Project 3. iDNA

iDNA.xcodeproj/xcuserdata/macuser.xcuserdatad/xcdebugger/Breakpoints.xcbkptlist

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+<?xml version="1.0" encoding="UTF-8"?>
+<Bucket
+   type = "1"
+   version = "1.0">
+</Bucket>

iDNA.xcodeproj/xcuserdata/macuser.xcuserdatad/xcschemes/iDNA.xcscheme

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+<?xml version="1.0" encoding="UTF-8"?>
+<Scheme
+   version = "1.3">
+   <BuildAction
+      parallelizeBuildables = "YES"
+      buildImplicitDependencies = "YES">
+      <BuildActionEntries>
+         <BuildActionEntry
+            buildForTesting = "YES"
+            buildForRunning = "YES"
+            buildForProfiling = "YES"
+            buildForArchiving = "YES"
+            buildForAnalyzing = "YES">
+            <BuildableReference
+               BuildableIdentifier = "primary"
+               BlueprintIdentifier = "6373D4F71689E47B00EE7CDA"
+               BuildableName = "iDNA.app"
+               BlueprintName = "iDNA"
+               ReferencedContainer = "container:iDNA.xcodeproj">
+            </BuildableReference>
+         </BuildActionEntry>
+      </BuildActionEntries>
+   </BuildAction>
+   <TestAction
+      selectedDebuggerIdentifier = "Xcode.DebuggerFoundation.Debugger.GDB"
+      selectedLauncherIdentifier = "Xcode.DebuggerFoundation.Launcher.GDB"
+      shouldUseLaunchSchemeArgsEnv = "YES"
+      buildConfiguration = "Debug">
+      <Testables>
+         <TestableReference
+            skipped = "NO">
+            <BuildableReference
+               BuildableIdentifier = "primary"
+               BlueprintIdentifier = "6373D51B1689E47C00EE7CDA"
+               BuildableName = "iDNATests.octest"
+               BlueprintName = "iDNATests"
+               ReferencedContainer = "container:iDNA.xcodeproj">
+            </BuildableReference>
+         </TestableReference>
+      </Testables>
+      <MacroExpansion>
+         <BuildableReference
+            BuildableIdentifier = "primary"
+            BlueprintIdentifier = "6373D4F71689E47B00EE7CDA"
+            BuildableName = "iDNA.app"
+            BlueprintName = "iDNA"
+            ReferencedContainer = "container:iDNA.xcodeproj">
+         </BuildableReference>
+      </MacroExpansion>
+   </TestAction>
+   <LaunchAction
+      selectedDebuggerIdentifier = "Xcode.DebuggerFoundation.Debugger.GDB"
+      selectedLauncherIdentifier = "Xcode.DebuggerFoundation.Launcher.GDB"
+      launchStyle = "0"
+      useCustomWorkingDirectory = "NO"
+      buildConfiguration = "Debug"
+      debugDocumentVersioning = "YES"
+      allowLocationSimulation = "YES">
+      <BuildableProductRunnable>
+         <BuildableReference
+            BuildableIdentifier = "primary"
+            BlueprintIdentifier = "6373D4F71689E47B00EE7CDA"
+            BuildableName = "iDNA.app"
+            BlueprintName = "iDNA"
+            ReferencedContainer = "container:iDNA.xcodeproj">
+         </BuildableReference>
+      </BuildableProductRunnable>
+      <AdditionalOptions>
+      </AdditionalOptions>
+   </LaunchAction>
+   <ProfileAction
+      shouldUseLaunchSchemeArgsEnv = "YES"
+      savedToolIdentifier = ""
+      useCustomWorkingDirectory = "NO"
+      buildConfiguration = "Release"
+      debugDocumentVersioning = "YES">
+      <BuildableProductRunnable>
+         <BuildableReference
+            BuildableIdentifier = "primary"
+            BlueprintIdentifier = "6373D4F71689E47B00EE7CDA"
+            BuildableName = "iDNA.app"
+            BlueprintName = "iDNA"
+            ReferencedContainer = "container:iDNA.xcodeproj">
+         </BuildableReference>
+      </BuildableProductRunnable>
+   </ProfileAction>
+   <AnalyzeAction
+      buildConfiguration = "Debug">
+   </AnalyzeAction>
+   <ArchiveAction
+      buildConfiguration = "Release"
+      revealArchiveInOrganizer = "YES">
+   </ArchiveAction>
+</Scheme>

