
-import eu.etaxonomy.taxeditor.ui.element.AbstractFormSection;
-import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
-import eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionElement;
-
-/**
- *
- * @author pplitzner
- * @date 17.12.2013
- *
- */
-public class AmplificationDetailElement extends AbstractEntityCollectionElement<Amplification> {
-
- private TermComboElement<DefinedTerm> comboDnaMarker;
-
- public AmplificationDetailElement(CdmFormFactory formFactory,
- AbstractFormSection section, Amplification entity,
- SelectionListener removeListener, int style) {
- super(formFactory, section, entity, removeListener, null, style);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * eu.etaxonomy.taxeditor.section.AbstractEntityCollectionElement#setEntity
- * (eu.etaxonomy.cdm.model.common.IVersionableEntity)
- */
- /** {@inheritDoc} */
- @Override
- public void setEntity(Amplification entity) {
- this.entity = entity;
- comboDnaMarker.setSelection(entity.getDnaMarker());
- }
-
-
- /*
- * (non-Javadoc)
- *
- * @see
- * eu.etaxonomy.taxeditor.section.AbstractEntityCollectionElement#createControls
- * (eu.etaxonomy.taxeditor.forms.ICdmFormElement, int)
- */
- /** {@inheritDoc} */
- @Override
- public void createControls(ICdmFormElement element, int style) {
- comboDnaMarker = formFactory.createTermComboElement(DefinedTerm.class,
- element, "DNA Marker", null, style);
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionElement#handleEvent(java.lang.Object)
- */
- @Override
- public void handleEvent(Object eventSource) {
- if (eventSource == comboDnaMarker) {
- getEntity().setDnaMarker(comboDnaMarker.getSelection());
- }
-
- }
-
-}
*/
package eu.etaxonomy.taxeditor.ui.section.occurrence;
-import org.eclipse.swt.widgets.Label;
-
import eu.etaxonomy.cdm.model.agent.AgentBase;
import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.molecular.Amplification;
-import eu.etaxonomy.cdm.model.molecular.Cloning;
-import eu.etaxonomy.cdm.model.molecular.Primer;
-import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
-import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.taxeditor.ui.campanula.compatibility.ICdmFormElement;
import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
-import eu.etaxonomy.taxeditor.ui.element.LayoutConstants;
+import eu.etaxonomy.taxeditor.ui.element.CheckboxElement;
import eu.etaxonomy.taxeditor.ui.element.NumberWithLabelElement;
import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
import eu.etaxonomy.taxeditor.ui.element.TimePeriodElement;
private TermComboElement<DefinedTerm> comboMarker;
private TimePeriodElement dateAmplification;
private EntitySelectionElement<AgentBase> selectionAmplificationStaff;
- private TextWithLabelElement textAmplificationSuccess;
+ private CheckboxElement checkBoxAmplificationSuccess;
private TextWithLabelElement textAmplificationSuccessDetails;
private TermComboElement<DefinedTerm> comboAmplificationMaterialOrMethod;
private TextWithLabelElement textGelPhoto;
private TermComboElement<DefinedTerm> comboPurificationMaterialOrMethod;
- //forward primer
- private TextWithLabelElement textPrimerForwardName;
- private TextWithLabelElement textPrimerForwardSequence;
- private EntitySelectionElement<Reference> selectionPrimerForwardReference;
- //reverse primer
- private TextWithLabelElement textPrimerReverseName;
- private TextWithLabelElement textPrimerReverseSequence;
- private EntitySelectionElement<Reference> selectionPrimerReverseReference;
- //cloning
- private TextWithLabelElement textCloningStrain;
- private TimePeriodElement dateCloning;
- private EntitySelectionElement<AgentBase> selectionCloningStaff;
- private TermComboElement<DefinedTerm> comboCloningMaterialOrMethod;
/**
comboMarker = formFactory.createTermComboElement(DefinedTerm.class, formElement, "Marker", entity.getDnaMarker(), style);
dateAmplification = formFactory.createTimePeriodElement(formElement, "Amplification Date", entity.getTimeperiod(), style);
