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DlgGSEAnalysis.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.beans.value.ObservableValue;
import javafx.collections.ObservableList;
import javafx.scene.control.*;
import javafx.stage.FileChooser;
import javafx.stage.Window;
import tappas.DataApp.DataType;
import tappas.DataApp.EnumData;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.*;
import java.util.function.UnaryOperator;
/**
*
* @author Hector del Risco - [email protected] & Pedro Salguero - [email protected]
*/
public class DlgGSEAnalysis extends DlgBase {
Label lblListTest, lblSelection1, lblSelection2, lblSets, lblRank1, lblRank2;
TextField txtName, txtSigValue, txtRLFile1, txtRLFile2, txtSets;
Button btnRLFile1, btnRLFile2, btnSets;
RadioButton rbGenes, rbProteins, rbTrans, rbFeatures, rbSets;
ChoiceBox cbRankedLists1, cbRankedLists2, cbMethods;
// Hyperlink lnkClearAll, lnkCheckAll;
TreeViewFeatures tvFeatures;
CheckBox chkMulti;
String paramId = "";
public DlgGSEAnalysis(Project project, Window window) {
super(project, window);
}
public Params showAndWait(Params dfltParams) {
if(createDialog("GSEAParams.fxml", "Gene Set Enrichment Analysis Parameters", true, "Help_Dlg_GSEA.html")) {
if(dfltParams == null)
dfltParams = new Params();
// get control objects
txtName = (TextField) scene.lookup("#txtName");
lblListTest = (Label) scene.lookup("#lblListTest");
lblRank1 = (Label) scene.lookup("#lblRank1");
lblRank2 = (Label) scene.lookup("#lblRank2");
lblSelection1 = (Label) scene.lookup("#lblSelection1");
lblSelection2 = (Label) scene.lookup("#lblSelection2");
cbRankedLists1 = (ChoiceBox) scene.lookup("#cbRankedLists1");
cbRankedLists2 = (ChoiceBox) scene.lookup("#cbRankedLists2");
txtRLFile1 = (TextField) scene.lookup("#txtRLFile1");
txtRLFile2 = (TextField) scene.lookup("#txtRLFile2");
btnRLFile1 = (Button) scene.lookup("#btnRLFile1");
btnRLFile2 = (Button) scene.lookup("#btnRLFile2");
chkMulti = (CheckBox) scene.lookup("#chkMulti");
rbGenes = (RadioButton) scene.lookup("#rbGenes");
rbProteins = (RadioButton) scene.lookup("#rbProteins");
rbTrans = (RadioButton) scene.lookup("#rbTrans");
txtSigValue = (TextField) scene.lookup("#txtThreshold");
cbMethods = (ChoiceBox) scene.lookup("#cbMethods");
rbFeatures = (RadioButton) scene.lookup("#rbFeatures");
rbSets = (RadioButton) scene.lookup("#rbSets");
lblSets = (Label) scene.lookup("#lblSets");
txtSets = (TextField) scene.lookup("#txtSets");
btnSets = (Button) scene.lookup("#btnSets");
TreeView tvf = (TreeView) scene.lookup("#tvFeatures");
// lnkClearAll = (Hyperlink) scene.lookup("#lnkClearAll");
// lnkCheckAll = (Hyperlink) scene.lookup("#lnkCheckAll");
// set default values
paramId = dfltParams.paramId;
txtName.setText(dfltParams.name);
tvFeatures = new TreeViewFeatures(project, this);
tvFeatures.initialize(tvf, dfltParams.hmFeatures, true);
txtSigValue.setText("" + dfltParams.sigValue);
if(dfltParams.dataType.equals(DataType.PROTEIN))
rbProteins.setSelected(true);
else if(dfltParams.dataType.equals(DataType.TRANS))
rbTrans.setSelected(true);
else
rbGenes.setSelected(true);
onDataTypeChange(cbRankedLists1, lblSelection1, txtRLFile1, btnRLFile1);
onDataTypeChange(cbRankedLists2, lblSelection2, txtRLFile2, btnRLFile2);
// custom annotation sets - will probably change once it's used
if(dfltParams.customFile.isEmpty())
rbFeatures.setSelected(true);
else {
rbSets.setSelected(true);
txtSets.setText(dfltParams.customFile);
}
chkMulti.setSelected(false);
chkMulti.setDisable(true);
cbMethods.getSelectionModel().selectedIndexProperty().addListener((ObservableValue<? extends Number> ov, Number oldValue, Number newValue) -> {
