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rrbox · Aug 13, 2022 · 2d5d8db · 2d5d8db
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,9 @@
+.DS_Store
+/.build
+/Packages
+/*.xcodeproj
+xcuserdata/
+DerivedData/
+.swiftpm/config/registries.json
+.swiftpm/xcode/package.xcworkspace/contents.xcworkspacedata
+.netrc
diff --git a/.swiftpm/xcode/package.xcworkspace/xcshareddata/IDEWorkspaceChecks.plist b/.swiftpm/xcode/package.xcworkspace/xcshareddata/IDEWorkspaceChecks.plist
@@ -0,0 +1,8 @@
+<?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>IDEDidComputeMac32BitWarning</key>
+	<true/>
+</dict>
+</plist>
diff --git a/.swiftpm/xcode/xcshareddata/xcschemes/Nucleotide-test.xcscheme b/.swiftpm/xcode/xcshareddata/xcschemes/Nucleotide-test.xcscheme
@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Scheme
+   LastUpgradeVersion = "1340"
+   version = "1.3">
+   <BuildAction
+      parallelizeBuildables = "YES"
+      buildImplicitDependencies = "YES">
+      <BuildActionEntries>
+         <BuildActionEntry
+            buildForTesting = "YES"
+            buildForRunning = "YES"
+            buildForProfiling = "YES"
+            buildForArchiving = "YES"
+            buildForAnalyzing = "YES">
+            <BuildableReference
+               BuildableIdentifier = "primary"
+               BlueprintIdentifier = "Nucleotide"
+               BuildableName = "Nucleotide"
+               BlueprintName = "Nucleotide"
+               ReferencedContainer = "container:">
+            </BuildableReference>
+         </BuildActionEntry>
+      </BuildActionEntries>
+   </BuildAction>
+   <TestAction
+      buildConfiguration = "Debug"
+      selectedDebuggerIdentifier = "Xcode.DebuggerFoundation.Debugger.LLDB"
+      selectedLauncherIdentifier = "Xcode.DebuggerFoundation.Launcher.LLDB"
+      shouldUseLaunchSchemeArgsEnv = "YES">
+      <Testables>
+      </Testables>
+   </TestAction>
+   <LaunchAction
+      buildConfiguration = "Debug"
+      selectedDebuggerIdentifier = "Xcode.DebuggerFoundation.Debugger.LLDB"
+      selectedLauncherIdentifier = "Xcode.DebuggerFoundation.Launcher.LLDB"
+      launchStyle = "0"
+      useCustomWorkingDirectory = "NO"
+      ignoresPersistentStateOnLaunch = "NO"
+      debugDocumentVersioning = "YES"
+      debugServiceExtension = "internal"
+      allowLocationSimulation = "YES">
+   </LaunchAction>
+   <ProfileAction
+      buildConfiguration = "Release"
+      shouldUseLaunchSchemeArgsEnv = "YES"
+      savedToolIdentifier = ""
+      useCustomWorkingDirectory = "NO"
+      debugDocumentVersioning = "YES">
+      <MacroExpansion>
+         <BuildableReference
+            BuildableIdentifier = "primary"
+            BlueprintIdentifier = "Nucleotide"
+            BuildableName = "Nucleotide"
+            BlueprintName = "Nucleotide"
+            ReferencedContainer = "container:">
+         </BuildableReference>
+      </MacroExpansion>
+   </ProfileAction>
+   <AnalyzeAction
+      buildConfiguration = "Debug">
+   </AnalyzeAction>
+   <ArchiveAction
+      buildConfiguration = "Release"
+      revealArchiveInOrganizer = "YES">
+   </ArchiveAction>
+</Scheme>
diff --git a/.swiftpm/xcode/xcshareddata/xcschemes/Nucleotide.xcscheme b/.swiftpm/xcode/xcshareddata/xcschemes/Nucleotide.xcscheme
@@ -0,0 +1,91 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Scheme
+   LastUpgradeVersion = "1340"
+   version = "1.3">
+   <BuildAction
+      parallelizeBuildables = "YES"
+      buildImplicitDependencies = "YES">
+      <BuildActionEntries>
+         <BuildActionEntry
+            buildForTesting = "YES"
+            buildForRunning = "YES"
+            buildForProfiling = "YES"
+            buildForArchiving = "YES"
+            buildForAnalyzing = "YES">
+            <BuildableReference
+               BuildableIdentifier = "primary"
+               BlueprintIdentifier = "Nucleotide"
+               BuildableName = "Nucleotide"
+               BlueprintName = "Nucleotide"
+               ReferencedContainer = "container:">
+            </BuildableReference>
+         </BuildActionEntry>
