From 4dcdadceaca2d21901ec0cde531adbc7e3efe827 Mon Sep 17 00:00:00 2001 From: jrtechs Date: Sun, 11 Nov 2018 21:38:40 -0500 Subject: [PATCH 01/59] Started working on paragraph formatter. --- other/paragraphFormatting.py | 98 ++++++++++++++++++++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 other/paragraphFormatting.py diff --git a/other/paragraphFormatting.py b/other/paragraphFormatting.py new file mode 100644 index 0000000..0e6b745 --- /dev/null +++ b/other/paragraphFormatting.py @@ -0,0 +1,98 @@ + +def extraSpace(S, M, i, j): + """ + Computes the number of extra characters at the end of + the line. + Between each word there is only once space. + + :param S: List of words + :param M: Max length of line + :param i: start word index + :param j: end word index + """ + extraSpaces = M - j + i + for x in range(i, j + 1): + extraSpaces -= len(S[x]) + return extraSpaces + + +def badnessLine(S, M, i, j): + """ + Computes Line badness. This is the number of + extra spaces or infinity if the length exceeds M + + :param S: List of words + :param M: Max length of line + :param i: start word index + :param j: end word index + """ + es = extraSpace(S, M, i, j) + if es < 0: + return float("infinity") + return es + + +def minBad(S, M, i): + """ + Computes the badness of a paragraph as the + badness of the worst line in the paragraph not + including the last line. + + *this is recursive + + :param S: List of words + :param M: Max length of line + :param i: start word index + """ + if len(S) == 0: + return 0 + + # Calculate the current line's badness + curBad = 0 + + k = i + while curBad > badnessLine(S, M, i, k): + curBad = badnessLine(S, M, i, k) + k = k + 1 + + return max(curBad, badnessLine(S, M, k)) + + + +def minBadDynamic(S, M): + """ + Write a procedure minBadDynamic that implements + the function mb' using dynamic program- + ming. It should take only two parameters: S and M + + :param S: List of words + :param M: Max length of line + """ + pass + + +def minBadDynamicChoice(S, M): + """ + Write a procedure minBadDynamicChoice that implements + the function mb 0 using dynamic + programming. In addition to returning mb(S, M ), it + should also return the choices made + + :param S: List of words + :param M: Max length of line + """ + pass + + +def printParagraph(S, M): + """ + which takes two parameters: S and M that displays the words in S on + the screen using the choices of minBadDynamicChoice. + + What is the asymptotic running time of your + algorithm? + + :param S: List of words + :param M: Max length of line + """ + pass From a053d0213d65613e78f10334b0729d541ecf81dc Mon Sep 17 00:00:00 2001 From: jrtechs Date: Mon, 12 Nov 2018 17:29:13 -0500 Subject: [PATCH 02/59] Updated the matrix chain problem to backtrack and print the solution. --- other/minMul.py | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/other/minMul.py b/other/minMul.py index a2434c1..5cfbbc4 100644 --- a/other/minMul.py +++ b/other/minMul.py @@ -6,6 +6,13 @@ Jeffery Russell """ +def generateMinOrdering(C, i, j): + if i == j: + return str(i) + return "(" + generateMinOrdering(C, i, C[i -1][j -1]) + generateMinOrdering(C, C[i -1][ j -1] +1, j) + ")" + + + def minMul(S): """ Simple function to print the matrixes used in @@ -41,7 +48,10 @@ def minMul(S): for i in range(0, n): for y in range(0, n): print(str(c[i][y]) + " ", end =" ") - print() + print() + + print(generateMinOrdering(c, 1, len(S))) + """ @@ -49,7 +59,8 @@ Makes sure that other programs don't execute the main """ if __name__ == '__main__': try: - minMul([(10,100),(100, 5),(5, 50)]) - #minMul([(5,10),(10,3),(3,12), (12,5), (5,50), (50,6)]) + #minMul([(10,100),(100, 5),(5, 50)]) + minMul([(5,10),(10,3),(3,12), (12,5), (5,50), (50,6)]) + #minMul([(30,35),(35,15),(15,5), (5,10), (10,20), (20,25)]) except KeyboardInterrupt: exit() \ No newline at end of file From 3fbc19d8d506976e8d8a669219ff6241bc4ea6e6 Mon Sep 17 00:00:00 2001 From: jrtechs Date: Wed, 14 Nov 2018 07:52:36 -0500 Subject: [PATCH 03/59] Designed a dynamic programming technique for the paragraph formatter. --- other/paragraphFormatting.py | 94 ++++++++++++++++++++++++++++++------ 1 file changed, 79 insertions(+), 15 deletions(-) diff --git a/other/paragraphFormatting.py b/other/paragraphFormatting.py index 0e6b745..41bfa38 100644 --- a/other/paragraphFormatting.py +++ b/other/paragraphFormatting.py @@ -1,3 +1,10 @@ +import math + +""" +Jeffery Russell +11-13-18 +""" + def extraSpace(S, M, i, j): """ @@ -28,7 +35,7 @@ def badnessLine(S, M, i, j): """ es = extraSpace(S, M, i, j) if es < 0: - return float("infinity") + return math.inf return es @@ -44,19 +51,17 @@ def minBad(S, M, i): :param M: Max length of line :param i: start word index """ - if len(S) == 0: + if badnessLine(S, M, i, len(S) -1) != math.inf: return 0 - # Calculate the current line's badness - curBad = 0 - - k = i - while curBad > badnessLine(S, M, i, k): - curBad = badnessLine(S, M, i, k) - k = k + 1 - - return max(curBad, badnessLine(S, M, k)) + min = math.inf + for k in range(i + 1, len(S)): + end = minBad(S, M, k) + front = badnessLine(S, M, i, k - 1) + max = end if end > front else front + min = min if min < max else max + return min def minBadDynamic(S, M): @@ -68,20 +73,63 @@ def minBadDynamic(S, M): :param S: List of words :param M: Max length of line """ - pass + cost = [math.inf for i in range(len(S))] + + for i in range(0, len(S)): + if badnessLine(S, M, 0, i) != math.inf: + cost[i] = badnessLine(S, M, 0, i) + if i == len(S) -1: + return 0 #Everything fit on one line + else: + min = math.inf + for k in range(0, i): + before = cost[k] + after = badnessLine(S, M, k + 1, i) + if i == len(S) -1 and badnessLine(S, M, k+1, i) != math.inf: + after = 0 # Last Line + max = before if before > after else after + min = min if min < max else max + cost[i] = min + return cost[len(S) -1] def minBadDynamicChoice(S, M): """ Write a procedure minBadDynamicChoice that implements - the function mb 0 using dynamic + the function mb' using dynamic programming. In addition to returning mb(S, M ), it should also return the choices made :param S: List of words :param M: Max length of line """ - pass + cost = [math.inf for i in range(len(S))] + + # List of tuples indicating start/end indices of line + choice = [[] for i in range(len(S))] + + for