I would like to call an R script from Java. I have done google searches on the topic, but almost all of the results I have seen would require me to add a dependency to some third party library. Can anyone show me a good way to accomplish the same thing without adding any dependencies to my code?
I am using a windows machine, so perhaps I might use the command line to start R (if it is not already open) and to run a specific R script. But I have never written command line code (or called it from Java) so I would need code examples.
I am including working sample code that I wrote for one possible approach below, using my command line idea. In my in-line-comments below, you can see that Step Three in AssembleDataFile.java is intentionally left blank by me. If you think that you can make the command line idea work, then please show me what code to write in Step Three.
Also, feel free to suggest another approach that, hopefully, does not involve adding any more dependencies to my code.
And, as always, I very much appreciate any links you might post to articles/tutorials/etc related to this question.
Here is what I have so far:
AssembleDataFile.java
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintWriter;
public class AssembleDataFile {
static String delimiter;
static String localPath = "C:\\test\\cr\\";
static String[][] myDataArray;
public static void main(String[] args) {
String inputPath = localPath+"pd\\";
String fileName = "MSData.txt";
delimiter = "\\t";
// Step One: Import data in two parts
try {
// 1A: get length of data file
BufferedReader br1 = new BufferedReader(new FileReader(inputPath+fileName));
int numRows = 0;
int numCols = 0;
String currentRow;
while ((currentRow = br1.readLine()) != null) {
numRows += 1;
numCols = currentRow.split(delimiter).length;}
br1.close();
//1B: populate data into array
myDataArray = new String[numRows][numCols+1];
BufferedReader br2 = new BufferedReader(new FileReader(inputPath+fileName));
String eachRow;
int rowIdx = 0;
while ((eachRow = br2.readLine()) != null) {
String[] splitRow = eachRow.split(delimiter);
for(int z = 0;z < splitRow.length;z++){myDataArray[rowIdx][z] = splitRow[z];}
rowIdx += 1;}
br2.close();
// Step Two: Write data to csv
String rPath = localPath+"r\\";
String sFileName = rPath+"2colData.csv";
PrintWriter outputWriter = new PrintWriter(sFileName);
for(int q = 0;q < myDataArray.length; q++){
outputWriter.println(myDataArray[q][8]+", "+myDataArray[q][9]);
}
outputWriter.close();
//Step Three: Call R script named My_R_Script.R that uses 2ColData.csv as input
// not sure how to write this code. Can anyone help me write this part?
// For what it is worth, one of the R scripts that I intend to call is included below
//
//added the following lines here, per Vincent's suggestion:
String rScriptFileName = rPath+"My_R_Script.R";
Runtime.getRuntime().exec("mypathto\\R\\bin\\Rscript "+rScriptFileName);
//
//
//Step Four: Import data from R and put it into myDataArray's empty last column
try {Thread.sleep(30000);}//make this thread sleep for 30 seconds while R creates the needed file
catch (InterruptedException e) {e.printStackTrace();}
String matchFileName = rPath+"Matches.csv";
BufferedReader br3 = new BufferedReader(new FileReader(matchFileName));
String thisRow;
int rowIndex = 0;
while ((thisRow = br3.readLine()) != null) {
String[] splitRow = thisRow.split(delimiter);
myDataArray[rowIndex][numCols] = splitRow[0];
rowIndex += 1;}
br3.close();
//Step Five: Check work by printing out one row from myDataArray
//Note that the printout has one more column than the input file had.
for(int u = 0;u<=numCols;u++){System.out.println(String.valueOf(myDataArray[1][u]));}
}
catch (FileNotFoundException e) {e.printStackTrace();}
catch (IOException ie){ie.printStackTrace();}
}
}
My_R_Script.R
myCSV <- read.csv(file="2colData.csv",head=TRUE,sep=",")
pts = SpatialPoints(myCSV)
Codes = readShapeSpatial("mypath/myshapefile.shp")
write.csv(ZipCodes$F[overlay(pts,Codes)], "Matches.csv", quote=FALSE, row.names=FALSE)
EDIT:
Here is the error message that is being thrown when I add Runtime.getRuntime().exec("Rscript "+rScriptFileName); to the code above:
java.io.IOException: Cannot run program "Rscript": CreateProcess error=2, The system cannot find the file specified
at java.lang.ProcessBuilder.start(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at AssembleDataFile.main(AssembleDataFile.java:52)
Caused by: java.io.IOException: CreateProcess error=2, The system cannot find the file specified
at java.lang.ProcessImpl.create(Native Method)
at java.lang.ProcessImpl.<init>(Unknown Source)
at java.lang.ProcessImpl.start(Unknown Source)
... 5 more
SECOND EDIT:
The code above now works because I followed Vincent's suggestions. However, I had to put in a sleep command in order to give the R script enough time to run. Without the sleep command, the java code above throws an error saying that the Matches.csv file does not exist. I am concerned that a 30 second sleep period is too rough of an instrument. Can anyone show me code that gets the java program to wait until the R program has a chance to create Matches.csv? I hesitate to use thread tools because I have read that poorly designed threads can cause bugs that are nearly impossible to localize and fix.