if(Params.lstMethods.get(cbMethods.getSelectionModel().getSelectedIndex()).id.equals(Params.Method.GOGLM.name())){
chkMulti.setSelected(false);
lblRank2.setDisable(true);
cbRankedLists2.setDisable(true);
}
});
chkMulti.disableProperty().bind(cbMethods.valueProperty().isNotEqualTo("MDGSA"));
lblRank2.setDisable(true);
txtRLFile2.setDisable(true);
lblSelection2.setDisable(true);
cbRankedLists2.setDisable(true);
btnRLFile2.setDisable(true);
lblRank2.setDisable(true);
txtRLFile2.setDisable(true);
lblSelection2.setDisable(true);
cbRankedLists2.setDisable(true);
btnRLFile2.setDisable(true);
setProjectName();
for(MethodData method : Params.lstMethods) {
cbMethods.getItems().add(method.name);
}
UnaryOperator<TextFormatter.Change> filter = (TextFormatter.Change change) -> {
if (change.getControlNewText().length() > Params.MAX_NAME_LENGTH) {
showDlgMsg("Name may not exceed " + Params.MAX_NAME_LENGTH + " characters");
return null;
} else {
showDlgMsg("");
return change;
}
};
txtName.setTextFormatter(new TextFormatter(filter));
btnRLFile1.setOnAction((event) -> { getRLFile(txtRLFile1); });
btnRLFile2.setOnAction((event) -> { getRLFile(txtRLFile2); });
//tvf.disableProperty().bindBidirectional(rbSets.selectedProperty());
rbSets.selectedProperty().addListener((ObservableValue<? extends Boolean> ov, Boolean oldValue, Boolean newValue) -> {
if(newValue){
tvf.setDisable(false);
}
});
lblSets.setDisable(true);
txtSets.setDisable(true);
btnSets.setDisable(true);
rbFeatures.selectedProperty().addListener((ObservableValue<? extends Boolean> ov, Boolean oldValue, Boolean newValue) -> {
if(newValue){
lblSets.setDisable(true);
txtSets.setDisable(true);
btnSets.setDisable(true);
}
});
btnSets.setOnAction((event) -> { getSetsFile(); });
// setup
// setup database categories
chkMulti.selectedProperty().addListener((ObservableValue<? extends Boolean> ov, Boolean oldValue, Boolean newValue) -> {
if(newValue){
lblRank2.setDisable(false);
cbRankedLists2.setDisable(false);
rbFeatures.setDisable(true);
tvf.setDisable(true);
rbSets.setDisable(true);
lblSets.setDisable(true);
txtSets.setDisable(true);
btnSets.setDisable(true);
}else{
lblRank2.setDisable(true);
cbRankedLists2.setDisable(true);
txtRLFile2.setDisable(true);
lblSelection2.setDisable(true);
btnRLFile2.setDisable(true);
rbFeatures.setDisable(false);
rbFeatures.setSelected(true);
tvf.setDisable(false);
rbSets.setDisable(false);
}
});
rbFeatures.getToggleGroup().selectedToggleProperty().addListener((ObservableValue<? extends Toggle> ov, Toggle oldValue, Toggle newValue) -> {
annotationFeaturesOnSelectionChanged();
});
rbGenes.getToggleGroup().selectedToggleProperty().addListener((ObservableValue<? extends Toggle> ov, Toggle oldValue, Toggle newValue) -> {
onDataTypeChange(cbRankedLists1, lblSelection1, txtRLFile1, btnRLFile1);
onDataTypeChange(cbRankedLists2, lblSelection2, txtRLFile2, btnRLFile2);
});
cbRankedLists1.getSelectionModel().selectedIndexProperty().addListener((ObservableValue<? extends Number> ov, Number oldValue, Number newValue) -> {
onRankedListChanged(cbRankedLists1, lblSelection1, txtRLFile1, btnRLFile1);
});
cbRankedLists2.getSelectionModel().selectedIndexProperty().addListener((ObservableValue<? extends Number> ov, Number oldValue, Number newValue) -> {
onRankedListChanged(cbRankedLists2, lblSelection2, txtRLFile2, btnRLFile2);
});
cbMethods.getSelectionModel().select(Params.getMethodCboIdx(dfltParams.method.name()));
// set ranked list
cbRankedLists1.getSelectionModel().select(Params.getRankedListIndexFromID(dfltParams.rankedList1.name()));
