From 4511eb73c5de533fd00c8917b5fada6096138305 Mon Sep 17 00:00:00 2001
From: AymarN <aymar.nahum@jecorde.com>
Date: Sat, 25 Mar 2023 22:20:13 -0400
Subject: [PATCH] Change the fileResource Object

---
 Week2/Codon Count/CodonCount.class | Bin 3483 -> 4267 bytes
 Week2/Codon Count/CodonCount.ctxt  |   3 ---
 Week2/Codon Count/CodonCount.java  |  29 +++++++++++++++++++---
 Week2/Codon Count/README.TXT       |  12 +++++++++
 Week2/Codon Count/package.bluej    |  38 +++++++++++++++++++++++++++++
 5 files changed, 75 insertions(+), 7 deletions(-)
 create mode 100644 Week2/Codon Count/README.TXT
 create mode 100644 Week2/Codon Count/package.bluej

diff --git a/Week2/Codon Count/CodonCount.class b/Week2/Codon Count/CodonCount.class
index 6f84168d7d7abae714930a1a420581dbb468da3a..804d6e01281ffd92c9f573ece5777eddede017eb 100644
GIT binary patch
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diff --git a/Week2/Codon Count/CodonCount.ctxt b/Week2/Codon Count/CodonCount.ctxt
index 17007ba..d31cde4 100644
--- a/Week2/Codon Count/CodonCount.ctxt	
+++ b/Week2/Codon Count/CodonCount.ctxt	
@@ -4,13 +4,10 @@ comment1.params=
 comment1.target=CodonCount()
 comment2.params=start\ dna
 comment2.target=void\ buildCodonMap(int,\ java.lang.String)
-comment2.text=\n\ This\ method\ will\ build\ a\ new\ map\ of\ codons\ mapped\ to\ their\ \n\ counts\ from\ the\ string\ dna\ with\ the\ reading\ frame\ with\ the\ position\ \n\ start(\ a\ value\ of\ 0,1\ or\ 2).You\ will\ call\ this\ method\ several\ times,\n\ so\ make\ sure\ your\ map\ is\ emptybefore\ building.\n
 comment3.params=
 comment3.target=java.lang.String\ getMostCommonCodon()
-comment3.text=\n\ This\ method\ returns\ a\ String,\ the\ codon\ in\ a\ reading\ frame\ that\ \n\ has\ the\ largest\ count.\ If\ there\ are\ several\ such\ codons,return\n\ any\ one\ of\ them.This\ method\ assumes\ the\ HashMap\ of\ codons\ to\n\ counts\ has\ already\ been\ built.\n
 comment4.params=start\ end
 comment4.target=void\ printCodonCounts(int,\ int)
-comment4.text=Write\ a\ void\ method\ named\ printCodonCounts\ that\ has\ two\ int\ parameters,\nstart\ and\ end.\ This\ method\ prints\ all\ the\ codons\ in\ the\ HashMap\ along\n\ with\ their\ count\ if\ their\ count\ is\ between\ start\ and\ end,\ inclusive\n
 comment5.params=
 comment5.target=void\ Test()
 numComments=6
diff --git a/Week2/Codon Count/CodonCount.java b/Week2/Codon Count/CodonCount.java
index b06be73..cf6bab8 100644
--- a/Week2/Codon Count/CodonCount.java	
+++ b/Week2/Codon Count/CodonCount.java	
@@ -4,10 +4,14 @@
  * Find out how many times each codon occurs in a stand of DNA based on 
  * reading frames.
  * @author (Aymar N) 
- * @version (07.03.2019)
+ * @version (04.01.2023 V2)
  */
 
-import edu.duke.*;
+//import edu.duke.*;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.FileNotFoundException;
 import java.util.HashMap;
 
 public class CodonCount {
@@ -104,8 +108,25 @@ public void printCodonCounts(int start, int end) {
     
     public void Test() {
        //String dna = "CGTTCAAGTTCAA";
-       FileResource DNA = new FileResource("dnaMystery1.txt");
-       String dna = DNA.asString();
+       String s = "";
+       String dna = "";
+       try(BufferedReader DNA = new BufferedReader(new FileReader("dnaMystery1.txt"));)
+       {
+           //FileResource DNA = new FileResource("dnaMystery1.txt");
+           while((s = DNA.readLine())!= null){
+               dna += s;
+           }
+           //String dna = DNA.asString();
+
+       }
+       catch(FileNotFoundException e){
+           e.printStackTrace();
+       }
+       catch(IOException e){
+           e.printStackTrace();
+       }
+      
+       
        int start = 1;
        int end = 5;
         
diff --git a/Week2/Codon Count/README.TXT b/Week2/Codon Count/README.TXT
new file mode 100644
index 0000000..7342ea5
--- /dev/null
+++ b/Week2/Codon Count/README.TXT	
@@ -0,0 +1,12 @@
+------------------------------------------------------------------------
+This is the project README file. Here, you should describe your project.
+Tell the reader (someone who does not know anything about this project)
+all they need to know. The comments should usually include at least:
+------------------------------------------------------------------------
+
+PROJECT TITLE:
+PURPOSE OF PROJECT:
+VERSION or DATE:
+HOW TO START THIS PROJECT:
+AUTHORS:
+USER INSTRUCTIONS:
diff --git a/Week2/Codon Count/package.bluej b/Week2/Codon Count/package.bluej
new file mode 100644
index 0000000..963e55b
--- /dev/null
+++ b/Week2/Codon Count/package.bluej	
@@ -0,0 +1,38 @@
+#BlueJ package file
+editor.fx.0.height=744
+editor.fx.0.width=1382
+editor.fx.0.x=-8
+editor.fx.0.y=-8
+objectbench.height=93
+objectbench.width=760
+package.divider.horizontal=0.6
+package.divider.vertical=0.8
+package.editor.height=393
+package.editor.width=670
+package.editor.x=260
+package.editor.y=48
+package.frame.height=600
+package.frame.width=800
+package.numDependencies=0
+package.numTargets=2
+package.showExtends=true
+package.showUses=true
+project.charset=UTF-8
+readme.height=60
+readme.name=@README
+readme.width=49
+readme.x=10
+readme.y=10
+target1.height=70
+target1.name=dnaMystery1.txt
+target1.type=TextTarget
+target1.width=120
+target1.x=10
+target1.y=90
+target2.height=70
+target2.name=CodonCount
+target2.showInterface=false
+target2.type=ClassTarget
+target2.width=120
+target2.x=70
+target2.y=10