validation + Control refactoring

compomics · Mar 3, 2018 · c9f102e · c9f102e
1 parent d5fcd22
commit c9f102e
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Showing 16 changed files with 713 additions and 373 deletions.
diff --git a/src/main/java/com/compomics/coss/Controller/MainFrameController.java b/src/main/java/com/compomics/coss/Controller/MainFrameController.java
diff --git a/src/main/java/com/compomics/coss/Controller/Validation.java b/src/main/java/com/compomics/coss/Controller/Validation.java
@@ -10,6 +10,7 @@
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
+import org.apache.avro.generic.GenericData;
 
 /**
  *
@@ -21,27 +22,28 @@ public Validation() {
 
     }
 
-    public void compareNmerge(List<ArrayList<ComparisonResult>> targetResult, List<ArrayList<ComparisonResult>> decoyResult) {
+    public List<ArrayList<ComparisonResult>> compareNmerge(List<ArrayList<ComparisonResult>> targetResult, List<ArrayList<ComparisonResult>> decoyResult) {
 
-        List<ArrayList<ComparisonResult>> validatedResult = null;
+        List<ArrayList<ComparisonResult>> validatedResult = new ArrayList<>();
         //calculate FDR=Ndecoy/Ntargethits
 
         int c = 0;
-        int decoySSM = 0;
-
         for (ArrayList<ComparisonResult> rTarget : targetResult) {
             ArrayList<ComparisonResult> rDecoy = decoyResult.get(c++);
             if (rTarget.get(0).compareTo(rDecoy.get(0)) < 0) {
 
-                rTarget.clear();
-                rTarget.addAll(rDecoy);
-                decoySSM++;
-
+                validatedResult.add(rDecoy);
+
+            }
+            else{
+                validatedResult.add(rTarget);
             }
+
 
         }
-        Collections.sort(targetResult, (ArrayList<ComparisonResult> o1, ArrayList<ComparisonResult> o2) -> Double.valueOf(o1.get(0).getScore()).compareTo(o2.get(0).getScore()));
+        Collections.sort(validatedResult, (ArrayList<ComparisonResult> o1, ArrayList<ComparisonResult> o2) -> Double.valueOf(o1.get(0).getScore()).compareTo(o2.get(0).getScore()));
 
+        return validatedResult;
     }
 
     public int validate(List<ArrayList<ComparisonResult>> result, double threshold) {

diff --git a/src/main/java/com/compomics/coss/Model/ConfigData.java b/src/main/java/com/compomics/coss/Model/ConfigData.java
@@ -3,7 +3,7 @@
 
 import com.compomics.ms2io.IndexKey;
 import java.io.File;
-import com.compomics.ms2io.SpectrumReader;
+import com.compomics.ms2io.SpectraReader;
 import java.util.List;
 /**
  *this class holds the configuration data for spectral comparison
@@ -15,8 +15,8 @@ public class ConfigData {
     File specLibraryFile;
     List<IndexKey> expIndex;
     List<IndexKey> libIndex;
-    SpectrumReader rdExperimental;
-    SpectrumReader rdLibrary;
+    SpectraReader rdExperimental;
+    SpectraReader rdLibrary;
 
     String outputPath;
     int ScoringFun;//index
@@ -50,19 +50,19 @@ public List<IndexKey> getExpSpectraIndex() {
         return this.expIndex;
     }
 
-    public SpectrumReader getExpSpecReader(){
+    public SpectraReader getExpSpecReader(){
         return this.rdExperimental;
     }
 
-    public void setExpSpecReader(SpectrumReader rd){
+    public void setExpSpecReader(SpectraReader rd){
         this.rdExperimental=rd;
     }
 
-    public void setLibSpecReader(SpectrumReader rd){
+    public void setLibSpecReader(SpectraReader rd){
         this.rdLibrary=rd;
     }
 
