Merge pull request #1276 from veg/develop

2.5.28
veg · Feb 16, 2021 · c6e3c83 · c6e3c83
2 parents 927e226 + 462a9a6
commit c6e3c83
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Showing 31 changed files with 380 additions and 166 deletions.
diff --git a/res/TemplateBatchFiles/Distances/JC69 b/res/TemplateBatchFiles/Distances/JC69
@@ -1,13 +1,9 @@
-function InitializeDistances (dummy)
-{
-	summingVector = {4,1}["1"];
-	return 0;
+function InitializeDistances (dummy) {
 }
 
-function ComputeDistanceFormula (s1,s2)
-{
-	GetDataInfo 		 (siteDifferenceCount, filteredData, s1, s2, DIST_OPTION);
-	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
+function ComputeDistanceFormula (s1,s2) {
+	GetDataInfo 		 (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
+	totalSitesCompared = +siteDifferenceCount;
 
 	if (totalSitesCompared)
 	{

diff --git a/res/TemplateBatchFiles/Distances/K2P b/res/TemplateBatchFiles/Distances/K2P
@@ -6,7 +6,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
 	if (totalSitesCompared)

diff --git a/res/TemplateBatchFiles/Distances/K2P_RV b/res/TemplateBatchFiles/Distances/K2P_RV
@@ -15,7 +15,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo 		 (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo 		 (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
 
 	if (totalSitesCompared)

diff --git a/res/TemplateBatchFiles/Distances/Modified_Nei_Gojobori b/res/TemplateBatchFiles/Distances/Modified_Nei_Gojobori
@@ -46,7 +46,7 @@ function ComputeDistanceFormula (s1,s2)
 	_SITE_OS_COUNT = {stateCharCount,stateCharCount};
 	_SITE_ON_COUNT = {stateCharCount,stateCharCount};
 
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 
 	_SITE_OS_COUNT = matrixTrick2*(_OBSERVED_S_$siteDifferenceCount)*Transpose(matrixTrick2);
 	_SITE_ON_COUNT = matrixTrick2*(_OBSERVED_NS_$siteDifferenceCount)*Transpose(matrixTrick2);

diff --git a/res/TemplateBatchFiles/Distances/Nei_Gojobori b/res/TemplateBatchFiles/Distances/Nei_Gojobori
@@ -40,7 +40,7 @@ function ComputeDistanceFormula (s1,s2)
 	_SITE_OS_COUNT = {stateCharCount,stateCharCount};
 	_SITE_ON_COUNT = {stateCharCount,stateCharCount};
 
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 
 	_SITE_OS_COUNT = matrixTrick2*(_OBSERVED_S_$siteDifferenceCount)*Transpose(matrixTrick2);
 	_SITE_ON_COUNT = matrixTrick2*(_OBSERVED_NS_$siteDifferenceCount)*Transpose(matrixTrick2);

diff --git a/res/TemplateBatchFiles/Distances/PC b/res/TemplateBatchFiles/Distances/PC
@@ -7,7 +7,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo 		 (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo 		 (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector));
 	totalDifference    = Transpose(summingVector)*(siteDifferenceCount$tracingVector*summingVector);
 

diff --git a/res/TemplateBatchFiles/Distances/PC_MH b/res/TemplateBatchFiles/Distances/PC_MH
@@ -7,7 +7,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 	totalDifference    = Transpose(summingVector)*(siteDifferenceCount$tracingVector*summingVector);
 	totalSitesCompared = Transpose(summingVector)*(siteDifferenceCount*summingVector);
 	totalDifference = totalDifference[0]/totalSitesCompared[0];

diff --git a/res/TemplateBatchFiles/Distances/PC_RV b/res/TemplateBatchFiles/Distances/PC_RV
@@ -16,7 +16,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 	totalDifference    = Transpose(summingVector)*(siteDifferenceCount$tracingVector*summingVector);
 	totalSitesCompared = Transpose(summingVector)*(siteDifferenceCount*summingVector);
 	return _distance_alpha*((totalDifference[0]/totalSitesCompared[0])^(-1/_distance_alpha)-1);

diff --git a/res/TemplateBatchFiles/Distances/T3P b/res/TemplateBatchFiles/Distances/T3P
@@ -11,7 +11,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
 	if (totalSitesCompared)

diff --git a/res/TemplateBatchFiles/Distances/TN84 b/res/TemplateBatchFiles/Distances/TN84
@@ -16,7 +16,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
 	if (totalSitesCompared)

diff --git a/res/TemplateBatchFiles/Distances/TN93 b/res/TemplateBatchFiles/Distances/TN93
@@ -26,7 +26,7 @@ function InitializeDistances (void)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DEFAULT);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
 	if (totalSitesCompared)

diff --git a/res/TemplateBatchFiles/Distances/TN93_RV b/res/TemplateBatchFiles/Distances/TN93_RV
@@ -25,7 +25,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
 	if (totalSitesCompared)

diff --git a/res/TemplateBatchFiles/Distances/p_Distance b/res/TemplateBatchFiles/Distances/p_Distance
@@ -6,7 +6,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
 	if (totalSitesCompared)
 	{

diff --git a/res/TemplateBatchFiles/Distances/p_Distance_aa b/res/TemplateBatchFiles/Distances/p_Distance_aa
@@ -12,7 +12,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 	totalDifference    = Transpose(summingVector)*(siteDifferenceCount$tracingVector*summingVector);
 	totalSitesCompared = Transpose(summingVector)*(siteDifferenceCount*summingVector);
 	return 1-totalDifference[0]/totalSitesCompared[0];

diff --git a/res/TemplateBatchFiles/Distances/p_Distance_binary b/res/TemplateBatchFiles/Distances/p_Distance_binary
@@ -6,7 +6,7 @@ function InitializeDistances (dummy)
 
 function ComputeDistanceFormula (s1,s2)
 {
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 	totalSitesCompared = (Transpose(summingVector)*(siteDifferenceCount*summingVector))[0];
 	if (totalSitesCompared)
 	{

diff --git a/res/TemplateBatchFiles/Distances/p_Distance_codon b/res/TemplateBatchFiles/Distances/p_Distance_codon
@@ -34,7 +34,7 @@ function ComputeDistanceFormula (s1,s2)
 {	
 	_SITE_ON_COUNT = {stateCharCount,stateCharCount};
 
-	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, DISTANCE_AMBIG_OPTION);
+	GetDataInfo (siteDifferenceCount, filteredData, s1, s2, RESOLVE_AMBIGUITIES);
 
 
 	if (distChoice == 0)