You just want to call an external application: wouldn't the following work?
Runtime.getRuntime().exec("Rscript myScript.R");
You can easily adapt this code: http://svn.rforge.net/org/trunk/rosuda/REngine/Rserve/test/StartRserve.java
Among other things it finds R and runs a fixed script in R - you can replace that script with with your script and ignore the last two methods.
Do not wait for the process to finish with Thread.sleep()...
Use the waitFor() method instead.
Process child = Runtime.getRuntime().exec(command, environments, dataDir);
int code = child.waitFor();
switch (code) {
case 0:
//normal termination, everything is fine
break;
case 1:
//Read the error stream then
String message = IOUtils.toString(child.getErrorStream());
throw new RExecutionException(message);
}
BufferedReader reader = null;
Process shell = null;
try {
shell = Runtime.getRuntime().exec(new String[] { "/usr/bin/Rscript", "/media/subin/works/subzworks/RLanguage/config/predict.R" });
reader = new BufferedReader(new InputStreamReader(shell.getInputStream()));
String line;
while ((line = reader.readLine()) != null) {
System.out.println(line);
}
} catch (IOException e) {
e.printStackTrace();
}
...would require me to add a dependency to some third party library...
Why is that so bad? You make it sound like "...would require me to assault a honeybadger with a baseball bat..." I don't see the harm, especially if it works.
Maybe RCaller can help you. No JNI required.
Related
I have launched my program that have two loop like this :
for(int i=0;i<100;i++)
String[] articles = getArticles(i);
for(int j=0;j<articles.length;j++)
process(articles[j]);
Can I modify the running program so it stop at i = 1? If how to do that?
The program will take days to finish and I want to stop but I must know where it was stoped so the next time I can resume it.
Unfortunately you won't be able to stop a running program at a predictable spot unless debugger is on.
Stop your program, change the code, and start it up again.
It is possible (lots of things are). But it can be very, very hard - unless you are skilled at looking at Java bytecode and know your OS internals, I would not try.
Assuming you are running under linux, you can suspend and restart processes via kill -STOP <pid> and kill -CONT <pid>. You can also take a stack-trace of a running java process via jstack, and look at the running threads and decompiled code.
You could do this
static boolean stopLoop = false;
static int[] runLoop(int i, int j) {
for(;i<100;i++) {
if(stopLoop) return new int[i, j];
String[] articles = getArticles(i);
for(;j<articles.length;j++) {
process(articles[i]);
}
j = 0;
}
}
(You probably wanted to write process(articles[j]); in your inner loop.)
You can save last value of i and j into a file after processing of each article, then you can terminate your program anytime you want, and next time just read the values of i and j from your file and you don't have to process them again.
Or set 100 article processes per program run, or process for 20 minutes, there are so many possibilities.
There is no straightforward way to do this, but with a little extra legwork it can be done. One way is to output the latest successful iteration to persistent storage (like a file), then read the file if it exists to find out where to start. The example below shows one way to do it:
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintWriter;
public class Test
{
public static void main(String[] args)
{
int start;
// Try to get the last successful run
File file = new File(System.getenv("HOME"), ".myprog");
if(file.exists()) {
try(BufferedReader reader = new BufferedReader(new FileReader(file))) {
String line = reader.readLine();
if(line == null) {
throw new NumberFormatException("Empty file, no number");
}
start = Integer.parseInt(line);
} catch(IOException | NumberFormatException ex) {
System.err.println("Unable to read progress: " + ex.getMessage());
System.err.println("Starting from the beginning");
start = 0;
}
} else {
start = 0;
}
// ... Your declarations go here
for(int i = start; i < 100; i++) {
String[] articles = getArticles(i);
for(int j=0;j<articles.length;j++) {
process(articles[i]);
}
// Record last successful run (this reopens the file every time)
try(PrintWriter writer = new PrintWriter(file)) {
writer.println(i);
} catch(IOException ex) {
System.err.println("Unable to record progress: " + ex.getMessage());
}
}
}
}
Note that I run on a Linux machine, so I called my file ~/.myprog. You may want to change that.
