Dustin Schreader

Sorry, I found the problem I forgot to write out the entire thing: java -cp . Test. So it does work now. disregard the post.

Saptaparna Dhar wrote:Thank you for your assistance.
I have set the path as suggested and now I compile the program by simply typing javac <classname>.java

Mr. John, the output which I got by typing java in the command prompt is--

Usage: java [-options] class [args...] (to execute a class) or java [-options] -jar jarfile [args...] (to execute a jar file) where options include: -d32 use a 32-bit data model if available -d64 use a 64-bit data model if available -client to select the "client" VM -server to select the "server" VM -hotspot is a synonym for the "client" VM [deprecated] The default VM is client. -cp <class search path of directories and zip/jar files> -classpath <class search path of directories and zip/jar files> A ; separated list of directories, JAR archives, and ZIP archives to search for class files. -D<name>=<value> set a system property -verbose[:class|gc|jni] enable verbose output -version print product version and exit -version:<value> require the specified version to run -showversion print product version and continue -jre-restrict-search | -no-jre-restrict-search include/exclude user private JREs in the version search -? -help print this help message -X print help on non-standard options -ea[:<packagename>...|:<classname>] -enableassertions[:<packagename>...|:<classname>] enable assertions with specified granularity -da[:<packagename>...|:<classname>] -disableassertions[:<packagename>...|:<classname>] disable assertions with specified granularity -esa | -enablesystemassertions enable system assertions -dsa | -disablesystemassertions disable system assertions -agentlib:<libname>[=<options>] load native agent library <libname>, e.g. -agentlib:hprof see also, -agentlib:jdwp=help and -agentlib:hprof=help -agentpath:<pathname>[=<options>] load native agent library by full pathname -javaagent:<jarpath>[=<options>] load Java programming language agent, see java.lang.instrument -splash:<imagepath> show splash screen with specified image See http://java.sun.com/javase/reference for more details.

I have a related issue. I am getting the above message and I have entered the command:
java -cp RunTestAndDisplayResults
Why does this screen appear in the windows command prompt and what can I do to run my program. I created a simple hello world program and used:
java -cp HelloWorld
and I got the output Hello world, so it must have executed fine actually the same thing is happening to my hello world program too. I do also have a jar file that I needed for jsch-0.1.48.jar in the same folder as the java and .class files. I'd Also like to mention that I ran this in eclipse and it works just fine. I've never used the command prompt to execute java before. Thank you!

I ended up doing this and it worked.. sort of.
//enter items to go into array System.out.println("Enter items to be stored in array. When done enter letter x."); vertex.arrayAL.add(0); int w = 2; System.out.print("Enter a[1]:\t"); while (in.hasNextInt()){ System.out.print("Enter a[" + w + "]:\t"); arrayVal = in.nextInt(); vertex.arrayAL.add(arrayVal); w++; }
The problem is the next part of my code is picking up the letter x that is typed in last to end the while loop and runs the last else statement to throw back x is not an option!
System.out.println("Do you want to use bypass or next vertex?"); System.out.print("b - bypass, n - next vertex: \t"); while(!byVert.equals("n") || !byVert.equals("N") || !byVert.equals("b") || !byVert.equals("B")){ //slight problem using previous letter as in.next so it will //cause the last else statement to go off every time but it still works byVert = in.next(); if (byVert.equals("b") || byVert.equals("B")){ vertex.Bypass(prefixLength, maxLength, maxDigit); }else if (byVert.equals("n") || byVert.equals("N")){ vertex.nextVertex(prefixLength, maxLength, maxDigit); }else System.out.println(byVert + " is not an option!"); }

I've created a do while loop that does insert items into an array list like I want it to but the problem is the output to console. I want the user to enter items into an array so I have a prompt like so:

Enter a[1]: 1 2 Enter a[2]: 3 Enter a[3]: 4 Enter a[4]: 5

As you notice it does not print Enter a[2]: to the correct part of the screen, it's like it skips the second iteration to print the prompt yet it still stores to in array[2]. Here is my code:

