Changed gonum vectorsto

evolbioinfo · Sep 30, 2019 · 6c135f6 · 6c135f6
1 parent bfa8636
commit 6c135f6
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Showing 4 changed files with 10 additions and 4 deletions.
diff --git a/models/dna/f81.go b/models/dna/f81.go
@@ -47,6 +47,7 @@ func (m *F81Model) InitModel(piA, piC, piG, piT float64) (err error) {
 }
 
 func (m *F81Model) computeEigens() (err error) {
+	var u mat.CDense
 	// Compute eigen values, left and right eigenvectors of Q
 	eigen := &mat.Eigen{}
 	if ok := eigen.Factorize(m.qmatrix, mat.EigenRight); !ok {
@@ -58,7 +59,7 @@ func (m *F81Model) computeEigens() (err error) {
 	for i, b := range eigen.Values(nil) {
 		val[i] = real(b)
 	}
-	u := eigen.VectorsTo(nil)
+	eigen.VectorsTo(&u)
 	reigenvect := mat.NewDense(4, 4, nil)
 	leigenvect := mat.NewDense(4, 4, nil)
 	reigenvect.Apply(func(i, j int, val float64) float64 { return real(u.At(i, j)) }, reigenvect)

diff --git a/models/dna/gtr.go b/models/dna/gtr.go
@@ -47,6 +47,8 @@ func (m *GTRModel) InitModel(d, f, b, e, a, c, piA, piC, piG, piT float64) (err
 }
 
 func (m *GTRModel) computeEigens() (err error) {
+	var u mat.CDense
+
 	// Compute eigen values, left and right eigenvectors of Q
 	eigen := &mat.Eigen{}
 	if ok := eigen.Factorize(m.qmatrix, mat.EigenRight); !ok {
@@ -58,7 +60,7 @@ func (m *GTRModel) computeEigens() (err error) {
 	for i, b := range eigen.Values(nil) {
 		val[i] = real(b)
 	}
-	u := eigen.VectorsTo(nil)
+	eigen.VectorsTo(&u)
 	reigenvect := mat.NewDense(4, 4, nil)
 	leigenvect := mat.NewDense(4, 4, nil)
 	reigenvect.Apply(func(i, j int, val float64) float64 { return real(u.At(i, j)) }, reigenvect)

diff --git a/models/dna/tn93.go b/models/dna/tn93.go
@@ -42,6 +42,8 @@ func (m *TN93Model) InitModel(kappa1, kappa2, piA, piC, piG, piT float64) (err e
 }
 
 func (m *TN93Model) computeEigens() (err error) {
+	var u mat.CDense
+
 	// Compute eigen values, left and right eigenvectors of Q
 	eigen := &mat.Eigen{}
 	if ok := eigen.Factorize(m.qmatrix, mat.EigenRight); !ok {
@@ -53,7 +55,7 @@ func (m *TN93Model) computeEigens() (err error) {
 	for i, b := range eigen.Values(nil) {
 		val[i] = real(b)
 	}
-	u := eigen.VectorsTo(nil)
+	eigen.VectorsTo(&u)
 	reigenvect := mat.NewDense(4, 4, nil)
 	leigenvect := mat.NewDense(4, 4, nil)
 	reigenvect.Apply(func(i, j int, val float64) float64 { return real(u.At(i, j)) }, reigenvect)

diff --git a/models/protein/model.go b/models/protein/model.go
@@ -95,6 +95,7 @@ func (model *ProtModel) InitModel(aafreqs []float64) error {
 	var i, j int
 	var sum float64
 	var ok bool
+	var u mat.CDense
 
 	ns := 20
 
@@ -132,7 +133,7 @@ func (model *ProtModel) InitModel(aafreqs []float64) error {
 	}
 	model.reigenvect = mat.NewDense(ns, ns, nil)
 	model.leigenvect = mat.NewDense(20, 20, nil)
-	u := model.eigen.VectorsTo(nil)
+	model.eigen.VectorsTo(&u)
 	model.eval = make([]float64, ns)
 	for i, b := range model.eigen.Values(nil) {
 		model.eval[i] = real(b)