I have a project where program has to open notepad file and after entering text and saving that notepad file program should display number of words in that file and it should delete the entered content in the file.
iam getting this error Error not derjava.lang.NullPointerException after running the program.
though after entering some text in Mytext.txt and saving it?
my question is why BufferedReader is reading empty file even though iam saving the file with some content.
Appreciate the help..
public class Notepad_Example {
public static void main(String[] jfb) {
try {
ProcessBuilder proc = new ProcessBuilder("notepad.exe", "C:\\Java Projects\\Reverse String\\src\\Mytext.txt");
proc.start();
BufferedReader br;
String s;
br = new BufferedReader(new FileReader("C:\\Java Projects\\Reverse String\\src\\Mytext.txt"));
s = br.readLine();
char c[] = new char[s.length()];
int j = 0;
for (int i = 0; i < s.length(); i++) {
if (s.charAt(i) != ' ') {
c[i] = s.charAt(i);
} else {
j++;
}
}
System.out.println("number of words are " + (j + 1));
br.close();
} catch (Exception hj) {
System.out.println("Error not der" + hj);
}
try {
FileWriter fw = new FileWriter("C:\\Java Projects\\Reverse String\\src\\Mytext.txt");
fw.close();
} catch (Exception hj) {
System.out.println("Error not der" + hj);
}
}
}
The issue you are having is here:
ProcessBuilder proc=new ProcessBuilder("notepad.exe","C:\\Java Projects\\Reverse String\\src\\Mytext.txt");
proc.start();
proc.start() is returning the freshly started process. You'll have to give the user the chance to edit and save the file and close the editor before you can read from that file. That is you have to wait for that process to finish before you can start using the results (the saved file) of that process.
So do instead something like this:
Process process = proc.start();
int result = process.waitFor();
if (result == 0) {
// Do your rest here
} else {
// give error message as the process did not finish without error.
}
Some further remarks:
The rest of your code also appears to have some issues.
You are only reading one line of that file. What if the user is using new lines?
The exception handling is not very good, at the very least print the stack trace of the exception which will give you further hints of where an exception was occuring
If you are using Java 7, read on try with resources; if you are using Java 6, add finally blocks to make sure your resources (the streams) are getting closed.
When you run proc.start(); it is not going to block and waitfor the process to end, it will continue running.
You will need to call the proc.waitFor() method, to block until it has finished.
NOTE
we have had some weird behaviour when using the process builder...
we used to start the process with a
new ProcessBuilder("notepad.exe", "C:\\Java Projects\\Reverse String\\src\\Mytext.txt");
but that started to fail wen we upgraded to Win7 and Java7 - we we not sure where this problem really originated, but we changed out Code like this:
String[] cmd = new String[]{"notepad.exe", "C:\\Java Projects\\Reverse String\\src\\Mytext.txt"};
new ProcessBuilder(cmd);
and since then it worked correct!
I have the code below, which simply reads all the files from a folder. There are 20,000 files in this folder. The code works good on a local folder (d:/files), but fails on a network path (//robot/files) after reading about 1,000 - 2,000 files.
Update: the folders are copies of each other.
What causes this problem and how to fix it?
package cef_debug;
import java.io.*;
public class Main {
public static void main(String[] args) throws Throwable {
String folder = args[0];
File[] files = (new File(folder)).listFiles();
String line;
for (int i = 0; i < files.length; i++) {
BufferedReader br = new BufferedReader(new FileReader(files[i]));
while ((line = br.readLine()) != null) {
}
br.close();
}
}
}
I get the following error when reading from a network path (//robot/files):
Exception in thread "main" java.io.IOException: Too many open files
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:106)
at java.io.FileReader.<init>(FileReader.java:55)
at cef_debug.Main.main(Main.java:12)
Java Result: 1
Line 12 is the line:
BufferedReader br = new BufferedReader(new FileReader(files[i]));
There is a documented bug for some java versions and some file opens to hit a limit of 2035. It is possible that you might've just hit that.