cbRankedLists2.getSelectionModel().select(Params.getRankedListIndexFromID(dfltParams.rankedList2.name()));
if(dfltParams.method.name().equals(Params.Method.MDGSA.name()) && dfltParams.useMulti.equals("TRUE"))
chkMulti.setSelected(true);
dialog.setOnCloseRequest((DialogEvent event) -> {
if(dialog.getResult() != null && dialog.getResult().containsKey("ERRMSG")) {
showDlgMsg((String)dialog.getResult().get("ERRMSG"));
dialog.setResult(null);
event.consume();
}
});
dialog.setResultConverter((ButtonType b) -> {
HashMap<String, String> params = null;
System.out.println(b.getButtonData().toString());
if (b.getButtonData() == ButtonBar.ButtonData.OK_DONE)
params = validate(dialog);
return params;
});
// lnkClearAll.setOnAction((event) -> {
// if(tvf.isDisable())
// clearAllFeatures(tvf);
// else
// clearAllFeatures(tvf);
// });
//
// lnkCheckAll.setOnAction((event) -> {
// if(tvf.isDisable())
// checkAllFeatures(tvf);
// else
// checkAllFeatures(tvf);
// });
Optional<HashMap> result = dialog.showAndWait();
if(result.isPresent())
return(new Params(result.get()));
}
return null;
}
//hyperlink funtions
private void clearAllFeatures(TreeView aux) {
TreeItem<String> rootItem = aux.getRoot();
ObservableList<TreeItem<String>> lst = rootItem.getChildren();
for(TreeItem ti : lst) {
CheckBoxTreeItem<String> item = (CheckBoxTreeItem<String>) ti;
ObservableList<TreeItem<String>> sublst = item.getChildren();
for(TreeItem subti : sublst) {
CheckBoxTreeItem<String> subitem = (CheckBoxTreeItem<String>) subti;
subitem.setSelected(false);
}
item.setSelected(false);
}
}
private void checkAllFeatures(TreeView aux) {
TreeItem<String> rootItem = aux.getRoot();
ObservableList<TreeItem<String>> lst = rootItem.getChildren();
for(TreeItem ti : lst) {
CheckBoxTreeItem<String> item = (CheckBoxTreeItem<String>) ti;
ObservableList<TreeItem<String>> sublst = item.getChildren();
for(TreeItem subti : sublst) {
CheckBoxTreeItem<String> subitem = (CheckBoxTreeItem<String>) subti;
subitem.setSelected(true);
}
item.setSelected(true);
}
}
private void onDataTypeChange(ChoiceBox cb, Label lbl, TextField txt, Button btn) {
ArrayList<String> lst = new ArrayList<>();
cb.getSelectionModel().clearSelection();
cb.getItems().clear();
String lstLabel;
if(rbGenes.isSelected()) {
lstLabel = Params.LIST_LABEL.replace("@", "Genes");
// for now users will have no way to get a ranked list for time series - no values available from maSigPro
//if(!project.data.isTimeCourseExpType()) {
lst.add(Params.lstRankedLists.get(Params.RankedList.DIUTRANS.ordinal()).name);
lst.add(Params.lstRankedLists.get(Params.RankedList.DIUPROT.ordinal()).name);
lst.add(Params.lstRankedLists.get(Params.RankedList.DIUTRANSEXT.ordinal()).name);
lst.add(Params.lstRankedLists.get(Params.RankedList.DIUPROTEXT.ordinal()).name);
lst.add(Params.lstRankedLists.get(Params.RankedList.DEA.ordinal()).name);
//}
}
else if(rbProteins.isSelected()) {
lstLabel = Params.LIST_LABEL.replace("@", "Proteins");
// for now users will have no way to get a ranked list for time series - no values available from maSigPro
//if(!project.data.isTimeCourseExpType()) {
lst.add(Params.lstRankedLists.get(Params.RankedList.DEA.ordinal()).name); // + " for Proteins");
//}
}
else {
lstLabel = Params.LIST_LABEL.replace("@", "Transcripts");
// for now users will have no way to get a ranked list for time series - no values available from maSigPro
//if(!project.data.isTimeCourseExpType()) {
lst.add(Params.lstRankedLists.get(Params.RankedList.DEA.ordinal()).name); // + " for Transcripts");
//}
}
lblListTest.setText(lstLabel);
lst.add(Params.lstRankedLists.get(Params.RankedList.FROMFILE.ordinal()).name);
for(String name : lst)
