mspire 0.2.4 → 0.3.0

data/specs/ms/spectrum_spec.rb

@@ -0,0 +1,89 @@
+
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require 'ms/spectrum'
+
+describe MS::Spectrum, 'equal_after_rounding?' do 
+  before(:all) do
+    @spectrum = MS::Spectrum.new
+  end
+  it 'returns equal after rounding' do
+    [[123.32145, 123.32, true], [123.328, 123.32, false], [123, 124, false], [122.94532, 123, true], [123, 123, true], [6.233355, 6.2334, true], [1029.212890625, 1029.212891, true]].each do |ar|
+      (precise, less_precise, answ) = ar
+      @spectrum.equal_after_rounding?(precise.to_f, less_precise.to_f).should == answ
+    end
+  end
+
+
+end
+describe MS::Spectrum, 'with a few values' do
+  before(:each) do
+    @mz = [1.2, 4.23332, 5.345734, 6.233355, 7.889]
+    @spec = MS::Spectrum.new(@mz,Array.new(5,100))
+  end
+  it 'finds an index given an exact m/z' do
+    @mz.each_with_index do |x,i|
+      @spec.index(x).should == i
+    end
+    [1, 4.233, 5.346, 6.2334, 7.89].each_with_index do |x,i|
+      @spec.index(x).should == i
+    end
+  end
+
+  it 'index returns nil if the m/z does not exist' do
+    [0.9, 1.28, 0, -10, 100, 4.233322, 4.233310, 4.3, 8.001, 7.905].each_with_index do |x,i|
+      @spec.index(x).should == nil
+    end
+  end
+  it 'finds an index given a rounded m/z' do
+    [1, 4, 5, 6, 8].each_with_index do |x,i|
+      @spec.index(x).should == i
+    end
+  end
+
+end
+
+describe MS::Spectrum, 'of full values' do
+  before(:each) do
+    @spec = MS::Spectrum.new(Ref::MZ,Array.new(Ref::MZ.size,100))
+  end
+
+  it 'finds an index given an exact m/z' do
+    @spec.index(1121.91625976562).should == 665
+    @spec.index(1029.212890625).should == 597
+    
+    #@spec.index(1029.212891).should == 665
+  end
+
+  it 'finds an index given approximate m/z' do
+    @spec.index(1121.91626).should == 665
+    @spec.index(1029.212891).should == 597
+  end
+
+
+
+end
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+class Ref
+    MZ = [300.801086425781, 301.70166015625, 302.771240234375, 303.972473144531, 304.845275878906, 305.704711914062, 306.92919921875, 307.755126953125, 309.0087890625, 309.868713378906, 310.956420898438, 312.174194335938, 312.815185546875, 314.045654296875, 315.086730957031, 316.046752929688, 317.3525390625, 318.233642578125, 319.613647460938, 321.082092285156, 322.192321777344, 322.95458984375, 323.894653320312, 325.020385742188, 325.743286132812, 326.779418945312, 327.823303222656, 328.613891601562, 329.550903320312, 330.544738769531, 331.53125, 332.574829101562, 334.576965332031, 335.536254882812, 336.649353027344, 337.825805664062, 339.057189941406, 340.065063476562, 340.720581054688, 341.499572753906, 342.942199707031, 343.76025390625, 344.600280761719, 345.855041503906, 346.655639648438, 347.846435546875, 348.9169921875, 349.891235351562, 350.635437011719, 351.70458984375, 352.663940429688, 353.673217773438, 354.972717285156, 355.828247070312, 356.828125, 357.716613769531, 358.844848632812, 360.2294921875, 360.850402832031, 361.569580078125, 362.565002441406, 363.612182617188, 365.454711914062, 366.121337890625, 366.760559082031, 367.6083984375, 368.523986816406, 369.439453125, 370.830444335938, 371.803466796875, 372.514587402344, 374.044555664062, 374.806091308594, 375.821472167969, 377.040344238281, 377.854248046875, 378.756591796875, 379.71533203125, 380.576477050781, 381.725463867188, 382.475708007812, 383.616394042969, 384.813537597656, 386.129638671875, 387.6005859375, 388.932556152344, 390.297546386719, 391.094055175781, 392.089965820312, 392.823608398438, 394.235961914062, 394.960632324219, 395.694702148438, 396.635864257812, 397.776733398438, 399.250183105469, 400.538269042969, 401.433288574219, 402.387023925781, 402.995971679688, 403.692077636719, 404.801391601562, 405.716735839844, 406.731872558594, 408.219970703125, 