i in range(0, len(S)): + if badnessLine(S, M, 0, i) != math.inf: + cost[i] = badnessLine(S, M, 0, i) + choice[i] = [(0, i)] + if i == len(S) - 1: + return 0, [(0,i)] # One line + else: + min = math.inf + choiceCanidate = [] + for k in range(0, i): # Finds the optimal solution + before = cost[k] # Previously computed minimum + after = badnessLine(S, M, k + 1, i) # Badness of new slice + if i == len(S) - 1 and badnessLine(S, M, k+1, i) != math.inf: + after = 0 # Last line + max = before if before > after else after + if min > max: + # Captures where slice is being taken + choiceCanidate = choice[k] + [(k+1, i)] + min = max + choice[i] = choiceCanidate + cost[i] = min + return cost[len(S) -1], choice[len(S) -1] def printParagraph(S, M): @@ -92,7 +140,23 @@ def printParagraph(S, M): What is the asymptotic running time of your algorithm? + This program will run asymptotically in O(n^2) due + to the characteristic of calculating the minBad + for each sub sequence and then looping through a + maximum of |S| to find the optimal solution. + :param S: List of words :param M: Max length of line """ - pass + cost, choice = minBadDynamicChoice(S, M) + print() + for i in range(0, len(choice)): + for x in range(choice[i][0], choice[i][1] + 1): + print(str(S[x]), end=" ") + print() + + +print(minBadDynamicChoice(["aaa", "aaa"], 6)) +printParagraph(["jjjjjj","aaa", "bb", "cc", "ff", "mm", "ddddd", "ddddd"], 6) + +printParagraph(["jjjjjj"], 6) \ No newline at end of file From 2f8d25877d715faabe4c28e3421903719fa10efd Mon Sep 17 00:00:00 2001 From: jrtechs Date: Tue, 27 Nov 2018 11:31:53 -0500 Subject: [PATCH 04/59] Created simple program to backup windows sticky notes. --- windows/Sticky Notes Backuper/Readme.txt | 14 ++++++++++++++ windows/Sticky Notes Backuper/grabStickyNotes.bat | 9 +++++++++ .../replaceCurrentStickyNotes.bat | 9 +++++++++ 3 files changed, 32 insertions(+) create mode 100644 windows/Sticky Notes Backuper/Readme.txt create mode 100644 windows/Sticky Notes Backuper/grabStickyNotes.bat create mode 100644 windows/Sticky Notes Backuper/replaceCurrentStickyNotes.bat diff --git a/windows/Sticky Notes Backuper/Readme.txt b/windows/Sticky Notes Backuper/Readme.txt new file mode 100644 index 0000000..d0781e5 --- /dev/null +++ b/windows/Sticky Notes Backuper/Readme.txt @@ -0,0 +1,14 @@ +This is a very simple program. + +Double click on grab StickyNotes.bat to backup your sticky notes +into the current directory. + +Double click ReplaceCurrentStickyNotes.bat to replace your +stickynotes with the ones in the current directory. + + + + +** Note this will only work with windows 10 and up. +Windows 10 uses the .sqlite format where windows 7 +used a .snt file. \ No newline at end of file diff --git a/windows/Sticky Notes Backuper/grabStickyNotes.bat b/windows/Sticky Notes Backuper/grabStickyNotes.bat new file mode 100644 index 0000000..14dcf4b --- /dev/null +++ b/windows/Sticky Notes Backuper/grabStickyNotes.bat @@ -0,0 +1,9 @@ +:: Author : Jeffery Russell 11-27-18 + +@echo off + +pushd %~dp0 +dir +copy %LocalAppData%\Packages\Microsoft.MicrosoftStickyNotes_8wekyb3d8bbwe\LocalState\plum.sqlite + +pause \ No newline at end of file diff --git a/windows/Sticky Notes Backuper/replaceCurrentStickyNotes.bat b/windows/Sticky Notes Backuper/replaceCurrentStickyNotes.bat new file mode 100644 index 0000000..22df29d --- /dev/null +++ b/windows/Sticky Notes Backuper/replaceCurrentStickyNotes.bat @@ -0,0 +1,9 @@ +:: Author : Jeffery Russell 11-27-18 + +@echo off + +pushd %~dp0 +dir +copy plum.sqlite %LocalAppData%\Packages\Microsoft.MicrosoftStickyNotes_8wekyb3d8bbwe\LocalState\plum.sqlite + +pause \ No newline at end of file From 5129e5e13321b6d78d475a3afd254f87134223ef Mon Sep 17 00:00:00 2001 From: jrtechs Date: Fri, 11 Jan 2019 13:55:20 -0500 Subject: [PATCH 05/59] Python implementation of the knapsack problem. --- other/knapSack.py | 52 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 other/knapSack.py diff --git a/other/knapSack.py b/other/knapSack.py new file mode 100644 index 0000000..4bfdece --- /dev/null +++ b/other/knapSack.py @@ -0,0 +1,52 @@ +""" +Jeffery Russell +12-1-18 +""" + + +def knapsack(V, W, capacity): + """ + Dynamic programming implementation of the knapsack problem + + :param V: List of the values + :param W: List of weights + :param capacity: max capacity of knapsack + :return: List of tuples of objects stolen in form (w, v) + """ + choices = [[[] for i in range(capacity + 1)] for j in range(len(V) + 1)] + cost = [[0 for i in range(capacity + 1)] for j in range(len(V) + 1)] + + for i in range(0, len(V)): + for j in range(0, capacity + 1): + if W[i] > j: # don't include another item + cost[i][j] = cost[i -1][j] + choices[i][j] = choices[i - 1][j] + else: # Adding another item + cost[i][j] = max(cost[i-1][j], cost[i-1][j - W[i]] + V[i]) + if cost[i][j] != cost[i-1][j]: + choices[i][j] = choices[i - 1][j - W[i]] + [(W[i], V[i])] + else: + choices[i][j] = choices[i - 1][j] + return choices[len(V) -1][capacity] + + +def printSolution(S): + """ + Takes the output of knapsack and prints it in a + pretty format. + + :param S: list of tuples representing items stolen + :return: None + """ + print("Thief Took:") + for i in S: + print("Weight: " + str(i[0]) + "\tValue: \t" + str(i[1])) + + print() + print("Total Value Stolen: " + str(sum(int(v[0]) for v in S))) + print("Total Weight in knapsack: " + str(sum(int(v[1]) for v in S))) + + +values = [99,1,1,1,1, 1,1] +weights = [5,1,2,3,4,5,1] +printSolution(knapsack(values, weights, 6)) \ No newline at end of file From dcfe1999826d69f9011848d3c6758be33c2218ab Mon Sep 17 00:00:00 2001 From: jrtechs Date: Sun, 20 Jan 2019 20:06:45 -0500 Subject: [PATCH 06/59] Created simple web page which prompts user to load a JSON file and it graphs it using visjs. --- graphing/basicGraph.html | 92 ++++++++++++++++++++++++++++++++++++++++ graphing/ex.json | 1 + 2 files changed, 93 insertions(+) create mode 100644 graphing/basicGraph.html create mode 100644 graphing/ex.json diff --git a/graphing/basicGraph.html b/graphing/basicGraph.html new file mode 100644 index 0000000..e75c3fc --- /dev/null +++ b/graphing/basicGraph.html @@ -0,0 +1,92 @@ + + + + Graph2d | Performance + + + + + + + + + + + + +
+ +Click the button then choose a file to graph. + +

