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.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;
+-(void) mutate:(int) percent;
+-(const NSString*) getNucleotide;
+-(const NSString*) getNewNucleotide:(NSString*) oldNuc;
+-(void) DNAFromString:(NSString*)source withMaxLen:(int) maxLen;
+
+@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
+
+const NSString * nucleotides[4] = {@"A", @"T", @"G", @"C"}; //array of nucleotides
+
+//initialization
+-(id) init {
+    self=[super init];
+    if (self) {
+        DNA=[[NSMutableArray alloc] init];
+    }
+    return self;
+}
+
+//initialization whith DNA of given length
+-(id) initWithLength:(int)DNALength {
+    self = [super init];
+    if (self) {
+        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;
+}
+
+//get DNA string to show in textfield
+-(NSString*) getDNAString {
+    NSMutableString *DNAString=[[NSMutableString alloc] init];
+    for (NSString *element in DNA){
+        [DNAString appendString:element];
+    }
+    return DNAString;
+}
+
+//get random nucleotide from nucs array
+-(const NSString*) getNucleotide {
+    return nucleotides[arc4random()%4];                //return random nucleotide
+}
+
+//count hamming distance to another cell
+-(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;
+}
+
+//crossbreed with anoter cell
+-(Cell*) crossbreedWith:(Cell*) partner {
+    Cell *child=[[Cell alloc] init];                   //create a child cell
+    NSInteger DNALength=[self->DNA count];
+    int rand=arc4random()%3;
+    switch (rand) {                                    //choose 1 of 3 crossbreeed ways
+        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;                                   
+}
+
+//mutate cell
+-(void) mutate:(int) percent {
+    int dnaLength = [DNA count];
+    if (percent == 0)                                // if percent = 0, do nothing
+        return;                                      
+    if (dnaLength != 100)                            // if DNA length isn't 100, recount
+        percent = percent * dnaLength / 100;         
+
+    // create an array of BOOL, where there are as many YES elems, as number of nucs we need to mutate
+    BOOL mas [dnaLength];
+    int count = dnaLength;                          
+    while (count--)                                 
+        mas [count] = count < percent? YES : NO;    
+
+    // shuffle BOOL array
+    count = dnaLength;                               
+    int tempIndex;                                   // buffer to save index of changed elem
+    BOOL tempValue;                                  // buffer to save value of changed elem
+    while (count--) {                                
+        tempIndex = arc4random() % dnaLength;        // get random index 
+        tempValue = mas [tempIndex];                 // get value of BOOL at random index
+        mas [tempIndex] = mas [count];               // exchange elem at index "count"
+        mas [count] = tempValue;                     // whith elem at random index
+    }
+
+    // mutation itself
+    count = dnaLength;                               
+    while (count--)                                  
+        if (mas[count])                              // if mas[count] = YES, mutate nuc
+            [DNA replaceObjectAtIndex:count withObject:[self getNewNucleotide:[DNA objectAtIndex:count]]];
+}     
+
+//get new random nuc
+-(const NSString*) getNewNucleotide:(NSString *)oldNuc {
+    int count;
+    for (count = 0; count < 4; count++)
+        if (nucleotides[count] == oldNuc)
+            break;                                  // get nuc index from 0 to 3 in nucs array, save   it in count
+    count = (count + 1 + arc4random() % 3) % 4;     // change index to random index not equal to it
+    return nucleotides[count];                      // return elem of nucs array at this index
+}
+
+//create DNA from string
+-(void) DNAFromString:(NSString*)source withMaxLen:(int) maxLen {
+    [self->DNA removeAllObjects];
+    NSString *nuc;
+    for (int i=0; i<[source length]||i<maxLen; i++) {
+        nuc = [NSString stringWithFormat:@"%c", [source characterAtIndex:i]]; //get char from string
+        [self->DNA addObject:nuc];                  //add char to DNA string
+    }
+}
+
+@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"
+
+@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 NSTextField *bestDNAField;
+
+    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;
+- (IBAction)loadGoal:(id)sender;
+
+
+- (void) evolution;
+- (void) setPopSize;
+- (void) setDNALen;
+- (void) setMutRate;
+- (void) setGen;
+- (void) setBestMatch;
+- (void) createGoal;
+@end