From the comments:
To clarify the issue, on win32 system there are three ways to open a
file:
1: Using Win32 API
2: Using MFC class framework lib.
3: using C-Library API (open() and fopen())
Other than the third option, i.e. option 1 and 2 have practically no
limitation in opening number of files. The third method is restricted
(for the reason not known to me) to open only approx. 2035 files. That
is why MS JVM is able to open unlimited (practically) files, but SUN
JVM fails after 2035 files (my guess is it is using 3rd method to
open file).
Now, this is an old issue fixed quite some time ago, but it is possible that they would be using the same function on network access, where the bug could still exist.
Even without closing the handle or the stream, windows should be able to open >10000 file handles and keep them open, as demonstrated by this test code in the bug comments:
import java.util.*;
import java.io.*;
// if run with "java maxfiles 10000", will create 10k files in the current folder
public class maxfiles
{
static int count = 0;
static List files = new ArrayList();
public static void main(String args[]) throws Exception
{
for (int n = 0; n < Integer.parseInt(args[0]); n++) {
File f = new File("file" + count++);
//save ref, so not gc'ed
files.add(new PrintStream(new FileOutputStream(f)));
}
Iterator it = files.iterator();
while (it.hasNext()) {
PrintStream out = ( PrintStream) it.next();
out.println("foo");
out.flush();
}
System.out.println("current files open: " + files.size());
} //~main
}
You could test running it on the network share, and report a bug if it fails. You could also try with a different JDK. At least with OpenJDK source, I couldn't see any other calls except WinAPI calls, so I'd try if the behaviour is the same.
Try:
package cef_debug;
import java.io.*;
public class Main {
public static void main(String[] args) throws Throwable {
String folder = args[0];
File[] files = (new File(folder)).listFiles();
String line;
for (int i = 0; i < files.length; i++) {
try {
BufferedReader br = new BufferedReader(new FileReader(files[i]));
while ((line = br.readLine()) != null) {
}
} finally {
try {
if (br != null){
br.close();
}
} catch (IOException e) {
e.printStackTrace();
}
}
}
}
}
First, this is my code :
import java.io.*;
import java.util.Date;
import com.banctecmtl.ca.vlp.shared.exceptions.*;
public class PowershellTest implements Runnable {
public static final String PATH_TO_SCRIPT = "C:\\Scripts\\ScriptTest.ps1";
public static final String SERVER_IP = "XX.XX.XX.XXX";
public static final String MACHINE_TO_MOD = "MachineTest";
/**
* #param args
* #throws OperationException
*/
public static void main(String[] args) throws OperationException {
new PowershellTest().run();
}
public PowershellTest(){}
#Override
public synchronized void run() {
String input = "";
String error = "";
boolean isHanging = false;
try {
Runtime runtime = Runtime.getRuntime();
Process proc = runtime.exec("powershell -file " + PATH_TO_SCRIPT +" "+ SERVER_IP +" "+ MACHINE_TO_MOD);
proc.getOutputStream().close();
InputStream inputstream = proc.getInputStream();
InputStreamReader inputstreamreader = new InputStreamReader(inputstream);
BufferedReader bufferedreader = new BufferedReader(inputstreamreader);
proc.waitFor();
String line;
while (!isHanging && (line = bufferedreader.readLine()) != null) {
input += (line + "\n");
Date date = new Date();
while(!bufferedreader.ready()){
this.wait(1000);
//if its been more then 1 minute since a line has been read, its hanging.
if(new Date().getTime() - date.getTime() >= 60000){
isHanging = true;
break;
}
}
}
inputstream.close();
inputstream = proc.getErrorStream();
inputstreamreader = new InputStreamReader(inputstream);
bufferedreader = new BufferedReader(inputstreamreader);
isHanging = false;
while (!isHanging && (line = bufferedreader.readLine()) != null) {
error += (line + "\n");
Date date = new Date();
while(!bufferedreader.ready()){
this.wait(1000);
//if its been more then 1 minute since a line has been read, its hanging.
if(new Date().getTime() - date.getTime() >= 60000){
isHanging = true;
break;
}
}
}
inputstream.close();
proc.destroy();
} catch (IOException e) {
//throw new OperationException("File IO problem.", e);
} catch (InterruptedException e) {
//throw new OperationException("Script thread problem.",e);
}
System.out.println("Error : " + error + "\nInput : " + input);
}
}
I'm currently trying to run a powershell script that will start/stop a vm (VMWARE) on a remote server. The script work from command line and so does this code. The thing is, I hate how I have to use a thread (and make it wait for the script to respond, as explained further) for such a job. I had to do it because both BufferedReader.readline() and proc.waitFor() hang forever.