-    public SpectrumReader getLibSpecReader(){
+    public SpectraReader getLibSpecReader(){
         return this.rdLibrary;
     }
 

diff --git a/src/main/java/com/compomics/coss/View/MainGUI.java b/src/main/java/com/compomics/coss/View/MainGUI.java
@@ -20,13 +20,15 @@
 import javax.swing.JPanel;
 import javax.swing.JTabbedPane;
 import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.JProgressBar;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
+import javax.swing.JTextField;
 import javax.swing.WindowConstants;
 import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
 
 
 /**
@@ -45,6 +47,7 @@ public class MainGUI extends JFrame {
        * constructor of the class 
        * @param settings setting panel to be added on the main GUI
        * @param result result panel to be added on the main GUI
+     * @param targetView
        * @param controler  controller class responsible for coordinating the process 
        */
     public MainGUI(SettingPanel settings, ResultPanel result, TargetDB_View targetView, MainFrameController controler) {
@@ -120,35 +123,12 @@ private void initComponents() {
         pnlLog = new JPanel(new FlowLayout(FlowLayout.LEFT));
         pnlLog.setLayout(new BorderLayout());
 
-        btnStartSearch=new JButton("Start Searching");
-        btnCancel=new  JButton("Cancel");       
-        prgProgress=new JProgressBar(0, 100);
-
-
-
-
-        JPanel innerControlPanel=new JPanel(new FlowLayout());
-        innerControlPanel.add(btnStartSearch);
-        innerControlPanel.add(btnCancel);
-
-        JPanel pnlValidationControl = new JPanel(new FlowLayout());
-
-
-        pnlCommands.add(innerControlPanel, BorderLayout.NORTH);
-        pnlCommands.add(prgProgress, BorderLayout.SOUTH);
-
-
         txtlog = new JTextArea();
         scrLogArea=new JScrollPane();
         txtlog.setColumns(20);
         txtlog.setRows(5);
         scrLogArea.setViewportView(txtlog);
-
-
-
-
-
-
+
         //this.setSize(dmnsn);
         this.setExtendedState(JFrame.MAXIMIZED_BOTH);
         tab = new JTabbedPane(JTabbedPane.TOP, JTabbedPane.WRAP_TAB_LAYOUT);
@@ -170,17 +150,7 @@ private void initComponents() {
         pnlLower.add(pnlCommands);
         pnlLower.add(pnlLog);
 
-
-
-//        //base panel it is the base panel holding the upper and the lower split panel
-//        splBase = new JSplitPane(JSplitPane.VERTICAL_SPLIT, pnlUpper, pnlLower);
-//        splBase.setResizeWeight(0.9);
-//        splBase.setDividerLocation(0.9);
-//        splBase.setEnabled(false);
-//        //splBase.setOneTouchExpandable(true);
-//        
-//       
-
+
         //SettingPanel settings = new SettingPanel();
         pnlsetting.add(settings);
 
@@ -215,30 +185,8 @@ public void windowClosing(final WindowEvent we
             }
         }
         );
-
-        //start search button listenr
-        btnStartSearch.addActionListener(new ActionListener() {
-                    @Override
-                    public void actionPerformed(ActionEvent e) {
-
-
-                        control.startSearch();
-
-                    }
-                }
-                );
-
-
-        //cancel button listener
-        btnCancel.addActionListener(new ActionListener() {
-            public void actionPerformed(ActionEvent ev) {
-
-                control.stopSearch();
 
-            }
-        }
-        );
-
+
         save.addActionListener(new ActionListener() {
             public void actionPerformed(ActionEvent ev) {
                 try {
@@ -277,10 +225,16 @@ public void actionPerformed(ActionEvent e) {
         tab.addChangeListener((ChangeEvent e) -> {
             if (e.getSource() instanceof JTabbedPane) {
                 JTabbedPane pane = (JTabbedPane) e.getSource();
-                changeControlView(pane.getSelectedIndex());
+                int ind = pane.getSelectedIndex();
+                control.cmdViewDisplay(ind);
+
             }          
         });
 