+
+
+
+

+
+

+
+
+
diff --git a/graphing/ex.json b/graphing/ex.json
new file mode 100644
index 0000000..6615c8e
--- /dev/null
+++ b/graphing/ex.json
@@ -0,0 +1 @@
+[{"x": "2014-06-1", "y": -6},{"x": "2014-06-11", "y": 0},{"x": "2014-06-12", "y": 25},{"x": "2014-06-13", "y": 30},{"x": "2014-06-14", "y": 10},{"x": "2014-06-15", "y": 15},{"x": "2014-06-16", "y": 30}]

From 72e484e046a4ee955016cf5a937a95d5b232c581 Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Tue, 29 Jan 2019 20:53:13 -0500
Subject: [PATCH 07/59] Created some basic framework classes to use for my
 testing of multi threaded file io.

---
 multiThreadedFileIO/FileReader.java  | 44 ++++++++++++++++
 multiThreadedFileIO/ReadTask.java    | 20 ++++++++
 multiThreadedFileIO/TaskManager.java | 76 ++++++++++++++++++++++++++++
 3 files changed, 140 insertions(+)
 create mode 100644 multiThreadedFileIO/FileReader.java
 create mode 100644 multiThreadedFileIO/ReadTask.java
 create mode 100644 multiThreadedFileIO/TaskManager.java

