From 839d8e3820c6097f89bdc096e264485d063c1943 Mon Sep 17 00:00:00 2001
From: David Runge <david.runge@frqrec.com>
Date: Tue, 14 Aug 2012 20:34:46 +0200
Subject: Classes and howto

---
 SNP.sc | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 SNP.sc

(limited to 'SNP.sc')

diff --git a/SNP.sc b/SNP.sc
new file mode 100644
index 0000000..5249971
--- /dev/null
+++ b/SNP.sc
@@ -0,0 +1,54 @@
+SNP{//TODO: use vectorial represntations only, strip chromosome (redundant, as stored in SNPDict already), 
+	var <chromosome;//chromosome as Symbol
+	var <vecChromosome;//corresponding number
+	var <id;//rsid of the SNP
+	var <position;//position of SNP on own chromosome
+	var <base;//base of the SNP (single or pair)
+	var <vecBase;//vectorial representation of the base (pair)
+	var <>resolver;//the other (two) combination(s) of the position
+	var <vecResolver;//vectorial representation of the other combination(s)
+
+	*new{
+		arg aChromosome, aPosition = 0, aId, aBase, aResolver;
+		^super.new.init(aChromosome, aPosition, aId, aBase, aResolver);
+	}
+
+	init{
+		arg aChromosome, aPosition, aId, aBase, aResolver;
+		chromosome = aChromosome.asSymbol;
+		vecChromosome = SNPInfo.convertChromosome(chromosome);
+		position = aPosition.asFloat;
+		id = aId.asSymbol;
+		base = aBase.asSymbol;
+		resolver = aResolver.asArray;
+		vecBase = SNPInfo.baseToVec(base);
+		vecResolver = SNPInfo.baseToVec(resolver);
+	}
+	
+	hasResolver{//check if this SNP has a resolver
+		var resolved = true;
+		if(resolver.isArray,{
+			resolver.do({
+				arg item,i;
+				if(item==\none,{
+					resolved = false
+				});
+			});
+			^resolved;
+		},{
+			if(resolver!=\none,{
+				^true;
+			},{
+				^false;
+			});
+		});
+	}
+
+	updateResolver{//update a resolver and its vector representation
+		arg newResolver;
+		if(newResolver!=resolver,{
+			resolver = newResolver;
+			vecResolver = SNPInfo.baseToVec(resolver);
+		});
+	}
+}
-- 
cgit v1.2.3-54-g00ecf