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DrillDownGSEA.java
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DrillDownGSEA.java
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/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package tappas;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.concurrent.Task;
import javafx.scene.control.*;
import javafx.scene.control.cell.PropertyValueFactory;
import javafx.scene.layout.Pane;
import javafx.stage.Window;
import tappas.DrillDownFEA.FEADrillDownData;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.*;
/**
*
* @author Hector del Risco - [email protected] & Pedro Salguero - [email protected]
*/
public class DrillDownGSEA extends DlgBase {
static int id = 0;
static String exportFilename = "";
Label lblHeader, lblDescription;
Button btnHelpTbl, btnExportTbl;
TableView tblMembers;
Pane paneMenu;
ProgressIndicator pi;
int toolId;
DataApp.DataType dataType;
String idColName;
String featureId;
String fileFeatures;
String fileFeatures2;
String panel;
boolean again = false; //to search in the another feature list
ArrayList<String> lstTestItems;
TaskHandler.ServiceExt service = null;
ObservableList<FEADrillDownData> data = null;
public DrillDownGSEA(Project project, Window window) {
super(project, window);
toolId = ++id;
}
public HashMap<String, String> showAndWait(DataApp.DataType dataType, String featureId, String description, String fileFeatures, String fileFeatures2, ArrayList<String> lstTestItems) {
if(createToolDialog("DrillDownGSEA.fxml", "GSEA Features Drill Down Data", null)) {
this.dataType = dataType;
this.featureId = featureId;
this.fileFeatures = fileFeatures;
this.fileFeatures2 = fileFeatures2;
this.lstTestItems = lstTestItems;
dialog.setTitle("GSEA Drill Down Data for " + featureId);
panel = TabGeneDataViz.Panels.TRANS.name();
switch(dataType) {
case PROTEIN:
idColName = "Protein";
panel = TabGeneDataViz.Panels.PROTEIN.name();
break;
case GENE:
idColName = "Gene";
break;
case TRANS:
default:
idColName = "Transcript";
break;
}
// get control objects
lblHeader = (Label) scene.lookup("#lblHeader");
lblDescription = (Label) scene.lookup("#lblDescription");
pi = (ProgressIndicator) scene.lookup("#piImage");
tblMembers = (TableView) scene.lookup("#tblMembers");
paneMenu = (Pane) scene.lookup("#paneMenu");
// setup dialog
exportFilename = "tappAS_GSEA_"+featureId+".tsv";
lblHeader.setText(idColName + "s containing " + featureId);
lblDescription.setText(description);
tblMembers.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
ObservableList<TableColumn> cols = tblMembers.getColumns();
cols.get(0).setText(idColName);
cols.get(0).setCellValueFactory(new PropertyValueFactory<>("Member"));
cols.get(1).setCellValueFactory(new PropertyValueFactory<>("Gene"));
cols.get(2).setCellValueFactory(new PropertyValueFactory<>("GeneDescription"));
if(dataType.equals(DataApp.DataType.GENE))
cols.remove(1);
SubTabBase.addRowNumbersCol(tblMembers);
ContextMenu cm = new ContextMenu();
addGeneDVItem(cm, tblMembers, panel);
app.export.setupTableExport(this, cm, true);
tblMembers.setContextMenu(cm);
app.export.addCopyToClipboardHandler(tblMembers);
// setup menu buttons
double yoffset = 3.0;
btnExportTbl = app.ctls.addImgButton(paneMenu, "export.png", "Export table data...", yoffset, 32, true);
btnExportTbl.setOnAction((event) -> { onButtonExport(); });
yoffset += 36;
btnHelpTbl = app.ctls.addImgButton(paneMenu, "help.png", "Help", yoffset, 32, true);
btnHelpTbl.setOnAction((event) -> { DlgHelp dlg = new DlgHelp(); dlg.show(title, "Help_DrillDown_GSEA.html", Tappas.getWindow()); });
// process dialog - modeless
dialog.setOnShown(e -> { runThread();});
dialog.showAndWait();
}
return null;
}
@Override
protected void onButtonExport() {
DlgExportData.Config cfg = new DlgExportData.Config(true, idColName + "s list (IDs only)", false, "");
DlgExportData.Params results = app.ctlr.getExportDataParams(cfg, null, null);
if(results != null) {
HashMap<String, String> hmColNames = new HashMap<>();
Export.ExportSelection selection = Export.ExportSelection.All;
if(results.dataSelection.equals(DlgExportData.Params.DataSelection.SELECTEDROWS))
