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DlgBase.java
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DlgBase.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.ObservableList;
import javafx.event.ActionEvent;
import javafx.fxml.FXMLLoader;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.control.*;
import javafx.scene.control.cell.CheckBoxTreeCell;
import javafx.scene.layout.AnchorPane;
import javafx.stage.Modality;
import javafx.stage.StageStyle;
import javafx.stage.Window;
import tappas.DataApp.EnumData;
import tappas.DbProject.AFStatsData;
import tappas.DrillDownFDAData.FDADrillDownData;
import java.io.*;
import java.time.LocalDate;
import java.time.LocalTime;
import java.util.*;
/**
*
* @author Hector del Risco - [email protected] & Pedro Salguero - [email protected]
*/
public class DlgBase extends AppObject {
Dialog<HashMap> dialog;
Scene scene;
Label lblMsg = null;
ButtonType btnOK, btnHelp, btnCancel;
Window window;
String title;
public DlgBase(Project project, Window window) {
super(project, null);
this.window = window;
}
public void showDlgMsg(String msg) {
if(lblMsg != null)
lblMsg.setText(msg);
if(!msg.isEmpty())
app.ctls.alertInformation(title, msg);
}
public boolean createFloatingWindow(Node node, String title) {
return createDialogInternal("", node, title, true, true, false, "");
}
public boolean createToolDialog(String fxml, String title, String helpHtml) {
return createDialogInternal(fxml, null, title, true, true, false, helpHtml);
}
public boolean createDialog(String fxml, String title, boolean btnOKFlg, boolean btnCancelFlg, String helpHtml) {
return createDialogInternal(fxml, null, title, false, btnOKFlg, btnCancelFlg, helpHtml);
}
public boolean createDialog(String fxml, String title, boolean btnCancelFlg, String helpHtml) {
return createDialogInternal(fxml, null, title, false, true, btnCancelFlg, helpHtml);
}
//
// Protected Functions
//
protected void onButtonExport() {
// override
}
protected void onButtonExportChart() {
// override
}
protected boolean isValidNumInt(String strnum) {
boolean valid = false;
try {
int num = Integer.parseUnsignedInt(strnum.trim());
valid = true;
} catch(Exception e) {
System.out.println("Not a valid integer value.");
}
return valid;
}
protected boolean isValidNumDbl(String strnum) {
boolean valid = false;
try {
double num = Double.parseDouble(strnum.trim());
valid = true;
} catch(Exception e) {
System.out.println("Not a valid double value.");
}
return valid;
}
protected void populateAnnotationFeatures(TreeView tv, HashMap<String, HashMap<String, Object>> hmSels) {
tv.setCellFactory(CheckBoxTreeCell.<String>forTreeView());
TreeItem<String> rootItem = new TreeItem<> ("Annotation File");
rootItem.setExpanded(true);
AFStatsData sd;
HashMap<String, Object> hm;
HashMap<String, HashMap<String, AFStatsData>> hmStats = project.data.getAFStats();
for (String source : hmStats.keySet()) {
hm = null;
CheckBoxTreeItem<String> item = new CheckBoxTreeItem<> (source);
item.selectedProperty().addListener((obsValue, oldValue, newValue) -> annotationFeaturesOnSelectionChanged());
if(hmSels.containsKey(source)) {
hm = hmSels.get(source);
if(hm.size() > 0 && hm.size() != hmStats.get(source).size())
item.setIndeterminate(true);
else
item.setSelected(true);
}
boolean addflg = false;
HashMap<String, AFStatsData> hmFeatures = hmStats.get(source);
for (String feature : hmFeatures.keySet()) {
if(!project.data.isRsvdFeature(source, feature)) {
sd = hmFeatures.get(feature);
if(sd.idCount > 0) {
addflg = true;
CheckBoxTreeItem<String> subitem = new CheckBoxTreeItem<> (feature);
