- added media section to DetailsViews for Amplification (gel photo) and SingelRead (pherogram)
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AbstractUnboundEntityCollectionSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationCloningDetailElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationCloningDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationGelPhotoCollectionDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationGeneralDetailElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationGeneralDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/AmplificationPrimerDetailElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SequenceReferenceCollectionDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SingleReadGeneralDetailElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SingleReadGeneralDetailSection.java -text
+eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/SingleReadPherogramCollectionDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/TissueSampleGeneralDetailElement.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/dna/TissueSampleGeneralDetailSection.java -text
eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/occurrence/media/LivingPlantPhotoGeneralDetailElement.java -text
import eu.etaxonomy.taxeditor.ui.section.occurrence.derivedUnit.PreservedSpecimenSourceCollectionDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationCloningDetailElement;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationCloningDetailSection;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationGelPhotoCollectionDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationGeneralDetailElement;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationPrimerDetailElement;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.DnaSampleGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SequenceGeneralDetailElement;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SequenceGeneralDetailSection;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SingleReadPherogramCollectionDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SequenceReferenceCollectionDetailElement;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SequenceReferenceCollectionDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SingleReadGeneralDetailElement;
return section;
}
+ public SingleReadPherogramCollectionDetailSection createSingleReadPherogramCollectionDetailSection(ConversationHolder conversation, ICdmFormElement parentElement, ISelectionProvider selectionProvider, int style){
+ SingleReadPherogramCollectionDetailSection section = new SingleReadPherogramCollectionDetailSection(this, conversation, parentElement, style);
+ addAndAdaptSection(parentElement, section);
+ return section;
+ }
+
public SequenceReferenceCollectionDetailSection createSequenceReferenceCollectionDetailSection(ConversationHolder conversation, ICdmFormElement parentElement, int style){
SequenceReferenceCollectionDetailSection section = new SequenceReferenceCollectionDetailSection(this, conversation, parentElement, style);
addAndAdaptSection(parentElement, section);
return section;
}
+ public AmplificationGelPhotoCollectionDetailSection createAmplificationGelPhotoCollectionDetailSection(ConversationHolder conversation, ICdmFormElement parentElement, int style){
+ AmplificationGelPhotoCollectionDetailSection section = new AmplificationGelPhotoCollectionDetailSection(this, conversation, parentElement, 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);
--- /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.dna;
+
+import java.util.Collection;
+import java.util.Collections;
+
+import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
+import eu.etaxonomy.cdm.model.media.Media;
+import eu.etaxonomy.cdm.model.molecular.Amplification;
+import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
+import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
+import eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection;
+
+/**
+ * @author pplitzner
+ * @date 26.02.2014
+ *
+ */
+public class AmplificationGelPhotoCollectionDetailSection extends AbstractEntityCollectionSection<Amplification, Media> {
+
+ /**
+ * @param formFactory
+ * @param conversation
+ * @param parentElement
+ * @param title
+ * @param style
+ */
+ public AmplificationGelPhotoCollectionDetailSection(CdmFormFactory formFactory, ConversationHolder conversation,
+ ICdmFormElement parentElement, int style) {
+ super(formFactory, conversation, parentElement, "Gel Photo", style);
+ }
+
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#getCollection(java.lang.Object)
+ */
+ @Override
+ public Collection<Media> getCollection(Amplification entity) {
+ if(entity.getGelPhoto()!=null){
+ return Collections.singleton(entity.getGelPhoto());
+ }
+ return Collections.EMPTY_LIST;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#createNewElement()
+ */
+ @Override
+ public Media createNewElement() {
+ if(getEntity().getGelPhoto()==null){
+ return Media.NewInstance();
+ }
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#addElement(java.lang.Object)
+ */
+ @Override
+ public void addElement(Media element) {
+ if(getEntity().getGelPhoto()==null){
+ getEntity().setGelPhoto(element);
+ }
+
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#removeElement(java.lang.Object)
+ */
+ @Override
+ public void removeElement(Media element) {
+ getEntity().setGelPhoto(null);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#getEmptyString()
+ */
+ @Override
+ public String getEmptyString() {
+ return "No gel photos yet";
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#getTooltipString()
+ */
+ @Override
+ protected String getTooltipString() {
+ return "Add a gel photo";
+ }
+
+}
*/
package eu.etaxonomy.taxeditor.ui.section.occurrence.dna;
-import org.eclipse.ui.forms.widgets.ExpandableComposite;
-
import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.molecular.SequenceString;
import eu.etaxonomy.taxeditor.ui.combo.TermComboElement;
import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
