From 673d79a4c7ff530783270f45450de73e69267f9c Mon Sep 17 00:00:00 2001
From: David Runge <dave@sleepmap.de>
Date: Mon, 30 Mar 2015 02:31:44 +0200
Subject: SNPInfo.sc: Retabbing document.

---
 SNPInfo.sc | 283 ++++++++++++++++++++++++++++++-------------------------------
 1 file changed, 141 insertions(+), 142 deletions(-)

diff --git a/SNPInfo.sc b/SNPInfo.sc
index a037e4a..a9a00cf 100644
--- a/SNPInfo.sc
+++ b/SNPInfo.sc
@@ -1,155 +1,154 @@
 SNPInfo{//helper class for calculations and constants used in the other classes
-	const <baseSingle = #[\A, \C, \G, \T];
-	const <basePair = #[\AA, \AC, \AG, \AT, \CC, \CG, \CT, \GG, \GT, \TT];
-	const <unknownBasePair = #[\AA, \CC, \GG, \TT];
-	const <emptyBasePair = #[\none, \none];
-	const <emptyBase = #[\none];
-//	const <chromosomesLength = #[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569];
-	const <chromosomesLength = #[247199719, 242751149, 199446827, 191263063, 180837866, 170896993, 158821424, 146274826, 140442298, 135374737, 134452384, 132289534, 114127980, 106360585, 100338915, 88822254, 78654742, 76117153, 63806651, 62435965, 46944323, 49528953, 154913754, 57741652, 16569];
-	const <chromosomesFactor = #[ 1, 1.0183256393155, 1.2394266818795, 1.2924592711349, 1.3669687907067, 1.4464837248482, 1.556463308124, 1.6899676161638, 1.7601514822835, 1.8260402529905, 1.8385670201281, 1.868626425126, 2.1659869823333, 2.324166597993, 2.4636475190109, 2.7830831561649, 3.142845716791, 3.2476217154365, 3.8741998698537, 3.9592519952242, 5.265806453317, 4.9910144274602, 1.5957247992325, 4.2811334701681, 14919.410887803 ];
-//	const <chromosomesFactor = #[1, 1.0248818404643, 1.2586989312271, 1.3039238578163, 1.3777202708052, 1.4566257978907, 1.5662480524924, 1.7029500665129, 1.7650631334069, 1.8390163889117, 1.8462117858074, 1.8621374094106, 2.1641997484794, 2.3218601681945, 2.4309688587862, 2.7585778581012, 3.0697700147583, 3.1923592004677, 4.2153713518124, 3.9547570730079, 5.1787069346401, 4.85825415617, 1.6052664523139, 4.1980065842769, 15043.190355483];
-	const <lengthAtOneMs = 69.236283611;//in hours
-	const <sCompany = #["ftdna-illumina", "23andme", "23andme-exome-vcf", "decodeme"];
-	const <a = #[1,0,0,0];
-	const <c = #[0,1,0,0];
-	const <g = #[0,0,1,0];
-	const <t = #[0,0,0,1];
-	const <e = #[0,0,0,0];
+  const <baseSingle = #[\A, \C, \G, \T];
+  const <basePair = #[\AA, \AC, \AG, \AT, \CC, \CG, \CT, \GG, \GT, \TT];
+  const <unknownBasePair = #[\AA, \CC, \GG, \TT];
+  const <emptyBasePair = #[\none, \none];
+  const <emptyBase = #[\none];
+//  const <chromosomesLength = #[249250621, 243199373, 198022430, 191154276, 180915260, 171115067, 159138663, 146364022, 141213431, 135534747, 135006516, 133851895, 115169878, 107349540, 102531392, 90354753, 81195210, 78077248, 59128983, 63025520, 48129895, 51304566, 155270560, 59373566, 16569];
+  const <chromosomesLength = #[247199719, 242751149, 199446827, 191263063, 180837866, 170896993, 158821424, 146274826, 140442298, 135374737, 134452384, 132289534, 114127980, 106360585, 100338915, 88822254, 78654742, 76117153, 63806651, 62435965, 46944323, 49528953, 154913754, 57741652, 16569];
+  const <chromosomesFactor = #[ 1, 1.0183256393155, 1.2394266818795, 1.2924592711349, 1.3669687907067, 1.4464837248482, 1.556463308124, 1.6899676161638, 1.7601514822835, 1.8260402529905, 1.8385670201281, 1.868626425126, 2.1659869823333, 2.324166597993, 2.4636475190109, 2.7830831561649, 3.142845716791, 3.2476217154365, 3.8741998698537, 3.9592519952242, 5.265806453317, 4.9910144274602, 1.5957247992325, 4.2811334701681, 14919.410887803 ];
+//  const <chromosomesFactor = #[1, 1.0248818404643, 1.2586989312271, 1.3039238578163, 1.3777202708052, 1.4566257978907, 1.5662480524924, 1.7029500665129, 1.7650631334069, 1.8390163889117, 1.8462117858074, 1.8621374094106, 2.1641997484794, 2.3218601681945, 2.4309688587862, 2.7585778581012, 3.0697700147583, 3.1923592004677, 4.2153713518124, 3.9547570730079, 5.1787069346401, 4.85825415617, 1.6052664523139, 4.1980065842769, 15043.190355483];
+  const <lengthAtOneMs = 69.236283611;//in hours
+  const <sCompany = #["ftdna-illumina", "23andme", "23andme-exome-vcf", "decodeme"];
+  const <a = #[1,0,0,0];
+  const <c = #[0,1,0,0];
+  const <g = #[0,0,1,0];
+  const <t = #[0,0,0,1];
+  const <e = #[0,0,0,0];
   const <colorA = "#80ff00";
   const <colorC = "#ff0000";
   const <colorG = "#8000ff";
   const <colorT = "#00ffff";
-	classvar <workingSCompany = #[1];//the companies working with this software (so far)
+  classvar <workingSCompany = #[1];//the companies working with this software (so far)
 