System.out.println("Enter items to be stored in array. When done enter a letter."); vertex.arrayAL.add(0); int w = 1; do{ System.out.print("Enter a[" + w + "]:\t"); arrayVal = in.nextInt(); vertex.arrayAL.add(arrayVal); w++; }while (in.hasNextInt()); int[] array = vertex.createArray(); for (int f = 0; f < array.length; f++) System.out.println(array[f]);

I'm trying to get characters from or actually just single letters from an arraylist. Am I able to use charAt on an array list, I'm getting an error when I try it: cannot find symbol on lines 73, 75, 77, 79. Should I use substring instead?
/* * To change this template, choose Tools | Templates * and open the template in the editor. */ package profile; import java.util.*; import org.apache.commons.lang.StringUtils; /** * * @author doodthatscool */ public class Profile { /** * @param args the command line arguments */ public static void main(String[] args) { // TODO code application logic here Scanner in = new Scanner(System.in); //create array list for sequences ArrayList seqAL = new ArrayList(); //create array to store positions of start int[] posArray = new int[seqAL.size()]; //create array for A int[] a = new int[seqAL.size()]; //create array for G int[] g = new int[seqAL.size()]; //create array for C int[] c = new int[seqAL.size()]; //create array for T int[] t = new int[seqAL.size()]; String sequence = ""; String consensus = ""; String newSeq = ""; int mLength = 0; int startPos = 0; int score = 0; // grab seqence until user inputs nothing // use void ensureCapacity(int CAP) to increase performence System.out.println("Press enter after each sequence and type X and enter when completed."); while (!sequence.equals("X") || !sequence.equals("x")) { sequence = in.nextLine(); seqAL.add(sequence); }//end while loop //get length for motif System.out.println("Enter the length for Motif."); mLength = in.nextInt(); //get starting positions for each motif for (int i = 0; i < seqAL.size(); i++) { System.out.println("Enter motif starting position for sequence " + i + "."); posArray[i] = in.nextInt(); }//end for loop //output alignment of sequences defined by s for (int j = 0; j < seqAL.size(); j++) { sequence = seqAL.get(j).toString(); newSeq = sequence.substring(posArray[j], mLength + posArray[j]); System.out.println(newSeq); }//end for loop //Count up all the A,C,G,T for (int k = 0; k < seqAL.size(); k++) { if (seqAL.charAt(k).equals('A')) { a[k] = a[k] + 1; } else if (seqAL.charAt(k).equals('C')) { c[k] = c[k] + 1; } else if (seqAL.charAt(k).equals('G')) { g[k] = g[k] + 1; } else if (seqAL.substring(k).equals('T')) { t[k] = t[k] + 1; } }//end for loop //output profile sequence System.out.print("A"); for (int w = 0; w < a.length; w++) { System.out.print(a[w]); } //System.out.print(StringUtils.countMatches(,); System.out.print("C"); for (int w = 0; w < c.length; w++) { System.out.print(c[w]); } System.out.print("G"); for (int w = 0; w < g.length; w++) { System.out.print(g[w]); } System.out.print("T"); for (int w = 0; w < t.length; w++) { System.out.print(t[w]); } for (int k = 0; k > a.length; k++) { //output consensus sequence //check if a is the largest if(a[k] > c[k] || a[k] > g[k] || a[k] > t[k]) { consensus = consensus.concat("A"); score = score + a[k]; } //check if c is the largest if(c[k] > a[k] || c[k] > g[k] || c[k] > t[k]) { consensus = consensus.concat("C"); score = score + c[k]; } //check if g is the largest if(g[k] > c[k] || g[k] > a[k] || g[k] > t[k]) { consensus = consensus.concat("G"); score = score + g[k]; } //check if t is the largest if(t[k] > c[k] || t[k] > g[k] || t[k] > a[k]) { consensus = consensus.concat("T"); score = score + t[k]; } }//end for loop //print consensus System.out.println("Consensus sequence: " + consensus); System.out.println("Score of consensus: " + score); } }

The only problem with that is when I want to create an ArrayList<Patient> patientList.... from the CSV file the scanner reads in the arraylist does not except the data from the CSV file because it's a string. I get an error saying cannot find symbol method Patient(java.lang.String).