diff --git a/multiThreadedFileIO/FileReader.java b/multiThreadedFileIO/FileReader.java
new file mode 100644
index 0000000..520fa81
--- /dev/null
+++ b/multiThreadedFileIO/FileReader.java
@@ -0,0 +1,44 @@
+import java.io.BufferedReader;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+
+/**
+ * Simple class for reading files as strings. 
+ *
+ * @author Jeffery Russell
+ */
+public class FileReader
+{
+
+    public static String readFile(String filePath)
+    {
+        String fileContent = new String();
+
+        try
+        {
+            BufferedReader br = new BufferedReader(
+                    new InputStreamReader(new FileInputStream(filePath)));
+            String line;
+
+            while ((line = br.readLine()) != null)
+            {
+                fileContent = fileContent.concat(line);
+            }
+            br.close();
+        }
+        catch (IOException e)
+        {
+            e.printStackTrace();
+        }
+        return fileContent;
+    }
+
+
+    public static void main(String[] args)
+    {
+        System.out.println("Test");
+        System.out.println(FileReader.readFile("./testData/data1.txt"));
+    }
+}
\ No newline at end of file
diff --git a/multiThreadedFileIO/ReadTask.java b/multiThreadedFileIO/ReadTask.java
new file mode 100644
index 0000000..249f608
--- /dev/null
+++ b/multiThreadedFileIO/ReadTask.java
@@ -0,0 +1,20 @@
+/**
+ * Simple method to be used by the task manager to do
+ * file io.
+ *
+ * @author Jeffery Russell
+ */
+public class ReadTask
+{
+    private String fileName;
+
+    public ReadTask(String fileName)
+    {
+        this.fileName = fileName;
+    }
+
+    public void runTask()
+    {
+        FileReader.readFile(fileName);
+    }
+}
\ No newline at end of file
diff --git a/multiThreadedFileIO/TaskManager.java b/multiThreadedFileIO/TaskManager.java
new file mode 100644
index 0000000..63b5ce1
--- /dev/null
+++ b/multiThreadedFileIO/TaskManager.java
@@ -0,0 +1,76 @@
+import java.util.List;
+import java.util.Vector;
+
+/**
+ * A class which enables user to run a large chunk of
+ * tasks in parallel efficiently.
+ *
+ * @author Jeffery 1-29-19
+ */
+public class TaskManager
+{
+    /** Number of threads to use at once */
+    private int threadCount;
+
+    /** Meaningless tasks to run in parallel */
+    private List tasks;
+
+
+    public TaskManager(int threadCount)
+    {
+        this.threadCount = threadCount;
+        //using vectors because they are thread safe
+        this.tasks = new Vector<>();
+    }
+
+
+    public void addTask(ReadTask t)
+    {
+        tasks.add(t);
+    }
+
+
+    /**
+     * This is the fun method.
+     *
+     * This will run all of the tasks in parallel using the
+     * desired amount of threads untill all of the jobs are
+     * complete.
+     */
+    public void runTasks()
+    {
+        int desiredThreads = threadCount > tasks.size() ?
+                tasks.size() : threadCount;
+
+        Thread[] runners = new Thread[desiredThreads];
+
+        System.out.println("Total Tasks: " + tasks.size());
+        System.out.println("Threads Used:" + desiredThreads);
+
+
+        for(int i = 0; i < desiredThreads; i++)
+        {
+            runners[i] = new Thread(()->
+            {
+                while(!tasks.isEmpty())
+                {
+                    ReadTask t = tasks.remove(0);
+                    t.runTask();
+                }
+            });
+            runners[i].start();
+        }
+
+        for(int i = 0; i < desiredThreads; i++)
+        {
+            try
+            {
+                runners[i].join();
+            }
+            catch (Exception e)
+            {
+                e.printStackTrace();
+            }
+        }
+    }
+}
\ No newline at end of file

From f1ae532387d33e2693675d8b8cde6239820b6742 Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Thu, 31 Jan 2019 13:12:36 -0500
Subject: [PATCH 08/59] Wrote tests to compare the read time of files vs number
 of cpu threads used.

---
 multiThreadedFileIO/DataCreator.java          | 71 +++++++++++++++++++
 .../MultiThreadedFileReadTest.java            | 40 +++++++++++
 multiThreadedFileIO/TaskManager.java          | 25 +++++--
 multiThreadedFileIO/graph.py                  | 13 ++++
 4 files changed, 142 insertions(+), 7 deletions(-)
 create mode 100644 multiThreadedFileIO/DataCreator.java
 create mode 100644 multiThreadedFileIO/MultiThreadedFileReadTest.java
 create mode 100644 multiThreadedFileIO/graph.py