cb.getItems().add(name);
if(cb.getItems().size() > 0)
cb.getSelectionModel().select(0);
onRankedListChanged(cb, lbl, txt, btn);
}
private void onRankedListChanged(ChoiceBox cb, Label lbl, TextField txt, Button btn) {
// must use getSelectedIndex - called from changed listener
ArrayList<String> lst = new ArrayList<>();
if(cb.getSelectionModel().getSelectedIndex() != -1) {
int idx = Params.getRankedListIndexFromName((String)cb.getItems().get(cb.getSelectionModel().getSelectedIndex()));
Params.RankedList rl = Params.RankedList.valueOf(Params.lstRankedLists.get(idx).id);
switch(rl) {
case FROMFILE:
lbl.setDisable(false);
txt.setDisable(false);
btn.setDisable(false);
break;
default:
lbl.setDisable(true);
txt.setDisable(true);
btn.setDisable(true);
break;
}
}
annotationFeaturesOnSelectionChanged();
}
private void getRLFile(TextField txt) {
File f = getFileName();
if(f != null)
txt.setText(f.getPath());
}
private void getSetsFile() {
File f = getSetsFileName();
if(f != null)
txtSets.setText(f.getPath());
}
private File getFileName() {
FileChooser fileChooser = new FileChooser();
fileChooser.setTitle(("Select Ranked list File"));
fileChooser.getExtensionFilters().addAll(
new FileChooser.ExtensionFilter("Ranked list files", "*.txt", "*.tsv"),
new FileChooser.ExtensionFilter("All Files", "*.*"));
String expFolder = app.userPrefs.getImportRankedListGSEAFolder();
if(!expFolder.isEmpty()) {
File f = new File(expFolder);
if(f.exists() && f.isDirectory())
fileChooser.setInitialDirectory(f);
else
app.userPrefs.setImportRankedListGSEAFolder("");
}
File selectedFile = fileChooser.showOpenDialog(dialog.getOwner());
if(selectedFile!=null)
app.userPrefs.setImportRankedListGSEAFolder(selectedFile.getParent());
return selectedFile;
}
private File getSetsFileName() {
FileChooser fileChooser = new FileChooser();
fileChooser.setTitle(("Select Annotation Feature Sets File in GMT format (*.gmt)"));
fileChooser.getExtensionFilters().addAll(
new FileChooser.ExtensionFilter("Annotation feature sets files", "*.gmt"),
new FileChooser.ExtensionFilter("All Files", "*.*"));
File selectedFile = fileChooser.showOpenDialog(dialog.getOwner());
return selectedFile;
}
private HashMap<String, String> validate(Dialog dialog) {
HashMap<String, String> results = new HashMap<>();
String errmsg = "";
System.out.println("Validate dialog");
int idx = Params.getMethodListIdxByName((String) cbMethods.getSelectionModel().getSelectedItem());
results.put(Params.METHOD_PARAM, Params.lstMethods.get(idx).id);
// get analysis name
String txt = txtName.getText().trim();
if(!txt.isEmpty()) {
// check if not an existing parameter id
if(paramId.isEmpty()) {
// check that name is not already used
ArrayList<DataApp.EnumData> lstGSEAParams = project.data.analysis.getGSEAParamsList();
for(DataApp.EnumData data : lstGSEAParams) {
if(txt.toLowerCase().equals(data.name.toLowerCase())) {
errmsg = "The name specified is already in use.";
break;
}
}
}
if(errmsg.isEmpty())
results.put(Params.NAME_PARAM, txt);
}
else
errmsg = "You must provide a name for the analysis.";
if(!errmsg.isEmpty()) {
txtName.requestFocus();
results.put("ERRMSG", errmsg);
return results;
}
// get the data type
DataType dataType;
if(rbTrans.isSelected())
dataType = DataType.TRANS;
else if(rbProteins.isSelected())
dataType = DataType.PROTEIN;
else
dataType = DataType.GENE;
results.put(Params.DATATYPE_PARAM, dataType.name());
// get the ranked list
idx = Params.getRankedListIndexFromName((String)cbRankedLists1.getItems().get(cbRankedLists1.getSelectionModel().getSelectedIndex()));
String lsitId = Params.lstRankedLists.get(idx).id;
results.put(Params.RANKEDLIST1_PARAM, lsitId);