409.398498535156, 410.421936035156, 411.209594726562, 412.011962890625, 412.739013671875, 413.435119628906, 414.143432617188, 415.083251953125, 416.492919921875, 417.629638671875, 418.542541503906, 419.22216796875, 419.897338867188, 420.7880859375, 421.839172363281, 422.86328125, 424.165710449219, 425.020263671875, 425.712097167969, 427.219360351562, 427.953247070312, 429.039367675781, 429.842346191406, 430.9833984375, 431.811462402344, 432.787719726562, 434.198486328125, 434.911071777344, 435.6279296875, 437.321166992188, 438.197448730469, 441.392822265625, 442.794372558594, 443.688232421875, 444.597534179688, 445.466247558594, 446.227966308594, 446.914245605469, 447.546936035156, 448.173278808594, 449.515563964844, 450.155517578125, 451.076049804688, 451.80859375, 452.888122558594, 454.161865234375, 455.119873046875, 456.791748046875, 457.733276367188, 458.702209472656, 459.986145019531, 460.669982910156, 461.494323730469, 462.233276367188, 463.476440429688, 464.808959960938, 465.488830566406, 466.521667480469, 467.236267089844, 468.25927734375, 469.573364257812, 470.788391113281, 471.397033691406, 472.3251953125, 473.016174316406, 473.884033203125, 474.768127441406, 475.71484375, 476.4599609375, 477.563171386719, 478.803833007812, 479.960021972656, 480.684143066406, 482.565612792969, 483.507568359375, 484.445495605469, 485.277221679688, 485.967590332031, 486.720397949219, 487.870178222656, 488.918029785156, 489.744018554688, 491.068664550781, 491.833435058594, 492.650573730469, 493.965026855469, 495.259765625, 496.394714355469, 497.059448242188, 498.060180664062, 499.154357910156, 501.302062988281, 502.07275390625, 504.229919433594, 505.106811523438, 505.800537109375, 508.017761230469, 508.681884765625, 509.696044921875, 510.333312988281, 512.247802734375, 513.393798828125, 514.066650390625, 515.622314453125, 516.840087890625, 518.3681640625, 519.65673828125, 521.18798828125, 521.8134765625, 522.556640625, 525.173583984375, 526.93017578125, 527.8955078125, 528.546630859375, 530.037109375, 530.682250976562, 531.6689453125, 533.123291015625, 534.359375, 535.144409179688, 535.915893554688, 537.208251953125, 537.831787109375, 538.450927734375, 539.700805664062, 540.919921875, 541.69873046875, 542.658203125, 544.65087890625, 546.431884765625, 547.52587890625, 549.49169921875, 551.28564453125, 552.2568359375, 554.173461914062, 554.998901367188, 555.777709960938, 556.683837890625, 557.781616210938, 558.829345703125, 559.62548828125, 561.412719726562, 566.22509765625, 568.303344726562, 569.317138671875, 570.64501953125, 571.35302734375, 572.68603515625, 573.504028320312, 574.764892578125, 576.551025390625, 578.062744140625, 579.164184570312, 579.979125976562, 580.649169921875, 581.505859375, 582.594116210938, 583.317016601562, 583.935546875, 584.800659179688, 585.533325195312, 586.652099609375, 588.186767578125, 589.5595703125, 591.04345703125, 593.177368164062, 594.206787109375, 595.06591796875, 595.67822265625, 596.616333007812, 598.947021484375, 599.933471679688, 601.442138671875, 602.24853515625, 603.02880859375, 604.325927734375, 605.169189453125, 606.299560546875, 608.28369140625, 609.507202148438, 610.47900390625, 611.820556640625, 616.285278320312, 617.404052734375, 618.650390625, 619.768432617188, 621.320068359375, 622.8955078125, 624.17431640625, 625.194091796875, 625.898803710938, 627.26611328125, 628.497802734375, 630.142333984375, 630.95556640625, 631.862182617188, 632.593872070312, 634.557373046875, 635.619506835938, 636.28173828125, 638.259521484375, 639.084716796875, 641.210693359375, 642.184326171875, 642.822143554688, 643.704345703125, 644.605224609375, 645.71630859375, 646.426391601562, 648.9580078125, 650.461791992188, 651.25927734375, 652.406005859375, 653.15771484375, 654.167236328125, 655.859619140625, 656.52783203125, 657.96044921875, 658.822143554688, 659.909545898438, 