+         <BuildActionEntry
+            buildForTesting = "YES"
+            buildForRunning = "YES"
+            buildForProfiling = "NO"
+            buildForArchiving = "NO"
+            buildForAnalyzing = "YES">
+            <BuildableReference
+               BuildableIdentifier = "primary"
+               BlueprintIdentifier = "NucleotideTests"
+               BuildableName = "NucleotideTests"
+               BlueprintName = "NucleotideTests"
+               ReferencedContainer = "container:">
+            </BuildableReference>
+         </BuildActionEntry>
+      </BuildActionEntries>
+   </BuildAction>
+   <TestAction
+      buildConfiguration = "Debug"
+      selectedDebuggerIdentifier = "Xcode.DebuggerFoundation.Debugger.LLDB"
+      selectedLauncherIdentifier = "Xcode.DebuggerFoundation.Launcher.LLDB"
+      shouldUseLaunchSchemeArgsEnv = "YES">
+      <Testables>
+         <TestableReference
+            skipped = "NO">
+            <BuildableReference
+               BuildableIdentifier = "primary"
+               BlueprintIdentifier = "NucleotideTests"
+               BuildableName = "NucleotideTests"
+               BlueprintName = "NucleotideTests"
+               ReferencedContainer = "container:">
+            </BuildableReference>
+         </TestableReference>
+      </Testables>
+   </TestAction>
+   <LaunchAction
+      buildConfiguration = "Debug"
+      selectedDebuggerIdentifier = "Xcode.DebuggerFoundation.Debugger.LLDB"
+      selectedLauncherIdentifier = "Xcode.DebuggerFoundation.Launcher.LLDB"
+      launchStyle = "0"
+      useCustomWorkingDirectory = "NO"
+      ignoresPersistentStateOnLaunch = "NO"
+      debugDocumentVersioning = "YES"
+      debugServiceExtension = "internal"
+      allowLocationSimulation = "YES">
+   </LaunchAction>
+   <ProfileAction
+      buildConfiguration = "Release"
+      shouldUseLaunchSchemeArgsEnv = "YES"
+      savedToolIdentifier = ""
+      useCustomWorkingDirectory = "NO"
+      debugDocumentVersioning = "YES">
+      <MacroExpansion>
+         <BuildableReference
+            BuildableIdentifier = "primary"
+            BlueprintIdentifier = "Nucleotide"
+            BuildableName = "Nucleotide"
+            BlueprintName = "Nucleotide"
+            ReferencedContainer = "container:">
+         </BuildableReference>
+      </MacroExpansion>
+   </ProfileAction>
+   <AnalyzeAction
+      buildConfiguration = "Debug">
+   </AnalyzeAction>
+   <ArchiveAction
+      buildConfiguration = "Release"
+      revealArchiveInOrganizer = "YES">
+   </ArchiveAction>
+</Scheme>
diff --git a/LICENCE b/LICENCE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 RedRimmedBox
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/Package.swift b/Package.swift
@@ -0,0 +1,28 @@
+// swift-tools-version: 5.6
+// The swift-tools-version declares the minimum version of Swift required to build this package.
+
+import PackageDescription
+
+let package = Package(
+    name: "Nucleotide",
+    products: [
+        // Products define the executables and libraries a package produces, and make them visible to other packages.
+        .library(
+            name: "Nucleotide",
+            targets: ["Nucleotide"]),
+    ],
+    dependencies: [
+        // Dependencies declare other packages that this package depends on.
+        // .package(url: /* package url */, from: "1.0.0"),
+    ],
+    targets: [
+        // Targets are the basic building blocks of a package. A target can define a module or a test suite.
+        // Targets can depend on other targets in this package, and on products in packages this package depends on.
+        .target(
+            name: "Nucleotide",
+            dependencies: []),
+        .testTarget(
+            name: "NucleotideTests",
+            dependencies: ["Nucleotide"]),
+    ]
+)
diff --git a/README.md b/README.md
@@ -0,0 +1,3 @@
+# Nucleotide
+
+現在開発中です.
diff --git a/Sources/Nucleotide/Nucleotide.swift b/Sources/Nucleotide/Nucleotide.swift
@@ -0,0 +1,111 @@
+//
+//  Nucreotide.swift
+//
+//
+//  Created by rrbox on 2022/08/13.