diff --git a/multiThreadedFileIO/DataCreator.java b/multiThreadedFileIO/DataCreator.java
new file mode 100644
index 0000000..e551be1
--- /dev/null
+++ b/multiThreadedFileIO/DataCreator.java
@@ -0,0 +1,71 @@
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.math.*;
+
+/**
+ * Simple class to generate random data for
+ * file IO tests.
+ *
+ * @author Jeffery Russell 1-31-19
+ */
+public class DataCreator
+{
+    /**
+     * Generates an obscure random character
+     * @return
+     */
+    private static char rndChar()
+    {
+        // or use Random or whatever
+        int rnd = (int) (Math.random() * 52);
+        char base = (rnd < 26) ? 'A' : 'a';
+        return (char) (base + rnd % 26);
+    }
+
+
+    /**
+     * Simple function to save contents to the disk
+     *
+     * @param s
+     * @param fileName
+     */
+    private static void saveToDisk(String s, String fileName)
+    {
+        BufferedWriter writer;
+        try
+        {
+            File file = new File(fileName);
+            file.createNewFile();
+            writer = new BufferedWriter(new FileWriter(file));
+            writer.write(s);
+            writer.flush();
+            writer.close();
+        }
+        catch (Exception e)
+        {
+            e.printStackTrace();
+        }
+    }
+
+
+    /**
+     * Creates 5MB of random test data to use
+     */
+    public static void main(String[] arguments)
+    {
+        System.out.println("Creating Test Files");
+        for(int i = 0; i < 100; i++)
+        {
+            //10k random characters for each file
+            //each file is 10kb * 500 files, total size of 5MB
+            String s = "";
+            for(int j = 0; j < 1000000; j++)
+            {
+                s = s + rndChar();
+            }
+            saveToDisk(s, "./testData/" + i + ".txt");
+            System.out.println(s);
+        }
+    }
+}
\ No newline at end of file
diff --git a/multiThreadedFileIO/MultiThreadedFileReadTest.java b/multiThreadedFileIO/MultiThreadedFileReadTest.java
new file mode 100644
index 0000000..32c63df
--- /dev/null
+++ b/multiThreadedFileIO/MultiThreadedFileReadTest.java
@@ -0,0 +1,40 @@
+import java.util.*;
+
+/**
+ * File to test the performance of multi threaded file
+ * io by reading a large quantity of files in parallel
+ * using a different amount of threads.
+ *
+ * @author Jeffery Russell 1-31-19
+ */
+public class MultiThreadedFileReadTest
+{
+    public static void main(String[] args)
+    {
+        List x = new ArrayList<>();
+        List y = new ArrayList<>();
+        for(int i = 1; i <= 64; i++)
+        {
+            long threadTotal = 0;
+            for(int w = 0; w < 20; w++)
+            {
+                TaskManager boss = new TaskManager(i);
+
+                for(int j = 0; j < 500; j++)
+                {
+                    boss.addTask(new ReadTask("./testData/" + i + ".txt"));
+                }
+                long startTime = System.nanoTime();
+                boss.runTasks();
+                long endTime = System.nanoTime();
+                long durationMS = (endTime - startTime)/1000000;
+                threadTotal+= durationMS;
+            }
+
+            x.add(i);
+            y.add(threadTotal/20.0); //finds average
+        }
+        System.out.println(x);
+        System.out.println(y);
+    }
+}
\ No newline at end of file
diff --git a/multiThreadedFileIO/TaskManager.java b/multiThreadedFileIO/TaskManager.java
index 63b5ce1..2929b31 100644
--- a/multiThreadedFileIO/TaskManager.java
+++ b/multiThreadedFileIO/TaskManager.java
@@ -44,18 +44,29 @@ public class TaskManager
 
         Thread[] runners = new Thread[desiredThreads];
 
-        System.out.println("Total Tasks: " + tasks.size());
-        System.out.println("Threads Used:" + desiredThreads);
-
-
         for(int i = 0; i < desiredThreads; i++)
         {
             runners[i] = new Thread(()->
             {
-                while(!tasks.isEmpty())
+                ReadTask t = null;
+                while(true)
                 {
-                    ReadTask t = tasks.remove(0);
-                    t.runTask();
+                    //need synchronized block to prevent
+                    //race condition
+                    synchronized (tasks)
+                    {
+                        if(!tasks.isEmpty())
+                            t = tasks.remove(0);
+                    }
+                    if(t == null)
+                    {
+                        break;
+                    }
+                    else
+                    {
+                        t.runTask();
+                        t = null;
+                    }
                 }
             });
             runners[i].start();
diff --git a/multiThreadedFileIO/graph.py b/multiThreadedFileIO/graph.py
new file mode 100644
index 0000000..469f90b
--- /dev/null
+++ b/multiThreadedFileIO/graph.py
@@ -0,0 +1,13 @@
+import matplotlib.pyplot as plt
+
+
+xList = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]
+yList = [230.5, 124.0, 84.65, 63.9, 51.6, 44.2, 39.15, 34.9, 31.9, 28.7, 27.2, 25.05, 24.25, 22.8, 21.25, 20.45, 19.8, 19.4, 18.6, 17.45, 17.0, 16.95, 16.4, 24.15, 15.2, 15.2, 15.0, 14.3, 14.7, 14.65, 14.65, 14.75, 13.85, 15.1, 14.35, 35.75, 15.3, 14.45, 14.25, 13.65, 14.45, 14.6, 13.95, 14.65, 14.5, 14.3, 14.85, 14.15, 15.0, 16.25, 14.25, 14.4, 14.15, 14.45, 14.25, 14.85, 14.3, 14.35, 15.35, 13.6, 14.3, 14.2, 14.3, 13.95]
+
+
+
+plt.plot(xList, yList)
+plt.xlabel('Number of Threads')
+plt.ylabel('Execution Time (MS)')
+
+plt.show()
\ No newline at end of file

From 43a19cf3f9c8dd3006b6112a1eb6239f3e660f2d Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Fri, 22 Feb 2019 21:45:03 -0500
Subject: [PATCH 09/59] Started working on genetic algorithm in javascript.

---
 geneticAlgorithm/geneticAlgo.html | 104 ++++++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100644 geneticAlgorithm/geneticAlgo.html

diff --git a/geneticAlgorithm/geneticAlgo.html b/geneticAlgorithm/geneticAlgo.html
new file mode 100644
index 0000000..cdbd682
--- /dev/null
+++ b/geneticAlgorithm/geneticAlgo.html
@@ -0,0 +1,104 @@
+
+
+
+    
+
+
+
+
+
+
+
+
+
\ No newline at end of file

From 98bd2dd1c4643b0e9c5b5d6a41c35a5da18c49ff Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Sat, 23 Feb 2019 10:36:19 -0500
Subject: [PATCH 10/59] Finished writing the genetic algorithm.

