[LutinJ2R-commits] r116 - trunk/src/main/java/org/nuiton/j2r/types

30 Jul 2009

Author: jcouteau
Date: 2009-07-30 16:05:04 +0200 (Thu, 30 Jul 2009)
New Revision: 116

Modified:
   trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java
   trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java
   trunk/src/main/java/org/nuiton/j2r/types/RList.java
Log:
Remove duplicate code, improve code (for sonar :) )

Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java
===================================================================

--- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java	2009-07-26 17:11:04 UTC (rev 115)
+++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java	2009-07-30 14:05:04 UTC (rev 116)
@@ -19,8 +19,10 @@
 import java.io.BufferedReader;
 import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.FileWriter;
+import java.io.IOException;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -41,6 +43,19 @@
     private List<String> rowNames;
     //Vector containing the vectors of the data.frame
     private List<List<? extends Object>> data;
+    private String setNamesString = "names(%s)<-c(%s)";
+    private String setNameString = "names(%s)[%s]<-\"%s\"";
+    private String getNamesString = "names(%s)";
+    private String getNameString = "names(%s)[%s]";
+    private String getRowNamesString = "row.names(%s)";
+    private String getRowNameString = "row.names(%s)[%s]";
+    private String setRowNamesString = "row.names(%s)<-c(%s)";
+    private String setRowNameString = "row.names(%s)[%s]<-\"%s\"";
+    private String indexExceptionText =
+            "Cannot perform operation, index is superior to size.\nIndex : %s\nSize : %s";
+    private String dataInconsistencyText =
+            "There is an inconsistency between the local and distant data.\nLocal data size : %s\nDistant data size : %s";
+    private String noVariable = "No variable name given";
 
     public RDataFrame(REngine engine) throws RException {
         super();
@@ -121,12 +136,12 @@
      *             when the row.names size get from R is bigger than the local
      *             data size.
      */
-    public List<String> getNames() throws RException, IndexOutOfBoundsException {
+    public List<String> getNames() throws RException {
 
         if (engine.isAutoCommit()) {
             //Get back the names from R.
-            String[] namesArray = (String[]) engine.eval("names(" +
-                    this.variable + ")");
+            String[] namesArray = (String[]) engine.eval(String.format(
+                    getNamesString, this.variable));
 
             //Check if size is correct, if yes, modify local data.
             if (namesArray.length <= this.data.size()) {
@@ -137,11 +152,10 @@
                 return names;
             } else {
                 //if size is not correct, throw a RException.
-                throw new IndexOutOfBoundsException(
-                        "Data inconsistency, local data is smaller (size : " +
-                        this.data.size() +
-                        ") than the names ArrayList in R (size : " +
-                        namesArray.length + ")");
+                throw new IndexOutOfBoundsException(String.format(
+                        dataInconsistencyText, this.data.size(),
+                        namesArray.length));
+
             }
         } else {
             return this.names;
@@ -164,14 +178,14 @@
      * @throws IndexOutOfBoundsException
      *             if the x index is out of bounds.
      */
-    public String getName(int x) throws RException, IndexOutOfBoundsException {
+    public String getName(int x) throws RException {
 
         //check if the index is valid
         if (x < names.size()) {
             if (engine.isAutoCommit()) {
                 //Get back the names from R.
-                String name = (String) engine.eval("names(" + this.variable +
-                        ")[" + (x + 1) + "]");
+                String name = (String) engine.eval(String.format(getNameString,
+                        this.variable, x + 1));
 
                 //Check if the String is returned.
                 if ((name != null) && (!name.equals(""))) {
@@ -180,7 +194,8 @@
             }
         } else {
             //if String is not returned, throw an IndexOutOfBOundsException.
-            throw new IndexOutOfBoundsException("Your index is not valid");
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, this.names.size()));
         }
 
         return this.names.get(x);
@@ -197,29 +212,31 @@
      *             when the names ArrayList is longer than the data.frame
      *             length.
      */
-    public void setNames(List<String> names) throws RException,
-            IndexOutOfBoundsException {
+    public void setNames(List<String> names) throws RException {
 
         //Check if the size is correct, if yes, do the modifications and send them to R.
         if (names.size() <= data.size()) {
             this.names = names;
 