selection = Export.ExportSelection.Highlighted;
if(results.dataType.equals(DlgExportData.Params.DataType.TABLEROWS.name()))
app.export.exportTableDataToFile(tblMembers, selection, exportFilename);
else if(results.dataType.equals(DlgExportData.Params.DataType.LIST.name())) {
hmColNames.put(idColName, "");
app.export.exportTableDataListToFile(tblMembers, selection, hmColNames, exportFilename);
}
}
}
//
// Internal Functions
//
private void addGeneDVItem(ContextMenu cm, TableView tbl, String panel) {
MenuItem item = new MenuItem("Show gene data visualization");
cm.getItems().add(item);
item.setOnAction((event) -> {
// get highlighted row's data and show gene data visualization
ObservableList<Integer> lstIdxs = tbl.getSelectionModel().getSelectedIndices();
if(lstIdxs.size() != 1) {
String msg = "You have multiple gene rows highlighted.\nHighlight a single row with the gene you want to visualize.";
app.ctls.alertInformation("Display Gene Data Visualization", msg);
}
else {
FEADrillDownData dd = (FEADrillDownData) tbl.getItems().get((tbl.getSelectionModel().getSelectedIndex()));
String gene = dd.getGene();
String genes[] = gene.split(",");
if(genes.length > 1) {
List<String> lst = Arrays.asList(genes);
Collections.sort(lst);
ChoiceDialog dlg = new ChoiceDialog(lst.get(0), lst);
dlg.setTitle("Gene Data Visualization");
dlg.setHeaderText("Select gene to visualize");
Optional<String> result = dlg.showAndWait();
if(result.isPresent()) {
gene = result.get();
showGeneDataVisualization(gene, panel);
}
}
else
showGeneDataVisualization(gene, panel);
}
});
}
private void showGeneDataVisualization(String gene, String panel) {
HashMap<String, Object> args = new HashMap<>();
args.put("panels", panel);
app.tabs.openTabGeneDataViz(project, project.getDef().id, gene, project.data.getResultsGeneTrans().get(gene), "Project '" + project.getDef().name + "'", args);
}
//
// Data Load
//
private void runThread() {
// get script path and run service/task
service = new DataService();
service.initialize();
service.start();
}
private class DataService extends TaskHandler.ServiceExt {
@Override
public void initialize() {
data = null;
}
@Override
protected void onRunning() {
pi.setVisible(true);
}
@Override
protected void onStopped() {
pi.setVisible(false);
}
@Override
protected void onFailed() {
java.lang.Throwable e = getException();
if(e != null)
app.logWarning("DrillDownGSEA failed - task aborted. Exception: " + e.getMessage());
else
app.logWarning("DrillDownGSEA - task aborted.");
app.ctls.alertWarning("Drill Down Gen Set Enrichment Analysis", "DrillDownGSEA - task aborted");
}
@Override
protected void onSucceeded() {
if(data != null) {
if(data.isEmpty() && !again){ //the feature is in the another list
String aux = fileFeatures;
fileFeatures = fileFeatures2;
fileFeatures2 = aux;
again = true;
runThread();
}else{
tblMembers.setItems(data);
if(!data.isEmpty())
tblMembers.getSelectionModel().select(0);
}
}
else
app.ctls.alertWarning("GSEA Drill Down Data", "Unable to load drill down data.");
}
@Override
protected Task<Void> createTask() {
Task task = new Task<Void>() {
@Override
protected Void call() throws Exception {
try {
if(Files.exists(Paths.get(fileFeatures))) {
ObservableList<FEADrillDownData> lst = FXCollections.observableArrayList();
List<String> lines = Files.readAllLines(Paths.get(fileFeatures), StandardCharsets.UTF_8);
for(String line : lines) {
line = line.trim();
if(!line.isEmpty() && line.charAt(0) != '#') {
String[] fields = line.split("\t");
if(fields.length > 2) {
String gene = project.data.getGenes(dataType, fields[0]);
if(fields[1].equals(featureId)) {
String geneDescription = project.data.getGeneDescriptions(dataType, fields[0]);
lst.add(new FEADrillDownData(fields[0], gene, geneDescription, "YES"));
}
}
else {
app.logError("Invalid line, " + line + ", in list file '" + fileFeatures + "'.");
lst.clear();
break;
}
}
}
FXCollections.sort(lst);
data = lst;
}
}
catch (Exception e) {
app.logError("Unable to load list file '" + fileFeatures + "': " + e.getMessage());
}
return null;
}
};
taskInfo = new TaskHandler.TaskInfo("GSEA Drill Down Data " + toolId, task);
return task;
}
}
}