public IC50TableModel( // net.bioclipse.brunn.pojos.Plate plate,
// KTable table,
// IC50 editor,
Replicates replicates) {
columnNames = new ArrayList<String>();
Collections.addAll(columnNames, new String[] {"Compound Names", "IC50"});
/*
* set up the matrix if there are any results for the plate
*/
if (replicates
.getPlate()
.getWell(1, 'a')
.getSampleContainer()
.getWorkList()
.getAbstractOperations()
.size()
> 0) {
fillContent(replicates);
extractEntries();
}
List<String[]> rows = new ArrayList<String[]>();
for (String compound : entries.keySet()) {
rows.add(entries.get(compound));
}
Collections.sort(
rows,
new Comparator<String[]>() {
public int compare(String[] o1, String[] o2) {
int c = o1[0].compareTo(o2[0]);
if (c != 0) return c;
c =
Double.compare(
Double.parseDouble(
o1[1].contains(" ") ? o1[1].substring(0, o1[1].indexOf(' ')) : o1[1]),
Double.parseDouble(
o2[1].contains(" ") ? o2[1].substring(0, o2[1].indexOf(' ')) : o2[1]));
if (c != 0) return c;
return 0;
}
});
matrix = rows.toArray(new String[0][0]);
this.rows = matrix.length;
this.cols = columnNames.size();
initialize();
}
// reads dataset from replicate table
private void fillContent(Replicates replicates) {
replicatesContent.clear();
String[][] matrix = replicates.getReplicatesContent();
String[] headers = matrix[0];
for (int i = 0; i < headers.length; i++) {
if (headers[i].equals("si%")
|| headers.equals("si")
|| headers.equals("SI")
|| headers.equals("Si")) {
headers[i] = "SI%";
}
replicatesContent.put(headers[i], null);
}
for (int i = 1; i < matrix.length; i++) {
if (Character.isDigit(matrix[i][3].charAt(0))) {
for (int j = 0; j < headers.length; j++) {
replicatesContent.put(
headers[j], addToStringArray(replicatesContent.get(headers[j]), matrix[i][j]));
}
}
}
splitConcAndUnit();
storeIC50();
}