             //Create the r instruction (names(var)<-c("name 1",...,"name x")).
-            String rexp = "names(" + this.variable + ")<-c(";
+
+            String namesString = "";
             for (int i = 0; i < this.names.size(); i++) {
-                rexp += "\"" + names.get(i) + "\",";
+                //add a "," to separate names beginning after the first name is displayed.
+                if (i != 0) {
+                    namesString += ",";
+                }
+                //add the column name between quotes.
+                namesString += "\"" + names.get(i) + "\"";
             }
-            rexp = rexp.substring(0, rexp.length() - 1) + ")";
 
             //Send the r instruction to the engine.
-            engine.voidEval(rexp);
+            engine.voidEval(String.format(setNamesString, this.variable,
+                    namesString));
         } else {
             //if size is not correct, throw a IndexOutOfBoundsException.
-            throw new IndexOutOfBoundsException(
-                    "Cannot assign the names attribute, the names List is too long.\nThe size of names (" +
-                    names.size() +
-                    ") must be shorter or equal to the data.frame length(" +
-                    data.size() + ").");
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    names.size(), data.size()));
         }
     }
 
@@ -235,23 +252,21 @@
      * @throws IndexOutOfBoundsException
      *             when the index is out of the data.frame bounds.
      */
-    public void setName(int x, String name) throws RException,
-            IndexOutOfBoundsException {
+    public void setName(int x, String name) throws RException {
         //check if the index is valid
         if (x < names.size()) {
             names.set(x, name);
 
             //create the r instruction (names(var)[x]<-"name")
-            String rexp = "names(" + this.variable + ")[" + (x + 1) + "]<-\"" +
-                    name + "\"";
+            String rexp = String.format(setNameString, this.variable, x + 1,
+                    name);
 
             //Send the R instruction to the engine.
             engine.voidEval(rexp);
         } else {
-            //if index is out of bounds, throw a IndexOutOfBOundsException
-            throw new IndexOutOfBoundsException(
-                    "Cannot assign the name, the index is out of bounds.\nIndex :" +
-                    x + "; data.frame size : " + data.size() + ".");
+            //if index is out of bounds, throw a IndexOutOfBoundsException
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, data.size()));
         }
     }
 
@@ -266,12 +281,11 @@
      *             when the row.names size get from R is bigger than the local
      *             data size.
      */
-    public List<String> getRowNames() throws RException,
-            IndexOutOfBoundsException {
+    public List<String> getRowNames() throws RException {
         if (engine.isAutoCommit()) {
             //Get back the names from R.
-            String[] rowNamesArray = (String[]) engine.eval("row.names(" +
-                    this.variable + ")");
+            String[] rowNamesArray = (String[]) engine.eval(String.format(
+                    getRowNamesString, this.variable));
 
             //Check if size is correct, if yes, modify local data.
             if (rowNamesArray.length <= this.data.get(0).size()) {
@@ -282,11 +296,9 @@
                 return rowNames;
             } else {
                 //if size is not correct, throw a RException.
-                throw new IndexOutOfBoundsException(
-                        "Data inconsistency, local data is smaller (size : " + this.data.get(0).
-                        size() + ") than the names ArrayList in R (size : " +
-                        rowNamesArray.length +
-                        ").\nYou may want to force an update");
+                throw new IndexOutOfBoundsException(String.format(
+                        dataInconsistencyText, rowNamesArray.length, this.data.
+                        get(0)));
             }
         } else {
             return this.rowNames;
@@ -307,11 +319,11 @@
      */
     public String getRowName(int y) throws RException {
         //check if the index is valid
-        if (y < names.size()) {
+        if (y < rowNames.size()) {
             if (engine.isAutoCommit()) {
                 //Get back the names from R.
-                String name = (String) engine.eval(
-                        "row.names(" + this.variable + ")[" + (y + 1) + "]");
+                String name = (String) engine.eval(String.format(
+                        getRowNameString, this.variable, y + 1));
 
                 //Check if the String is returned.
                 if ((name != null) && (!name.equals(""))) {
@@ -320,7 +332,8 @@
             }
         } else {
             //if String is not returned, throw an IndexOutOfBOundsException.
-            throw new IndexOutOfBoundsException("Your index is not valid");
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    y, rowNames.size()));
         }
         return this.rowNames.get(y);
 