if(lsitId.equals(Params.RankedList.FROMFILE.name())) {
String filepath = txtRLFile1.getText().trim();
errmsg = checkRankedListFile(filepath, results);
if(errmsg.isEmpty())
results.put(Params.FROMFILE1_PARAM, filepath);
else
txtRLFile1.requestFocus();
}
else if(lsitId.equals(Params.RankedList.DEA.name())) {
if(!project.data.analysis.hasDEAData(dataType)) {
errmsg = "You do not have DEA results for selected ranked list.";
cbRankedLists1.requestFocus();
}
}
else if(lsitId.equals(Params.RankedList.DIUTRANS.name()) || lsitId.equals(Params.RankedList.DIUTRANSEXT.name())) {
if(!project.data.analysis.hasDIUDataTrans()) {
errmsg = "You do not have transcripts DIU results for selected test list.";
cbRankedLists1.requestFocus();
}
}
else if(lsitId.equals(Params.RankedList.DIUPROT.name()) || lsitId.equals(Params.RankedList.DIUPROTEXT.name())) {
if(!project.data.analysis.hasDIUDataProtein()) {
errmsg = "You do not have protein DIU results for selected test list.";
cbRankedLists1.requestFocus();
}
}
if(chkMulti.isSelected()){
results.put(Params.USEMULTI_PARAM, "TRUE");
// get the ranked list
idx = Params.getRankedListIndexFromName((String)cbRankedLists2.getItems().get(cbRankedLists2.getSelectionModel().getSelectedIndex()));
String lsitId2 = Params.lstRankedLists.get(idx).id;
if(lsitId.equals(lsitId2))
errmsg = "You can not have selected the same ranked list for a multidimensional mdgsa analysis.";
if(errmsg.isEmpty()){
results.put(Params.RANKEDLIST2_PARAM, lsitId2);
if(lsitId2.equals(Params.RankedList.FROMFILE.name())) {
String filepath = txtRLFile2.getText().trim();
errmsg = checkRankedListFile(filepath, results);
if(errmsg.isEmpty())
results.put(Params.FROMFILE2_PARAM, filepath);
else
txtRLFile1.requestFocus();
}
else if(lsitId2.equals(Params.RankedList.DEA.name())) {
if(!project.data.analysis.hasDEAData(dataType)) {
errmsg = "You do not have DEA results for selected ranked list.";
cbRankedLists2.requestFocus();
}
}
else if(lsitId2.equals(Params.RankedList.DIUTRANS.name()) || lsitId2.equals(Params.RankedList.DIUTRANSEXT.name())) {
if(!project.data.analysis.hasDIUDataTrans()) {
errmsg = "You do not have transcripts DIU results for selected test list.";
cbRankedLists2.requestFocus();
}
}
else if(lsitId2.equals(Params.RankedList.DIUPROT.name()) || lsitId2.equals(Params.RankedList.DIUPROTEXT.name())) {
if(!project.data.analysis.hasDIUDataProtein()) {
errmsg = "You do not have protein DIU results for selected test list.";
cbRankedLists2.requestFocus();
}
}
}
}
if(errmsg.isEmpty()) {
txt = txtSigValue.getText().trim();
if(txt.length() > 0) {
try {
Double val = Double.parseDouble(txt);
if(val >= DlgBase.DlgParams.MIN_PVAL_THRESHOLD && val <= DlgBase.DlgParams.MAX_PVAL_THRESHOLD)
results.put(Params.SIGVAL_PARAM, txt);
else
errmsg = "Invalid significance value entered (" + DlgBase.DlgParams.MIN_PVAL_THRESHOLD + " to " + DlgBase.DlgParams.MAX_PVAL_THRESHOLD + " allowed).";
} catch(Exception e) {
errmsg = "Invalid significance value number entered.";
}
}
else
errmsg = "You must enter a significance value.";
if(errmsg.isEmpty()) {
if(chkMulti.isSelected()){
//for multivariant just use GeneOntology
results.put(Params.FEATURE_PARAM, "GeneOntology");
}else{
// check if using annotation file features
if(rbFeatures.isSelected())
errmsg = tvFeatures.validate(Params.FEATURE_PARAM, results);
else {
// load annotation sets file if provided
String filepath = txtSets.getText().trim();
if(filepath.length() > 0) {
ArrayList<Utils.Set> lst = Utils.loadSetsFile(filepath);
if(!lst.isEmpty()) {
// let's prevent out of controls sets - need to find out what value is reasonable later!!!
