v1.0.7

Analyses - Fixed DFI for Single Time series - Fixed DEA for Single Time series - FEA now has the option to select all the features in one click General -RBPs feature now are showed in Transcript View -GO annotation has been updated (February 01 2021). -Miscellaneous changes.
ConesaLab · Apr 5, 2021 · dda2cc5 · dda2cc5
1 parent 80ba4ec
commit dda2cc5
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Showing 7 changed files with 11,993 additions and 11,427 deletions.
diff --git a/DlgFEAnalysis.java b/DlgFEAnalysis.java
@@ -6,6 +6,7 @@
 package tappas;
 
 import javafx.beans.value.ObservableValue;
+import javafx.collections.ObservableList;
 import javafx.scene.control.*;
 import javafx.stage.FileChooser;
 import javafx.stage.Window;
@@ -28,6 +29,7 @@ public class DlgFEAnalysis extends DlgBase {
     Label lblBkgndSelection;
     TextField txtName, txtSigValue, txtSamplingCnt;
     ChoiceBox cbCompare, cbMethod, cbUseWOCat;
+    Hyperlink lnkClearAll, lnkCheckAll;
     TextField txtTestFile, txtBkgndFile;
     Button btnTestFile, btnBkgndFile;
     RadioButton rbGenes, rbProteins, rbTrans;
@@ -65,6 +67,9 @@ public Params showAndWait(Params dfltParams) {
             cbMethod = (ChoiceBox) scene.lookup("#cbMethod");
             cbUseWOCat = (ChoiceBox) scene.lookup("#cbUseWOCat");
             TreeView tvf = (TreeView) scene.lookup("#tvFeatures");
+
+            lnkClearAll = (Hyperlink) scene.lookup("#lnkClearAll");
+            lnkCheckAll = (Hyperlink) scene.lookup("#lnkCheckAll");
             Label lblSamplingCnt = (Label) scene.lookup("#lblSamplingCnt");
 
             // setup dialog
@@ -110,7 +115,22 @@ else if(dfltParams.dataType.equals(DataType.TRANS))
                 txtSamplingCnt.setDisable(samdis1);
             });
             onDataTypeChange();
-
+
+            // setup database categories
+            lnkClearAll.setOnAction((event) -> {
+                if(tvf.isDisable())
+                    clearAllFeatures(tvf);
+                else
+                    clearAllFeatures(tvf);
+            });
+
+            lnkCheckAll.setOnAction((event) -> {
+                if(tvf.isDisable())
+                    checkAllFeatures(tvf);
+                else
+                    checkAllFeatures(tvf);
+            });
+
             // set test list
             int idx = Params.getTestListIndexFromID(dfltParams.testList.name());
             for(int i = 0; i < cbTestLists.getItems().size(); i++) {
@@ -172,6 +192,34 @@ else if(dfltParams.dataType.equals(DataType.TRANS))
     //
     // Internal Functions
     //
+    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() {
         ArrayList<String> lstTest = new ArrayList<>();
         ArrayList<String> lstBkgnd = new ArrayList<>();

diff --git a/DlgGSEAnalysis.java b/DlgGSEAnalysis.java
@@ -6,6 +6,7 @@
 package tappas;
 
 import javafx.beans.value.ObservableValue;
+import javafx.collections.ObservableList;
 import javafx.scene.control.*;
 import javafx.stage.FileChooser;
 import javafx.stage.Window;
@@ -28,6 +29,7 @@ public class DlgGSEAnalysis extends DlgBase {
     Button btnRLFile1, btnRLFile2, btnSets;
     RadioButton rbGenes, rbProteins, rbTrans, rbFeatures, rbSets;
     ChoiceBox cbRankedLists1, cbRankedLists2, cbMethods;
+//    Hyperlink lnkClearAll, lnkCheckAll;
     TreeViewFeatures tvFeatures;
     CheckBox chkMulti;
 
@@ -67,6 +69,9 @@ public Params showAndWait(Params dfltParams) {
             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;
@@ -157,7 +162,9 @@ else if(dfltParams.dataType.equals(DataType.TRANS))
 
             btnSets.setOnAction((event) -> { getSetsFile(); });
 
-            // setup 
+            // setup
+            // setup database categories
+
             chkMulti.selectedProperty().addListener((ObservableValue<? extends Boolean> ov, Boolean oldValue, Boolean newValue) -> {
                 if(newValue){
                     lblRank2.setDisable(false);
@@ -222,13 +229,57 @@ else if(dfltParams.dataType.equals(DataType.TRANS))
                     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();