@@ -339,29 +352,29 @@
      *             when the row names ArrayList is longer than the data.frame
      *             length
      */
-    public void setRowNames(List<String> rowNames) throws RException,
-            IndexOutOfBoundsException {
+    public void setRowNames(List<String> rowNames) throws RException {
 
         //Check if the size is correct, if yes, do the modifications and send them to R.
         if (rowNames.size() == data.get(0).size()) {
             this.rowNames = rowNames;
 
             //Create the r instruction (row.names(var)<-c("name 1",...,"name x")).
-            String rexp = "row.names(" + this.variable + ")<-c(";
+            String rowNamesString = "";
             for (int i = 0; i < this.rowNames.size(); i++) {
-                rexp += "\"" + rowNames.get(i) + "\",";
+                if (i != 0) {
+                    rowNamesString += ",";
+                }
+                rowNamesString += "\"" + rowNames.get(i) + "\"";
             }
-            rexp = rexp.substring(0, rexp.length() - 1) + ")";
+            String rexp = String.format(setRowNamesString, this.variable,
+                    rowNamesString);
 
             //Send the r instruction to the engine.
             engine.voidEval(rexp);
         } else {
             //if size is not correct, throw a RException.
-            throw new IndexOutOfBoundsException(
-                    "Cannot assign the names attribute, the ArrayList is too long.\nThe size of names (" +
-                    rowNames.size() +
-                    ") must be shorter or equal to the data.frame length(" + data.get(0).
-                    size() + ").");
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    rowNames.size(), data.get(0).size()));
         }
     }
 
@@ -377,23 +390,21 @@
      * @throws IndexOutOfBoundsException
      *             when the index is out of the data.frame bounds.
      */
-    public void setRowName(int x, String rowName) throws RException,
-            IndexOutOfBoundsException {
+    public void setRowName(int x, String rowName) throws RException {
         //check if the index is valid
         if (x < rowNames.size()) {
             rowNames.set(x, rowName);
 
             //create the r instruction (row.names(var)[x]<-"rowName")
-            String rexp = "row.names(" + this.variable + ")[" + (x + 1) +
-                    "]<-\"" + rowName + "\"";
+            String rexp = String.format(setRowNameString, this.variable, x + 1,
+                    rowName);
 
             //Send the R instruction to the engine.
             engine.voidEval(rexp);
         } else {
             //if index is out of bounds, throw a RException
-            throw new IndexOutOfBoundsException(
-                    "Cannot assign the name, the index is out of bounds.\nIndex :" +
-                    x + "; data.frame size : " + data.size() + ".");
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, data.size()));
         }
     }
 
@@ -436,8 +447,7 @@
     @Override
     public String toRString() throws RException {
         if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot instantiate data.frame in R, no variable name given");
+            throw new RException(noVariable);
         }
         String returnString = this.variable + "<-data.frame(";
         if (!(this.data.isEmpty())) {
@@ -509,20 +519,18 @@
      * @throws ArrayStoreException
      *             if the target destination cannot accept double value
      */
-    public void set(int x, int y, double data) throws RException,
-            IndexOutOfBoundsException, ArrayStoreException {
+    public void set(int x, int y, double data) throws RException {
 
