/**
* Gets Interaction Detection element. It is possible that an interaction is missing important
* attributes, such as Experimental System Name, XRef DB, and XRef ID. All of these attributes are
* required by PSI. Rather than throwing an exception here, the data_mapper manually specifies
* "Not Specified" for all missing attributes.
*
* @param interaction Interaction.
* @return InteractionDetection Object.
*/
private CvType getInteractionDetection(
org.cytoscape.coreplugin.psi_mi.model.Interaction interaction) {
CvType interactionDetection = new CvType();
String idStr = null;
try {
idStr = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_NAME);
} catch (ClassCastException e) {
idStr = null;
}
if (idStr == null) {
idStr = "Not Specified";
}
String idRef = null;
try {
idRef = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_ID);
} catch (ClassCastException e) {
idRef = null;
}
// If there is no ID Ref, find a best match.
if (idRef == null) {
if (idStr.equals(EXP_AFFINITY_PRECIPITATION) || idStr.equals(EXP_AFFINITY_CHROMOTOGRAPHY)) {
idStr = "affinity chromatography technologies";
idRef = "MI:0004";
} else if (idStr.equals(EXP_TWO_HYBRID)) {
idStr = "classical two hybrid";
idRef = "MI:0018";
} else if (idStr.equals(EXP_PURIFIED_COMPLEX)) {
idStr = "copurification";
idRef = "MI:0025";
} else {
idRef = "Not Specified";
}
}
NamesType names = createName(idStr, null);
interactionDetection.setNames(names);
String dbRef = null;
try {
dbRef = (String) interaction.getAttribute(InteractionVocab.EXPERIMENTAL_SYSTEM_XREF_DB);
} catch (ClassCastException e) {
dbRef = null;
}
if (dbRef == null) {
dbRef = "PSI-MI";
}
XrefType xref = createXRef(dbRef, idRef);
interactionDetection.setXref(xref);
return interactionDetection;
}
/**
* Gets Experiment Description.
*
* @param interaction Interaction object.
* @return Castor InteractionElementTypeChoice object.
*/
private InteractionElementType.ExperimentList getExperimentDescription(
org.cytoscape.coreplugin.psi_mi.model.Interaction interaction, int index) {
// Create New Experiment List
InteractionElementType.ExperimentList expList = new InteractionElementType.ExperimentList();
// Create New Experiment Description
ExperimentType expType = new ExperimentType();
// Set Experimental ID
expType.setId(index);
// Set Bibliographic Reference
BibrefType bibRef = null;
Object pmid = interaction.getAttribute(InteractionVocab.PUB_MED_ID);
if ((pmid != null) && pmid instanceof String) {
bibRef = createBibRef(PUB_MED_DB, (String) pmid);
expType.setBibref(bibRef);
}
// Set Interaction Detection
CvType interactionDetection = getInteractionDetection(interaction);
expType.setInteractionDetectionMethod(interactionDetection);
// Set Choice Element
expList.getExperimentRefOrExperimentDescription().add(expType);
return expList;
}
/**
* Gets a complete list of NonRedundant Proteins.
*
* @return HashMap of NonRedundant Proteins.
*/
private HashMap getNonRedundantInteractors() {
HashMap interactorMap = new HashMap();
for (int i = 0; i < interactions.size(); i++) {
org.cytoscape.coreplugin.psi_mi.model.Interaction interaction =
(org.cytoscape.coreplugin.psi_mi.model.Interaction) interactions.get(i);
List interactors = interaction.getInteractors();
for (int j = 0; j < interactors.size(); j++) {
Interactor interactor = (Interactor) interactors.get(j);
addToHashMap(interactor, interactorMap);
}
}
return interactorMap;
}
/**
* Gets the Interaction Participant List.
*
* @param interaction Interaction object.
* @return Castor Participant List.
*/
private InteractionElementType.ParticipantList getParticipantList(
org.cytoscape.coreplugin.psi_mi.model.Interaction interaction) {
InteractionElementType.ParticipantList participantList =
new InteractionElementType.ParticipantList();
List interactors = interaction.getInteractors();
for (int i = 0; i < interactors.size(); i++) {
Interactor interactor = (Interactor) interactors.get(i);
String name = interactor.getName();
ParticipantType participant1 = createParticipant(name);
participantList.getParticipant().add(participant1);
}
return participantList;
}