-	*calcPosition{//normalize all positions on chromosomes to the longest (the first) by chromosomesFactor of chromosomesFactor
-		arg chromosome, position;
-		var factor = 0.0, outPos = 0.0;
-		switch(chromosome.asSymbol,
-			\1,{factor = chromosomesFactor[0]},
-			\2,{factor = chromosomesFactor[1]},
-			\3,{factor = chromosomesFactor[2]},
-			\4,{factor = chromosomesFactor[3]},
-			\5,{factor = chromosomesFactor[4]},
-			\6,{factor = chromosomesFactor[5]},
-			\7,{factor = chromosomesFactor[6]},
-			\8,{factor = chromosomesFactor[7]},
-			\9,{factor = chromosomesFactor[8]},
-			\10,{factor = chromosomesFactor[9]},
-			\11,{factor = chromosomesFactor[10]},
-			\12,{factor = chromosomesFactor[11]},
-			\13,{factor = chromosomesFactor[12]},
-			\14,{factor = chromosomesFactor[13]},
-			\15,{factor = chromosomesFactor[14]},
-			\16,{factor = chromosomesFactor[15]},
-			\17,{factor = chromosomesFactor[16]},
-			\18,{factor = chromosomesFactor[17]},
-			\19,{factor = chromosomesFactor[18]},
-			\20,{factor = chromosomesFactor[19]},
-			\21,{factor = chromosomesFactor[20]},
-			\22,{factor = chromosomesFactor[21]},
-			\X,{factor = chromosomesFactor[22]},
-			\Y,{factor = chromosomesFactor[23]},
-			\MT,{factor = chromosomesFactor[24]}
-		);
-		^outPos = round(position.asFloat*factor);//round to the next possible slot
-	}
-	
-	*convertChromosome{//convert funky names of chromosomes to valid numbers
-		arg chrom;
-		switch(chrom,
-			\X, {^23},
-			\Y, {^24},
-			\MT,{^25},
-			"X", {^23},
-			"Y", {^24},
-			"MT",{^25},
-			{^chrom.asInt}
-		);
-	}
-	
-	*baseToVec{//calculate unique vectors on basis of the base given
-		arg base;
-		var out = [[],[]];
-		if(base.isArray, {//unwrap items in Array
-			base.do({
-				arg item, i;
-				if(item.notNil, {
-					out.put(i, this.baseToVec(item));
-				});
-			});
-			^out;
-		},{
-			if(this.isBasePair(base),{//if it's a base pair calc
-				switch(base,
-					\AA, {^a},
-					\AC, {^(a-c)},
-					\AG, {^(a-g)},
-					\AT, {^(a-t)},
-					\CC, {^c},
-					\CG, {^(c-g)},
-					\CT, {^(c-t)},
-					\GG, {^g},
-					\GT, {^(g-t)},
-					\TT, {^t},
-				);
-			},{
-				if(this.isBase(base),{//if it's a single base, return
-					switch(base,
-						\A, {^a},
-						\C, {^c},
-						\G, {^g},
-						\T, {^t}
-					);
-				},{
-					if(base == \none,{//if it's unknown, return empty
-						^e;
-					});
-				});
-			});
-		});
-	}
+  *calcPosition{//normalize all positions on chromosomes to the longest (the first) by chromosomesFactor of chromosomesFactor
+    arg chromosome, position;
+    var factor = 0.0, outPos = 0.0;
+    switch(chromosome.asSymbol,
+      \1,{factor = chromosomesFactor[0]},
+      \2,{factor = chromosomesFactor[1]},
+      \3,{factor = chromosomesFactor[2]},
+      \4,{factor = chromosomesFactor[3]},
+      \5,{factor = chromosomesFactor[4]},
+      \6,{factor = chromosomesFactor[5]},
+      \7,{factor = chromosomesFactor[6]},
+      \8,{factor = chromosomesFactor[7]},
+      \9,{factor = chromosomesFactor[8]},
+      \10,{factor = chromosomesFactor[9]},
+      \11,{factor = chromosomesFactor[10]},
+      \12,{factor = chromosomesFactor[11]},
+      \13,{factor = chromosomesFactor[12]},
+      \14,{factor = chromosomesFactor[13]},
+      \15,{factor = chromosomesFactor[14]},
+      \16,{factor = chromosomesFactor[15]},
+      \17,{factor = chromosomesFactor[16]},
+      \18,{factor = chromosomesFactor[17]},
+      \19,{factor = chromosomesFactor[18]},
+      \20,{factor = chromosomesFactor[19]},
+      \21,{factor = chromosomesFactor[20]},
+      \22,{factor = chromosomesFactor[21]},
+      \X,{factor = chromosomesFactor[22]},
+      \Y,{factor = chromosomesFactor[23]},
+      \MT,{factor = chromosomesFactor[24]}
+    );
+    ^outPos = round(position.asFloat*factor);//round to the next possible slot
+  }
 