         if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
+            throw new RException(noVariable);
         }
         if (x >= this.data.size()) {
-            throw new IndexOutOfBoundsException("The x value is too high : " + x +
-                    ">=" + this.data.size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, this.data.size()));
         }
         if (y >= this.data.get(0).size()) {
-            throw new IndexOutOfBoundsException("The y value is too high : " + y +
-                    ">=" + this.data.get(0).size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    y, this.data.get(0).size()));
         }
         if (this.data.get(x).get(y) instanceof Double) {
             ((ArrayList<Double>) this.data.get(x)).set(y, data);
@@ -553,16 +561,15 @@
      */
     public void set(int x, int y, Boolean data) throws RException {
         if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
+            throw new RException(noVariable);
         }
         if (x >= this.data.size()) {
-            throw new IndexOutOfBoundsException("The x value is too high : " + x +
-                    ">=" + this.data.size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, this.data.size()));
         }
         if (y >= this.data.get(0).size()) {
-            throw new IndexOutOfBoundsException("The y value is too high : " + y +
-                    ">=" + this.data.get(0).size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    y, this.data.get(0).size()));
         }
         if (this.data.get(x).get(y) instanceof Boolean) {
             ((ArrayList<Boolean>) this.data.get(x)).set(y, data);
@@ -598,16 +605,15 @@
      */
     public void set(int x, int y, String data) throws RException {
         if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
+            throw new RException(noVariable);
         }
         if (x >= this.data.size()) {
-            throw new IndexOutOfBoundsException("The x value is too high : " + x +
-                    ">=" + this.data.size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, this.data.size()));
         }
         if (y >= this.data.get(0).size()) {
-            throw new IndexOutOfBoundsException("The y value is too high : " + y +
-                    ">=" + this.data.get(0).size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    y, this.data.get(0).size()));
         }
         if (this.data.get(x).get(y) instanceof String) {
             ((ArrayList<String>) this.data.get(x)).set(y, data);
@@ -637,16 +643,15 @@
      */
     public void set(int x, int y, int data) throws RException {
         if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
+            throw new RException(noVariable);
         }
         if (x >= this.data.size()) {
-            throw new IndexOutOfBoundsException("The x value is too high : " + x +
-                    ">=" + this.data.size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, this.data.size()));
         }
         if (y >= this.data.get(0).size()) {
-            throw new IndexOutOfBoundsException("The y value is too high : " + y +
-                    ">=" + this.data.get(0).size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    y, this.data.size()));
         }
         if (this.data.get(x).get(y) instanceof Integer) {
             ((ArrayList<Integer>) this.data.get(x)).set(y, data);
@@ -675,12 +680,12 @@
     public Object get(int x, int y) throws RException,
             IndexOutOfBoundsException {
         if (x >= this.data.size()) {
-            throw new IndexOutOfBoundsException("The x value is too high : " + x +
-                    ">=" + this.data.size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, this.data.size()));
         }
         if (y >= this.data.get(0).size()) {
-            throw new IndexOutOfBoundsException("The y value is too high : " + y +
-                    ">=" + this.data.get(0).size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    y, this.data.get(0).size()));
         }
         if (engine.isAutoCommit()) {
             Object returnObject = engine.eval(this.variable + "[" + (y + 1) +
@@ -703,26 +708,6 @@
     }
 
     /**
-     * Method to set the data.frame variable name
-     * 
-     * @param variable
-     *            the new variable name
-     * @throws RException
-     *             if something wrong happen while assigning the data.frame to
-     *             the new variable in R.
-     */
-    public void setVariable(String variable) throws RException {
-        this.variable = variable;
-        try {
-            engine.voidEval(toRString());
-        } catch (RException eee) {
-            throw new RException(
-                    "An error occured while trying to assign the data.frame in R",
-                    eee);
-        }
-    }
-
-    /**
      * Method to get the ArrayLists of the R data.frame (there is no
      * synchronizing with R, use the update() method to synchronize data with R
      * before using this method if you think data may have changed.
@@ -784,15 +769,15 @@
             }
 
             //update row names
-            String[] rowNamesArray = (String[]) engine.eval("row.names(" +
-                    this.variable + ")");
+            String[] rowNamesArray = (String[]) engine.eval(String.format(
+                    getRowNamesString, this.variable));
             for (int i = 0; i < rowNamesArray.length; i++) {
                 rowNames.add(rowNamesArray[i]);
             }
 
             //update names
-            String[] namesArray = (String[]) engine.eval("names(" +
-                    this.variable + ")");
+            String[] namesArray = (String[]) engine.eval(String.format(
+                    getNamesString, this.variable));
             for (int i = 0; i < namesArray.length; i++) {
                 names.add(namesArray[i]);
             }
@@ -853,7 +838,7 @@
             }
             file.close();
         } catch (Exception e) {
-            e.printStackTrace();
+            log.error(e);
         }
 
     }
@@ -871,62 +856,10 @@
      *            Does the csv file contain names of the columns.
      */
     public void importCsv(File inputFile, boolean rowNames, boolean names) {
-        String tmp;
-        Integer dataSize = 0;
-        try {
+        List<Object> tmp = new ArrayList<Object>();
+        tmp.add("string");
+        importCsv(inputFile, rowNames, names, (List) tmp);
 
