public void mapEdgeColumn(final EncoreInteraction interaction, final CyRow row) {
final Set<String> exp = interaction.getExperimentToPubmed().keySet();
row.set(DETECTION_METHOD_ID, new ArrayList<String>(exp));
final List<CrossReference> pubIDs = interaction.getPublicationIds();
final List<String> pubIdList = new ArrayList<String>();
final List<String> pubDBList = new ArrayList<String>();
for (CrossReference pub : pubIDs) {
pubIdList.add(pub.getIdentifier());
pubDBList.add(pub.getDatabase());
}
if (pubIdList.isEmpty() == false) row.set(PUB_ID, pubIdList);
if (pubDBList.isEmpty() == false) row.set(PUB_DB, pubDBList);
// Interaction (use UniqueID)
row.set(CyEdge.INTERACTION, interaction.getMappingIdDbNames());
final List<Confidence> scores = interaction.getConfidenceValues();
for (Confidence c : scores) {
String type = c.getType();
String value = c.getValue();
if (row.getTable().getColumn(type) == null)
row.getTable().createColumn(type, Double.class, true);
try {
double doubleVal = Double.parseDouble(value);
row.set(type, doubleVal);
} catch (NumberFormatException e) {
// logger.warn("Invalid number string: " + value);
// Ignore invalid number
}
}
}
/**
* Add a single entry
*
* @param row
* @param val
* @param columnName
*/
private final void addSingleColumn(
final CyRow row, final String val, final String columnName, final Class<?> dataType) {
// Ignore invalid entry.
if (val == null || val.equals("-")) {
return;
}
// Create column if necessary
if (row.getTable().getColumn(columnName) == null) {
row.getTable().createColumn(columnName, dataType, false);
}
Object newValue = val;
if (dataType == Boolean.class) newValue = Boolean.parseBoolean(val);
row.set(columnName, newValue);
}
private void processOtherNames(CyRow row, final Map<String, List<String>> accs) {
for (String originalDBName : accs.keySet()) {
final String dbName = validateNamespace(originalDBName);
if (row.getTable().getColumn(dbName) == null)
row.getTable().createListColumn(dbName, String.class, false);
List<String> currentList = row.getList(dbName, String.class);
if (currentList == null) currentList = new ArrayList<String>();
final Set<String> nameSet = new HashSet<String>(currentList);
final List<String> names = accs.get(originalDBName);
nameSet.addAll(names);
row.set(dbName, new ArrayList<String>(nameSet));
}
}
private void guessHumanReadableName(final CyRow row) {
boolean found = false;
// Special handler for STRING. This is a hack...
if (row.getTable().getColumn(STRING_ATTR_NAME) != null) {
final List<String> stringList = row.getList(STRING_ATTR_NAME, String.class);
if (stringList != null) found = findHumanReadableName(row, stringList, ncbiPattern, true);
}
if (found) return;
// try NCBI
if (row.getTable().getColumn(ENTREZ_GENE_ATTR_NAME) != null) {
final List<String> ncbiList = row.getList(ENTREZ_GENE_ATTR_NAME, String.class);
if (ncbiList != null) found = findHumanReadableName(row, ncbiList, ncbiPattern, true);
}
if (found) return;
// Try Uniprot
List<String> uniprotList = null;
if (row.getTable().getColumn(UNIPROT_ATTR_NAME) != null) {
uniprotList = row.getList(UNIPROT_ATTR_NAME, String.class);
if (uniprotList != null) found = findHumanReadableName(row, uniprotList, exact1Pattern, true);
}
if (found) return;
if (uniprotList != null) found = findHumanReadableName(row, uniprotList, uniprotPattern, false);
if (found) return;
// Unknown
if (row.getTable().getColumn("unknown") != null) {
final List<String> unknownList = row.getList("unknown", String.class);
if (unknownList != null)
found = findHumanReadableName(row, unknownList, uniprotPattern, false);
}
if (found) return;
if (found == false) {
// Give up. Use primary key
row.set(PREDICTED_GENE_NAME, row.get(CyNetwork.NAME, String.class));
}
}
/**
* Split the entry by the delimiter and simply creates list column from the values.
*
* @param row
* @param val
* @param columnName
*/
private final void addSimpleListColumn(
final CyRow row, final String val, final String columnName) {
// Ignore invalid entry.
