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DlgDPAnalysis.java
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DlgDPAnalysis.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.scene.control.*;
import javafx.stage.Window;
import tappas.DataApp.EnumData;
import java.util.*;
import static tappas.DataAnnotation.POLYA_FEATURE;
import static tappas.DataAnnotation.STRUCTURAL_SOURCE;
/**
*
* @author Pedro Salguero - [email protected]
*/
public class DlgDPAnalysis extends DlgBase {
TextField txtSigValue, txtFiltValue, txtLength, txtK;
ChoiceBox cbMethods, cbDegree, cbType, cbFiltering;
CheckBox chkFilt, chkMclust;
Label lblDegree, lblFilter, lblFilterBy, lblFilterDefault, lblType, lblK;
ArrayList<String> lstTerms;
DataApp.ExperimentType expType = project.data.getExperimentType();
public DlgDPAnalysis(Project project, Window window) {
super(project, window);
}
public Params showAndWait(Params dfltParams) {
String fxml = project.data.isTimeCourseExpType()? "DPAParams_TimeCourse.fxml" : "DPAParams.fxml";
if(createDialog(fxml, "Differential PolyAdenylation Analysis Parameters", true, "Help_Dlg_DPA.html")) {
if(dfltParams == null)
dfltParams = new Params(project);
// get control objects
txtSigValue = (TextField) scene.lookup("#txtThreshold");
txtLength = (TextField) scene.lookup("#txtLength");
cbMethods = (ChoiceBox) scene.lookup("#cbMethods");
cbDegree = (ChoiceBox) scene.lookup("#cbDegree");
cbType = (ChoiceBox) scene.lookup("#cbType");
lblDegree = (Label) scene.lookup("#lblDegree");
lblType = (Label) scene.lookup("#lblType");
txtFiltValue = (TextField) scene.lookup("#txtFiltValue");
lblFilter = (Label) scene.lookup("#lblFilter");
lblFilterBy = (Label) scene.lookup("#lblFilterBy");
lblFilterDefault = (Label) scene.lookup("#lblFilterDefault");
chkFilt = (CheckBox) scene.lookup("#chkFilt");
cbFiltering = (ChoiceBox) scene.lookup("#cbFiltering");
lblK = (Label) scene.lookup("#lblK");
txtK = (TextField) scene.lookup("#txtK");
chkMclust = (CheckBox) scene.lookup("#chkMclust");
// setup dialog
setProjectName();
for(MethodData method : Params.lstMethods){
if(method.expType.equals(expType))
cbMethods.getItems().add(method.name);
}
cbMethods.getSelectionModel().select(Params.getMethodCboIdx(dfltParams.method.name(), expType));
txtSigValue.setText("" + dfltParams.sigValue);
txtLength.setText("" + dfltParams.lengthValue);
int maxDegree = Math.max(1, project.data.getTimePoints() - 1);
//Visible options - CaseControl is another fxml
//all
if(dfltParams.filter) {
chkFilt.setSelected(true);
}else{
chkFilt.setSelected(false);
}
txtFiltValue.setText("" + dfltParams.filterFC);
txtFiltValue.setVisible(true);
lblFilter.setVisible(true);
lblFilterBy.setVisible(true);
lblFilterDefault.setVisible(true);
cbFiltering.setVisible(true);
txtFiltValue.disableProperty().bind(chkFilt.selectedProperty().not());
lblFilterBy.disableProperty().bind(chkFilt.selectedProperty().not());
cbFiltering.disableProperty().bind(chkFilt.selectedProperty().not());
for(EnumData tp : Params.lstFiltering)
cbFiltering.getItems().add(tp.name);
cbFiltering.getSelectionModel().select(Params.getFilterCboIdx(dfltParams.filteringType.name()));
lblFilterBy.setText(dfltParams.filteringType.name().equals("FOLD")? "Fold expression difference:" : "Prop. expression difference:");
cbFiltering.valueProperty().addListener((obs, oldValue, newValue) -> {
System.out.println(newValue);