subitem.selectedProperty().addListener((observableValue, oldnum, newnum) -> annotationFeaturesOnSelectionChanged());
if(hm != null && (hm.containsKey(feature) || hm.isEmpty()))
subitem.setSelected(true);
item.getChildren().add(subitem);
}
}
}
if(addflg)
rootItem.getChildren().add(item);
}
tv.setShowRoot(false);
tv.setRoot(rootItem);
}
protected void populateAnnotationFeaturesPositional(TreeView tv, HashMap<String, HashMap<String, Object>> hmSels) {
tv.setCellFactory(CheckBoxTreeCell.<String>forTreeView());
TreeItem<String> rootItem = new TreeItem<> ("Annotation File");
rootItem.setExpanded(true);
AFStatsData sd;
HashMap<String, Object> hm;
HashMap<String, HashMap<String, AFStatsData>> hmStats = project.data.getAFStats();
HashMap<String, ArrayList<String>> hmPositional = project.data.getAFStatsPositional();
for (String source : hmPositional.keySet()) {
if(!hmStats.containsKey(source))
continue;
hm = null;
CheckBoxTreeItem<String> item = new CheckBoxTreeItem<> (source);
item.selectedProperty().addListener((obsValue, oldValue, newValue) -> annotationFeaturesOnSelectionChanged());
if(hmSels.containsKey(source)) {
hm = hmSels.get(source);
if(hm.size() > 0 && hm.size() != hmStats.get(source).size())
item.setIndeterminate(true);
else
item.setSelected(true);
}
boolean addflg = false;
HashMap<String, AFStatsData> hmFeatures = hmStats.get(source);
for (String feature : hmFeatures.keySet()) {
//Just get Features that appear in hmPositional
if(hmPositional.get(source).contains(feature) && !project.data.isRsvdFeature(source, feature)) {
sd = hmFeatures.get(feature);
if(sd.idCount > 0) {
addflg = true;
CheckBoxTreeItem<String> subitem = new CheckBoxTreeItem<> (feature);
subitem.selectedProperty().addListener((observableValue, oldnum, newnum) -> annotationFeaturesOnSelectionChanged());
if(hm != null && (hm.containsKey(feature) || hm.isEmpty()))
subitem.setSelected(true);
item.getChildren().add(subitem);
}
}
}
if(addflg)
rootItem.getChildren().add(item);
}
tv.setShowRoot(false);
tv.setRoot(rootItem);
}
protected void populateAnnotationFeaturesPresence(TreeView tv, HashMap<String, HashMap<String, Object>> hmSels) {
tv.setCellFactory(CheckBoxTreeCell.<String>forTreeView());
TreeItem<String> rootItem = new TreeItem<> ("Annotation File");
rootItem.setExpanded(true);
AFStatsData sd;
HashMap<String, Object> hm;
HashMap<String, HashMap<String, AFStatsData>> hmStats = project.data.getAFStats();
HashMap<String, ArrayList<String>> hmPresence = project.data.getAFStatsPresence();
for (String source : hmPresence.keySet()) {
if(!hmStats.containsKey(source))
continue;
hm = null;
CheckBoxTreeItem<String> item = new CheckBoxTreeItem<> (source);
item.selectedProperty().addListener((obsValue, oldValue, newValue) -> annotationFeaturesOnSelectionChanged());
if(hmSels.containsKey(source)) {
hm = hmSels.get(source);
if(hm.size() > 0 && hm.size() != hmStats.get(source).size())
item.setIndeterminate(true);
else
item.setSelected(true);
}
boolean addflg = false;
HashMap<String, AFStatsData> hmFeatures = hmStats.get(source);
for (String feature : hmFeatures.keySet()) {
//Just get Features that appear in hmPresence
if(hmPresence.get(source).contains(feature) && !project.data.isRsvdFeature(source, feature)) {
sd = hmFeatures.get(feature);
if(sd.idCount > 0) {
addflg = true;
CheckBoxTreeItem<String> subitem = new CheckBoxTreeItem<> (feature);
subitem.selectedProperty().addListener((observableValue, oldnum, newnum) -> annotationFeaturesOnSelectionChanged());
if(hm != null && (hm.containsKey(feature) || hm.isEmpty()))
subitem.setSelected(true);
item.getChildren().add(subitem);
}
}
}
if(addflg)
rootItem.getChildren().add(item);
}
tv.setShowRoot(false);
tv.setRoot(rootItem);
}
