public static void collectCounts()

in ctakes-smoking-status/src/main/java/org/apache/ctakes/smokingstatus/patientLevel/PatientLevelSmokingStatus.java [66:224]
123 lines of code
19 McCabe index (conditional complexity)

	public static void collectCounts(String delim){
		try {
			FileReader fr = new FileReader(inputFile);
			BufferedReader reader = new BufferedReader(fr);
			String line = null;
			try {
				//Format of the input information to be processed:
				//Example: docSet35_0106487312_12_200812_12_2008701
				//docSet35 - is something that retrieval api assigns by default to output to a subset (in this case I think that is doc_link_id)
				//01064873 - is the MCN
				//12_12_2008 - this should have been the start date range(which it is not in this case because of programming error)
				//12_12_2008 - this should have been the end date range (which is is not in this case because of programming error)
				//The last n-digits is a sequential numbers.
				boolean currentSmoker = false;
				boolean nonSmoker = false;
				boolean pastSmoker = false;
				boolean smoker = false;

				//collect the counts and fill the hash map
				while ( (line = reader.readLine()) != null) {
					if(line.length()<1) continue;
					line = line.trim();
					System.out.println("Line: " + line);
					String[] parts = line.split(delim);
					String[] parts1 = parts[0].split("_"); //0106487312
					String clinicNumber = parts1[1].substring(0, 8);
					
					System.out.println(parts[1]); //class label
					if (parts[1].equals("PAST_SMOKER")){
						pastSmoker = true;
						System.out.println("past smoker doc");
					}
					if (parts[1].equals("NON_SMOKER")){
						nonSmoker = true;
						System.out.println("non smoker doc");
					}
					if (parts[1].equals("CURRENT_SMOKER")){
						currentSmoker = true;
						System.out.println("current smoker doc");
					}
					if (parts[1].equals("SMOKER")){
						smoker = true;
						System.out.println("smoker doc");
					}
					
					//if a new clinic number
					if (!patientsStatuses.containsKey(clinicNumber)){
						//create a vector for currentSmoker, nonSmoker, pastSmoker, and smoker values
						Vector<Integer> smokingStatusElements = new Vector<Integer>(4);
						if (currentSmoker == true){
							//smokingStatusElements
							smokingStatusElements.insertElementAt(1, 0);
							smokingStatusElements.insertElementAt(0, 1);
							smokingStatusElements.insertElementAt(0, 2);
							smokingStatusElements.insertElementAt(0, 3);
							System.out.println("incrementing current");
						}
						else if (nonSmoker == true){
							smokingStatusElements.insertElementAt(0, 0);
							smokingStatusElements.insertElementAt(1, 1);
							smokingStatusElements.insertElementAt(0, 2);
							smokingStatusElements.insertElementAt(0, 3);
							System.out.println("incrementing non");
						}
						else if (pastSmoker == true){
							//smokingStatusElements[0] = 0;
							
							smokingStatusElements.insertElementAt(0, 0);
							smokingStatusElements.insertElementAt(0, 1);
							smokingStatusElements.insertElementAt(1, 2);
							smokingStatusElements.insertElementAt(0, 3);
							System.out.println("incrementing past");
							
							//System.out.println("past smoker");
						}
						else if (smoker == true){
							//smokingStatusElements[0] = 0;
							
							smokingStatusElements.insertElementAt(0, 0);
							smokingStatusElements.insertElementAt(0, 1);
							smokingStatusElements.insertElementAt(0, 2);
							smokingStatusElements.insertElementAt(1, 3);
							System.out.println("incrementing past");
							
							//System.out.println("past smoker");
						}
						//account for the UNKNOWN category
						else {
							smokingStatusElements.insertElementAt(0, 0);
							smokingStatusElements.insertElementAt(0, 1);
							smokingStatusElements.insertElementAt(0, 2);
							smokingStatusElements.insertElementAt(0, 3);
						}
					
						//clinicNumber = parts1[0] + "_" + clinicNumber;
						patientsStatuses.put(clinicNumber, smokingStatusElements);
					}
					
					//if an existing clinic number
					else {
						Vector<Integer> smokingStatusElements = (Vector<Integer>) patientsStatuses.get(clinicNumber);
						
						//increment the respective smoking status
						if (currentSmoker == true){
							int currentValue = ((Integer) smokingStatusElements.elementAt(0)).intValue();
							currentValue = currentValue + 1;
							smokingStatusElements.setElementAt(currentValue, 0);
							System.out.println("incrementing current: " + currentValue);
							patientsStatuses.put(clinicNumber, smokingStatusElements);
						}
						else if (nonSmoker == true){
							int currentValue = ((Integer) smokingStatusElements.elementAt(1)).intValue();
							currentValue = currentValue + 1;
							smokingStatusElements.setElementAt(currentValue, 1);
							System.out.println("incrementing non: " + currentValue);
							patientsStatuses.put(clinicNumber, smokingStatusElements);
						}
						else if (pastSmoker == true){
							int currentValue = ((Integer) smokingStatusElements.elementAt(2)).intValue();
							currentValue = currentValue + 1;
							smokingStatusElements.setElementAt(currentValue, 2);
							System.out.println("incrementing past: " + currentValue);
							patientsStatuses.put(clinicNumber, smokingStatusElements);
						}
						else if (smoker == true){
							int currentValue = ((Integer) smokingStatusElements.elementAt(3)).intValue();
							currentValue = currentValue + 1;
							smokingStatusElements.setElementAt(currentValue, 3);
							System.out.println("incrementing smoker: " + currentValue);
							patientsStatuses.put(clinicNumber, smokingStatusElements);
						}
						//account for the UNKNOWN category
						else {
							//do nothing
						}
					
						//patientsStatuses.put(clinicNumber, smokingStatusElements);
					}
					
					currentSmoker = false;
					nonSmoker = false;
					pastSmoker = false;
					smoker = false;
				}
			} catch (IOException e) {
				e.printStackTrace();
			}
			
			try {
				reader.close();
				fr.close();
			} catch (IOException e) {
				// TODO Auto-generated catch block
				e.printStackTrace();
			}
		} catch (FileNotFoundException e1) {
			e1.printStackTrace();
		}
	}