660.773681640625, 661.7734375, 664.002197265625, 664.96533203125, 666.625610351562, 668.973022460938, 669.7646484375, 670.6513671875, 672.27294921875, 673.169555664062, 674.858642578125, 675.718994140625, 676.745361328125, 677.466552734375, 678.604736328125, 680.147705078125, 681.142578125, 681.933349609375, 683.229736328125, 684.41357421875, 686.447509765625, 687.880859375, 689.662719726562, 690.491821289062, 691.112060546875, 694.089599609375, 694.885620117188, 695.734619140625, 698.015625, 699.21630859375, 700.71533203125, 702.184936523438, 703.388549804688, 704.596923828125, 705.3076171875, 706.487548828125, 707.610107421875, 708.528564453125, 709.323608398438, 710.18505859375, 711.12939453125, 712.266967773438, 713.28564453125, 715.2998046875, 716.581298828125, 717.333251953125, 718.65185546875, 719.658813476562, 721.110717773438, 722.131591796875, 723.205322265625, 724.197265625, 725.251342773438, 726.477783203125, 727.608154296875, 728.540283203125, 729.320678710938, 730.3056640625, 731.65185546875, 733.397705078125, 734.366943359375, 735.504150390625, 736.795166015625, 738.273315429688, 740.48046875, 741.299072265625, 742.173461914062, 742.86669921875, 744.785888671875, 746.8779296875, 748.128784179688, 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824.442260742188, 827.7109375, 829.531616210938, 830.426879882812, 832.463134765625, 833.255004882812, 834.453125, 835.244750976562, 836.306396484375, 837.582153320312, 838.958251953125, 840.4677734375, 841.878173828125, 843.275024414062, 844.0, 845.133544921875, 846.884399414062, 847.799926757812, 848.9990234375, 850.070434570312, 851.87646484375, 854.469604492188, 855.295166015625, 857.824829101562, 860.77685546875, 862.132202148438, 863.554321289062, 864.557250976562, 865.8017578125, 867.702270507812, 868.665649414062, 869.851806640625, 872.493774414062, 873.479125976562, 875.295043945312, 876.073608398438, 877.45458984375, 878.231567382812, 879.895141601562, 881.426513671875, 882.178955078125, 882.82421875, 884.2978515625, 885.93603515625, 887.682739257812, 888.5888671875, 889.888305664062, 891.596313476562, 892.661010742188, 893.334716796875, 894.553466796875, 897.082275390625, 899.702270507812, 901.876586914062, 903.037475585938, 904.111450195312, 906.00146484375, 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+end

data/specs/roc_spec.rb

@@ -0,0 +1,251 @@
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper'
 )
+require 'roc'
+
+describe 'an area under the curve calculator', :shared => true do
+
+  it 'calculates area under curve correctly' do
+    x_y_pairs = {
+      [[1,2,3],[2,3,4]]    => 6,
+      [[1,2,3],[-2,-3,-4]] => -6,
+      [[1,2,3],[4,3,2]]    => 6,
+      [[1,2,3],[-4,-3,-2]] => -6,
+      [[4,5,6],[2,1,2]]    => 3,
+      [[4,5,6],[-2,-1,-2]] => -3,
+    }
+    x_y_pairs.each do |k,v|
+      calculate(*k).should == v
+    end
+  end
+
+  def calculate(x,y)
+    @method.call(x,y)
+  end
+end
+
+describe ROC do
+  before(:all) do
+    @method = proc {|x,y| ROC.new.area_under_curve(x,y) }
+  end
+  it_should_behave_like 'an area under the curve calculator'
+
+  it 'gives doublets_to_separate' do
+    t = true
+    f = false
+    x,y = ROC.new.doublets_to_separate([[0,f],[1,f],[2,f],[3,t],[3,f],[0,f],[4,f],[1,t],[2,t]])
+    x.should == [1,2,3]
+    y.should == [0,0,1,2,3,4]
+  end
+
+  it 'gives tps_and_ppv' do
+    tp = %w(1 2 3 4 5 6 6 6 7 8 9 10 10 10 10 11 12 ).collect {|c| c.to_f } # 17 total
+    fp = %w(3.5 4 5 5 5 6 6 6.5 7 8 9 9.5 10 15).collect {|c| c.to_f } # 14 total
+    xe = [1, 2, 3, 4, 5, 8, 9, 10, 11, 15, 16, 17]
+    #       1, 2, 3, 4        5,   6,             7,             8,   9
+    #       10              11                12
+    ye = [1, 1, 1, 4.0/6.0, 0.5, 8.0/(7.0+8.0), 9.0/(9.0+9.0), 0.5, 11.0/(11.0+ 11.0),  15.0/(15.0+13.0), 16.0/(16.0+13.0), 17.0/(17.0+13.0)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye,"complex real-life-like scenario")