-            BufferedReader first = new BufferedReader(new FileReader(inputFile));
-            tmp = first.readLine();
-            String[] splitted = tmp.split("\\;");
-            if (rowNames) {
-                dataSize = splitted.length - 1;
-            } else {
-                dataSize = splitted.length;
-            }
-
-            BufferedReader br = new BufferedReader(new FileReader(inputFile));
-            if (this.data != null) {
-                this.data.clear();
-            }
-            if ((rowNames) && (this.rowNames != null)) {
-                this.rowNames.clear();
-            }
-            if (names) {
-                if (this.names != null) {
-                    this.names.clear();
-                }
-                tmp = br.readLine();
-                splitted = tmp.split("\\;");
-                for (int i = 1; i < splitted.length; i++) {
-                    this.names.add(splitted[i]);
-                }
-            }
-
-            List<List<? extends Object>> tempData =
-                    new ArrayList<List<? extends Object>>();
-
-            for (int i = 0; i < dataSize; i++) {
-                List<Object> column = new ArrayList<Object>();
-                tempData.add(column);
-            }
-
-            while ((tmp = br.readLine()) != null) {
-                splitted = tmp.split("\\;");
-                int index = 0;
-                if (rowNames) {
-                    this.rowNames.add(splitted[0]);
-                    index = 1;
-                }
-                for (int i = 0 + index; i < splitted.length; i++) {
-                    ((ArrayList<Object>) tempData.get(i - index)).add(
-                            (Object) splitted[i]);
-                }
-            }
-            br.close();
-            this.data = tempData;
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
     }
 
     /**
@@ -946,70 +879,17 @@
      */
     public void importCsv(File inputFile, boolean rowNames, boolean names,
             Object importType) {
-        String tmp;
-        Integer dataSize = 0;
-        try {
-
-            BufferedReader first = new BufferedReader(new FileReader(inputFile));
-            tmp = first.readLine();
-            String[] splitted = tmp.split("\\;");
-            if (rowNames) {
-                dataSize = splitted.length - 1;
-            } else {
-                dataSize = splitted.length;
-            }
-
-            BufferedReader br = new BufferedReader(new FileReader(inputFile));
-            if (this.data != null) {
-                this.data.clear();
-            }
-            if ((rowNames) && (this.rowNames != null)) {
-                this.rowNames.clear();
-
-            }
-            if (names) {
-                if (this.names != null) {
-                    this.names.clear();
-                }
-                tmp = br.readLine();
-                splitted = tmp.split("\\;");
-                for (int i = 1; i < splitted.length; i++) {
-                    this.names.add(splitted[i]);
-                }
-            }
-
-            List<List<? extends Object>> tempData =
-                    new ArrayList<List<? extends Object>>();
-
-            for (int i = 0; i < dataSize; i++) {
-                List<Object> column = new ArrayList<Object>();
-                tempData.add(column);
-            }
-
-            while ((tmp = br.readLine()) != null) {
-                splitted = tmp.split("\\;");
-                int index = 0;
-                if (rowNames) {
-                    this.rowNames.add(splitted[0]);
-                    index = 1;
-                }
-                for (int i = 0 + index; i < splitted.length; i++) {
-                    if (importType instanceof String) {
-                        ((ArrayList<Object>) tempData.get(i - index)).add(
-                                (Object) splitted[i]);
-                    } else if (importType instanceof Double) {
-                        ((ArrayList<Object>) tempData.get(i - index)).add(Double.
-                                valueOf(splitted[i]));
-                    } else if (importType instanceof Integer) {
-                        ((ArrayList<Object>) tempData.get(i - index)).add(Integer.
-                                valueOf(splitted[i]));
-                    }
-                }
-            }
-            br.close();
-            this.data = tempData;
-        } catch (Exception e) {
-            e.printStackTrace();
+        List<Object> tmp = new ArrayList<Object>();
+        if (importType instanceof String) {
+            log.info("string");
+            tmp.add((String) importType);
+            importCsv(inputFile, rowNames, names, (List) tmp);
+        } else if (importType instanceof Double) {
+            tmp.add((Double) importType);
+            importCsv(inputFile, rowNames, names, tmp);
+        } else if (importType instanceof Integer) {
+            tmp.add((Integer) importType);
+            importCsv(inputFile, rowNames, names, tmp);
         }
     }
 