if (val == null || val.equals("-")) {
return;
}
// Create column if necessary
if (row.getTable().getColumn(columnName) == null) {
row.getTable().createListColumn(columnName, String.class, false);
}
final String[] entries = SPLITTER.split(val);
final List<String> ids = new ArrayList<String>();
for (final String entry : entries) {
if (entry != null) {
final String newEntry = entry.replaceAll("\"", "");
ids.add(newEntry);
}
}
if (!ids.isEmpty()) row.set(columnName, ids);
}
private final void addListColumn(
final CyRow row, final String val, final String columnName, final Class<?> listType) {
if (val == null || val.equals("-")) {
return;
}
String newColName = null;
// Create column if necessary
if (columnName != null) {
if (row.getTable().getColumn(columnName) == null) {
row.getTable().createListColumn(columnName, listType, false);
row.getTable().createListColumn(columnName + " ID", String.class, false);
}
newColName = columnName;
}
final String[] entries = SPLITTER.split(val);
final List<String> ids = new ArrayList<String>();
final List<String> descriptions = new ArrayList<String>();
for (final String entry : entries) {
final String[] contents = parseValues(entry);
if (newColName == null) {
if (row.getTable().getColumn(contents[0]) == null) {
row.getTable().createListColumn(contents[0], listType, false);
row.getTable().createListColumn(contents[0] + " ID", String.class, false);
}
newColName = contents[0];
}
if (contents[1] != null) ids.add(contents[1]);
if (contents[2] != null) descriptions.add(contents[2]);
}
if (!ids.isEmpty()) row.set(newColName + " ID", ids);
if (!descriptions.isEmpty()) row.set(newColName, descriptions);
}
private void mergeRow(String keyName, CyRow sourceRow, CyRow targetRow) {
for (CyColumn column : sourceRow.getTable().getColumns()) {
if (cancelled) return;
String columnName = column.getName();
if (columnName.equals(keyName)) continue;
Class<?> type = column.getType();
if (type.equals(List.class)) {
Class<?> elementType = column.getListElementType();
List<?> list = sourceRow.getList(columnName, elementType);
targetRow.set(columnName, list);
} else {
Object value = sourceRow.get(columnName, type);
targetRow.set(columnName, value);
}
}
}
public void mapEdgeColumn(
final String[] entries,
final CyRow row,
final CyEdge edge,
final String sourceName,
final String targetName) {
// Column 7: Detection method
final String[] detectionMethods = SPLITTER.split(entries[6]);
final List<String> methods = new ArrayList<String>();
final List<String> methodID = new ArrayList<String>();
for (final String entry : detectionMethods) {
final String[] methodContents = parseValues(entry);
if (methodContents[1] != null) methodID.add(methodContents[1]);
if (methodContents[2] != null) methods.add(methodContents[2]);
}
if (!methods.isEmpty()) row.set(DETECTION_METHOD_NAME, methods);
if (!methodID.isEmpty()) row.set(DETECTION_METHOD_ID, methodID);
// Column 8: Authors
final String[] authorsParts = SPLITTER.split(entries[7]);
final List<String> authors = new ArrayList<String>();
for (final String entry : authorsParts) {
String updatedAuthor = entry.replaceAll("\"", "");
authors.add(updatedAuthor);
}
if (!authors.isEmpty()) row.set(AUTHOR, authors);
final List<String> pubIdList = new ArrayList<String>();
final List<String> pubDBList = new ArrayList<String>();
final String[] pubID = SPLITTER.split(entries[8]);
for (final String entry : pubID) {
String id = parseValues(entry)[1];
String db = parseValues(entry)[0];
if (id != null && db != null) {
pubDBList.add(db);
pubIdList.add(id);
}
}
if (!pubIdList.isEmpty()) row.set(PUB_ID, pubIdList);
if (!pubDBList.isEmpty()) row.set(PUB_DB, pubDBList);
final String[] dbNames = SPLITTER.split(entries[12]);
row.set(SOURCE_DB, parseValues(dbNames[0])[0]);
// Interaction Types - Use first one as primary type.
final String[] typeParts = SPLITTER.split(entries[11]);
final List<String> types = new ArrayList<String>();
for (final String entry : typeParts) {
final String type = parseValues(entry)[2];
if (type != null) types.add(type);
}
if (!types.isEmpty()) {
row.set(INTERACTION_TYPE, types);
row.set(PRIMARY_INTERACTION_TYPE, types.get(0));
}
// Set interaction: this is an ID.
final String[] interactionID = SPLITTER.split(entries[13]);
final String interaction = parseValues(interactionID[0])[1];
row.set(CyEdge.INTERACTION, interaction);
// Create name
row.set(CyNetwork.NAME, sourceName + " (" + interaction + ") " + targetName);
final String[] scores = SPLITTER.split(entries[14]);
for (String score : scores) {
final String[] scoreArray = parseValues(score);
String scoreType = "Confidence-Score-" + scoreArray[0];
String value = scoreArray[1];
if (value == null) {
continue;
}
if (row.getTable().getColumn(scoreType) == null)
row.getTable().createColumn(scoreType, Double.class, true);
try {
double doubleVal = Double.parseDouble(value);
row.set(scoreType, doubleVal);
} catch (NumberFormatException e) {
// logger.warn("Invalid number string: " + value);
// Ignore invalid number
}
}
// For MITAB 2.7
if (entries.length > 15) {
addListColumn(row, entries[16], "Source Biological Role", String.class);
addListColumn(row, entries[17], "Target Biological Role", String.class);
addListColumn(row, entries[18], "Source Experimental Role", String.class);
addListColumn(row, entries[19], "Target Experimental Role", String.class);
addListColumn(row, entries[40], "Source Participant Detection Method", String.class);
addListColumn(row, entries[41], "Target Participant Detection Method", String.class);
addListColumn(row, entries[15], "Complex Expansion", String.class);
addListColumn(row, entries[24], "Xref", String.class);
addSimpleListColumn(row, entries[27], "Annotation");
addListColumn(row, entries[28], "Host Organism Taxonomy", String.class);
addSimpleListColumn(row, entries[29], "Parameters");
addSingleColumn(row, entries[30], "Creation Date", String.class);
addSingleColumn(row, entries[31], "Update Date", String.class);
addSingleColumn(row, entries[35], "Negative", Boolean.class);
}
}