selectionAmplificationStaff = formFactory.createSelectionElement(AgentBase.class, getConversationHolder(), formElement, "Amplification staff", entity.getActor(), EntitySelectionElement.ALL, style);
- textAmplificationSuccess = formFactory.createTextWithLabelElement(formElement, "Amplification Success", entity.getSuccessful(), style);
+ checkBoxAmplificationSuccess = formFactory.createCheckbox(formElement, "Amplification Success", entity.getSuccessful(), style);
textAmplificationSuccessDetails = formFactory.createTextWithLabelElement(formElement, "Ampl. Success Details", entity.getSuccessText(), style);
// comboAmplificationMaterialOrMethod = formFactory.createTermComboElement(DefinedTerm.class, formElement, "Ampl. Mat. & Meth.", entity.get, style)
numberGelVoltage = formFactory.createNumberTextWithLabelElement(formElement, "Gel Voltage (V)", entity.getElectrophoresisVoltage(), style);
textGelPhoto = formFactory.createTextWithLabelElement(formElement, "Gel Photo", "XXX", style);
comboPurificationMaterialOrMethod = formFactory.createTermComboElement(DefinedTerm.class, formElement, "Purification Mat. & Meth.",
entity.getPurification()==null?null:entity.getPurification().getDefinedMaterialOrMethod(), style);
-
- Label createHorizontalSeparator1 = formFactory.createHorizontalSeparator(formElement, style);
- createHorizontalSeparator1.setLayoutData(LayoutConstants.FILL_HORIZONTALLY(2, 1));
- //first primer
- Primer forwardPrimer = entity.getForwardPrimer();
- String initialName;
- String initalSequenceString;
- Reference initialReference;
- if(forwardPrimer==null){
- initialName = "";
- initalSequenceString = null;
- initialReference = null;
- }
- else{
- initialName = forwardPrimer.getLabel();
- initialReference = forwardPrimer.getPublishedIn();
- if(forwardPrimer.getSequence()==null){
- initalSequenceString = "";
- }
- else{
- initalSequenceString = forwardPrimer.getSequence().getSequenceString();
- }
- }
- textPrimerForwardName = formFactory.createTextWithLabelElement(formElement, "Forward Primer", initialName, style);
- textPrimerForwardSequence = formFactory.createTextWithLabelElement(formElement, "Fw. Primer Sequence", initalSequenceString, style);
- selectionPrimerForwardReference = formFactory.createSelectionElement(Reference.class, getConversationHolder(), formElement, "Fw. Primer Reference", initialReference, EntitySelectionElement.ALL, style);
-
- //second primer
- Primer reversePrimer = entity.getForwardPrimer();
- String initialNameReverse;
- String initalSequenceStringReverse;
- Reference initialReferenceReverse;
- if(reversePrimer==null){
- initialNameReverse = "";
- initalSequenceStringReverse = null;
- initialReferenceReverse = null;
- }
- else{
- initialNameReverse = reversePrimer.getLabel();
- initialReferenceReverse = reversePrimer.getPublishedIn();
- if(reversePrimer.getSequence()==null){
- initalSequenceStringReverse = "";
- }
- else{
- initalSequenceStringReverse = reversePrimer.getSequence().getSequenceString();
- }
- }
- textPrimerReverseName = formFactory.createTextWithLabelElement(formElement, "Reverse Primer", initialNameReverse, style);
- textPrimerReverseSequence = formFactory.createTextWithLabelElement(formElement, "Rv. Primer Sequence", initalSequenceStringReverse, style);
- selectionPrimerReverseReference = formFactory.createSelectionElement(Reference.class, getConversationHolder(), formElement, "Rv. Primer Reference", initialReferenceReverse, EntitySelectionElement.ALL, style);
-
- Label createHorizontalSeparator = formFactory.createHorizontalSeparator(formElement, style);
- createHorizontalSeparator.setLayoutData(LayoutConstants.FILL_HORIZONTALLY(2, 1));
-
- Cloning cloning = entity.getCloning();
- textCloningStrain = formFactory.createTextWithLabelElement(formElement, "Cloning Strain", cloning==null?"":cloning.getStrain(), style);