@@ -1035,10 +915,7 @@
         String tmp;
         Integer dataSize = 0;
         try {
-
-            BufferedReader first = new BufferedReader(new FileReader(inputFile));
-            tmp = first.readLine();
-            String[] splitted = tmp.split("\\;");
+            String[] splitted = getLines(inputFile);
             if (rowNames) {
                 dataSize = splitted.length - 1;
             } else {
@@ -1080,7 +957,21 @@
                     index = 1;
                 }
                 for (int i = 0 + index; i < splitted.length; i++) {
-                    if (importTypes.get(i - index) instanceof String) {
+                    //test the size of the inputType list. If 1 import all the
+                    //columns as the type of the first
+                    if (importTypes.size() == 1) {
+                        if (importTypes.get(0) instanceof String) {
+                            ((ArrayList<Object>) tempData.get(i - index)).add(
+                                    (Serializable) splitted[i]);
+                        } else if (importTypes.get(0) instanceof Double) {
+                            ((ArrayList<Object>) tempData.get(i - index)).add(Double.
+                                    valueOf(splitted[i]));
+                        } else if (importTypes.get(0) instanceof Integer) {
+                            ((ArrayList<Object>) tempData.get(i - index)).add(Integer.
+                                    valueOf(splitted[i]));
+                        }
+
+                    } else if (importTypes.get(i - index) instanceof String) {
                         ((ArrayList<Object>) tempData.get(i - index)).add(
                                 (Serializable) splitted[i]);
                     } else if (importTypes.get(i - index) instanceof Double) {
@@ -1095,7 +986,16 @@
             br.close();
             this.data = tempData;
         } catch (Exception e) {
-            e.printStackTrace();
+            log.error(e);
         }
     }
+
+    private String[] getLines(File inputFile) throws IOException,
+            FileNotFoundException {
+        String tmp;
+        BufferedReader first = new BufferedReader(new FileReader(inputFile));
+        tmp = first.readLine();
+        String[] splitted = tmp.split("\\;");
+        return splitted;
+    }
 }

Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java
===================================================================
--- trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java	2009-07-26 17:11:04 UTC (rev 115)
+++ trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java	2009-07-30 14:05:04 UTC (rev 116)
@@ -221,4 +221,24 @@
     public String getVariable() {
         return this.variable;
     }
+
+        /**
+     * Method to set the list variable name
+     *
+     * @param variable
+     *            the new variable name
+     * @throws RException
+     *             if something wrong happen while assigning the list to the new
+     *             variable in R.
+     */
+    public void setVariable(String variable) throws RException {
+        this.variable = variable;
+        try {
+            engine.voidEval(toRString());
+        } catch (RException eee) {
+            throw new RException(
+                    "An error occured while trying to assign the list in R",
+                    eee);
+        }
+    }
 }

Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java
===================================================================
--- trunk/src/main/java/org/nuiton/j2r/types/RList.java	2009-07-26 17:11:04 UTC (rev 115)
+++ trunk/src/main/java/org/nuiton/j2r/types/RList.java	2009-07-30 14:05:04 UTC (rev 116)
@@ -30,6 +30,15 @@
     private Log log = LogFactory.getLog(RList.class);
     private List<String> names;
     private List<Object> data;
+    private String setNamesString = "names(%s)<-c(%s)";
+    private String setNameString = "names(%s)[%s]<-\"%s\"";
+    private String getNamesString = "names(%s)";
+    private String getNameString = "names(%s)[%s]";
+    private String indexExceptionText =
+            "Cannot perform operation, index is superior to size.\nIndex : %s\nSize : %s";
+    private String dataInconsistencyText =
+            "There is an inconsistency between the local and distant data.\nLocal data size : %s\nDistant data size : %s";
+    private String noVariable = "No variable name given";
 
     public RList(REngine engine) {
         super();
@@ -62,16 +71,13 @@
      *         the R list
      * @throws RException
      *             if an error occurs while getting back the names from R.
-     * @throws IndexOutOfBoundsException
-     *             when the row.names size get from R is bigger than the local
-     *             data size.
      */
-    public List<String> getNames() throws RException, IndexOutOfBoundsException {
+    public List<String> getNames() throws RException {
 
         if (engine.isAutoCommit()) {
             //Get back the names from R.
-            String[] namesArray = (String[]) engine.eval("names(" +
-                    this.variable + ")");
+            String[] namesArray = (String[]) engine.eval(String.format(
+                    getNamesString, this.variable));
 
