notpron

commit 20300a51328d8f8c0243090ceaff6a3972e45220
parent 6e88bc07a3085bd2460a0950a0868d6f9a189198
Author: Dominik Schmidt <das1993@hotmail.com>
Date:   Wed,  2 Sep 2015 20:44:51 +0200

D-Programm für DNS-Strang verbessert.

Diffstat:
Objects/Program/D/BasePair.d
 | 
186
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++------

1 file changed, 172 insertions(+), 14 deletions(-)
diff --git a/Objects/Program/D/BasePair.d b/Objects/Program/D/BasePair.d
@@ -1,22 +1,70 @@
 import std.stdio;
 import std.range;
+import std.algorithm;
 
 
+static immutable AminoAcid.Desc aD[]=[
+	AminoAcid.Desc("Alanine", "Ala", 'A'),
+	AminoAcid.Desc("Cyxteine", "Cys", 'C'),
+	AminoAcid.Desc("Aspartic acid", "Asp", 'D'),
+	AminoAcid.Desc("Glutamic acid", "Glu", 'E'),
+	AminoAcid.Desc("Phenylalanine", "Phe", 'F'),
+	AminoAcid.Desc("Glycine", "Gly", 'G'),
+	AminoAcid.Desc("Histidine", "His", 'H'),
+	AminoAcid.Desc("Isoleucine", "Ile", 'I'),
+	AminoAcid.Desc("Lysine", "Lys", 'K'),
+	AminoAcid.Desc("Leucine", "Leu", 'L'),
+	AminoAcid.Desc("Methionine", "Met", 'M'),
+	AminoAcid.Desc("Asparagine", "Asn", 'N'),
+	AminoAcid.Desc("Proline", "Pro", 'P'),
+	AminoAcid.Desc("Glutamine", "Gln", 'Q'),
+	AminoAcid.Desc("Arginine", "Arg", 'R'),
+	AminoAcid.Desc("Serine", "Ser", 'S'),
+	AminoAcid.Desc("Threonine", "Thr", 'T'),
+	AminoAcid.Desc("Valine", "Val", 'V'),
+	AminoAcid.Desc("Tryptophan", "Trp", 'W'),
+	AminoAcid.Desc("Tyrosine", "Tyr", 'Y'),
+];
+immutable(AminoAcid.Desc)* findAA(char shortcut){
+	auto res=aD.assumeSorted.find!"a.shortcut==b"(shortcut);
+	if(res.empty){
+		return null;
+	}
+	return &(res.front());
+}
+
 struct AminoAcid{
-	string name;
+	struct Desc{
+		string longname;
+		string shortname;
+		char shortcut;
+	}
+	immutable(AminoAcid.Desc) *desc;
 	bool start;
 	bool stop;
-	this(string str, bool start=false, bool stop=false){
-		name=str;
-		this.start=start;
-		this.stop=stop;
-	}
 	this(char sname, bool start=false, bool stop=false){
-		name=""~sname;
+		desc=findAA(sname);
 		this.start=start;
 		this.stop=stop;
 	}
+	string toString(bool shrt=true){
+		if(start){
+			return "START";
+		}
+		else if(stop){
+			return "STOP";
+		}
+		else if(desc==null)
+			return "*";
+		return (shrt) ? desc.shortname : desc.longname;
+	}
+	char toChar(){
+		if(desc==null)
+			return ' ';
+		return desc.shortcut;
+	}
 }
+
 struct AminoAcidTable{
 	private immutable static char[] AminoAcids	= "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
 	private immutable static char[] Starts = "---M---------------M---------------M----------------------------";
@@ -35,16 +83,126 @@ struct AminoAcidTable{
 			table[am]=AminoAcid(AminoAcids[i],(Starts[i]!='-'),(AminoAcids[i]=='*'));
 		}
 	}
+	
+	AminoAcid* opIndex(in DNS.Codon c){
+		return (c.c in table);
+	}
+	
+	AminoAcid* opIndex(in RNS.Codon c){
+		return opIndex(c.dns);
+	}
+	
+	auto opCall(Range)(Range r) if(isInputRange!Range && (is(ElementType!Range == RNS.Codon) || is(ElementType!Range == DNS.Codon))){
+		return r.map!(a=>*this[a]);
+	}
+	
+	auto opCall(in DNS d){
+		return d.seq.map!(a=>*this[a]);
+	}
+	auto opCall(in RNS d){
+		return d.seq.map!(a=>*this[a]);
+	}
+}
+template CodonSeq(){
+	struct Codon{
+		char[3]c;
+		this(char[3] c){
+			this.c=c;
+		}
+		this(Range)(Range r){
+			foreach(i; 0..3){
+				c[i]=cast(char)r.front;
+				r.popFront();
+			}
+		}
+	}
+}
+///Swaps A with B and C with A
+void BaseSwap(ref char str[3], in char A, in char B, in char C){
+	foreach(ref c; str){
+		if(c==A){
+			c=B;
+		}
+		else if(c==C){
+			c=A;
+		}
+	}
+}
+///Swaps A with B and vice versa
+void BaseSwap(ref char str[3], in char A, in char B){
+	foreach(ref c; str){
+		if(c==A){
+			c=B;
+		}
+		else if(c==B){
+			c=A;
+		}
+	}
+}
+
+RNS.Codon rns(in DNS.Codon d){
+	RNS.Codon c=RNS.Codon(d.c);
+	c.c.BaseSwap('A','U','T');
+	c.c.BaseSwap('G','C');
+	return c;
+}
+DNS.Codon dns(in RNS.Codon d){
+	DNS.Codon c=DNS.Codon(d.c);
+	c.c.BaseSwap('A','T','U');
+	c.c.BaseSwap('G','C');
+	return c;
+}
+
+struct DNS{
+	mixin CodonSeq;
+	Codon seq[];
+	this(Range)(Range r) if(isInputRange!Range && is(ElementType!Range==Codon)){
+		r.copy(seq.appender);
+	}
+	this(Range)(Range r) if(isInputRange!Range && isSomeChar!(ElementType!Range)){
+		foreach(s; r.chunks(3)){
+			seq~=Codon(s);
+		}
+	}
+	auto rns(){
+		return seq.map!(a=>a.rns);
+	}
+	auto aa(ref AminoAcidTable aat){
+		return aat(seq);
+	}
+}
+struct RNS{
+	mixin CodonSeq;
+	Codon seq[];
+	this(Range)(Range r) if(isInputRange!Range && isSomeChar!(ElementType!Range)){
+		foreach(s; r.chunks(3)){
+			seq~=Codon(s);
+		}
+	}
+	this(Range)(Range r) if(isInputRange!Range && is(ElementType!Range==Codon)){
+		auto app=appender(seq);
+		r.copy(app);
+		seq=app.data;
+	}
+	auto dns(){
+		return seq.map!(a=>a.dns);
+	}
+	auto aa(ref AminoAcidTable aat){
+		return aat(seq);
+	}
 }
 
 static AminoAcidTable aat;
 
-void main(){
-	string str="GTTGCTCTTGAAAATACTATTAATGAA";
+auto aaString(Range)(Range r){
+	return r.map!(a=>a.toChar());
+}
+auto aalString(Range)(Range r){
+	return r.map!(a=>a.toString()).joiner(",\t");
+}
+
+void main(string args[]){
 	aat.initialize();
-	writeln(aat.table.byValue());
-	foreach(seq; str.chunks(3)){
-		char[] d=seq.map!(a=>cast(char)a).array;
-		write(aat.table[d[0..3]].name);
-	}
+	DNS d=DNS(args[1]);
+	writeln(aat(d).aaString());
 }