---
 geneticAlgorithm/geneticAlgo.html | 178 +++++++++++++++++++++++++++---
 1 file changed, 164 insertions(+), 14 deletions(-)

diff --git a/geneticAlgorithm/geneticAlgo.html b/geneticAlgorithm/geneticAlgo.html
index cdbd682..a79839b 100644
--- a/geneticAlgorithm/geneticAlgo.html
+++ b/geneticAlgorithm/geneticAlgo.html
@@ -1,8 +1,6 @@
 
 
-
     
+        let exampleOrganism = new Chromosome(geneList);
 
+        runGeneticOptimization(exampleOrganism, basicCostFunction, 100, 50, 0.01, 0.3, 20, 10);
+
+    
 
 
 

From 4376164ab8b22bfba22826e4c9384e1f274768e9 Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Sat, 23 Feb 2019 13:06:36 -0500
Subject: [PATCH 11/59] Created plotting graph for the genetic algorithm.

---
 geneticAlgorithm/geneticAlgo.html | 185 +++++++++++++++++++++++++++++-
 1 file changed, 182 insertions(+), 3 deletions(-)

diff --git a/geneticAlgorithm/geneticAlgo.html b/geneticAlgorithm/geneticAlgo.html
index a79839b..8d9c8d8 100644
--- a/geneticAlgorithm/geneticAlgo.html
+++ b/geneticAlgorithm/geneticAlgo.html
@@ -1,5 +1,14 @@
 
 
+    
+    
+
+    
+
     
+
 
 
 
 
+    

+
+    
+    
+
+    

+        

+            
Population Variables

+        

+        

+            

+                

+                    
+                    
+                

+                

+                    
+                    
+                

+            

+            

+                

+                    
+                    
+                

+                

+                    
+                    
+                

+            

+            

+            
+        

+    

+
 
 
 

From 9f0bf214b980af65a915c966ba44d683f43e59fc Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Sat, 23 Feb 2019 14:03:26 -0500
Subject: [PATCH 12/59] Added a line chart displaying the average cost and best
 cost.

---
 geneticAlgorithm/geneticAlgo.html | 112 ++++++++++++++++++++++--------
 1 file changed, 83 insertions(+), 29 deletions(-)

diff --git a/geneticAlgorithm/geneticAlgo.html b/geneticAlgorithm/geneticAlgo.html
index 8d9c8d8..e8f31d9 100644
--- a/geneticAlgorithm/geneticAlgo.html
+++ b/geneticAlgorithm/geneticAlgo.html
@@ -114,11 +114,13 @@
         const naturalSelection = function(population, keepNumber, fitnessFunction)
         {
             let fitnessArray = [];
+            let total = 0;
             for(let i = 0; i < population.length; i++)
             {
                 const fitness = fitnessFunction(population[i]);
                 console.log(fitness);
                 fitnessArray.push({fit:fitness, chrom: population[i]});
+                total+= fitness;
             }
 
             fitnessArray.sort(predicateBy("fit"));
@@ -130,7 +132,7 @@
             {
                 survivors.push(fitnessArray[i].chrom);
             }
-            return {survivors: survivors, bestFit: bestFitness, bestChrom: bestChromosome};
+            return {average: total/population.length, survivors: survivors, bestFit: bestFitness, bestChrom: bestChromosome};
         };
 
         const blendGene = function(gene1, gene2, blendCoef)
@@ -254,12 +256,10 @@
                         bestCostG = Number.MAX_VALUE, bestChromosomeG = genericChromosomeG;
         const runGeneticOptimizationforGraph = function()
         {
-
-
-
-
             let generationResult = naturalSelection(populationG, keepNumberG, costFunctionG);
 
+            stats.push([generationG, generationResult.bestFit, generationResult.average]);
+
             if(bestCostG > generationResult.bestFit)
             {
                 bestChromosomeG = generationResult.bestChrom;
@@ -269,7 +269,6 @@
 
             generationG++;
 
-
             console.log("Generation " + generationG + " Best Cost: " + bestCostG);
 
             console.log(generationResult);
@@ -279,12 +278,13 @@
             mutatePopulation(populationG, mutationRateG);
 
             createGraph();
-
         };
 
+
+        let stats = [];
         const createGraph = function()
         {
-                        var dataPoints = [];
+            var dataPoints = [];
 
             console.log(dataPoints);
 
@@ -307,6 +307,29 @@
             var chart = new google.visualization.ScatterChart(document.getElementById('chart_div'));
 
             chart.draw(data, options);
+
+            //line chart stuff
+              var line_data = new google.visualization.DataTable();
+            line_data.addColumn('number', 'Generation');
+              line_data.addColumn('number', 'Best');
+              line_data.addColumn('number', 'Average');
+
+                  line_data.addRows(stats);
+
+              console.log(stats);
+
+              var lineChartOptions = {
+                hAxis: {
+                  title: 'Generation'
+                },
+                vAxis: {
+                  title: 'Cost'
+                },
+                colors: ['#AB0D06', '#007329']
+              };
+
+              var chart = new google.visualization.LineChart(document.getElementById('line_chart'));
+              chart.draw(line_data, lineChartOptions);
         };
 
 
@@ -328,31 +351,63 @@
         generationG = 0;
 
 
-        function resetPopulation()
+        function verifyForm()
         {
+            if(Number($("#populationSize").val()) <= 1)
+            {
+                alert("Population size must be greater than one.");
+                return false;
+            }
+
+            if(Number($("#mutationRate").val()) > 1 ||
+                Number($("#mutationRate").val()) < 0)
+            {
+                alert("Mutation rate must be between zero and one.");
+                return false;
+            }
 
-            autoRunning = false;
-            $("#runAutoOptimizer").val("Auto Run");
+            if(Number($("#survivalSize").val()) < 0)
+            {
+                alert("Survival size can't be less than one.");
+                return false;
+            }
+
+            if(Number($("#newBlood").val()) < 0)
+            {
+                alert("New organisms can't be a negative number.");
+                return false;
+            }
+            return true;
+        }
 