The script, when ran from cmd, is long to execute. it stall for 30 sec to 1 min from validating authentification with the server and executing the actual script. From what I saw from debugging, the readline hang when it start receiving those delays from the script.
I'm also pretty sure it's not a memory problem since I never had any OOM error in any debugging session.
Now I understand that Process.waitFor() requires me to flush the buffer from both the error stream and the regular stream to work and so that's mainly why I don't use it (I need the output to manage VM specific errors, certificates issues, etc.).
I would like to know if someone could explain to me why it hangs and if there is a way to just use the typical readline() without having it to hang so hard. Even if the script should have ended since a while, it still hang (I tried to run both the java application and a cmd command using the exact same thing I use in the java application at the same time, left it runingfor 1h, nothing worked). It is not just stuck in the while loop, the readline() is where the hanging is.
Also this is a test version, nowhere close to the final code, so please spare me the : this should be a constant, this is useless, etc. I will clean the code later. Also the IP is not XX.XX.XX.XXX in my code, obviously.
Either explanation or suggestion on how to fix would be greatly appreciated.
Ho btw here is the script I currently use :
Add-PSSnapin vmware.vimautomation.core
Connect-VIServer -server $args[0]
Start-VM -VM "MachineTest"
If you need more details I will try to give as much as I can.
Thanks in advance for your help!
EDIT : I also previously tested the code with a less demanding script, which job was to get the content of a file and print it. Since no waiting was needed to get the information, the readline() worked well. I'm thus fairly certain that the problem reside on the wait time coming from the script execution.
Also, forgive my errors, English is not my main language.
Thanks in advance for your help!
EDIT2 : Since I cannot answer to my own Question :
Here is my "final" code, after using threads :
import java.io.*;
public class PowershellTest implements Runnable {
public InputStream is;
public PowershellTest(InputStream newIs){
this.is = newIs;
}
#Override
public synchronized void run() {
String input = "";
String error = "";
try {
InputStreamReader inputstreamreader = new InputStreamReader(is);
BufferedReader bufferedreader = new BufferedReader(inputstreamreader);
String line;
while ((line = bufferedreader.readLine()) != null) {
input += (line + "\n");
}
is.close();
} catch (IOException e) {
//throw new OperationException("File IO problem.", e);
}
System.out.println("Error : " + error + "\nInput : " + input);
}
}
And the main simply create and start 2 thread (PowerShellTest instances), 1 with the errorStream and 1 with the inputStream.
I believe I made a dumb error when I first coded the app and fixed it somehow as I reworked the code over and over. It still take a good 5-6 mins to run, which is somehow similar if not longer than my previous code (which is logical since the errorStream and inputStream get their information sequentially in my case).
Anyway, thanks to all your answer and especially Miserable Variable for his hint on threading.
First, don't call waitFor() until after you've finished reading the streams. I would highly recommend you look at ProcessBuilder instead of simply using Runtime.exec, and split the command up yourself rather than relying on Java to do it for you:
ProcessBuilder pb = new ProcessBuilder("powershell", "-file", PATH_TO_SCRIPT,
SERVER_IP, MACHINE_TO_MOD);
pb.redirectErrorStream(true); // merge stdout and stderr
Process proc = pb.start();
redirectErrorStream merges the error output into the normal output, so you only have to read proc.getInputStream(). You should then be able to just read that stream until EOF, then call proc.waitFor().
You are currently waiting to complete reading from inputStream before starting to read from errorStream. If the process writes to its stderr before stdout maybe you are getting into a deadlock situation.
Try reading from both streams from concurrently running threads. While you are at it, also remove proc.getOutputStream().close();. It shouldn't affect the behavior, but it is not required either.
I am using a Java Project that gives an user interface for doing some user events. It is not being executed as Runnable thread in main() as in most Swing/Gui applications. Rather it has several class and form files in the source code and is run from command line using another Java program.