+//
+
+public struct Nucleotide: OptionSet {
+    public var rawValue: UInt8
+    public init(rawValue: UInt8) {
+        self.rawValue = rawValue
+    }
+}
+
+extension Nucleotide {
+    static let a = Self.init(rawValue: 0b11)
+    static let c = Self.init(rawValue: 0b11 << 2)
+    static let g = Self.init(rawValue: 0b11 << 4)
+    static let t = Self.init(rawValue: 0b11 << 6)
+    static let u = Self.init(rawValue: 0b11 << 6)
+}
+
+// fasta 形式
+extension Nucleotide {
+    static let r: Self = [.a, .g]
+    static let y: Self = [.t, .c]
+    static let k: Self = [.g, .t]
+    static let m: Self = [.a, .c]
+}
+
+extension Nucleotide {
+    static let s: Self = [.g, .c]
+    static let w: Self = [.a, .t]
+}
+
+extension Nucleotide {
+    static let b: Self = [.g, .t, .c]
+    static let d: Self = [.g, .a, .t]
+    static let h: Self = [.a, .c, .t]
+    static let v: Self = [.g, .c, .a]
+}
+
+extension Nucleotide {
+    static let n: Self = [.a, .g, .c, .t]
+    static let gap: Self = .init(rawValue: 0)
+}
+
+public protocol BaseType {
+    static var unicodeToBaseDict: [UnicodeScalar: Nucleotide] { get }
+    static var baseToUnicodeDict: [UInt8: UnicodeScalar] { get }
+}
+
+extension BaseType {
+    static func unicodeConvertToBase(_ unicode: UnicodeScalar) -> Nucleotide? {
+        return Self.unicodeToBaseDict[unicode]
+    }
+
+    static func baseConvertToUnicode(_ base: Nucleotide) -> UnicodeScalar? {
+        return Self.baseToUnicodeDict[base.rawValue]
+    }
+}
+
+
+public enum DNA: BaseType {
+    public static let unicodeToBaseDict: [UnicodeScalar: Nucleotide] = [
+        "A": .a,
+        "C": .c,
+        "G": .g,
+        "T": .t,
+    ]
+
+    public static let baseToUnicodeDict: [UInt8: UnicodeScalar] = [
+        Nucleotide.a.rawValue: "A",
+        Nucleotide.t.rawValue: "T",
+        Nucleotide.c.rawValue: "C",
+        Nucleotide.g.rawValue: "G",
+    ]
+
+}
+
+public enum RNA: BaseType {
+    public static let unicodeToBaseDict: [UnicodeScalar: Nucleotide] = [
+        "A": .a,
+        "C": .c,
+        "G": .g,
+        "U": .u,
+    ]
+
+    public static let baseToUnicodeDict: [UInt8: UnicodeScalar] = [
+        Nucleotide.a.rawValue: "A",
+        Nucleotide.u.rawValue: "U",
+        Nucleotide.c.rawValue: "C",
+        Nucleotide.g.rawValue: "G",
+    ]
+
+}
+
+public struct BaseSequence<T: BaseType>: ExpressibleByStringLiteral, CustomStringConvertible {
+    var sequence: [UInt8]
+
+    public init(stringLiteral value: StringLiteralType) {
+        self.sequence = value.unicodeScalars.reduce(into: []) { partialResult, s in
+            partialResult.append(T.unicodeConvertToBase(s)!.rawValue)
+        }
+    }
+
+    public var description: String {
+        "\(T.self): \(self.sequence.reduce(into: "") {$0 += String(T.baseConvertToUnicode(Nucleotide(rawValue: $1))!)})"
+    }
+
+}
diff --git a/Tests/NucleotideTests/NucleotideTests.swift b/Tests/NucleotideTests/NucleotideTests.swift
@@ -0,0 +1,35 @@
+import XCTest
+@testable import Nucleotide
+
+extension String {
+    subscript(at: Int) -> Character { self[self.index(self.startIndex, offsetBy: at)] }
+}
+
+final class NucleotideTests: XCTestCase {
+    var seq: BaseSequence<DNA>?
+    override func setUp() async throws {
+
+    }
+
+//    文字列をプログラミング内の配列データに変換する際にかかる時間を計測
+    func testStringToSeqData() throws {
+        // This is an example of a functional test case.
+        // Use XCTAssert and related functions to verify your tests produce the correct
+        // results.
+
+        // 1000万塩基分の文字列を変換する時間を計測します.
+        self.measure {
+            self.seq = .init(stringLiteral: String(repeating: "A", count: 10000000))
+        }
+//        計測結果
+//        10万塩基: 0.009 sec
+//        100万塩基: 0.063 sec
+//        1000万塩基: 0.611 sec
+//        1億塩基: 6.140 sec
+
+//        予想
+//        10億塩基: 1 min
+//        30億塩基: 3 min
+
+    }
+}