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unroll/optimize some JavaConversions #1326

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unroll/optimize some JavaConversions #1326

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16 changes: 8 additions & 8 deletions adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,12 @@
*/
package org.bdgenomics.adam.models

import htsjdk.samtools.{ SAMFileHeader, SAMSequenceRecord, SAMSequenceDictionary }
import htsjdk.samtools.{ SAMFileHeader, SAMSequenceDictionary, SAMSequenceRecord }
import htsjdk.variant.vcf.VCFHeader
import org.bdgenomics.formats.avro.{ NucleotideContigFragment, Contig }
import org.bdgenomics.formats.avro.{ Contig, NucleotideContigFragment }

import scala.collection.JavaConversions.{ asScalaIterator, seqAsJavaList }
import scala.collection._
import scala.collection.JavaConversions._

/**
* Singleton object for creating SequenceDictionaries.
Expand All @@ -48,7 +49,7 @@ object SequenceDictionary {
* @return A SequenceDictionary with populated sequence records.
*/
def apply(dict: SAMSequenceDictionary): SequenceDictionary = {
new SequenceDictionary(dict.getSequences.map(SequenceRecord.fromSAMSequenceRecord).toVector)
new SequenceDictionary(dict.getSequences.iterator().map(SequenceRecord.fromSAMSequenceRecord).toVector)
}

/**
Expand Down Expand Up @@ -98,7 +99,7 @@ object SequenceDictionary {
*/
def fromSAMSequenceDictionary(samDict: SAMSequenceDictionary): SequenceDictionary = {
val samDictRecords = samDict.getSequences
new SequenceDictionary(samDictRecords.map(SequenceRecord.fromSAMSequenceRecord).toVector)
new SequenceDictionary(samDictRecords.iterator().map(SequenceRecord.fromSAMSequenceRecord).toVector)
}
}

Expand Down Expand Up @@ -143,7 +144,7 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab
* @param name The name of the contig to extract.
* @return True if we have a sequence record for this contig.
*/
def containsRefName(name: String): Boolean = byName.containsKey(name)
def containsRefName(name: String): Boolean = byName.contains(name)

/**
* Adds a sequence record to this dictionary.
Expand Down Expand Up @@ -178,7 +179,7 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab
* @return Returns a SAM formatted sequence dictionary.
*/
def toSAMSequenceDictionary: SAMSequenceDictionary = {
new SAMSequenceDictionary(records.map(_ toSAMSequenceRecord).toList)
new SAMSequenceDictionary(records.iterator.map(_.toSAMSequenceRecord).toList)
}

/**
Expand Down Expand Up @@ -222,7 +223,6 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab

private[adam] def toAvro: Seq[Contig] = {
records.map(_.toADAMContig)
.toSeq
}

/**
Expand Down