Arrays filling improvement and some tidy up.

src/main/java/epic/util/Arrays.scala

@@ -48,9 +48,9 @@ object Arrays {
     val ret = new Array[C](arr1.length * arr2.length)
     var off = 0
     var i = 0
-    while(i < arr1.length) {
+    while (i < arr1.length) {
       var j = 0
-      while(j < arr2.length) {
+      while (j < arr2.length) {
         ret(off) = f(arr1(i), arr2(j))
         off += 1
         j += 1
@@ -65,9 +65,9 @@ object Arrays {
     val ret = new Array[Int](arr1.length * arr2.length)
     var off = 0
     var i = 0
-    while(i < arr1.length) {
+    while (i < arr1.length) {
       var j = 0
-      while(j < arr2.length) {
+      while (j < arr2.length) {
         ret(off) = arr1(i) + arr2(j) * secondScale
         off += 1
         j += 1

src/main/scala/epic/constraints/CachedLabeledSpanConstraintsFactory.scala

@@ -2,7 +2,6 @@ package epic.constraints
 
 import epic.util.CacheBroker
 
-
 /**
  * A cached version of [[epic.constraints.LabeledSpanConstraints.Factory]].
  * Uses the [[epic.util.CacheBroker]] infrastructure

src/main/scala/epic/constraints/ChartConstraints.scala

@@ -19,29 +19,26 @@ import java.io.{DataOutput, DataInput}
 case class ChartConstraints[L](top: LabeledSpanConstraints[L],
                                 bot: LabeledSpanConstraints[L]) extends SpanConstraints with Serializable {
 
-
-  def isAllowedSpan(begin: Int, end: Int):Boolean = top.isAllowedSpan(begin, end) || bot.isAllowedSpan(begin, end)
+  def isAllowedSpan(begin: Int, end: Int): Boolean = top.isAllowedSpan(begin, end) || bot.isAllowedSpan(begin, end)
   /** TODO */ // TODO
-  def hasMaximalLabel(begin: Int, end: Int):Boolean = ???
-
+  def hasMaximalLabel(begin: Int, end: Int): Boolean = ???
 
   def maxSpanLengthStartingAt(begin: Int): Int = top.maxSpanLengthStartingAt(begin) max bot.maxSpanLengthStartingAt(begin)
 
   def flatten = top | bot
-  def &(other: ChartConstraints[L]) = if(this eq other) this else ChartConstraints(top & other.top, bot & other.bot)
+  def &(other: ChartConstraints[L]) = if (this eq other) this else ChartConstraints(top & other.top, bot & other.bot)
   def |(other: ChartConstraints[L]) = ChartConstraints(top | other.top, bot | other.bot)
 
-
 }
 
 object ChartConstraints {
+
   def noSparsity[L]: ChartConstraints[L] = ChartConstraints[L](LabeledSpanConstraints.noConstraints[L], LabeledSpanConstraints.noConstraints[L])
 
   def apply[L](top: TriangularArray[_ <: BitSet], bot: TriangularArray[_ <: BitSet]): ChartConstraints[L] = ChartConstraints(LabeledSpanConstraints(top), LabeledSpanConstraints(bot))
 
   trait Factory[L, W] extends SpanConstraints.Factory[W] {
     def constraints(w: IndexedSeq[W]): ChartConstraints[L]
-
     def |(cf: Factory[L, W]) = new OrFactory(this, cf)
   }
 
@@ -82,11 +79,9 @@ object ChartConstraints {
       case _ =>
         bot(t.begin,t.end) = BitSet(labelIndex(t.label))
     }
-
     ChartConstraints(LabeledSpanConstraints(top), LabeledSpanConstraints(bot))
   }
 
-
   implicit def serializerChartConstraints[L]:Serializer[ChartConstraints[L]] = new Serializer[ChartConstraints[L]] with Serializable {
     def serialize(out: DataOutput, value: ChartConstraints[L]) {
        implicitly[Serializer[LabeledSpanConstraints[L]]].serialize(out, value.top)
@@ -98,6 +93,6 @@ object ChartConstraints {
       val bot = implicitly[Serializer[LabeledSpanConstraints[L]]].deserialize(in, available)
       ChartConstraints(top, bot)
     }
-
   }
+
 }