lblFilterBy.setText(newValue.equals("Fold filtering")? "Fold expression difference:" : "Prop. expression difference:");
lblFilterDefault.setText(newValue.equals("Fold filtering")? "(default: 2)" : "(default: 0.2)");
txtFiltValue.promptTextProperty().set(newValue.equals("Fold filtering")? "1.0 to 99.0" : "0.01 to 0.99");
txtFiltValue.setText(newValue.equals("Fold filtering")? "2.0" : "0.2");
});
if(project.data.isTimeCourseExpType()) {
cbDegree.setVisible(true);
lblDegree.setVisible(true);
lblK.setVisible(true);
txtK.setVisible(true);
chkMclust.setVisible(true);
txtK.setText("" + dfltParams.k);
chkMclust.selectedProperty().addListener((ObservableValue<? extends Boolean> ov, Boolean oldValue, Boolean newValue) -> {
lblK.setText(newValue? "Max K clusters:" : "K clusters:");
});
for(int i = 1; i <= maxDegree; i++)
cbDegree.getItems().add("" + i);
if((dfltParams.degree - 1) < maxDegree)
cbDegree.getSelectionModel().select(dfltParams.degree - 1);
else
cbDegree.getSelectionModel().select(maxDegree - 1);
}
if(project.data.isSingleTimeSeriesExpType()) {
cbType.setVisible(false);
lblType.setVisible(false);
}else if(project.data.isMultipleTimeSeriesExpType()){
cbType.setVisible(true);
lblType.setVisible(true);
for(EnumData tp : Params.lstType)
cbType.getItems().add(tp.name);
cbType.getSelectionModel().select(Params.getTypeListIdx(dfltParams.strictType.name(), Params.lstType));
}
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;
});
Optional<HashMap> result = dialog.showAndWait();
if(result.isPresent())
return(new Params(result.get(), project));
}
return null;
}
private HashMap<String, String> validate(Dialog dialog) {
HashMap<String, String> results = new HashMap<>();
String errmsg = "";
int tidx;
// there is no way to screw up the choice boxes - must select a value
// so all we need to do is check for a valid threshold value
int idx = Params.getMethodListIdxByName((String) cbMethods.getSelectionModel().getSelectedItem(), expType);
results.put(Params.METHOD_PARAM, Params.lstMethods.get(idx).id);
String txt = "";
// Course time
if(project.data.isTimeCourseExpType()) {
if(errmsg.isEmpty()){
results.put(Params.DEGREE_PARAM, (String) cbDegree.getSelectionModel().getSelectedItem());
if(project.data.isMultipleTimeSeriesExpType()){
tidx = Params.getTypeListByName((String) cbType.getSelectionModel().getSelectedItem(), Params.lstType);
results.put(Params.STRICTTYPE_PARAM, Params.lstType.get(tidx).id);
}
}
if(errmsg.isEmpty()) {
// check for a valid K value
txt = txtK.getText().trim();
if(txt.length() > 0) {
try {
Double val = Double.parseDouble(txt);
if(val >= Params.MIN_K && val <= Params.MAX_K) {
results.put(Params.K_PARAM, txt);
}
else
errmsg = "Invalid K clusters value entered (" + Params.MIN_K + " to " + Params.MAX_K + " allowed).";
} catch(Exception e) {
errmsg = "Invalid K clusters value number entered.";
}
}
else
errmsg = "You must enter the K clusters value.";
if(errmsg.isEmpty()) {
results.put(Params.MCLUST_PARAM, chkMclust.isSelected()? "true" : "false");
}
else
txtK.requestFocus();
}
}
//All
//filter
results.put(Params.FILTER_PARAM, chkFilt.isSelected()? Boolean.TRUE.toString() : Boolean.FALSE.toString());
if(chkFilt.isSelected()) {
txt = txtFiltValue.getText().trim();
if(txt.length() > 0) {
try {
tidx = Params.getTypeListByName((String) cbFiltering.getSelectionModel().getSelectedItem(), Params.lstFiltering);
results.put(Params.FILTERINGTYPE_PARAM, Params.lstFiltering.get(tidx).id);
