--- a
+++ b/src/biodiscml/AdaptDatasetToTesting.java
@@ -0,0 +1,276 @@
+/*
+ * Get clinical and genes expression
+ * Make some feature extraction
+ */
+package biodiscml;
+
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.TreeMap;
+import utils.Weka_module;
+import utils.utils.TableObject;
+import static utils.utils.readTable;
+import weka.classifiers.Classifier;
+import weka.core.SerializationHelper;
+
+/**
+ *
+ * @author Mickael
+ */
+public class AdaptDatasetToTesting {
+
+    public static boolean debug = Main.debug;
+    public static boolean missingClass = false;
+
+    public AdaptDatasetToTesting() {
+    }
+
+    public boolean isMissingClass() {
+        return missingClass;
+    }
+
+    /**
+     * create dataset with a determined class
+     *
+     * @param theClass
+     * @param infiles
+     * @param outfile
+     */
+    public AdaptDatasetToTesting(String theClass, HashMap<String, String> infiles, String outfile, String separator, String model) {
+        //get model features
+        Weka_module weka = new Weka_module();
+        ArrayList<String> alModelFeatures = weka.getFeaturesFromClassifier(model); //features in the right order
+        HashMap<String, String> hmModelFeatures = new HashMap<>();//indexed hashed features
+        System.out.println("# Model features: ");
+
+        Boolean voteModel = false;
+        try {
+            voteModel = (((Classifier) SerializationHelper.read(model)).getClass().toString().contains("weka.classifiers.meta.Vote"));
+        } catch (Exception e) {
+            if (Main.debug) {
+                e.printStackTrace();
+            }
+        }
+        if (voteModel) {
+            System.out.println("    Combined Vote model");
+        }
+        for (String f : alModelFeatures) {
+            if (!f.startsWith("Model") && !f.startsWith("class")) {
+                hmModelFeatures.put(f, f);
+            }
+        }
+        hmModelFeatures.put("class", "class");
+        for (String s : hmModelFeatures.keySet()) {
+            System.out.println("\t" + s);
+        }
+
+        //convert hashmap to list
+        String[] files = new String[infiles.size()];
+        String[] prefixes = new String[infiles.size()];
+        int cpt = 0;
+        for (String f : infiles.keySet()) {
+            files[cpt] = f;
+            prefixes[cpt] = infiles.get(f);
+            cpt++;
+        }
+
+        //load datasets of features
+        if (debug) {
+            System.out.println("loading files");
+        }
+
+        ArrayList<TableObject> al_tables = new ArrayList<>();
+        int classIndex = -1;
+
+        for (int i = 0; i < files.length; i++) {
+            String file = files[i];
+            TableObject tbo = new TableObject(readTable(file, separator));
+            //locate class
+            if (tbo.containsClass(theClass)) {
+                classIndex = i;
+            }
+            al_tables.add(tbo);
+        }
+
+        //extract class 
+        ArrayList<String> myClass = new ArrayList<>();
+
+        try {
+            myClass = al_tables.get(classIndex).getTheClass(theClass);
+        } catch (Exception e) {
+            String f = "";
+            for (String s : infiles.keySet()) {
+                f += " " + s;
+            }
+            System.out.println("Class " + theClass + " not found in " + f + ". Class values are filled by ?");
+            missingClass = true;
+        }
+
+        // replace spaces by _ in class
+        for (int i = 0; i < myClass.size(); i++) {
+            String c = myClass.get(i).replace(" ", "_");
+            myClass.set(i, c);
+        }
+
+        //remove feature that are not needed by the model
+        //create outfile
+        System.out.println("create outfile " + outfile);
+
+        HashMap<String, ArrayList<String>> hmOutput = new HashMap<>();
+        try {
+            PrintWriter pw = new PrintWriter(new FileWriter(outfile));
+            ///////// PRINT HEADER
+            //pw.print(Main.mergingID);
+            hmOutput.put(Main.mergingID, new ArrayList<>());
+            for (int i = 0; i < al_tables.size(); i++) {
+                TableObject tbo = al_tables.get(i);
+                for (String s : tbo.hmData.keySet()) {
+                    String head = null;
+                    if (!prefixes[i].isEmpty()) {
+                        head = prefixes[i] + "__" + s;
+                    } else {
+                        head = s;
+                    }
+                    if (hmModelFeatures.containsKey(head)) {
+                        //pw.print("\t" + head);
+                        hmOutput.put(head, new ArrayList<>());
+                    }
+                }
+            }
+
+            //pw.println("\tclass");
+            hmOutput.put("class", new ArrayList<>());
+            //pw.flush();
+
+            //search for ids present in all datasets
+            HashMap<String, String> hm_ids = getCommonIds(al_tables);
+            if (al_tables.size() > 1) {
+                System.out.println("Total number of common instances between files:" + hm_ids.size());
+            } else {
+                System.out.println("Total number of instances between files:" + hm_ids.size());
+            }
+
+            ///////PREPARE CONTENT FOR PRINTING
+            TreeMap<String, Integer> tm = new TreeMap<>();
+            tm.putAll(al_tables.get(0).hmIDsList);
+            for (String id : tm.keySet()) {
+                if (hm_ids.containsKey(id)) { //if sample exist in all files
+                    //pw.print(id);
+                    hmOutput.get(Main.mergingID).add(id);
+                    for (int i = 0; i < al_tables.size(); i++) {
+                        TableObject tbo = al_tables.get(i);
+                        int idIndex = tbo.hmIDsList.get(id); //get index for sample
+                        for (String s : tbo.hmData.keySet()) { //for all features
+                            String feature = null;
+                            if (!prefixes[i].isEmpty()) {
+                                feature = prefixes[i] + "__" + s;
+                            } else {
+                                feature = s;
+                            }
+                            if (hmModelFeatures.containsKey(feature)) {
+                                //pw.print("\t" + tbo.hmData.get(s).get(idIndex));
+                                // print values and replace , per .
