/** Called from bicat.gui.window.Search */
public void search(int data, int list, int idx, String genes, String chips, boolean andSearch) {
if (engine.isDebug()) System.out.println("Starting search ...");
Dataset BcR = (Dataset) engine.getDatasetList().get(data);
LinkedList biclusterList = (LinkedList) BcR.getBCsList(list).get(idx);
biclusterList = search(biclusterList, genes, chips, andSearch);
// do management ...
BcR.updateSearchBiclustersLists(biclusterList, list, idx);
if (owner != null) {
owner.updateSearchMenu();
owner.buildTree();
owner.getTree().setSelectionPath(owner.getPreprocessedPath());
owner.getTree().setSelectionPath(owner.getPreprocessedPath());
int row = owner.getTree().getRowCount() - 1;
while (row >= 0) {
owner.getTree().collapseRow(row);
row--;
}
}
}
/**
* Called from bicat.gui.window.GenePairAnalysis
*
* @throws Exception
*/
public void genePairAnalysis(
int data, int list, int idx, int minCoocScore, int minCommonScore, boolean byCooc)
throws Exception {
Dataset BcR = (Dataset) engine.getDatasetList().get(data);
LinkedList biclusterList = (LinkedList) BcR.getBCsList(list).get(idx);
HashMap gpa = new HashMap();
if (engine.isDebug()) {
System.out.println("Starting gene pair analysis ...");
System.out.println("Hashmap for biclusterList: " + biclusterList.toString());
}
if (byCooc) gpa = gpaByCoocurrence(biclusterList, minCoocScore, BcR);
else gpa = gpaByCommonChips(biclusterList, minCommonScore);
if (engine.isDebug()) System.out.println("Hashmap size for gpa: " + gpa.size());
// do management ...
BcR.updateAnalysisBiclustersLists(gpa, list, idx);
if (owner != null) {
owner.updateAnalysisMenu();
owner.buildTree();
owner.getTree().setSelectionPath(owner.getPreprocessedPath());
owner.getTree().setSelectionPath(owner.getPreprocessedPath());
int row = owner.getTree().getRowCount() - 1;
while (row >= 0) {
owner.getTree().collapseRow(row);
row--;
}
}
}
/** Called from bicat.gui.window.Filter */
public void filter(
int data, int list, int idx, int minG, int maxG, int minC, int maxC, int nrBCs, int overlap) {
if (engine.isDebug()) System.out.println("Starting filter ...");
Dataset BcR = (Dataset) engine.getDatasetList().get(data);
LinkedList biclusterList = (LinkedList) BcR.getBCsList(list).get(idx);
int limit_G = BcR.getGeneCount();
int limit_C = BcR.getWorkingChipCount();
biclusterList = filterBySize(biclusterList, minG, maxG, minC, maxC, limit_G, limit_C);
biclusterList = filterByOverlap(biclusterList, nrBCs, overlap);
// do management ...
BcR.updateFilterBiclustersLists(biclusterList, list, idx);
if (owner != null) {
owner.updateFilterMenu();
owner.buildTree();
owner.getTree().setSelectionPath(owner.getPreprocessedPath());
int row = owner.getTree().getRowCount() - 1;
while (row >= 0) {
owner.getTree().collapseRow(row);
row--;
}
}
}