I wrote my own patient class and I am able to pass strings to the constructor. I just couldn't figure out how to convert string to generic type.. which I still don't really understand but someone had a similar code for the conversion. I think it was a little to much for me to handle. I'm just trying to read a string from a text file and insert that into an arraylist<Patient> and I couldn't figure out what to do to convert it.

Found a conversion example and slightly modified it. I don't understand why they would use interface but I got it to compile. Thanks for the help everyone!
interface Transformer<I, O> { O transform(I input); } private Patient conversion(Scanner s, Transformer<String, Patient> transformer) throws IOException { String element = s.next(); Patient elem = transformer.transform(element); return elem; } public void addPt(String ptCode, String ptName, String dr, String floor, Transformer<String, Patient> Transformer) throws IOException { ArrayList<Patient> patientList = new ArrayList<Patient>(); try { Scanner s = new Scanner(new File("database.CSV")); while (s.hasNextLine()) { Patient info = conversion(s, Transformer); patientList.add(info); } } catch (FileNotFoundException ex) { Logger.getLogger(ServiceMaster.class.getName()).log(Level.SEVERE, null, ex); } Patient newPatient = new Patient(ptCode, ptName, "Patient", dr, floor); Patient toString = newPatient.toString(); patientList.add(toString); }

Netbeans threw the logger automatically since I needed a try catch so I haven't had time to mess around with that yet. I wrote down pseudo code of all the classes. I have created a person class, a physician class, a patient class, and a person interface all methods having no more than one variable except the constructor. My addPt method looks cleaner already I think. I have looked through oracles class arraylist, tutorials on generics. I didn't know oracle had tutorials on conversions I will look those up now. Thank you!

Ok I've been doing some reading and found out a little more about generics and arraylists and scanners. Since patientList is an ArrayList of type <Patient> I should be able to do add(E e) or in my case patientList.add(Patient (s.next())); and since next() from the scanner returns a String I should be able to say that s.next() string is of type Patient correct? Well I guess it's not correct because I get the error cannot find symbol method Patient(java.lang.String) on line 7. I don't understand why it wants to see it as a method instead of making s.next() type Patient.
public void addPt(String ptCode, String ptName, String dr, String floor) { ArrayList<Patient> patientList = new ArrayList<Patient>(); try { Scanner s = new Scanner(new File("database.CSV")); while (s.hasNextLine()) { patientList.add(Patient (s.next())); } } catch (FileNotFoundException ex) { Logger.getLogger(ServiceMaster.class.getName()).log(Level.SEVERE, null, ex); } Patient newPatient = new Patient(ptCode, ptName, "Patient", dr, floor); Patient toString = newPatient.toString(); patientList.add(toString); }

I think I made progress but still no go with error line 7. Cannot find symbol variable next location variable s of type java.util.scanner.
public void addPt(String ptCode, String ptName, String dr, String floor, String time) { try{ Scanner s = new Scanner(new File("database.CSV")); ArrayList<Patient> patient = new ArrayList<Patient>(); while (s.hasNextLine()){ patient.add(new Patient(s.next)); } s.close(); for (int w = 0; w < patient.size(); w++) { Patient temp = patient.get(w); String[] results = temp.split(","); if (results[0].equals(ptCode) && results[5].equals("pt")) { JOptionPane.showMessageDialog(null, "Patient already exists", "error", JOptionPane.ERROR_MESSAGE); } else if (results[0].equals(ptCode)) { results[3] = floor; patient.add(new Patient(ptCode, ptName, dr, floor, "pt")); } else { patient.add(new Patient(ptCode, ptName, dr, floor, "pt")); } } // Create file FileWriter fstream = new FileWriter("database.CSV"); BufferedWriter out = new BufferedWriter(fstream); for( int i=0; i<patient.size(); i++){ out.write(patient.get(i)); } //Close the output stream out.close(); }catch (Exception e){//Catch exception if any System.out.println("Error: " + e.getMessage()); } }