protected void annotationFeaturesOnSelectionChanged() {
// override
}
protected void setProjectName() {
if(scene != null) {
AnchorPane paneProject = (AnchorPane) scene.lookup("#paneProject");
paneProject.getStyleClass().add("project" + project.getProjectNumber());
Label lblProjectName = (Label) scene.lookup("#lblProjectName");
lblProjectName.setText("Project \"" + project.getProjectName()+ "\"");
}
}
// protected void setProjectNameScrollPane() {
// if(scene != null) {
// ScrollPane scPane = (ScrollPane) scene.lookup("#scPane");
// AnchorPane acPane = (AnchorPane) scPane.getContent().lookup("#acPane");
//
// AnchorPane paneProject = (AnchorPane) acPane.lookup("#paneProject");
// paneProject.getStyleClass().add("project" + project.getProjectNumber());
// Label lblProjectName = (Label) acPane.lookup("#lblProjectName");
// lblProjectName.setText("Project \"" + project.getProjectName()+ "\"");
// }
// }
// run script and write output to log file
protected void runScript(TaskHandler.TaskInfo taskInfo, List<String> lst, String name, String logFilepath) {
try {
ProcessBuilder pb = new ProcessBuilder(lst);
System.out.println(lst);
pb.redirectErrorStream(true);
Process process = pb.start();
taskInfo.process = process;
// monitor process output
Writer writer = null;
try {
String line, dspline;
LocalDate date = LocalDate.now();
LocalTime time = LocalTime.now();
writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(logFilepath, true), "utf-8"));
dspline = name + " script is running...\n";
writer.write(dspline);
BufferedReader input = new BufferedReader(new InputStreamReader(process.getInputStream()));
while ((line = input.readLine()) != null) {
time = LocalTime.now();
dspline = time.toString() + " " + line + "\n";
writer.write(dspline);
}
try { input.close(); } catch(Exception e) { }
int ev = process.waitFor();
dspline = time.toString() + " " + name + " script ended. Exit value: " + ev + "\n";
writer.write(dspline);
} catch(Exception e) {
app.logError("Unable to capture " + name + " process output: " + e.getMessage());
} finally {
try {writer.close();} catch (Exception e) {;}
}
} catch(Exception e) {
app.logError("Unable to run " + name + " script: " + e.getMessage());
}
}
// override if needed
protected void onClose() {
dialog.close();
}
protected void addGeneDVItemFDA(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)
app.ctls.alertInformation("Display Gene Data Visualization", "You have multiple gene rows highlighted.\nHighlight a single row with the gene you want to visualize.");
else {
FDADrillDownData a = (FDADrillDownData) tbl.getItems().get((tbl.getSelectionModel().getSelectedIndex()));
String gene = a.getGene().trim();
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 show data visualization for.");
Optional<String> result = dlg.showAndWait();
if(result.isPresent()) {
gene = result.get();
showGeneDataVisualizationFDA(gene, panel);
}
}
else
showGeneDataVisualizationFDA(gene, panel);
}
});
// check if we can provide online references
if(WebRefs.hasOnlineReferences(project)) {
item = new MenuItem("Show gene online references in web browser");
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)
app.ctls.alertInformation("Display Gene Online Reference", "You have multiple gene rows highlighted.\nHighlight a single row with the gene to show online references for.");
else {
DataApp.SelectionDataResults rdata = (DataApp.SelectionDataResults) tbl.getItems().get((tbl.getSelectionModel().getSelectedIndex()));
String gene = rdata.getGene().trim();
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 Online Reference");
dlg.setHeaderText("Select gene to show online references for");