+
+
+
+
         setJMenuBar(menuBar);        
         BorderLayout layout=new BorderLayout();
         getContentPane().setLayout(layout);
@@ -307,15 +261,13 @@ public void actionPerformed(ActionEvent e) {
     public JPanel pnlsetting;
     public JPanel pnlresult;
 
-    private JPanel pnlCommands;
+    public JPanel pnlCommands;
     private JPanel pnlLog;
 
 
-    public JButton btnStartSearch;
-    private JButton btnCancel;
     public JTextArea txtlog;
     private JScrollPane scrLogArea;
-    public JProgressBar prgProgress;
+
 
     private void changeControlView(int selectedIndex) {
 

diff --git a/src/main/java/com/compomics/coss/View/RasterPanel.java b/src/main/java/com/compomics/coss/View/RasterPanel.java
@@ -2,7 +2,7 @@
 
 import com.compomics.ms2io.IndexKey;
 import com.compomics.ms2io.Spectrum;
-import com.compomics.ms2io.SpectrumReader;
+import com.compomics.ms2io.SpectraReader;
 import java.awt.Color;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
@@ -29,7 +29,7 @@
 public class RasterPanel extends JPanel implements MouseListener, MouseMotionListener {
 
     List<IndexKey> iKey;
-    SpectrumReader rd;
+    SpectraReader rd;
     double scale = 1;
     double retnTime = 0;
     BufferedImage temp;
@@ -49,7 +49,7 @@ public class RasterPanel extends JPanel implements MouseListener, MouseMotionLis
      * @param key index key to read the spectrum
      * @param rd spectrum reader object
      */
-    public RasterPanel(List<IndexKey> key, SpectrumReader rd) {
+    public RasterPanel(List<IndexKey> key, SpectraReader rd) {
         this.iKey = key;
         this.rd=rd;
 

diff --git a/src/main/java/com/compomics/coss/View/SearchCommandPnl.java b/src/main/java/com/compomics/coss/View/SearchCommandPnl.java
@@ -0,0 +1,76 @@
+/*
+ * 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 com.compomics.coss.View;
+
+import com.compomics.coss.Controller.MainConsolControler;
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import com.compomics.coss.Controller.MainFrameController;
+
+/**
+ *
+ * @author Genet
+ */
+public class SearchCommandPnl extends JPanel{
+
+    MainFrameController control;
+    public SearchCommandPnl(MainFrameController control) {
+        this.control=control;
+        init();
+    }
+
+    private void init(){
+
+
+        btnStartSearch=new JButton("Start Searching");
+        JButton btnCancel=new  JButton("Cancel");       
+        prgProgress=new JProgressBar(0, 100);  
+
+        JPanel innerControlPanel=new JPanel(new FlowLayout());
+        innerControlPanel.add(btnStartSearch);
+        innerControlPanel.add(btnCancel);
+
+         //start search button listenr
+        btnStartSearch.addActionListener(new ActionListener() {
+                    @Override
+                    public void actionPerformed(ActionEvent e) {
+
+
+                        control.startSearch();
+
+                    }
+                }
+                );
+
+
+        //cancel button listener
+        btnCancel.addActionListener(new ActionListener() {
+            public void actionPerformed(ActionEvent ev) {
+
+                control.stopSearch();
+
+            }
+        }
+        );
+
+
+        setLayout(new BorderLayout());
+        add(innerControlPanel, BorderLayout.NORTH);
+        add(prgProgress, BorderLayout.SOUTH);
+
+
+    }
+
+    public JButton btnStartSearch;    
+    public JProgressBar prgProgress;
+
+
+}
diff --git a/src/main/java/com/compomics/coss/View/SettingPanel.java b/src/main/java/com/compomics/coss/View/SettingPanel.java
@@ -252,7 +252,7 @@ public void valueChanged(TreeSelectionEvent e) {
         );
 
         //End of Matching panel layout
-        //this panel: the layout
+        //base input panel layout: panel to hold all the three different panels together
         javax.swing.GroupLayout pnlMainLayout = new javax.swing.GroupLayout(pnlInputs);
         pnlInputs.setLayout(pnlMainLayout);