+                                String out = tbo.hmData.get(s).get(idIndex).replace(",", ".").trim();
+                                if (out.isEmpty()) {
+                                    out = Main.missingValueToReplace;
+                                }
+                                hmOutput.get(feature).add(out);
+                            }
+                        }
+                    }
+
+                    if (missingClass) {
+                        hmOutput.get("class").add("?");
+                    } else {
+                        //pw.print("\t" + myClass.get(al_tables.get(classIndex).hmIDsList.get(id)));
+                        hmOutput.get("class").add(myClass.get(al_tables.get(classIndex).hmIDsList.get(id)));
+                        //pw.print("\t" + myClass.get(idIndex).replace("1", "true").replace("0", "false"));
+                    }
+
+                    //pw.println();
+                }
+            }
+            //PRINTING CONTENT IN THE RIGHT ORDER
+            if (voteModel || (alModelFeatures.size() != hmModelFeatures.size())) {
+                //ensure class is at the end of the list
+                alModelFeatures = new ArrayList<>();
+                for (String feature : hmModelFeatures.keySet()) {
+                    if (!feature.equals("class")) {
+                        alModelFeatures.add(feature);
+                    }
+                }
+                alModelFeatures.add("class");
+            }
+            //header
+            pw.print(Main.mergingID);
+            for (String feature : alModelFeatures) {
+                pw.print("\t" + feature);
+            }
+            pw.println();
+            pw.flush();
+            //content
+            for (int i = 0; i < hm_ids.size(); i++) {//for every instance
+                pw.print(hmOutput.get(Main.mergingID).get(i));
+                for (String feature : alModelFeatures) {
+                    try {
+                        pw.print("\t" + hmOutput.get(feature).get(i));
+                    } catch (Exception e) {
+                        System.out.println("Feature "+feature+" is not present in the test set. Replacing with missing data");
+                        pw.print("\t?");
+                    }
+                }
+                pw.println();
+            }
+            pw.flush();
+            pw.close();
+            if (debug) {
+                System.out.println("closing outfile " + outfile);
+            }
+            pw.close();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
+    }
+
+    /**
+     * get common ids between infiles
+     *
+     * @param al_tables
+     * @return
+     */
+    public static HashMap<String, String> getCommonIds(ArrayList<TableObject> al_tables) {
+        HashMap<String, String> hm_ids = new HashMap<>();
+        //if many infiles
+        if (al_tables.size() > 0) {
+            HashMap<String, Integer> hm_counts = new HashMap<>();
+            //get all ids, count how many times each one is seen
+            for (TableObject table : al_tables) {
+                for (String s : table.hmIDsList.keySet()) {
+                    //s = s.toLowerCase();
+                    if (hm_counts.containsKey(s)) {
+                        int tmp = hm_counts.get(s);
+                        tmp++;
+                        hm_counts.put(s, tmp);
+                    } else {
+                        hm_counts.put(s, 1);
+                    }
+                }
+            }
+            //check number of times ids have been seen
+            for (String s : hm_counts.keySet()) {
+                if (hm_counts.get(s) == al_tables.size()) {
+                    hm_ids.put(s, "");
+                }
+            }
+        } else {//for one infile
+            for (String s : al_tables.get(0).hmIDsList.keySet()) {
+                hm_ids.put(s, "");
+            }
+        }
+
+        return hm_ids;
+    }
+
+}