- dateCloning = formFactory.createTimePeriodElement(formElement, "Cloning Date", cloning==null?null:cloning.getTimeperiod(), style);
- selectionCloningStaff = formFactory.createSelectionElement(AgentBase.class, getConversationHolder(), formElement, "Cloning Staff", cloning==null?null:cloning.getActor(), EntitySelectionElement.ALL, style);
- comboCloningMaterialOrMethod = formFactory.createTermComboElement(DefinedTerm.class, formElement, "Cloning Mat. & Meth.", cloning==null?null:cloning.getDefinedMaterialOrMethod(), style);
}
/*
else if(eventSource==selectionAmplificationStaff){
getEntity().setActor(selectionAmplificationStaff.getEntity());
}
- else if(eventSource==textAmplificationSuccess){
- getEntity().setSuccessful(Boolean.valueOf(textAmplificationSuccess.getText()));
+ else if(eventSource==checkBoxAmplificationSuccess){
+ getEntity().setSuccessful(checkBoxAmplificationSuccess.getSelection());
}
else if(eventSource==textAmplificationSuccessDetails){
getEntity().setSuccessText(textAmplificationSuccessDetails.getText());
}
purification.setDefinedMaterialOrMethod(comboPurificationMaterialOrMethod.getSelection());
}
- else if(eventSource==textPrimerForwardName || eventSource==textPrimerForwardSequence || eventSource==selectionPrimerForwardReference){
- Primer forwardPrimer = getEntity().getForwardPrimer();
- if(forwardPrimer==null){
- forwardPrimer = Primer.NewInstance("");
- getEntity().setForwardPrimer(forwardPrimer);
- }
- if(eventSource==textPrimerForwardName){
- forwardPrimer.setLabel(textPrimerForwardName.getText());
- }
- else if(eventSource==textPrimerForwardSequence){
- Sequence sequence = forwardPrimer.getSequence();
- if(sequence==null){
- sequence = Sequence.NewInstance(textPrimerForwardSequence.getText());
- forwardPrimer.setSequence(sequence);
- }
- else{
- sequence.setSequenceString(textPrimerForwardSequence.getText());
- }
- }
- else if(eventSource==selectionPrimerForwardReference){
- forwardPrimer.setPublishedIn(selectionPrimerForwardReference.getSelection());
- }
- }
- else if(eventSource==textPrimerReverseName || eventSource==textPrimerReverseSequence || eventSource==selectionPrimerReverseReference){
- Primer reversePrimer = getEntity().getReversePrimer();
- if(reversePrimer==null){
- reversePrimer = Primer.NewInstance("");
- getEntity().setReversePrimer(reversePrimer);
- }
- if(eventSource==textPrimerReverseName){
- reversePrimer.setLabel(textPrimerReverseName.getText());
- }
- else if(eventSource==textPrimerReverseSequence){
- Sequence sequence = reversePrimer.getSequence();
- if(sequence==null){
- sequence = Sequence.NewInstance(textPrimerReverseSequence.getText());
- reversePrimer.setSequence(sequence);
- }
- else{
- sequence.setSequenceString(textPrimerReverseSequence.getText());
- }
- }
- else if(eventSource==selectionPrimerReverseReference){
- reversePrimer.setPublishedIn(selectionPrimerReverseReference.getSelection());
- }
- }
- else if(eventSource==textCloningStrain || eventSource==dateCloning|| eventSource==selectionCloningStaff || eventSource==comboCloningMaterialOrMethod){
- Cloning cloning = getEntity().getCloning();
- if(cloning==null){
- cloning = Cloning.NewInstance();
- getEntity().setCloning(cloning);
- }
- if(eventSource==textCloningStrain){
- cloning.setStrain(textCloningStrain.getText());
- }
- else if(eventSource==dateCloning){
- cloning.setTimeperiod(dateCloning.getTimePeriod());
- }
- else if(eventSource==selectionCloningStaff){
- cloning.setActor(selectionCloningStaff.getSelection());
- }
- else if(eventSource==comboCloningMaterialOrMethod){
- cloning.setDefinedMaterialOrMethod(comboCloningMaterialOrMethod.getSelection());
- }
- }
}
-
}
\ No newline at end of file
--- /dev/null
+// $Id$
+/**
+ * Copyright (C) 2014 EDIT
+ * European Distributed Institute of Taxonomy
+ * http://www.e-taxonomy.eu
+ *
+ * The contents of this file are subject to the Mozilla Public License Version 1.1
+ * See LICENSE.TXT at the top of this package for the full license terms.