if(lst.size() <= Params.MAX_NUM_SETS) {
int cnt = 0;
ArrayList<String> nflst = new ArrayList<>();
for(Utils.Set set : lst) {
for(String member : set.lstMembers) {
switch(dataType) {
case GENE:
if(project.data.hasGene(member))
cnt++;
else
nflst.add(member);
break;
}
}
}
// check if any genes found
if(cnt > 0) {
// check if missing genes
if(!nflst.isEmpty()) {
int badcnt = nflst.size();
int dspcnt = Math.min(25, badcnt);
String msg = "Non-matching " + app.data.getDataTypePlural(dataType.name()) + " found in custom sets:\n ";
for(int i = 0; i < dspcnt; i++) {
msg += nflst.get(i);
if(i < (dspcnt-2))
msg += ", ";
}
if(dspcnt < badcnt)
msg += "\nOnly showing the first " + dspcnt + app.data.getDataTypePlural(dataType.name()) + ".";
app.logInfo(msg);
String alertmsg = "Some of the " + app.data.getDataTypePlural(dataType.name()) + " specified in custom sets\nare not part of the project data\nand will be removed.\nDo you want to Proceeed?\n";
if(!app.ctls.alertConfirmation("Custom Annotation Sets", alertmsg, null))
errmsg = "Non-matching " + app.data.getDataTypePlural(dataType.name()) + " found in custom sets.";
}
}
else
errmsg = "No matching " + app.data.getDataTypePlural(dataType.name()) + " found in custom sets.";
}
else
errmsg = "Custom sets file exceeds limit of " + Params.MAX_NUM_SETS + " sets (" + lst.size() + ")";
}
else
errmsg = "Unable to load annotation sets data.";
if(errmsg.isEmpty())
results.put(Params.CUSTOMFILE_PARAM, filepath);
}
else
errmsg = "You must enter the annotation sets file path and name.";
}
}
}
else
txtSigValue.requestFocus();
}
if(!errmsg.isEmpty())
results.put("ERRMSG", errmsg);
return results;
}
// We want to provide meaningful messages to the user - so there is a lot of checking taking place
private String checkRankedListFile(String path, HashMap<String, String> results) {
String errmsg = "";
app.logInfo("Checking specified ranked list file: " + path);
if(path.length() > 0) {
try {
File f = new File(path);
if(f.exists()) {
long size = f.length();
if(size >= Params.MIN_RL_FILE_SIZE && size <= Params.MAX_RL_FILE_SIZE) {
if(f.canRead()) {
try (BufferedReader br = new BufferedReader(new FileReader(f))) {
String line = br.readLine();
if(line != null) {
if(!line.trim().isEmpty() && !line.startsWith("#")) {
String[] fields = line.split("\t");
if(fields.length >= 1) {
}
}
}
else
errmsg = "Unable to read ranked list file data.";
}
}
else
errmsg = "Ranked list file does not have read access. Check file permissions.";
}
else {
if(size > Params.MAX_RL_FILE_SIZE)
errmsg = "Ranked list file exceeds maximum size allowed of " + (Params.MAX_RL_FILE_SIZE/1000000) + "MB";
else
errmsg = "Ranked list file does not have sufficient data (" + size + "bytes).";
}
}
else
errmsg = "Unable to find specified Ranked list file.";
} catch(Exception e) {
errmsg = "Unable to open specified Ranked list file.";
}
}
else
errmsg = "You must specify the Ranked list file's location.";
if(!errmsg.isEmpty())
app.logInfo("Ranked list file check failed: " + errmsg);
else
app.logInfo("Ranked list file passed initial check.");
return errmsg;
}
//
// Data Classes
//
public static class Params extends DlgParams {
public static final String NAME_PARAM = "name";
public static final String DATATYPE_PARAM = "dataType";
public static final String RANKEDLIST1_PARAM = "rankedList1";
public static final String FROMFILE1_PARAM = "file1";
public static final String RANKEDLIST2_PARAM = "rankedList2";