But when I am trying to read a certain file by clicking on some input button, the system fails to read the file. The system writes the custom error message into a file named log.txt saved within the project folder.
I have tried
1. Setting breakpoints (the application does not stop at breakpoint)
2. Doing console prints i.e. System.out.println (there is no print on console)
So both the ways of debugging has failed. I am using Eclipse 3.5.2 SDK (Galileo). How can I debug the user events on my applicattion?
The outline of the source class DataImportPanel in project DDMT is listed below. It is giving an exception in the method DataImportPanel.openHeteroFile(File).
DDMT.core.DataImportPanel
...
DDMT.core.DataImportPanel.heteroDistributionModel
...
DDMT.core.DataImportPanel.initComponents()
DDMT.core.DataImportPanel.initComponents().new ActionListener() {...}
...
DDMT.core.DataImportPanel.initComponents().new MouseAdapter() {...}
DDMT.core.DataImportPanel.initComponents().new ActionListener() {...}
DDMT.core.DataImportPanel.jButton2ActionPerformed(ActionEvent)
...
DDMT.core.DataImportPanel.jButton3ActionPerformed(ActionEvent)
DDMT.core.DataImportPanel.openHeteroFile(File)
DDMT.core.DataImportPanel.jButton8ActionPerformed(ActionEvent)
DDMT.core.DataImportPanel.openFile(File)
DDMT.core.DataImportPanel.jButton15ActionPerformed(ActionEvent)
DDMT.core.DataImportPanel.jRadioButton1ActionPerformed(ActionEvent)
DDMT.core.DataImportPanel.buttonGroup1
...
DDMT.core.DataImportPanel.jButton8
DDMT.core.DataImportPanel.jButton9
DDMT.core.DataImportPanel.jLabel1
...
DDMT.core.DataImportPanel.jList1
...
DDMT.core.DataImportPanel.jPanel1
...
DDMT.core.DataImportPanel.jRadioButton1
...
DDMT.core.DataImportPanel.jScrollPane1
...
DDMT.core.DataImportPanel.jTabbedPane1
DDMT.core.DataImportPanel.DistributionTypes
DDMT.core.DataImportPanel.DoubleCellRenderer
Here is the openHeteroFile which is throwing the Data Import exception
private void openHeteroFile(File f)
{
File file = null;
try{
file = f;
file.createNewFile();
FileReader reader = new FileReader(file);
BufferedReader bReader = new BufferedReader(reader);
//The vector that holds the number of columns
attributeNames = new ArrayList<String>();
//Read in the number of pairs
String line = bReader.readLine();
//load the file
heteroDistributionModel = new DefaultListModel();
line = bReader.readLine();
while( line != null )
{
//Set up the RegEx matches
heteroDistM = heteroDistP.matcher(line);
firstM = firstP.matcher(line);
firstM.find();
String output1 = firstM.group()+" (";
for( int j = 0; j< nodeTypes[0].length; j++)
{
if( controlClass.nodes[Integer.parseInt(firstM.group())].getNodeType().equals( nodeTypes[1][j]) )
{
output1 = output1+nodeTypes[0][j]+")";
}
}
String output2 = new String();
while( heteroDistM.find() )
{
attributeNames.add(heteroDistM.group(1));
output2 = output2 + " "+heteroDistM.group(1);
}
heteroDistributionModel.addElement(new String[]{output1, output2});
line = bReader.readLine();
}
for (String attr : attributeNames)
System.out.println(attr); //debug
jList3.setModel(heteroDistributionModel);
jList3.setCellRenderer(new DoubleCellRenderer());
bReader.close();
reader.close();
}catch(IOException ex)
{
controlClass.showError("Data Import: Error: File "+file.getPath()+" is not a valid Heterogeneous data file!");
}catch(Exception ex)
{
ex.printStackTrace(); //debug
controlClass.showError("Data Import: Error: Unknown problem reading file "+file.getPath()+"!");
}
}
There is a little green ladybug right next to the run button that starts the debugger.
I would make sure the proper calls are being made. Also check your brackets, breaks, and returns to make sure the code is actually being read. Please post a SSCCE (Short, Self Contained, Correct Example) so we can view your code to help you out better.
Edit (after OP added some code)
I'm pretty sure your issue is where you file.createNewFile();