+ */
+package eu.etaxonomy.taxeditor.ui.section.occurrence;
+
+import eu.etaxonomy.cdm.model.molecular.Amplification;
+import eu.etaxonomy.cdm.model.molecular.Primer;
+import eu.etaxonomy.cdm.model.molecular.Sequence;
+import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.taxeditor.ui.campanula.compatibility.ICdmFormElement;
+import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
+import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
+import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
+import eu.etaxonomy.taxeditor.ui.selection.EntitySelectionElement;
+
+/**
+ * @author pplitzner
+ * @date 15.01.2014
+ *
+ */
+public class AmplificationPrimerDetailElement extends AbstractCdmDetailElement<Amplification> {
+
+ //forward primer
+ private TextWithLabelElement textPrimerForwardName;
+ private TextWithLabelElement textPrimerForwardSequence;
+ private EntitySelectionElement<Reference> selectionPrimerForwardReference;
+ //reverse primer
+ private TextWithLabelElement textPrimerReverseName;
+ private TextWithLabelElement textPrimerReverseSequence;
+ private EntitySelectionElement<Reference> selectionPrimerReverseReference;
+
+
+ /**
+ * @param formFactory
+ * @param formElement
+ */
+ public AmplificationPrimerDetailElement(CdmFormFactory formFactory, ICdmFormElement formElement) {
+ super(formFactory, formElement);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#createControls
+ * (eu.etaxonomy.taxeditor.forms.ICdmFormElement, java.lang.Object, int)
+ */
+ @Override
+ protected void createControls(ICdmFormElement formElement, Amplification entity, int style) {
+ //first primer
+ Primer forwardPrimer = entity.getForwardPrimer();
+ String initialName;
+ String initalSequenceString;
+ Reference initialReference;
+ if(forwardPrimer==null){
+ initialName = "";
+ initalSequenceString = null;
+ initialReference = null;
+ }
+ else{
+ initialName = forwardPrimer.getLabel();
+ initialReference = forwardPrimer.getPublishedIn();
+ if(forwardPrimer.getSequence()==null){
+ initalSequenceString = "";
+ }
+ else{
+ initalSequenceString = forwardPrimer.getSequence().getSequenceString();
+ }
+ }
+ textPrimerForwardName = formFactory.createTextWithLabelElement(formElement, "Forward Primer", initialName, style);
+ textPrimerForwardSequence = formFactory.createTextWithLabelElement(formElement, "Fw. Primer Sequence", initalSequenceString, style);
+ selectionPrimerForwardReference = formFactory.createSelectionElement(Reference.class, getConversationHolder(), formElement, "Fw. Primer Reference", initialReference, EntitySelectionElement.ALL, style);
+
+ //second primer
+ Primer reversePrimer = entity.getForwardPrimer();
+ String initialNameReverse;
+ String initalSequenceStringReverse;
+ Reference initialReferenceReverse;
+ if(reversePrimer==null){
+ initialNameReverse = "";
+ initalSequenceStringReverse = null;
+ initialReferenceReverse = null;
+ }
+ else{
+ initialNameReverse = reversePrimer.getLabel();
+ initialReferenceReverse = reversePrimer.getPublishedIn();
+ if(reversePrimer.getSequence()==null){
+ initalSequenceStringReverse = "";
+ }
+ else{
+ initalSequenceStringReverse = reversePrimer.getSequence().getSequenceString();
+ }
+ }
+ textPrimerReverseName = formFactory.createTextWithLabelElement(formElement, "Reverse Primer", initialNameReverse, style);
+ textPrimerReverseSequence = formFactory.createTextWithLabelElement(formElement, "Rv. Primer Sequence", initalSequenceStringReverse, style);
+ selectionPrimerReverseReference = formFactory.createSelectionElement(Reference.class, getConversationHolder(), formElement, "Rv. Primer Reference", initialReferenceReverse, EntitySelectionElement.ALL, style);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * eu.etaxonomy.taxeditor.section.AbstractCdmDetailElement#handleEvent(java
+ * .lang.Object)
+ */
+ @Override
+ public void handleEvent(Object eventSource) {
+ if(eventSource==textPrimerForwardName || eventSource==textPrimerForwardSequence || eventSource==selectionPrimerForwardReference){
+ Primer forwardPrimer = getEntity().getForwardPrimer();
+ if(forwardPrimer==null){
+ forwardPrimer = Primer.NewInstance("");
+ getEntity().setForwardPrimer(forwardPrimer);
+ }
+ if(eventSource==textPrimerForwardName){
+ forwardPrimer.setLabel(textPrimerForwardName.getText());
+ }
+ else if(eventSource==textPrimerForwardSequence){
+ Sequence sequence = forwardPrimer.getSequence();
+ if(sequence==null){
+ sequence = Sequence.NewInstance(textPrimerForwardSequence.getText());