-import eu.etaxonomy.taxeditor.ui.element.LayoutConstants;
import eu.etaxonomy.taxeditor.ui.element.NumberWithLabelElement;
import eu.etaxonomy.taxeditor.ui.element.TextWithLabelElement;
import eu.etaxonomy.taxeditor.ui.element.UriWithLabelElement;
private TextWithLabelElement textBoldProcessID;
private UriWithLabelElement textBoldUri;
- private SequenceReferenceCollectionDetailSection sectionReferenceCollection;
-
/**
* @param formFactory
* @param formElement
textBoldUri = formFactory.createUriWithLabelElement(formElement, "BOLD URI", entity.getBoldUri(), style);
textBoldUri.setEnabled(false);
- sectionReferenceCollection = formFactory.createSequenceReferenceCollectionDetailSection(getConversationHolder(), formElement, ExpandableComposite.TWISTIE);
- sectionReferenceCollection.setLayoutData(LayoutConstants.FILL_HORIZONTALLY(2, 1));
- sectionReferenceCollection.setEntity(entity);
}
/*
/** {@inheritDoc} */
@Override
public void addElement(Reference element) {
- if(element!=null){
- getEntity().addCitation(element);
- }
+ //never gets called
}
/* (non-Javadoc)
//TODO sequence can be null if DerivateView is opened again. Why?? When initially created it is not null
SequenceString editedSequence = entity.getSequence();
- int readLength = 0;
+ Integer readLength = 0;
String editedSequenceString = "";
if(editedSequence!=null){
- readLength = editedSequence.getLength();
+ Integer length = editedSequence.getLength();
+ if(length!=null){
+ readLength = length;
+ }
editedSequenceString = editedSequence.getString();
}
textReadLength = formFactory.createNumberTextWithLabelElement(formElement, "Read Length", readLength, style);
--- /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.dna;
+
+import java.util.Collection;
+import java.util.Collections;
+
+import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
+import eu.etaxonomy.cdm.model.media.Media;
+import eu.etaxonomy.cdm.model.molecular.SingleRead;
+import eu.etaxonomy.taxeditor.ui.element.CdmFormFactory;
+import eu.etaxonomy.taxeditor.ui.element.ICdmFormElement;
+import eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection;
+
+/**
+ * @author pplitzner
+ * @date 03.03.2014
+ *
+ */
+public class SingleReadPherogramCollectionDetailSection extends AbstractEntityCollectionSection<SingleRead, Media> {
+
+ /**
+ * @param formFactory
+ * @param conversation
+ * @param parentElement
+ * @param title
+ * @param style
+ */
+ public SingleReadPherogramCollectionDetailSection(CdmFormFactory formFactory, ConversationHolder conversation,
+ ICdmFormElement parentElement, int style) {
+ super(formFactory, conversation, parentElement, "Pherogram", style);
+ }
+
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#getCollection(java.lang.Object)
+ */
+ @Override
+ public Collection<Media> getCollection(SingleRead entity) {
+ if(entity.getPherogram()!=null){
+ return Collections.singleton(entity.getPherogram());
+ }
+ return Collections.EMPTY_LIST;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#createNewElement()
+ */
+ @Override
+ public Media createNewElement() {
+ if(getEntity().getPherogram()==null){
+ return Media.NewInstance();
+ }
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#addElement(java.lang.Object)
+ */
+ @Override
+ public void addElement(Media element) {
+ if(getEntity().getPherogram()==null){
+ getEntity().setPherogram(element);
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#removeElement(java.lang.Object)
+ */
+ @Override
+ public void removeElement(Media element) {
+ getEntity().setPherogram(null);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#getEmptyString()
+ */
+ @Override
+ public String getEmptyString() {
+ return "No pherogram yet";
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.taxeditor.ui.section.AbstractEntityCollectionSection#getTooltipString()
+ */
+ @Override
+ protected String getTooltipString() {
+ return "Add a pherogram";
+ }
+}
import eu.etaxonomy.taxeditor.ui.section.occurrence.derivedUnit.PreservedSpecimenDeterminationDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.derivedUnit.PreservedSpecimenGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationCloningDetailSection;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationGelPhotoCollectionDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.AmplificationPrimerDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.DnaSampleGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SequenceGeneralDetailSection;
+import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SingleReadPherogramCollectionDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.SingleReadGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.dna.TissueSampleGeneralDetailSection;
import eu.etaxonomy.taxeditor.ui.section.occurrence.media.LivingPlantPhotoGeneralDetailSection;
AmplificationCloningDetailSection cloningSection = formFactory.createAmplificationCloningDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE);
+ formFactory.createHorizontalSeparator(parent, SWT.BORDER);
+
+ AmplificationGelPhotoCollectionDetailSection gelPhotoSection = formFactory.createAmplificationGelPhotoCollectionDetailSection(getConversationHolder(), parent, ExpandableComposite.TWISTIE);
+
addPart(generalSection);
addPart(primerSection);
addPart(cloningSection);
+ addPart(gelPhotoSection);
}
private void createSequenceSection(RootElement parent) {
destroySections();
+
SequenceGeneralDetailSection section = formFactory.createSequenceGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
addPart(section);
private void createSingleReadSection(RootElement parent) {
destroySections();
+
SingleReadGeneralDetailSection section = formFactory.createSingleReadGeneralDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
+ formFactory.createHorizontalSeparator(parent, SWT.BORDER);
+
+ SingleReadPherogramCollectionDetailSection pherogramSection = formFactory.createSingleReadPherogramCollectionDetailSection(getConversationHolder(), parent, this, ExpandableComposite.TWISTIE | ExpandableComposite.EXPANDED);
+
addPart(section);
+ addPart(pherogramSection);
}
private void createSpecimenScanSection(RootElement parent) {