public static final String FROMFILE2_PARAM = "file2";
public static final String SIGVAL_PARAM = "sigval";
public static final String CUSTOMFILE_PARAM = "customFile";
public static final String FEATURE_PARAM = "feature1";
private static final String METHOD_PARAM = "method";
private static final String USEMULTI_PARAM = "multi";
public static int MAX_NAME_LENGTH = 60;
public static final int MIN_RL_FILE_SIZE = 10;
public static final int MAX_RL_FILE_SIZE = 100000000;
public static final int MAX_NUM_SETS = 1000;
public static enum Method {
// all cases
MDGSA,
GOGLM
}
private static final List<MethodData> lstMethods = Arrays.asList(
new MethodData(Method.MDGSA.name(), "MDGSA"),
new MethodData(Method.GOGLM.name(), "GOglm")
);
private static final String LIST_LABEL = "@ Ranked List";
public static enum RankedList {
DIUTRANS, DIUTRANSEXT, DIUPROT, DIUPROTEXT, DEA, FROMFILE
}
private static final List<EnumData> lstRankedLists = Arrays.asList(
new EnumData(RankedList.DIUTRANS.name(), "Differential Isoform Usage Results (Transcripts)"),
new EnumData(RankedList.DIUTRANSEXT.name(), "DIU Analysis Results (Transcripts - including single isoform genes)"),
new EnumData(RankedList.DIUPROT.name(), "Differential Isoform Usage Results (Proteins)"),
new EnumData(RankedList.DIUPROTEXT.name(), "DIU Analysis Results (Proteins - including single isoform genes)"),
new EnumData(RankedList.DEA.name(), "Differential Expression Analysis Results"),
new EnumData(RankedList.FROMFILE.name(), "Use ranked list from file...")
);
private final DataApp.DataType dfltDataType = DataApp.DataType.GENE;
private final RankedList dfltRankedList1 = Params.RankedList.DIUTRANS;
private final RankedList dfltRankedList2 = Params.RankedList.DEA;
private final double dfltSigValue = 0.05;
private final String dfltUseMulti = "FALSE";
HashMap<String, HashMap<String, Object>> hmFeatures = new HashMap<>();
Method method;
public String name = "";
public DataApp.DataType dataType;
public RankedList rankedList1;
public RankedList rankedList2;
public String fromFile1 = "";
public String fromFile2 = "";
public double sigValue;
public String customFile = "";
public String paramId = "";
public String useMulti = "";
public Params() {
//Method dfltMethod = DlgGSEAnalysis.Params.Method.MDGSA;
Method dfltMethod = DlgGSEAnalysis.Params.Method.GOGLM;
method = dfltMethod;
name = "";
dataType = dfltDataType;
rankedList1 = dfltRankedList1;
rankedList2 = dfltRankedList2;
fromFile1 = "";
fromFile2 = "";
sigValue = dfltSigValue;
customFile = "";
useMulti = dfltUseMulti;
}
public Params(HashMap<String, String> hmParams) {
//Method dfltMethod = DlgGSEAnalysis.Params.Method.MDGSA;
Method dfltMethod = DlgGSEAnalysis.Params.Method.GOGLM;
method = hmParams.containsKey(METHOD_PARAM)? Method.valueOf(hmParams.get(METHOD_PARAM)) : dfltMethod;
name = hmParams.containsKey(NAME_PARAM)? hmParams.get(NAME_PARAM) : "";
useMulti = hmParams.containsKey(USEMULTI_PARAM)? hmParams.get(USEMULTI_PARAM) : dfltUseMulti;
dataType = hmParams.containsKey(DATATYPE_PARAM)? DataApp.DataType.valueOf(hmParams.get(DATATYPE_PARAM)) : dfltDataType;
rankedList1 = hmParams.containsKey(RANKEDLIST1_PARAM)? RankedList.valueOf(hmParams.get(RANKEDLIST1_PARAM)) : dfltRankedList1;
rankedList2 = hmParams.containsKey(RANKEDLIST2_PARAM)? RankedList.valueOf(hmParams.get(RANKEDLIST2_PARAM)) : dfltRankedList2;
fromFile2 = hmParams.containsKey(FROMFILE2_PARAM)? hmParams.get(FROMFILE2_PARAM) : "";