+ forwardPrimer.setSequence(sequence);
+ }
+ else{
+ sequence.setSequenceString(textPrimerForwardSequence.getText());
+ }
+ }
+ else if(eventSource==selectionPrimerForwardReference){
+ forwardPrimer.setPublishedIn(selectionPrimerForwardReference.getSelection());
+ }
+ }
+ else if(eventSource==textPrimerReverseName || eventSource==textPrimerReverseSequence || eventSource==selectionPrimerReverseReference){
+ Primer reversePrimer = getEntity().getReversePrimer();
+ if(reversePrimer==null){
+ reversePrimer = Primer.NewInstance("");
+ getEntity().setReversePrimer(reversePrimer);
+ }
+ if(eventSource==textPrimerReverseName){
+ reversePrimer.setLabel(textPrimerReverseName.getText());
+ }
+ else if(eventSource==textPrimerReverseSequence){
+ Sequence sequence = reversePrimer.getSequence();
+ if(sequence==null){
+ sequence = Sequence.NewInstance(textPrimerReverseSequence.getText());
+ reversePrimer.setSequence(sequence);
+ }
+ else{
+ sequence.setSequenceString(textPrimerReverseSequence.getText());
+ }
+ }
+ else if(eventSource==selectionPrimerReverseReference){
+ reversePrimer.setPublishedIn(selectionPrimerReverseReference.getSelection());
+ }
+ }
+ }
+}
--- /dev/null
+// $Id$
+/**
+* Copyright (C) 2014 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+package eu.etaxonomy.taxeditor.ui.section.occurrence;
+
+import org.eclipse.jface.viewers.ISelectionProvider;
+
+import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
+import eu.etaxonomy.cdm.model.molecular.Amplification;
+import eu.etaxonomy.taxeditor.ui.campanula.compatibility.ICdmFormElement;
+import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
+import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailElement;
+import eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailSection;
+
+/**
+ * @author pplitzner
+ * @date 15.01.2014
+ *
+ */
+public class AmplificationPrimerDetailSection extends AbstractCdmDetailSection<Amplification> {
+
+ /**
+ * @param formFactory
+ * @param conversation
+ * @param parentElement
+ * @param selectionProvider
+ * @param style
+ */
+ public AmplificationPrimerDetailSection(CdmFormFactory formFactory,
+ ConversationHolder conversation, ICdmFormElement parentElement,
+ ISelectionProvider selectionProvider, int style) {
+ super(formFactory, conversation, parentElement, selectionProvider, style);
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.section.AbstractCdmDetailSection#getHeading()
+ */
+ @Override
+ public String getHeading() {
+ return "Primer";
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailSection#createCdmDetailElement(eu.etaxonomy.taxeditor.ui.section.AbstractCdmDetailSection, int)
+ */
+ @Override
+ protected AbstractCdmDetailElement<Amplification> createCdmDetailElement(AbstractCdmDetailSection<Amplification> parentElement, int style) {
+ return formFactory.createAmplificationPrimerDetailElement(parentElement);
+ }
+
+}
textContigFile = formFactory.createTextWithLabelElement(formElement, "Contig File", "XXX", style);
textConsensusSequence = formFactory.createTextWithLabelElement(formElement, "Consensus Sequence 5'->3'", entity.getConsensusSequence().getString(), style);
textConsensusSequenceLength = formFactory.createNumberTextWithLabelElement(formElement, "Consensus Seq. Length", entity.getConsensusSequence().getLength(), style);
-// textBarcodeSequence = formFactory.createTextWithLabelElement(formElement, "Barcode Sequence 5'->3'", entity.getBarcodeSequencePart().getString(), style);
+ textBarcodeSequence = formFactory.createTextWithLabelElement(formElement, "Barcode Sequence 5'->3'", entity.getBarcodeSequencePart()==null?"":entity.getBarcodeSequencePart().getString(), style);
textGeneticAccessNo = formFactory.createTextWithLabelElement(formElement, "Genetic Acc. No.", entity.getGeneticAccessionNumber(), style);
textBoldProcessID = formFactory.createTextWithLabelElement(formElement, "BOLD Process ID", entity.getBoldProcessId(), style);
}
else if(eventSource==textGeneticAccessNo){
getEntity().setGeneticAccessionNumber(textGeneticAccessNo.getText());
- if(textGeneticAccessNo.getText()!=null && !textGeneticAccessNo.getText().isEmpty()){
+ }
+ else if(eventSource==textBoldProcessID){
+ getEntity().setBoldProcessId(textBoldProcessID.getText());
+ if(textBoldProcessID.getText()!=null && !textBoldProcessID.getText().isEmpty()){
textBoldLink.setText(getEntity().getBoldUri().toString());
}
else{
textBoldLink.setText("");
}
}
- else if(eventSource==textBoldProcessID){