diff --git a/dialogs/FEAParams.fxml b/dialogs/FEAParams.fxml
@@ -1,10 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<?import java.lang.*?>
+<?import javafx.geometry.*?>
 <?import javafx.geometry.Insets?>
 <?import javafx.scene.control.*?>
 <?import javafx.scene.layout.*?>
 <?import javafx.scene.text.*?>
-<AnchorPane id="AnchorPane" maxWidth="800.0" prefHeight="625.0" prefWidth="800.0" xmlns="http://javafx.com/javafx/8" xmlns:fx="http://javafx.com/fxml/1">
+
+<AnchorPane id="AnchorPane" maxWidth="800.0" prefHeight="601.0" prefWidth="800.0" xmlns="http://javafx.com/javafx/8" xmlns:fx="http://javafx.com/fxml/1">
    <children>
       <Label fx:id="lblMsg" alignment="CENTER" layoutX="5.0" layoutY="506.0" prefWidth="461.0" textFill="ORANGERED" AnchorPane.bottomAnchor="-12.0" AnchorPane.leftAnchor="5.0" AnchorPane.rightAnchor="5.0" />
       <Pane prefHeight="60.0" prefWidth="474.0" style="-fx-border-color: lightgray; -fx-border-radius: 5;" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="60.0">
@@ -67,9 +70,9 @@
             <Label fx:id="lblProjectName" alignment="CENTER" prefHeight="15.0" prefWidth="510.0" text="..." AnchorPane.leftAnchor="10.0" AnchorPane.rightAnchor="10.0" AnchorPane.topAnchor="9.0" />
          </children>
       </AnchorPane>
-      <Pane layoutY="430.0" maxWidth="350.0" minWidth="350.0" prefHeight="155.0" prefWidth="350.0" style="-fx-border-color: lightgray; -fx-border-radius: 5;" AnchorPane.leftAnchor="0.0" AnchorPane.topAnchor="430.0">
+      <Pane layoutY="419.0" maxWidth="350.0" minWidth="350.0" prefHeight="170.0" prefWidth="350.0" style="-fx-border-color: lightgray; -fx-border-radius: 5;" AnchorPane.leftAnchor="0.0" AnchorPane.topAnchor="419.0">
          <children>
-            <Label layoutX="10.0" layoutY="135.0" prefHeight="14.0" prefWidth="350.0" text="You may select one or more features from a single source" textFill="DARKGRAY">
+            <Label layoutX="10.0" layoutY="133.0" prefHeight="34.0" prefWidth="211.0" text="You may select one or more features from&#10;a single source" textFill="DARKGRAY">
                <font>
                   <Font size="11.0" />
                </font>
@@ -85,14 +88,16 @@
                   <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
                </rowConstraints>
             </GridPane>
+            <Hyperlink fx:id="lnkCheckAll" layoutX="283.0" layoutY="145.0" text="Check All" />
+            <Hyperlink fx:id="lnkClearAll" layoutX="221.0" layoutY="145.0" text="Clear All" />
          </children>
       </Pane>
-      <Label layoutX="10.0" layoutY="420.0" styleClass="textDlgSection" stylesheets="@../Style.css" text="Annotation Feature(s)" AnchorPane.leftAnchor="10.0" AnchorPane.topAnchor="420.0">
+      <Label layoutX="10.0" layoutY="409.0" styleClass="textDlgSection" stylesheets="@../Style.css" text="Annotation Feature(s)" AnchorPane.leftAnchor="10.0" AnchorPane.topAnchor="409.0">
          <font>
             <Font size="16.0" />
          </font>
       </Label>
-      <Pane layoutX="380.0" layoutY="430.0" maxWidth="420.0" minWidth="420.0" prefHeight="155.0" prefWidth="420.0" style="-fx-border-color: lightgray; -fx-border-radius: 5;" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="430.0">
+      <Pane layoutX="380.0" layoutY="419.0" maxWidth="420.0" minWidth="420.0" prefHeight="170.0" prefWidth="420.0" style="-fx-border-color: lightgray; -fx-border-radius: 5;" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="419.0">
          <children>
             <GridPane layoutX="10.0" layoutY="20.0" prefHeight="125.0" prefWidth="400.0">
                <children>
@@ -126,7 +131,7 @@
                </rowConstraints>
             </GridPane>
          </children></Pane>
-      <Label layoutX="389.0" layoutY="420.0" styleClass="textDlgSection" stylesheets="@../Style.css" text="Analysis Parameters" AnchorPane.leftAnchor="389.0" AnchorPane.topAnchor="420.0">
+      <Label layoutX="389.0" layoutY="409.0" styleClass="textDlgSection" stylesheets="@../Style.css" text="Analysis Parameters" AnchorPane.leftAnchor="389.0" AnchorPane.topAnchor="409.0">
          <font>
             <Font size="16.0" />
          </font>

diff --git a/dialogs/GSEAParams.fxml b/dialogs/GSEAParams.fxml
@@ -1,8 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
+<?import java.lang.*?>
 <?import javafx.scene.control.*?>
 <?import javafx.scene.layout.*?>
 <?import javafx.scene.text.*?>
+
 <AnchorPane id="AnchorPane" prefHeight="775.0" prefWidth="745.0" xmlns="http://javafx.com/javafx/8" xmlns:fx="http://javafx.com/fxml/1">
    <children>
       <Pane layoutY="697.0" prefHeight="50.0" prefWidth="800.0" style="-fx-border-color: lightgray; -fx-border-radius: 5;" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="697.0">