-            populationSizeG = $("#populationSize").val();
-            mutationRateG = $("#mutationRate").val();
-            keepNumberG = $("#survivalSize").val();
-            newBloodNumberG = $("#newBlood").val();
-            generationG = 0;
+        function resetPopulation()
+        {
+            if(verifyForm())
+            {
+                stats = [];
+                autoRunning = false;
+                $("#runAutoOptimizer").val("Auto Run");
 
-            populationG = createRandomPopulation(genericChromosomeG, populationSizeG);
-            createGraph();
+                populationSizeG = $("#populationSize").val();
+                mutationRateG = $("#mutationRate").val();
+                keepNumberG = $("#survivalSize").val();
+                newBloodNumberG = $("#newBlood").val();
+                generationG = 0;
+
+                populationG = createRandomPopulation(genericChromosomeG, populationSizeG);
+                createGraph();
+            }
         }
 
         populationG = createRandomPopulation(genericChromosomeG, populationSizeG);
 
 
-        window.onload = function () {
+        window.onload = function (){
+            google.charts.load('current', {packages: ['corechart', 'line']});
             google.charts.load('current', {'packages':['corechart']}).then(function()
             {
                 createGraph();
             })
-
         };
 
 
@@ -382,8 +437,6 @@
             runAutoOptimizer();
         }
 
-
-
         //runGeneticOptimization(exampleOrganism, basicCostFunction, 100, 50, 0.01, 0.3, 20, 10);
 
     
@@ -394,6 +447,8 @@
 
     

 
+    

+
     
     
 
@@ -401,32 +456,31 @@
         

             
Population Variables

         

-        

+        

             

                 

                     
-                    
+                    
                 

                 

                     
-                    
+                    
                 

             

             

                 

                     
-                    
+                    
                 

                 

                     
-                    
+                    
                 

             

             

             
-        

+        
     
-
 
 
 

From e5e809a58d840c96a7dd2162178bee1d2554c75d Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Thu, 18 Apr 2019 19:43:12 -0400
Subject: [PATCH 13/59] Added vim configuration file to repository.

---
 config/vimrc | 120 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 120 insertions(+)
 create mode 100644 config/vimrc

diff --git a/config/vimrc b/config/vimrc
new file mode 100644
index 0000000..9f9f3d2
--- /dev/null
+++ b/config/vimrc
@@ -0,0 +1,120 @@
+" sets spell check to be enabled to files which
+" end with either .md or .txt
+" 
+" To get auto complete type z= when you are
+" over the word.
+autocmd BufRead,BufNewFile *.md setlocal spell spelllang=en_us
+autocmd BufRead,BufNewFile *.txt setlocal spell spelllang=en_us
+
+
+""" Indentation and Tabs """
+"file based indentation
+filetype plugin indent on
+
+"copy indentation from current line when making a new line
+set autoindent
+" Smart indentation when programming: indent after {
+set smartindent 
+
+set tabstop=4     " number of spaces per tab
+set expandtab     " convert tabs to spaces
+set shiftwidth=4  " set a tab press equal to 4 spaces
+
+
+""" Looks and Appearance"""
+
+" Enable syntax highlighting
+syntax enable
+
+" Enable 256 colors palette in Gnome Terminal
+if $COLORTERM == 'gnome-terminal'
+    set t_Co=256
+endif
+
+try
+    colorscheme desert
+catch
+endtry
+
+set background=dark
+
+" Set extra options when running in GUI mode
+if has("gui_running")
+    set guioptions-=T
+    set guioptions-=e
+    set t_Co=256
+    set guitablabel=%M\ %t
+endif
+
+
+" File Encodings
+
+" Set utf8 as standard encoding and en_US as the standard language
+set encoding=utf8
+
+" Use Unix as the standard file type
+set ffs=unix,dos,mac
+
+
+" Productivity 
+
+" Set Line Numbers to show
+set number
+
+" Highlights the current line with a underscore
+set cursorline
+
+" Displays a red bar at 80 characters
+set colorcolumn=80
+
+" Shows a auto complete tab when you are typing a command
+" like :sp 
+set wildmenu
+
+" sets the size of the status bar at bottom to have a height of two
+set laststatus=2
+
+
+
+"  Searching when in command mode type /words to find
+" search as characters are entered
+set incsearch
+" highlight matched characters
+set hlsearch
+
+" Ignore case when searching
+set ignorecase
+
+
+
+"Disable ding sound on error, flashes cursor instead
+set visualbell
+
+" Display ruler on bottom right -- should be there by default
+set ruler
+
+" Enables mouse support
+set mouse=a
+
+" Auto updates file if an external source edits the file
+set autoread
+
+" Improves performance by only redrawing screen when needed
+set lazyredraw
+
+
+" Copy and paste
+" Selection
+" v and arrows select characters
+" V select entire lines
+" d on something selected cuts it -- also used for delete
+" y = yank = copy
+" P paste before cursor
+" p paste after cursor
+
+
+
+" Basic Vim navigation
+" :sp file  -- this will open a new file horizontally
+" :vsp file -- will open a file splitting vertically
+" ctrl-w w -- this will toggle to another open vim window

From cfc9f92cb49ead60ef554fcc043354663cee48f6 Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Sun, 21 Apr 2019 16:52:28 -0400
Subject: [PATCH 14/59] Created script to format markdown paragraphs following
 a stringent column max.