Double val = Double.parseDouble(txt);
if(Params.lstFiltering.get(tidx).id.equals("FOLD")){
if(val >= Params.MIN_FILTER && val <= Params.MAX_FILTER) {
results.put(Params.FILTERFC_PARAM, txt);
}
else
errmsg = "Invalid filter value entered (" + Params.MIN_FILTER + " to " + Params.MAX_FILTER + " allowed).";
}else if(val >= Params.MIN_FILTER_PROP && val <= Params.MAX_FILTER_PROP){
results.put(Params.FILTERFC_PARAM, txt);
}else
errmsg = "Invalid filter value entered (" + Params.MIN_FILTER_PROP + " to " + Params.MAX_FILTER_PROP + " allowed).";
} catch(Exception e) {
errmsg = "Invalid filter value number entered.";
}
}
else
errmsg = "You must enter a filter value.";
if(!errmsg.isEmpty()) {
txtFiltValue.requestFocus();
results.put("ERRMSG", errmsg);
}
}else{
results.put(Params.FILTERFC_PARAM, "0");
}
//sigValue
txt = txtSigValue.getText().trim();
if(txt.length() > 0) {
try {
Double val = Double.parseDouble(txt);
if(val >= Params.MIN_PVAL_THRESHOLD && val <= Params.MAX_PVAL_THRESHOLD) {
results.put(Params.SIGVAL_PARAM, txt);
}
else
errmsg = "Invalid significance value entered (" + Params.MIN_PVAL_THRESHOLD + " to " + Params.MAX_PVAL_THRESHOLD + " allowed).";
} catch(Exception e) {
errmsg = "Invalid significance value number entered.";
}
}
else
errmsg = "You must enter a significance value.";
if(!errmsg.isEmpty()) {txtSigValue.requestFocus();
results.put("ERRMSG", errmsg);
}else{
txt = txtLength.getText().trim();
if(txt.length() > 0) {
try {
int val = Integer.parseInt(txt);
if(val >= Params.MIN_PVAL_LENGTH && val <= Params.MAX_PVAL_LENGTH) {
results.put(Params.LENGTH_PARAM, txt);
}
else
errmsg = "Invalid length value entered (" + Params.MIN_PVAL_LENGTH + " to " + Params.MAX_PVAL_LENGTH + " allowed).";
} catch(Exception e) {
errmsg = "Invalid length value number entered.";
}
}
else
errmsg = "You must enter a length value.";
}
return results;
}
public static class Params extends DlgParams {
public static enum Method {
// case-control
DEXSEQ, //EDGER,
// time course
MASIGPRO
}
private static final List<MethodData> lstMethods = Arrays.asList(
//new MethodData(Method.EDGER.name(), "edgeR", DataApp.ExperimentType.Two_Group_Comparison),
new MethodData(Method.DEXSEQ.name(), "DEXSeq", DataApp.ExperimentType.Two_Group_Comparison),
new MethodData(Method.MASIGPRO.name(), "maSigPro", DataApp.ExperimentType.Time_Course_Multiple),
new MethodData(Method.MASIGPRO.name(), "maSigPro", DataApp.ExperimentType.Time_Course_Single)
);
public static enum StrictType {
// time course
LESSSTRICT, MORESTRICT
}
public static enum FilteringType {
FOLD, PROP
}
private static final List<EnumData> lstType = Arrays.asList(
new EnumData(StrictType.LESSSTRICT.name(), "Less strict"),
new EnumData(StrictType.MORESTRICT.name(), "More strict")
);
private static final List<EnumData> lstFiltering = Arrays.asList(
new EnumData(FilteringType.FOLD.name(), "Fold filtering"),
new EnumData(FilteringType.PROP.name(), "Proportion filtering")
);
// if time course experiment
public static final int MIN_K = 1;
public static final int MAX_K = 30;
public static final String K_PARAM = "k";
public static final String MCLUST_PARAM = "mclust";
private static final int dfltK = 9;
private static final boolean dfltMclust = false;
public static int MAX_DEAFULT_DEGREE = 3;
private static final String DEGREE_PARAM = "polynomial";
FilteringType dfltFilteringType = FilteringType.FOLD;