fromFile1 = hmParams.containsKey(FROMFILE1_PARAM)? hmParams.get(FROMFILE1_PARAM) : "";
sigValue = hmParams.containsKey(SIGVAL_PARAM)? Double.parseDouble(hmParams.get(SIGVAL_PARAM)) : dfltSigValue;
customFile = hmParams.containsKey(CUSTOMFILE_PARAM)? hmParams.get(CUSTOMFILE_PARAM) : "";
this.hmFeatures = new HashMap<>();
if(hmParams.containsKey(FEATURE_PARAM)) {
String[] fields = hmParams.get(FEATURE_PARAM).trim().split("\t");
if(fields.length > 0) {
HashMap<String, Object> hm = new HashMap<>();
hmFeatures.put(fields[0].trim(), hm);
for(int i = 1; i < fields.length; i++)
hm.put(fields[i].trim(), null);
}
}
}
@Override
public HashMap<String, String> getParams() {
HashMap<String, String> hm = new HashMap<>();
hm.put(METHOD_PARAM, method.name());
hm.put(NAME_PARAM, name);
hm.put(USEMULTI_PARAM, useMulti);
hm.put(DATATYPE_PARAM, dataType.name());
hm.put(RANKEDLIST1_PARAM, rankedList1.name());
if(!fromFile1.isEmpty())
hm.put(FROMFILE1_PARAM, fromFile1);
hm.put(RANKEDLIST2_PARAM, rankedList2.name());
if(!fromFile2.isEmpty())
hm.put(FROMFILE2_PARAM, fromFile2);
if(!customFile.isEmpty())
hm.put(CUSTOMFILE_PARAM, customFile);
hm.put(SIGVAL_PARAM, "" + sigValue);
for(String db : hmFeatures.keySet()) {
String features = db;
HashMap<String, Object> hmCats = hmFeatures.get(db);
for(String cat : hmCats.keySet())
features += "\t" + cat;
hm.put(FEATURE_PARAM, features);
break;
}
return hm;
}
public String getFeaturesName() {
String source = "";
String features = "";
// NOTE: only single source allowed
for(String src : hmFeatures.keySet()) {
source = src;
HashMap<String, Object> hmSF = hmFeatures.get(src);
for(String feature : hmSF.keySet())
features += (features.isEmpty()? " [" : ", ") + feature;
features += features.isEmpty()? "" : "]";
break;
}
return source + features;
}
// base class implements boolean save(String filepath)
//
// Static functions
//
public static Params load(String filepath) {
HashMap<String, String> params = new HashMap<>();
Utils.loadParams(params, filepath);
return (new Params(params));
}
private static int getMethodCboIdx(String id) {
int idx = 0;
for(MethodData ed : lstMethods) {
if(ed.id.equals(id))
break;
idx++;
}
if(idx >= lstMethods.size())
idx = 0;
System.out.println("We can't run the selected method. Default method is selected.");
return idx;
}
private static int getMethodListIdxByName(String name) {
int idx = 0;
for(MethodData ed : lstMethods) {
if(ed.name.equals(name))
break;
idx++;
}
if(idx >= lstMethods.size()){
idx = 0;
System.out.println("We can't run the selected method. Default method is selected.");
}
return idx;
}
private static int getRankedListIndexFromID(String id) {
int idx = 0;
for(EnumData ed : Params.lstRankedLists) {
if(ed.id.equals(id))
break;
idx++;
}
if(idx >= Params.lstRankedLists.size())
idx = 0;
return idx;
}
private static int getRankedListIndexFromName(String name) {
int idx = 0;
for(EnumData ed : Params.lstRankedLists) {
if(ed.name.equals(name))
break;
idx++;
}
if(idx >= Params.lstRankedLists.size())
idx = 0;
return idx;
}
}
protected static class MethodData implements Comparable<MethodData> {
public String id;
public String name;
public DataApp.ExperimentType expType;
public MethodData(String id, String name, DataApp.ExperimentType expType) {
this.id = id;
this.name = name;
this.expType = expType;
}
public MethodData(String id, String name) {
this.id = id;
this.name = name;
}
@Override
public int compareTo(MethodData entry) {
return (id.compareToIgnoreCase(entry.id));
}
}
}