Optional<String> result = dlg.showAndWait();
if(result.isPresent()) {
gene = result.get();
WebRefs.showGeneOnlineReferences(gene, project);
}
}
else
WebRefs.showGeneOnlineReferences(gene, project);
}
});
}
}
public void showGeneDataVisualizationFDA(String gene, String panel) {
HashMap<String, Object> hmArgs = new HashMap<>();
hmArgs.put("panels", panel);
app.tabs.openTabGeneDataViz(project, project.getDef().id, gene, project.data.getResultsGeneTrans().get(gene), "Project '" + project.getDef().name + "'", hmArgs);
}
//
// Internal Functions
//
private boolean createDialogInternal(String fxml, Node node, String title, boolean tool, boolean btnOKFlg, boolean btnCancelFlg, String helpHtml) {
boolean result = false;
this.title = title;
dialog = new Dialog();
dialog.setTitle(title);
if(tool) {
// using unified style in Windows 10 results in the dialog content being blank (not shown)
// change if issue is resolved or workaround found
dialog.initStyle(Utils.isWindowsOS()? StageStyle.DECORATED : StageStyle.UNIFIED);
dialog.initModality(Modality.NONE);
dialog.setResizable(true);
dialog.setOnCloseRequest(e -> { onClose(); });
}
else {
dialog.initModality(Modality.APPLICATION_MODAL);
dialog.setResizable(false);
dialog.initStyle(StageStyle.DECORATED);
}
dialog.initOwner(window);
try {
if(node == null)
node = (Node) FXMLLoader.load(app.ctlr.fxdc.getClass().getResource("/tappas/dialogs/" + fxml));
else {
String url = getClass().getResource("/tappas/Style.css").toExternalForm();
dialog.getDialogPane().getStylesheets().add(url);
dialog.getDialogPane().getStyleClass().add("float-dialog-pane");
}
dialog.getDialogPane().setContent(node);
dialog.getDialogPane().getScene().getWindow().sizeToScene();
if(btnOKFlg) {
btnOK = new ButtonType((tool? "Close" : "OK"), ButtonBar.ButtonData.OK_DONE);
dialog.getDialogPane().getButtonTypes().add(btnOK);
}
if(btnCancelFlg) {
btnCancel = new ButtonType("Cancel", ButtonBar.ButtonData.CANCEL_CLOSE);
dialog.getDialogPane().getButtonTypes().add(btnCancel);
}
if(helpHtml != null && !helpHtml.isEmpty()) {
btnHelp = new ButtonType("Help", ButtonBar.ButtonData.HELP);
dialog.getDialogPane().getButtonTypes().add(btnHelp);
System.out.println("bt: " + dialog.getDialogPane().getButtonTypes());
final Button btHelp = (Button) dialog.getDialogPane().lookupButton(btnHelp);
System.out.println("hlp: " + btHelp);
if(btHelp != null) {
btHelp.addEventFilter(ActionEvent.ACTION, event -> {
DlgHelp dlg = new DlgHelp();
dlg.show(title, helpHtml, Tappas.getWindow());
event.consume();
});
}
}
scene = dialog.getDialogPane().getContent().getScene();
lblMsg = (Label) scene.lookup("#lblMsg");
result = true;
} catch(Exception e) {
logger.logError("Unable to create dialog: " + e.getMessage());
}
return result;
}
//
// Data Classes
//
public static class DlgParams {
final static double MIN_PVAL_THRESHOLD = 0.0;
final static double MAX_PVAL_THRESHOLD = 1.0;
final static double MAX_PVAL_FC = 10000.0;
final static double MIN_R2CUTOFF = 0.4;
final static double MAX_R2CUTOFF = 0.8;
public static enum YesNo {
NO, YES
}
protected static final List<EnumData> lstYesNo = Arrays.asList(
new EnumData(YesNo.NO.name(), "No"),
new EnumData(YesNo.YES.name(), "Yes")
);
public DlgParams() {
}
public DlgParams(HashMap<String, String> hmParams) {
}
public HashMap<String, String> getParams() {
// override
HashMap<String, String> hm = new HashMap<>();
return hm;
}
public boolean save(String filepath) {
return Utils.saveParams(getParams(), filepath);
}
protected static int getYNIndex(String ynID) {
int idx = 0;
for(EnumData yn : lstYesNo) {
if(yn.id.equals(ynID))
break;
idx++;
}
if(idx >= lstYesNo.size())
idx = 0;
return idx;
}
}
}