- getEntity().setBoldProcessId(textBoldProcessID.getText());
- }
else if(eventSource==textBoldLink){
//cannot be set because it is generated from the genetic access number and a base URI
}
import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.reference.Reference;
+import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
import eu.etaxonomy.taxeditor.ui.campanula.compatibility.ICdmFormElement;
import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
import eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection;
/** {@inheritDoc} */
@Override
public Reference createNewElement() {
- return null;
+ return ReferenceFactory.newGeneric();
}
/* (non-Javadoc)
"Taxon is excluded", ((Taxon) entity).isExcluded(), style);
checkbox_unplaced = formFactory.createCheckbox(formElement,
"Taxon is unplaced", ((Taxon) entity).isUnplaced(), style);
+ checkbox_published = formFactory.createCheckbox(formElement,
+ "Taxon is published", ((Taxon) entity).isPublish(), style);
}
checkbox_doubtful = formFactory.createCheckbox(formElement,
entity.getClass().getSimpleName() + " is doubtful", entity.isDoubtful(), style);
-
- checkbox_published = formFactory.createCheckbox(formElement,
- "Taxon is published", ((TaxonBase) entity).isPublish(), style);
+
}
import eu.etaxonomy.taxeditor.ui.section.name.NonViralNameDetailSection;
import eu.etaxonomy.taxeditor.ui.section.name.ProtologueSection;
import eu.etaxonomy.taxeditor.ui.section.name.TypeDesignationSection;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationCloningDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationGeneralDetailSection;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.AmplificationPrimerDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.ArtworkGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.DerivedUnitBaseDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.DerivedUnitGeneralDetailSection;
TissueSampleGeneralDetailSection section = formFactory.createTissueSampleGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
- formFactory.createHorizontalSeparator(parent, SWT.BORDER);
-
addPart(section);
}
destroySections();
DnaSampleGeneralDetailSection section = formFactory.createDnaSampleGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
- formFactory.createHorizontalSeparator(parent, SWT.BORDER);
-
addPart(section);
}
private void createAmplificationSection(RootElement parent) {
destroySections();
- AmplificationGeneralDetailSection section = formFactory.createAmplificationGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
+ AmplificationGeneralDetailSection generalSection = formFactory.createAmplificationGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
formFactory.createHorizontalSeparator(parent, SWT.BORDER);
- addPart(section);
+ AmplificationPrimerDetailSection primerSection = formFactory.createAmplificationPrimerDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE);
+
+ formFactory.createHorizontalSeparator(parent, SWT.BORDER);
+
+ AmplificationCloningDetailSection cloningSection = formFactory.createAmplificationCloningDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE);
+
+
+ addPart(generalSection);
+ addPart(primerSection);
+ addPart(cloningSection);
}
private void createSequenceSection(RootElement parent) {
destroySections();
SequenceGeneralDetailSection section = formFactory.createSequenceGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
- formFactory.createHorizontalSeparator(parent, SWT.BORDER);
-
addPart(section);
}
destroySections();
SingleReadGeneralDetailSection section = formFactory.createSingleReadGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
- formFactory.createHorizontalSeparator(parent, SWT.BORDER);
-
addPart(section);
}
destroySections();
SpecimenScanGeneralDetailSection section = formFactory.createSpecimenScanGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
- formFactory.createHorizontalSeparator(parent, SWT.BORDER);
-
addPart(section);
}
destroySections();
LivingPlantPhotoGeneralDetailSection section = formFactory.createLivingPlantPhotoGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
- formFactory.createHorizontalSeparator(parent, SWT.BORDER);
-
addPart(section);
}
destroySections();
ArtworkGeneralDetailSection section = formFactory.createArtworkGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
- formFactory.createHorizontalSeparator(parent, SWT.BORDER);
-
addPart(section);
}
BGBM BDI Projects / taxeditor.git / commitdiff