Hello,
I'm getting an error when I try to add an element to an ArrayList from my Scanner and I think it has something to do with scanner s not being of type <Patient>. Am I right, how do I fix it? Error line 7.
public void addPt(String ptCode, String ptName, String dr, String floor, String time) { try{ Scanner s = new Scanner(new File("database.CSV")); ArrayList<Patient> patient = new ArrayList<Patient>(); while (s.hasNextLine()){ patient.add(s.next); } s.close(); for (int w = 0; w < patient.size(); w++) { Patient temp = patient.get(w); String[] results = temp.split(","); if (results[0].equals(ptCode) && results[5].equals("pt")) { JOptionPane.showMessageDialog(null, "Patient already exists", "error", JOptionPane.ERROR_MESSAGE); } else if (results[0].equals(ptCode)) { results[3] = floor; results[4] = getDate(); } else { patient.add(new Patient(ptCode, ptName, dr, floor, getDate(), "pt")); } } // Create file FileWriter fstream = new FileWriter("database.CSV"); BufferedWriter out = new BufferedWriter(fstream); for( int i=0; i<patient.size(); i++){ out.write(patient.get(i)); } //Close the output stream out.close(); }catch (Exception e){//Catch exception if any System.out.println("Error: " + e.getMessage()); } }

Thank you I will take a look.

So since I had a an array of arrays previously and now I want to use an arrayList it seems easy enough to add more and more elements to an ArrayList but how do I sort through the list like i did when I was using a for loop to sort through the array of arrays? It seems like I'd be sorting through each entire string of combined variables created by my patient class when, let's say I just wanted to compare against the code of the pt to do a search on them not the code, name, physician, floor, and time.
public void addPt(String ptCode, String ptName, String dr, String floor, String time) { Scanner s = new Scanner(new File("database.CSV")); ArrayList<Patient> patient = new ArrayList<Patient>(); while (s.hasNext()){ patient.add(s.next()); } s.close(); for (int w = 0; w < patient.length; w++) { if (/*?*/.equals(ptCode) && /*?*/.equals("patient")) { JOptionPane.showMessageDialog(null, "Patient already exists", "error", JOptionPane.ERROR_MESSAGE); } else if (/*?*/.equals(ptCode)) { //replace the current patient room info (from ptCode) according to the new room info provided if pt already exists } else { patient.add(new Patient(ptCode, ptName, dr, floor, getTime(), "pt")); } } try{ // Create file FileWriter fstream = new FileWriter("database.CSV"); BufferedWriter out = new BufferedWriter(fstream); for( int i=0; i<patient.size(); i++){ out.write(patient.get(i)); } //Close the output stream oout.close(); }catch (Exception e){//Catch exception if any System.out.println("Error: " + e.getMessage()); } }

So since I had a an array of arrays previously and now I want to use an arrayList it seems easy enough to add more and more elements to an ArrayList but how do I sort through the list like i did when I was using a for loop to sort through the array of arrays? It seems like I'd be sorting through each entire string of combined variables created by my patient class when, let's say I just wanted to compare against the code of the pt to do a search on them not the code, name, physician, floor, and time.
ArrayList<Patient> patient = new ArrayList<Patient>(); for (int w = 0; w< patient.length; w++) { if (/*?*/.equals(ptCode) && /*?*/.equals("patient")) { JOptionPane.showMessageDialog(null, "Patient already exists", "error", JOptionPane.ERROR_MESSAGE); } else if (/*?*/.equals(ptCode)) { //replace the current patient room info (from ptCode) according to the new room info provided if pt already exists } else { patient.add(new Patient(ptCode, ptName, dr, floor, getTime(), "pt")); } } try{ BufferedWriter out = new BufferedWriter("database.CSV"); for( int i=0; i<patient.size(); i++){ out.write(patient.get(i)); } //Close the output stream out.close(); }catch (Exception e){//Catch exception if any System.out.println("Error: " + e.getMessage()); }

Also, I've been trying to look up more on "this" I learned it a while ago in class and I'm still confused as to how I'd use it but Winston gave it in this example.
public class Patient { private int code; private String name; private String doctor; private int floor; private Calendar admitted; public Patient(int code, String name, String doctor, int floor, Date admitted) { this.code = code; this.name = name; this.doctor = doctor; this.floor = floor; this.admitted = new GregorianCalendar(admitted); } public String toString() { //code to return Patient info as a string } }
is this.code referring to the private int code; at the top of the class that that it can differentiate between the parameters of the method patient and the class variables? And if that's correct is that the only reason this. is used, to differentiate between variables?