iDNA.xcodeproj/xcuserdata/macuser.xcuserdatad/xcschemes/xcschememanagement.plist

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>SchemeUserState</key>
+	<dict>
+		<key>iDNA.xcscheme</key>
+		<dict>
+			<key>orderHint</key>
+			<integer>0</integer>
+		</dict>
+	</dict>
+	<key>SuppressBuildableAutocreation</key>
+	<dict>
+		<key>6373D4F71689E47B00EE7CDA</key>
+		<dict>
+			<key>primary</key>
+			<true/>
+		</dict>
+		<key>6373D51B1689E47C00EE7CDA</key>
+		<dict>
+			<key>primary</key>
+			<true/>
+		</dict>
+	</dict>
+</dict>
+</plist>

iDNA/Cell+Mutate.h

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+//
+//  Cell+Mutate.h
+//  DNA
+//
+//  Created by D_Unknown on 11/6/12.
+//  Copyright (c) 2012 D_Unknown. All rights reserved.
+//
+
+#import "Cell.h"
+
+@interface Cell (Mutate)
+
+-(void) mutate:(int) x;
+
+@end

iDNA/Cell+Mutate.m

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+//
+//  Cell+Mutate.m
+//  DNA
+//
+//  Created by D_Unknown on 11/6/12.
+//  Copyright (c) 2012 D_Unknown. All rights reserved.
+//
+
+#import "Cell+Mutate.h"
+
+@implementation Cell (Mutate)
+
+-(void) mutate:(int)x {
+    NSArray  *nucleotides=[NSArray arrayWithObjects: @"A", @"T", @"G", @"C", nil]; //array of nucleotides
+    int DNALen = [DNA count];
+    int NucsToMut=x*DNALen/100;
+    int rand_ind, rand_nuc;
+    NSMutableArray *mutated = [[NSMutableArray alloc] init];
+
+    for (int i=0; i<NucsToMut; i++) {
+        while (true) {
+            rand_ind = arc4random()%DNALen; //get random index in DNA for replacement
+            if([mutated containsObject:[NSNumber numberWithInt:rand_ind]])
+                continue; //check if it has been already replaced, if so get another index
+            do {
+                rand_nuc = arc4random()%4;//get random nuc
+            }
+            while([[DNA objectAtIndex:rand_ind] isEqualTo: [nucleotides objectAtIndex:rand_nuc]]); //check if nucleotide has changed. If it hasn't, repeat replacing
+            [DNA replaceObjectAtIndex:rand_ind withObject:[nucleotides objectAtIndex:rand_nuc]];//mutate!
+            [mutated addObject:[NSNumber numberWithInt:rand_ind]];
+            break;
+        }
+    }
+}     
+
+@end

iDNA/Cell.h

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+//
+//  Cell.h
+//  DNA
+//
+//  Created by D_Unknown on 11/6/12.
+//  Copyright (c) 2012 D_Unknown. All rights reserved.
+//
+
+#import <Foundation/Foundation.h>
+
+@interface Cell : NSObject
+{
+    NSMutableArray *DNA;
+    NSArray  *nucleotidesArray;
+
+}
+
+-(id) initWithLength:(int)DNALength;
+-(NSString*) getDNAString;
+-(int) hammingDistance:(Cell*) c;
+-(Cell*) crossbreedWith:(Cell*) partner;
+-(NSString*) getNucleotide;
+
+@end

