Cleanup

Author: olegs

README.md

@@ -33,7 +33,8 @@ Tests
 
 Usages
 ------
-Used in the following projects: 
+Used in the following projects:
+
 * [SPAN](https://github.com/JetBrains-Research/span) Semi-supervised Peak Analyzer
 * [JBR](https://github.com/JetBrains-Research/jbr) JBR Genome Browser
 * [FARM](https://github.com/JetBrains-Research/fishbone) hierarchical association rule mining and visualization method

build.gradle

@@ -92,6 +92,7 @@ if (rootProject == project) {
         }
     }
 }
+
 private String settingsFolder(final String propertyName, final String folderName) {
     if (!System.hasProperty(propertyName)) {
         return "${rootProject.buildDir}/.tests/$folderName"

src/main/kotlin/org/jetbrains/bio/BioinfToolsCLA.kt

@@ -90,7 +90,7 @@ object BioinfToolsCLA {
     /**
      * Configure logging to console / file. Returns path to log file.
      */
-        internal fun configureLogging(quiet: Boolean, debug: Boolean) {
+    internal fun configureLogging(quiet: Boolean, debug: Boolean) {
         if (quiet) {
             Logs.quiet()
         }

src/main/kotlin/org/jetbrains/bio/dataframe/DataFrameMapper.kt

@@ -86,6 +86,7 @@ object DataFrameMappers {
                             val witness = values.asBooleanArray()
                             column.wrap(BitterSet(witness.size) { witness[it] })
                         }
+
                         is StringColumn -> column.wrap(values.asStringArray())
                         else -> error("unsupported column type: ${column.javaClass.canonicalName}")
                     }
@@ -108,6 +109,7 @@ object DataFrameMappers {
                         is DoubleColumn -> writer.write(column.label, column.data)
                         is BooleanColumn -> writer.write(
                             column.label, with(column.data) { BooleanArray(size()) { get(it) } })
+
                         is StringColumn -> writer.write(column.label, column.data)
                         else -> error("unsupported column type: ${column.javaClass.canonicalName}")
                     }

src/main/kotlin/org/jetbrains/bio/dataframe/DataFramePredicates.kt

@@ -83,12 +83,14 @@ fun all(pf: RowPredicateFactory, vararg rest: RowPredicateFactory): RowPredicate
             val p1 = pfs[1](df)
             IntPredicate { p0.test(it) && p1.test(it) }
         }
+
         3 -> RowPredicateFactory { df ->
             val p0 = pfs[0](df)
             val p1 = pfs[1](df)
             val p2 = pfs[2](df)
             IntPredicate { p0.test(it) && p1.test(it) && p2.test(it) }
         }
+
         else -> RowPredicateFactory { df ->
             // XXX we could optimize it by processing pfs in threes.
             val ps = pfs.map { it(df) }

src/main/kotlin/org/jetbrains/bio/genome/Ensembl.kt

@@ -158,6 +158,7 @@ class GtfReader(val reader: BufferedReader, val genome: Genome) {
             // just not to write long if condition:
             "transcript", "exon", "CDS", "start_codon", "three_prime_utr" -> { /* noop */
             }
+
             else -> return type
         }
 
@@ -188,15 +189,19 @@ class GtfReader(val reader: BufferedReader, val genome: Genome) {
             "exon" -> {
                 transcriptInfo.exons.add(location)
             }
+
             "CDS" -> {
                 transcriptInfo.cds.add(location)
             }
+
             "transcript" -> {
                 transcriptInfo.transcript = location
             }
+
             "three_prime_utr" -> {
                 transcriptInfo.utr3.add(location)
             }
+
             "start_codon" -> {
                 // Used only for data validation
                 if (transcriptInfo.startCodon == -1) {

src/main/kotlin/org/jetbrains/bio/genome/Genome.kt

@@ -99,6 +99,7 @@ class Genome private constructor(
             gtfPath.name.endsWith(".gtf.gz") -> {
                 gtfPath.name.subSequence(0, gtfPath.name.length - ".gtf.gz".length)
             }
+
             gtfPath.extension == "gtf" -> gtfPath.stem
             else -> error("Unsupported GTF path: $gtfPath")
         }
@@ -245,7 +246,7 @@ class Genome private constructor(
     companion object {
         const val TEST_ORGANISM_BUILD = "to1"
 
-                internal val LOG = LoggerFactory.getLogger(Genome::class.java)
+        internal val LOG = LoggerFactory.getLogger(Genome::class.java)
 
         /** Use cache to avoid extra chrom.sizes loading. */
         private val CACHE = Maps.newConcurrentMap<String, Genome>()
@@ -278,6 +279,7 @@ class Genome private constructor(
                         "<n/a>", "<n/a>", "<n/a>", "<n/a>", "<n/a>",
                         null, "<n/a>", null
                     )
+
                     else -> {
                         if (!AnnotationsConfigLoader.initialized) {
                             // Init with default settings only if not initialized by user before us

src/main/kotlin/org/jetbrains/bio/genome/GenomeQuery.kt

@@ -66,7 +66,7 @@ class GenomeQuery(val genome: Genome, vararg names: String) {
     override fun hashCode() = Objects.hash(build, restriction)
 
     companion object {
-                internal val LOG = LoggerFactory.getLogger(GenomeQuery::class.java)
+        internal val LOG = LoggerFactory.getLogger(GenomeQuery::class.java)
 
         /**
          * Parses [String] as genome with possible custom chromosomes set.

src/main/kotlin/org/jetbrains/bio/genome/Transcripts.kt

@@ -336,12 +336,15 @@ object Transcripts {
         AssociationStrategy.SINGLE -> associatedTranscriptsSingle(
             location, limit, codingOnly
         )
+
         AssociationStrategy.TWO -> associatedTranscriptsTwo(
             location, limit, codingOnly
         )
+
         AssociationStrategy.BASAL_PLUS_EXT -> associatedTranscriptsPlus(
             location, codingOnly = codingOnly, distal = limit
         )
+
         AssociationStrategy.MULTIPLE -> associatedTranscriptsMultiple(
             location, codingOnly = codingOnly, limit = limit
         )

src/main/kotlin/org/jetbrains/bio/genome/containers/intersection/IntersectionInfo.kt

@@ -83,12 +83,14 @@ data class IntersectionInfo(
                         0 -> {
                             colNames = csvRecord!!.toList().subList(2, csvRecord.size())
                         }
+
                         1 -> {
                             requireNotNull(colNames)
                             colsMergedLociNumber = IntArray(colNames!!.size) { i ->
                                 csvRecord.get(i + 2).toInt()
                             }
                         }
+
                         else -> {
                             val records = csvRecord.toList()
                             val rowValues = DoubleArray(colNames!!.size)