tomjadams

public final class SpecificationLifecycleImpl implements SpecificationLifecycle {
    public <T extends Throwable> Either<T, ContextClass> createContext() {
        throw new UnsupportedOperationException();
    }

    public <T extends Throwable> Either<T, Unit> resetMockery() {
        throw new UnsupportedOperationException();
    }

    public <T extends Throwable> Either<T, Unit> wireActors() {

tomjadams

package com.googlecode.instinct.internal.runner;

import static com.googlecode.instinct.expect.Expect.expect;
import com.googlecode.instinct.integrate.junit4.InstinctRunner;
import com.googlecode.instinct.marker.annotate.BeforeSpecification;
import com.googlecode.instinct.marker.annotate.Dummy;
import com.googlecode.instinct.marker.annotate.Specification;
import com.googlecode.instinct.marker.annotate.Stub;
import com.googlecode.instinct.marker.annotate.Subject;
import fj.Unit;

tomjadams

private SpecificationResult runLifecycle(final long startTime, final SpecificationLifecycle lifecycle,
        final SpecificationMethod specificationMethod) {
    List<Option<Throwable>> lifecycleStepErrors = nil();
    final Either<Throwable, ContextClass> createContextResult = lifecycle.createContext(specificationMethod.getContextClass());
    lifecycleStepErrors = lifecycleStepErrors.cons(createContextResult.left().toOption());
    if (createContextResult.isLeft()) {
        return fail(startTime, specificationMethod, somes(lifecycleStepErrors), false);
    } else {
        final ContextClass contextClass = createContextResult.right().value();
        final Option<Throwable> contextValidationResult = methodValidator.checkContextConstructor(contextClass.getType());

tomjadams

package com.googlecode.furnace.parse

import sequence.GeneSequence
import scala.collection.mutable.{ArrayBuffer => MutableArray}
import scalaz.list.NonEmptyList, NonEmptyList._
import sequence.{Base, GeneSequence}
import sequence.Base._
import sequence.GeneSequence._

/**

tomjadams

scala> val list = List(1, 2, 3, 4, 5, 6, 7, 8, 9)
list: List[Int] = List(1, 2, 3, 4, 5, 6, 7, 8, 9)

scala> val iter = list.elements
iter: Iterator[Int] = non-empty iterator

scala> val firstTwoElements = iter.filter(_ < 5).zipWithIndex.takeWhile(_._2 < 2).map(_._1).toList
firstTwoElements: List[Int] = List(1, 2)

scala> assert(iter.toList == List(3, 4, 5, 6, 7, 8, 9)) 

tomjadams

object CommandLineBlast {
  lazy val blastHome = getenv("BLAST_HOME")
  lazy val tmpDir = getProperty("java.io.tmpdir")

  def blast(config: BlastConfiguration): AnalysisResult = {
    if (blastHome == null) {
      error("BLAST_HOME is not defined. It must point to the BLAST installation directory, e.g. BLAST_HOME=/opt/blast")
    } else {
      val executable = blastHome + "/bin/" + config.searchUtility.name
      val c = command(executable)("-p", config.program.name)("-e 1.0")("-d ecoli.nt")("-i test.txt")("-o test.out")

tomjadams

package com.googlecode.furnace.analyse.blast;

import static com.googlecode.instinct.expect.Expect.expect;
import com.googlecode.instinct.integrate.junit4.InstinctRunner;
import com.googlecode.instinct.internal.util.instance.ObjectFactory;
import com.googlecode.instinct.marker.annotate.BeforeSpecification;
import com.googlecode.instinct.marker.annotate.Dummy;
import com.googlecode.instinct.marker.annotate.Mock;
import com.googlecode.instinct.marker.annotate.Specification;
import com.googlecode.instinct.marker.annotate.Subject;

tomjadams

CmdUtils.CreateCommand({
  name: "showmore",
  takes: {"url to shorten": noun_arb_text},
  preview: "Replaces the selected URL with ashowmore.info shortened URL.",
  description: "Replaces the selected URL with a bit.ly-shortened URL.",
  icon: "http://bit.ly/favicon.png",
  execute: function( urlToShorten ) {
    var baseUrl = "http://showmore.info/links/";
    var params = {link_url: urlToShorten.text};
    jQuery.get(baseUrl, params, function(shortenedUrl) {

tomjadams

    <property name="project.longname" value="Instinct Behaviour Driven Development (BDD) Framework"/>
    <property name="project.shortname" value="instinct-core"/>
    <property name="project.version.major" value="0"/>
    <property name="project.version.minor" value="2.0"/>
    <property name="version-status" value=""/>
    <property name="project.version.full" value="${project.version.major}.${project.version.minor}${version-stat
us}"/>

    <property name="project.jar" value="${project.shortname}-${project.version.full}.jar"/>
    <property name="project.zip" value="${project.shortname}-${project.version.full}.zip"/>

tomjadams

package com.googlecode.furnace.grid

import org.gridgain.grid.{GridTaskSplitAdapter, GridJobResult, GridJob}
import analyse.{AnalysisResult, SequenceIdentifier}
import java.util.{List => JavaList}
import java.util.{Collection => JavaCollection}
import sequence.GeneSequence

final class GeneSequenceGridTask extends GridTaskSplitAdapter[Iterator[GeneSequence], List[AnalysisResult]] {
  def split(gridSize: Int, inputSequences: Iterator[GeneSequence]): JavaCollection[_ <: GridJob] = error("I'm not really a list")