iDNA/Cell.m

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+//
+//  Cell.m
+//  DNA
+//
+//  Created by D_Unknown on 11/6/12.
+//  Copyright (c) 2012 D_Unknown. All rights reserved.
+//
+
+#import "Cell.h"
+
+@implementation Cell
+
+-(id) init {
+    self=[super init];
+    if (self) {
+        DNA=[[NSMutableArray alloc] init];
+    }
+    return self;
+}
+
+-(id) initWithLength:(int)DNALength {
+    self = [super init];
+
+    if (self) {
+    nucleotidesArray = [NSArray arrayWithObjects: @"A", @"T", @"G", @"C", nil]; //array of nucleotides
+    DNA = [[NSMutableArray alloc] initWithCapacity:DNALength];
+
+    for(int i=0; i<DNALength; i++)
+        [DNA insertObject:[self getNucleotide] atIndex:i]; //fill DNA array with nucleotides
+    }
+    return self;
+}
+
+-(NSString*) getDNAString {
+    NSMutableString *DNAString=[[NSMutableString alloc] init];
+    for (NSString *element in DNA){
+        [DNAString appendString:element];
+    }
+    return DNAString;
+}
+
+-(NSString*) getNucleotide {
+    return [nucleotidesArray objectAtIndex:(arc4random()%4)]; //get random nucleotide
+}
+
+-(int) hammingDistance:(Cell*) c {
+    int dist=0;
+    for (NSUInteger i=0; i<[self->DNA count]; i++)
+        if([[self->DNA objectAtIndex:i] isNotEqualTo: [c->DNA objectAtIndex:i]])
+           dist++; //++ hamming distance if nucleotides are not equal
+    return dist;
+}
+
+-(Cell*) crossbreedWith:(Cell*) partner {
+    Cell *child=[[Cell alloc] init];
+    NSInteger DNALength=[self->DNA count];
+    int rand=arc4random()%3;
+    switch (rand) {
+        case 0: {
+            for (int i=0; i<DNALength/2; i++) {
+                [child->DNA addObject:[self->DNA objectAtIndex:i]];
+            }
+            for (int i=DNALength/2; i<DNALength; i++) {
+                [child->DNA addObject:[partner->DNA objectAtIndex:i]];
+            }
+            break;
+        }
+
+        case 1: {
+            BOOL first=YES;
+            for (int i=0; i<DNALength; i++) {
+                if (first) {
+                    [child->DNA addObject:[self->DNA objectAtIndex:i]];
+                    first=NO;
+                }
+                else {
+                    [child->DNA addObject:[partner->DNA objectAtIndex:i]];
+                    first=YES;
+                }
+            }
+            break;
+        }
+        case 2: {
+            for (int i=0; i<DNALength*0.2; i++) {
+                [child->DNA addObject:[self->DNA objectAtIndex:i]];
+            }
+            for (int i=DNALength*0.2; i<DNALength*0.8; i++) {
+                [child->DNA addObject:[partner->DNA objectAtIndex:i]];
+            }
+            for (int i=DNALength*0.8; i<DNALength; i++) {
+                [child->DNA addObject:[self->DNA objectAtIndex:i]];
+            }
+            break;
+        }
+
+    }
+
+    return child;
+}
+
+@end

iDNA/Document.h

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+//
+//  Document.h
+//  iDNA
+//
+//  Created by D_unknown on 12/25/12.
+//  Copyright (c) 2012 D_unknown. All rights reserved.
+//
+
+#import <Cocoa/Cocoa.h>
+#import "Cell.h"
+#import "Cell+Mutate.h"
+@interface Document : NSDocument {
+    NSMutableArray *population;
+    Cell *goalDNA;
+
+    NSInteger populationSize;
+    NSInteger DNALength;
+    NSInteger mutationRate;
+
+    NSInteger generation;
+    NSInteger bestMatch;
+    BOOL paused;
+    BOOL stopped;
+
+    IBOutlet NSTextField *popSizeField;
+    IBOutlet NSTextField *DNALenField;
+    IBOutlet NSTextField *mutRateField;
+
+    IBOutlet NSSlider *popSizeSlider;
+    IBOutlet NSSlider *DNALenSlider;
+    IBOutlet NSSlider *mutRateSlider;
+
+
+    IBOutlet NSTextField *genLabel;
+    IBOutlet NSTextField *bestMatchLabel;
+    IBOutlet NSProgressIndicator *bestMatchProg;
+
+    IBOutlet NSTextField *goalDNAField;
+
+    IBOutlet NSButton *startBut;
+    IBOutlet NSButton *loadBut;
+    IBOutlet NSButton *stopBut;    
+
+}
+
+- (IBAction)startEvolution:(id)sender;
+- (IBAction)populationSizeChange:(id)sender;
+- (IBAction)DNALengthChange:(id)sender;
+- (IBAction)mutationRateChange:(id)sender;
+- (IBAction)stopEvol:(id)sender;
+
+
+- (void) evolution;
+- (void) setPopSize;
+- (void) setDNALen;
+- (void) setMutRate;
+- (void) setGen;
+- (void) setBestMatch;
+- (void) createGoal;
+@end