             //Check if size is correct, if yes, modify local data.
             if (namesArray.length <= this.data.size()) {
@@ -82,10 +88,9 @@
                 return names;
             } else {
                 //if size is not correct, throw a RException.
-                throw new IndexOutOfBoundsException(
-                        "Data inconsistency, local data is smaller (size : " +
-                        this.data.size() + ") than the names in R (size : " +
-                        namesArray.length + ")");
+                throw new IndexOutOfBoundsException(String.format(
+                        dataInconsistencyText, this.data.size(),
+                        namesArray.length));
             }
         } else {
             return this.names;
@@ -104,18 +109,15 @@
      * 
      * @throws RException
      *             if an error occurs while getting back the name from R.
-     * 
-     * @throws IndexOutOfBoundsException
-     *             if the x index is out of bounds.
      */
-    public String getName(int x) throws RException, IndexOutOfBoundsException {
+    public String getName(int x) throws RException {
 
         //check if the index is valid
         if (x < names.size()) {
             if (engine.isAutoCommit()) {
                 //Get back the names from R.
-                String name = (String) engine.eval("names(" + this.variable +
-                        ")[" + (x + 1) + "]");
+                String name = (String) engine.eval(String.format(getNameString,
+                        this.variable, x + 1));
 
                 //Check if the String is returned.
                 if ((name != null) && (!name.equals(""))) {
@@ -124,8 +126,8 @@
             }
         } else {
             //if String is not returned, throw an IndexOutOfBOundsException.
-            throw new IndexOutOfBoundsException("Your index " + x +
-                    " is not valid");
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, names.size()));
         }
 
         return this.names.get(x);
@@ -140,29 +142,29 @@
      * @throws RException
      *             when the names list is longer than the list length.
      */
-    public void setNames(List<String> names) throws RException,
-            IndexOutOfBoundsException {
+    public void setNames(List<String> names) throws RException {
 
         //Check if the size is correct, if yes, do the modifications and send them to R.
         if (names.size() <= data.size()) {
             this.names = names;
 
             //Create the r instruction (names(var)<-c("name 1",...,"name x")).
-            String rexp = "names(" + this.variable + ")<-c(";
+            String namesString = "";
             for (int i = 0; i < this.names.size(); i++) {
-                rexp += "\"" + names.get(i) + "\",";
+                if (i != 0) {
+                    namesString += ",";
+                }
+                namesString += "\"" + names.get(i) + "\"";
             }
-            rexp = rexp.substring(0, rexp.length() - 1) + ")";
+            String rexp = String.format(setNamesString, this.variable,
+                    namesString);
 
             //Send the r instruction to the engine.
             engine.voidEval(rexp);
         } else {
             //if size is not correct, throw a IndexOutOfBoundsException.
-            throw new IndexOutOfBoundsException(
-                    "Cannot assign the names attribute, the names List is too long.\nThe size of names (" +
-                    names.size() +
-                    ") must be shorter or equal to the list length(" +
-                    data.size() + ").");
+            throw new IndexOutOfBoundsException(String.format(
+                    dataInconsistencyText, names.size(), data.size()));
         }
     }
 
@@ -175,11 +177,8 @@
      *            Name of the object.
      * @throws RException
      *             if an error occur while in R
-     * @throws IndexOutOfBoundsException
-     *             when the index is out of the list bounds.
      */
-    public void setName(int x, String name) throws RException,
-            IndexOutOfBoundsException {
+    public void setName(int x, String name) throws RException {
         //check if the index is valid
         if (x < data.size()) {
             for (int i = 0; i <= x; i++) {
@@ -199,16 +198,15 @@
             }
 
             //create the r instruction (names(var)[x]<-"name")
-            String rexp = "names(" + this.variable + ")[" + (x + 1) + "]<-\"" +
-                    name + "\"";
+            String rexp = String.format(setNameString, this.variable, x + 1,
+                    name);
 
             //Send the R instruction to the engine.
             engine.voidEval(rexp);
         } else {
             //if index is out of bounds, throw a IndexOutOfBOundsException
-            throw new IndexOutOfBoundsException(
-                    "Cannot assign the name, the index is out of bounds.\nIndex :" +
-                    x + "; data.frame size : " + data.size() + ".");
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, data.size()));
         }
     }
 
