/**
* @param type
* @return a map whose keys are the values corresponding to nodes of type 'type' and the values
* are the number of them
*/
private Map<String, Integer> extractNodes(NodeType type) {
Map<String, Integer> resultNodes = new HashMap<String, Integer>();
List<ISANode> node = graph.getNodes(type);
for (ISANode nodeOfInterest : node) {
// extract the values!
for (int rowIndex = 1; rowIndex < assayTable.length; rowIndex++) {
if (nodeOfInterest.getIndex() < assayTable[rowIndex].length) {
String[] row =
Arrays.copyOf(assayTable[rowIndex], assayTable[rowIndex].length, String[].class);
String value = row[nodeOfInterest.getIndex()];
if (value != null && !value.equals("")) {
if (!resultNodes.containsKey(value)) {
resultNodes.put(value, 1);
} else {
int newCount = resultNodes.get(value) + 1;
resultNodes.put(value, newCount);
}
}
}
}
}
return resultNodes;
}
/**
* *
*
* <p>Method to create the data groups. This method determines the labels to be used for groups.
*
* @param fileContents a matrix of Objects, which is the contents of the spreadsheet
* @param group a string indicating the column to consider to form the groups, e.g. Factor
* @param exactMatch true or false indicating whether the string match is exact or not
* @param includeColumnNames true or false indicating if the columns names are included in the
* result (e.g if true the result will be 'Factor Value[<specific value>]', otherwise it will
* be '<specific value>' only)
* @return Map<String, String>
*/
private Map<String, StudyGroup> getDataGroupsWithTypeByColumn(
Object[][] fileContents, String group, boolean exactMatch, boolean includeColumnNames) {
// map for resulting groups
// group name, study group object
Map<String, StudyGroup> groups = new HashMap<String, StudyGroup>();
String[] columnNames = Arrays.copyOf(fileContents[0], fileContents[0].length, String[].class);
boolean allowedUnit = false;
for (int row = 1; row < fileContents.length; row++) {
Map<String, String> groupDefinition = new HashMap<String, String>();
String groupVal = "";
int elementsNumber = 0;
for (int col = 0; col < columnNames.length; col++) {
String column = columnNames[col];
boolean match = false;
if (exactMatch) {
if (column.equalsIgnoreCase(group)) {
match = true;
} else if (allowedUnit && column.equalsIgnoreCase("unit")) {
match = true;
}
} else {
if (column.contains(group)) {
match = true;
} else if (allowedUnit && column.equalsIgnoreCase("unit")) {
match = true;
}
}
if (match) {
if (!fileContents[row][col].equals("")) {
groupVal +=
(elementsNumber > 0 ? "|" : "")
+ (includeColumnNames ? extractColumnType(column) + "=" : " ")
+ fileContents[row][col];
groupDefinition.put(extractColumnType(column), (String) fileContents[row][col]);
elementsNumber++;
allowedUnit = true;
}
} else
allowedUnit =
column.contains("Term Source REF") || column.contains("Term Accession Number");
}
if (!groupVal.equals("")) {
groupVal = groupVal.trim();
if (!groups.containsKey(groupVal)) {
groups.put(groupVal, new StudyGroup(group, groupVal));
}
StudyGroup studyGroup = groups.get(groupVal);
studyGroup.addGroupMember(getColValAtRow(fileContents, columnNames, "Sample Name", row));
studyGroup.setGroupDefinition(groupDefinition);
}
}
return groups;
}