private static final String FILTERINGTYPE_PARAM = "filteringType";
private static final String FILTER_PARAM = "filter";
private static final String FILTERFC_PARAM = "filter_FC";
public static double MIN_FILTER = 1.0;
public static double MAX_FILTER = 99.0;
public static double MIN_FILTER_PROP = 0.01;
public static double MAX_FILTER_PROP = 0.99;
private final double dfltFiltFCValue = 2.0;
// if multiple time course experiment
private static final String STRICTTYPE_PARAM = "strictType";
// shared by all
private static final String METHOD_PARAM = "method";
public static final String USING_PARAM = "using";
private static final String SIGVAL_PARAM = "sigval";
private static final String LENGTH_PARAM = "length";
public static final String FEATURE_PARAM = "feature";
//SourceFeature
public static final String source = STRUCTURAL_SOURCE;
public static final String feature = POLYA_FEATURE;
public String getSource(){return this.source;}
public String getFeature(){return this.feature;}
final static int MIN_PVAL_LENGTH = 1;
final static int MAX_PVAL_LENGTH = 160;
public static final int MAX_FEATURES = 99;
private Method dfltMethod = Method.DEXSEQ;
private double dfltSigValue = 0.05;
private int dfltLengthValue = 60;
Method method;
StrictType strictType;
double sigValue;
int lengthValue, degree, k;
boolean filter, mclust;
double filterFC;
FilteringType filteringType;
DataApp.ExperimentType expType;
public Params(Project project) {
this.expType = project.data.getExperimentType();
boolean dfltFilter = expType.equals(DataApp.ExperimentType.Two_Group_Comparison)? false : true;
Method dfltMethod = expType.equals(DataApp.ExperimentType.Two_Group_Comparison)? DlgDPAnalysis.Params.Method.DEXSEQ : DlgDPAnalysis.Params.Method.MASIGPRO;
StrictType dfltStrictType = expType.equals(DataApp.ExperimentType.Time_Course_Multiple)? StrictType.LESSSTRICT : null;
int dfltDegree = Math.min(MAX_DEAFULT_DEGREE, Math.max(1, project.data.getTimePoints() - 1));
FilteringType dfltFilteringType = DlgDPAnalysis.Params.FilteringType.FOLD;
this.method = dfltMethod;
this.sigValue = dfltSigValue;
this.lengthValue = dfltLengthValue;
this.degree = dfltDegree;
this.filter = dfltFilter;
this.filterFC = dfltFiltFCValue;
this.filteringType = dfltFilteringType;
this.strictType = dfltStrictType;
this.k = dfltK;
this.mclust = dfltMclust;
}
public Params(HashMap<String, String> hmParams, Project project) {
this.expType = project.data.getExperimentType();
boolean dfltFilter = expType.equals(DataApp.ExperimentType.Two_Group_Comparison)? false : true;
Method dfltMethod = expType.equals(DataApp.ExperimentType.Two_Group_Comparison)? DlgDPAnalysis.Params.Method.DEXSEQ : DlgDPAnalysis.Params.Method.MASIGPRO;
StrictType dfltStrictType = expType.equals(DataApp.ExperimentType.Time_Course_Multiple)? StrictType.LESSSTRICT : null;
int dfltDegree = Math.min(MAX_DEAFULT_DEGREE, Math.max(1, project.data.getTimePoints() - 1));
FilteringType dfltFilteringType = DlgDPAnalysis.Params.FilteringType.FOLD;
if(hmParams.isEmpty()) {
this.filter = dfltFilter;
this.filterFC = dfltFiltFCValue;
this.filteringType = dfltFilteringType;
this.degree = dfltDegree;
this.strictType = dfltStrictType;
this.method = dfltMethod;
this.sigValue = dfltSigValue;
this.lengthValue = dfltLengthValue;
this.k = dfltK;
this.mclust = dfltMclust;
}
else {
this.filter = hmParams.containsKey(FILTER_PARAM)? Boolean.valueOf(hmParams.get(FILTER_PARAM)) : dfltFilter;