@@ -242,26 +240,6 @@
     }
 
     /**
-     * Method to set the list variable name
-     * 
-     * @param variable
-     *            the new variable name
-     * @throws RException
-     *             if something wrong happen while assigning the list to the new
-     *             variable in R.
-     */
-    public void setVariable(String variable) throws RException {
-        this.variable = variable;
-        try {
-            engine.voidEval(toRString());
-        } catch (RException eee) {
-            throw new RException(
-                    "An error occured while trying to assign the list in R",
-                    eee);
-        }
-    }
-
-    /**
      * Method to export the list in a String for evaluation in R.
      * 
      * @return a R string representation of the list to create it in R.
@@ -270,10 +248,7 @@
      */
     @Override
     public String toRString() throws RException {
-        if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot instantiate data.frame in R, no variable name given");
-        }
+        testVariable();
 
         String returnString = this.variable + "<-list(";
         if ((this.data != null) && (!(this.data.isEmpty()))) {
@@ -317,10 +292,7 @@
      *             if no variable name has been given to the list
      */
     public void set(int x, double data) throws RException {
-        if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
-        }
+        testVariable();
         for (int i = 0; i <= x; i++) {
             try {
                 this.data.get(i);
@@ -350,10 +322,7 @@
      *             if no variable name has been given to the list
      */
     public void set(int x, Boolean data) throws RException {
-        if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
-        }
+        testVariable();
         for (int i = 0; i <= x; i++) {
             try {
                 this.data.get(i);
@@ -385,15 +354,9 @@
      *            value to set
      * @throws RException
      *             if no variable name has been given to the list
-     * @throws IndexOutOfBoundsException
-     *             if the x coordinate is not correct.
      */
-    public void set(int x, String data) throws RException,
-            IndexOutOfBoundsException {
-        if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
-        }
+    public void set(int x, String data) throws RException {
+        testVariable();
         for (int i = 0; i <= x; i++) {
             try {
                 this.data.get(i);
@@ -421,14 +384,9 @@
      *            value to set
      * @throws RException
      *             if no variable name has been given to the list
-     * @throws IndexOutOfBoundsException
-     *             if the x coordinate is not correct.
      */
     public void set(int x, int data) throws RException {
-        if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
-        }
+        testVariable();
         for (int i = 0; i <= x; i++) {
             try {
                 this.data.get(i);
@@ -459,10 +417,7 @@
      *             if no variable name has been given to the list
      */
     public void set(int x, REXP data) throws RException {
-        if ((this.variable.equals("")) || (this.variable == null)) {
-            throw new RException(
-                    "Cannot propage modification in R, no variable name given");
-        }
+        testVariable();
         for (int i = 0; i <= x; i++) {
             try {
                 this.data.get(i);
@@ -491,13 +446,11 @@
      * @return the Object located at the [x] coordinate
      * @throws RException
      *             if no variable name has been given to the list
-     * @throws IndexOutOfBoundsException
-     *             if the xcoordinate is not correct.
      */
-    public Object get(int x) throws RException, IndexOutOfBoundsException {
+    public Object get(int x) throws RException {
         if (x >= this.data.size()) {
-            throw new IndexOutOfBoundsException("The x value is too high : " + x +
-                    ">=" + this.data.size());
+            throw new IndexOutOfBoundsException(String.format(indexExceptionText,
+                    x, this.data.size()));
         }
         if (engine.isAutoCommit()) {
             Object returnObject = engine.eval(this.variable + "[[" + (x + 1) +
@@ -566,8 +519,8 @@
         }
 
         //update names
-        String[] namesArray = (String[]) engine.eval("names(" + this.variable +
-                ")");
+        String[] namesArray = (String[]) engine.eval(String.format(
+                getNamesString, this.variable));
         for (int i = 0; i < namesArray.length; i++) {
             names.add(namesArray[i]);
         }
@@ -591,4 +544,11 @@
             attributes.put(key, attribute);
         }
     }
+
+    public void testVariable() throws RException {
+        if ((this.variable.equals("")) || (this.variable == null)) {
+            throw new RException(
+                    noVariable);
+        }
+    }
 }

    

[LutinJ2R-commits] r116 - trunk/src/main/java/org/nuiton/j2r/types

jcouteau＠users.labs.libre-entreprise.org