+  *convertChromosome{//convert funky names of chromosomes to valid numbers
+    arg chrom;
+    switch(chrom,
+      \X, {^23},
+      \Y, {^24},
+      \MT,{^25},
+      "X", {^23},
+      "Y", {^24},
+      "MT",{^25},
+      {^chrom.asInt}
+    );
+  }
 
-	*createResolverForPair{//for known base pairs, create a resolver
-		arg base;
-		base = base.asSymbol;
-		switch(base,
-			\AC,{^[\AA, \CC]},
-			\AG,{^[\AA, \GG]},
-			\AT,{^[\AA, \TT]},
-			\CG,{^[\CC, \GG]},
-			\CT,{^[\CC, \TT]},
-			\GT,{^[\GG, \TT]},
-			{^[\none, \none]}
-		);
-	}
+  *baseToVec{//calculate unique vectors on basis of the base given
+    arg base;
+    var out = [[],[]];
+    if(base.isArray, {//unwrap items in Array
+      base.do({
+        arg item, i;
+        if(item.notNil, {
+          out.put(i, this.baseToVec(item));
+        });
+      });
+      ^out;
+    },{
+      if(this.isBasePair(base),{//if it's a base pair calc
+        switch(base,
+          \AA, {^a},
+          \AC, {^(a-c)},
+          \AG, {^(a-g)},
+          \AT, {^(a-t)},
+          \CC, {^c},
+          \CG, {^(c-g)},
+          \CT, {^(c-t)},
+          \GG, {^g},
+          \GT, {^(g-t)},
+          \TT, {^t},
+        );
+      },{
+        if(this.isBase(base),{//if it's a single base, return
+          switch(base,
+            \A, {^a},
+            \C, {^c},
+            \G, {^g},
+            \T, {^t}
+          );
+        },{
+          if(base == \none,{//if it's unknown, return empty
+            ^e;
+          });
+        });
+      });
+    });
+  }
 
-	*isUnknownBasePair{//check if it's an unknown pair
-		arg base;
-		if(unknownBasePair.includes(base.asSymbol),{//if the base is part of the unknown base pairs
-			^true;
-		},{
-			^false;
-		});
-	}
+  *createResolverForPair{//for known base pairs, create a resolver
+    arg base;
+    base = base.asSymbol;
+    switch(base,
+      \AC,{^[\AA, \CC]},
+      \AG,{^[\AA, \GG]},
+      \AT,{^[\AA, \TT]},
+      \CG,{^[\CC, \GG]},
+      \CT,{^[\CC, \TT]},
+      \GT,{^[\GG, \TT]},
+      {^[\none, \none]}
+    );
+  }
 
-	*isBase{//check if it's a single base
-		arg base;
-		if(baseSingle.includes(base.asSymbol),{//if the base is part of the unknown base pairs
-			^true;
-		},{
-			^false;
-		});
-	}
-	
-	*isBasePair{//check if it's a (known) base pair
-		arg base;
-		if(basePair.includes(base.asSymbol),{//if the base is part of the unknown base pairs
-			^true;
-		},{
-			^false;
-		});
-	}
+  *isUnknownBasePair{//check if it's an unknown pair
+    arg base;
+    if(unknownBasePair.includes(base.asSymbol),{//if the base is part of the unknown base pairs
+      ^true;
+    },{
+      ^false;
+    });
+  }
+
+  *isBase{//check if it's a single base
+    arg base;
+    if(baseSingle.includes(base.asSymbol),{//if the base is part of the unknown base pairs
+      ^true;
+    },{
+      ^false;
+    });
+  }
+
+  *isBasePair{//check if it's a (known) base pair
+    arg base;
+    if(basePair.includes(base.asSymbol),{//if the base is part of the unknown base pairs
+      ^true;
+    },{
+      ^false;
+    });
+  }
 
   //returns a hex color value for a base/ base pair
   *getColorFromBase{
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