this.filterFC = hmParams.containsKey(FILTERFC_PARAM)? Double.parseDouble(hmParams.get(FILTERFC_PARAM)) : dfltFiltFCValue;
this.filteringType = hmParams.containsKey(FILTERINGTYPE_PARAM)? FilteringType.valueOf(hmParams.get(FILTERINGTYPE_PARAM)) : dfltFilteringType;
this.degree = hmParams.containsKey(DEGREE_PARAM)? Integer.parseInt(hmParams.get(DEGREE_PARAM)) : dfltDegree;
this.strictType = hmParams.containsKey(STRICTTYPE_PARAM)? StrictType.valueOf(hmParams.get(STRICTTYPE_PARAM)) : null;
// these parameters must be provided by all if HashMap has values - exception otherwise
this.method = Method.valueOf(hmParams.get(METHOD_PARAM));
this.lengthValue = hmParams.containsKey(LENGTH_PARAM)? Integer.parseInt(hmParams.get(LENGTH_PARAM)) : dfltLengthValue;
this.sigValue = Double.parseDouble(hmParams.get(SIGVAL_PARAM));
this.k = hmParams.containsKey(K_PARAM)? Integer.parseInt(hmParams.get(K_PARAM)) : dfltK;
this.mclust = hmParams.containsKey(MCLUST_PARAM)? Boolean.valueOf(hmParams.get(MCLUST_PARAM).toLowerCase()) : dfltMclust;
}
}
public HashMap<String, String> getParams(Project project) {
HashMap<String, String> hm = new HashMap<>();
// get shared parameters
hm.put(METHOD_PARAM, method.name());
hm.put(SIGVAL_PARAM, "" + sigValue);
hm.put(LENGTH_PARAM, "" + lengthValue);
hm.put(FILTER_PARAM, "" + Boolean.toString(filter));
if(filter)
hm.put(FILTERFC_PARAM, "" + filterFC);
if(filteringType != null)
hm.put(FILTERINGTYPE_PARAM, "" + filteringType.name());
// only get parameters if relevant
if(project.data.isTimeCourseExpType()) {
hm.put(DEGREE_PARAM, "" + degree);
if(project.data.isMultipleTimeSeriesExpType()) {
if(strictType != null)
hm.put(STRICTTYPE_PARAM, "" + strictType.name());
}
hm.put(K_PARAM, "" + k);
hm.put(MCLUST_PARAM, Boolean.toString(mclust));
}
return hm;
}
// add save function to only save relevant experiment type parameters
public boolean save(String filepath, Project project) {
return Utils.saveParams(getParams(project), filepath);
}
//
// Static functions
//
public static Params load(String filepath, Project project) {
HashMap<String, String> params = new HashMap<>();
Utils.loadParams(params, filepath);
return (new Params(params, project));
}
private static int getMethodCboIdx(String id, DataApp.ExperimentType expType) {
int idx = 0;
int size = 0;
for(MethodData ed : lstMethods) {
if(ed.expType.equals(expType))
size++;
}
for(MethodData ed : lstMethods) {
if(ed.expType.equals(expType)) {
if(ed.id.equals(id))
break;
idx++;
}
}
if(idx >= size)
idx = 0;
return idx;
}
private static int getFilterCboIdx(String id) {
int idx = 0;
for(EnumData ed : lstFiltering) {
if(ed.id.equals(id)){
break;
}
idx++;
}
return idx;
}
private static int getMethodListIdxByName(String name, DataApp.ExperimentType expType) {
int idx = 0;
for(MethodData ed : lstMethods) {
if(ed.expType.equals(expType)) {
if(ed.name.equals(name))
break;
}
idx++;
}
if(idx >= lstMethods.size())
idx = 0;
return idx;
}
private static int getTypeListByName(String id, List<EnumData> lst) {
int idx = 0;
for(EnumData ed : lst) {
if(ed.name.equals(id))
break;
idx++;
}
if(idx >= lst.size())
idx = 0;
return idx;
}
private static int getTypeListIdx(String id, List<EnumData> lst) {
int idx = 0;
for(EnumData ed : lst) {
if(ed.id.equals(id))
break;
idx++;
}
if(idx >= lst.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;
}
@Override
public int compareTo(MethodData entry) {
return (id.compareToIgnoreCase(entry.id));
}
}
}