---
 other/markdownParagraphFormatter.py | 121 ++++++++++++++++++++++++++++
 1 file changed, 121 insertions(+)
 create mode 100644 other/markdownParagraphFormatter.py

diff --git a/other/markdownParagraphFormatter.py b/other/markdownParagraphFormatter.py
new file mode 100644
index 0000000..1840d0b
--- /dev/null
+++ b/other/markdownParagraphFormatter.py
@@ -0,0 +1,121 @@
+"""
+Jeffery Russell
+2019-4-21
+
+Simple program to reformat paragraphs in markdown text files
+to follow a specific col limit.
+"""
+
+import os
+import sys
+
+
+def formatChunk(stringContent, charLimit):
+    """
+    Formats a markdown section with with a specific
+    col limit. This only makes changes if the section is a
+    paragraph and nothing else.
+
+    The only guarantee for the input is that there
+    are no lines which only contain a new line or space.
+
+    :param stringContent: string of markdown chunk
+    :param charLimit: max character limit
+    :return: formatted string
+    """
+    if len(stringContent.strip(" ")) == 0:
+        return ""
+    elif not stringContent[0].isalpha():
+        return stringContent
+    result = ""
+    line = ""
+    stringContent = stringContent.replace("\n", " ")
+    words = stringContent.split(" ")
+
+    for word in words:
+        if len(line) == 0 or len(line) + len(word) < charLimit:
+            if not len(line) == 0:
+                line = line + " "
+            line = line + word
+        else:
+            result = result + line + "\n"
+            line = word
+    if line != "":
+        result = result + line + "\n"
+    return result
+
+
+def writeToFile(fileName, content):
+    """
+    Writes to a file, overwriting the existing
+    output.
+    :param fileName:
+    :param content:
+    :return:
+    """
+    f = open(fileName, "w+")
+    f.write(content)
+    f.close()
+
+
+def wrapMarkdownParagraphsToColLimit(fileName, charLimit):
+    """
+    Breaks apart a markdown file into chunks. A chunks are
+    separated by a blank lines. Each chunk is then
+    rendered according to our 80 char rules defined
+    in the formatChunk section.
+    :param fileName:
+    :param charLimit:
+    :return:
+    """
+    result = ""
+    tempResult = ""
+    with open(fileName) as file:
+        for line in file:
+            if line.strip(" ") == "\n":
+                result = result + formatChunk(tempResult, charLimit)
+                tempResult = ""
+                result = result + "\n"
+            else:
+                tempResult = tempResult + line
+            print(line)
+    if tempResult != "":
+        result = result + formatChunk(tempResult, charLimit)
+    return result
+
+
+def print_usage():
+    """
+    Prints script usage.
+    :return:
+    """
+    print("Usage: file name -t (optional)")
+    print("\t-p simply prints the formatted output.")
+    print("\tfile name -- runs the command overwriting the existing file.")
+
+
+def main():
+    """
+    Checks command line input and calls the proper formatting
+    functions.
+    :return:
+    """
+    if len(sys.argv) > 1:
+        fileName = os.getcwd() + "/" + sys.argv[1]
+        if len(sys.argv) == 3 and sys.argv[2].lower() == "-p":
+            print(wrapMarkdownParagraphsToColLimit(fileName, 70))
+        else:
+            writeToFile(fileName,
+                        wrapMarkdownParagraphsToColLimit(fileName, 70))
+    else:
+        print_usage()
+
+
+"""
+Makes sure that other scripts don't execute the main
+"""
+if __name__ == '__main__':
+    try:
+        main()
+    except KeyboardInterrupt:
+        panic()

From fe145214b1679a6954bde4268b7a99e4c658656d Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Tue, 23 Apr 2019 21:51:37 -0400
Subject: [PATCH 15/59] Updated code to work with code blocks when there are
 new lines in it.

---
 other/markdownParagraphFormatter.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/other/markdownParagraphFormatter.py b/other/markdownParagraphFormatter.py
index 1840d0b..dca9fad 100644
--- a/other/markdownParagraphFormatter.py
+++ b/other/markdownParagraphFormatter.py
@@ -70,15 +70,23 @@ def wrapMarkdownParagraphsToColLimit(fileName, charLimit):
     """
     result = ""
     tempResult = ""
+    inCodeBlock = False
+
     with open(fileName) as file:
         for line in file:
-            if line.strip(" ") == "\n":
+
+            if line.startswith("```"):
+                inCodeBlock = not inCodeBlock
+                result = result + line
+            elif inCodeBlock:
+                result = result + line
+            elif line.strip(" ") == "\n":
                 result = result + formatChunk(tempResult, charLimit)
                 tempResult = ""
                 result = result + "\n"
             else:
                 tempResult = tempResult + line
-            print(line)
+
     if tempResult != "":
         result = result + formatChunk(tempResult, charLimit)
     return result

From b92ba144f3c24534f472d7d8bbc3865d0c1cd801 Mon Sep 17 00:00:00 2001
From: jrtechs 
Date: Tue, 23 Apr 2019 22:04:25 -0400
Subject: [PATCH 16/59] Added comments to GA algo

---
 geneticAlgorithm/geneticAlgo.html | 150 ++++++++++++++++++++++++------
 1 file changed, 121 insertions(+), 29 deletions(-)

diff --git a/geneticAlgorithm/geneticAlgo.html b/geneticAlgorithm/geneticAlgo.html
index e8f31d9..c09a7a2 100644
--- a/geneticAlgorithm/geneticAlgo.html
+++ b/geneticAlgorithm/geneticAlgo.html
@@ -12,6 +12,12 @@