+
+    ## leading fp's
+    tp = [1,2,3]
+    fp = [0,0,1,2,3,4]
+    xe = [1,2,3]
+    ye = [1.0/(1+3), 2.0/(2+4), 3.0/(3+5)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye, "leading fps")
+
+    ## leading tp's
+    tp = [-1,2,3]
+    fp = [0,4]
+    xe = [1,2,3]
+    ye = [1.0/(1+0), 2.0/(2+1), 3.0/(3+1)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye, "leading tps")
+
+    ## equal tp's leading
+    tp = [0.0001,0.0001,0.0001,2]
+    fp = [0.01,4.0]
+    xe = [3,4]
+    ye = [3.0/(3+0), 4.0/(4+1)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye, "equal tps leading")
+
+    ## equal arrays with some repeated values
+    tp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    fp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    xe = [1,2,4,5,6,7]
+    ye = [0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
+    _test_tps_and_ppv_method(tp,fp,xe,ye, "equal arrays with some repeated values")
+
+  end
+
+  it 'gives numhits_and_ppv' do
+    ## leading fp's
+    tp = [1,2,3]
+    fp = [0,0,1,2,3,4]
+    xe = [2,4,6,8,9]
+    ye = [0.0/2, 1.0/4, 2.0/6, 3.0/8, 3.0/9]
+    _test_numhits_and_ppv_method(tp,fp,xe,ye, "leading fps")
+
+    ## leading tp's
+    tp = [-1,2,3]
+    fp = [0,4]
+    xe = [1, 2, 3, 4, 5]
+    ye = [1.0/1, 1.0/2, 2.0/3, 3.0/4, 3.0/5]
+    _test_numhits_and_ppv_method(tp,fp,xe,ye, "leading tps")
+
+    ## equal tp's leading
+    tp = [0.0001,0.0001,0.0001,2]
+    fp = [0.01,4.0]
+    xe = [3, 4, 5, 6]
+    ye = [3.0/3, 3.0/4, 4.0/5, 4.0/6]
+    _test_numhits_and_ppv_method(tp,fp,xe,ye, "equal tps leading")
+
+    ## equal arrays with some repeated values
+    tp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    fp = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    xe = [2, 4, 8, 10, 12, 14]
+    ye = [0.5, 0.5, 0.5, 0.5, 0.5, 0.5]
+    _test_numhits_and_ppv_method(tp,fp,xe,ye, "equal arrays with some repeated values")
+
+    ## @TODO: NEED TO FILL THIS OUT!
+=begin 
+    tp = %w(1 2 3 4 5 6 6 6 7 8 9 10 10 10 10 11 12 ).collect {|c| c.to_f } # 17 total
+    fp = %w(3.5 4 5 5 5 6 6 6.5 7 8 9 9.5 10 15).collect {|c| c.to_f } # 14 total
+    xe = [1, 2, 3, 4, ]
+    #       1, 2, 3, 4        5,   6,             7,             8,   9
+    #       10              11                12
+    ye = [1, 1, 1, 4.0/6.0, 0.5, 8.0/(7.0+8.0), 9.0/(9.0+9.0), 0.5, 11.0/(11.0+ 11.0),  15.0/(15.0+13.0), 16.0/(16.0+13.0), 17.0/(17.0+13.0)]
+    _test_tps_and_ppv_method(tp,fp,xe,ye,"complex real-life-like scenario")
+=end
+
+  end
+
+  def _test_numhits_and_ppv_method(tp,fp,xe,ye,message='')
+    roc = ROC.new
+    list = roc.separate_to_doublets(tp,fp)
+    (x,y) = roc.numhits_and_ppv(list)
+    y.size.should == x.size
+    x.should == xe
+    y.should == ye
+  end
+
+  def _test_tps_and_ppv_method(tp,fp,xe,ye,message='')
+    (x,y) = ROC.new.tps_and_ppv(tp,fp)
+    y.size.should == x.size
+    x.should == xe
+    y.should == ye
+  end
+
+end
+
+describe DecoyROC do
+
+  ###################################################################
+
+  it 'gives pred_and_ppv' do
+    hits = [1,2,3]
+    decoys = [0,0,1,2,3,4]
+    num_hits_e = [1,2,3]
+    num_fps = [3,4,5]
+    # expected = [-2.0/1, -2.0/2, -2.0/3] 
+    _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+  end
+
+  it 'gives pred_tps_ppv__leading_tps' do
+    ## leading tp's
+    hits = [-1,2,3]
+    decoys = [0,4]
+    num_hits_e = [1,2,3]
+    num_fps = [0,1,1]
+    _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+  end
+
+  it 'gives pred_tps_ppv__equal_tps_leading' do
+    hits = [0.0001,0.0001,0.0001,2]
+    decoys = [0.01,4.0]
+    num_hits_e = [3,4]
+    num_fps = [0,1]
+    _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+  end
+
+  it 'gives pred_tps_ppv__equal_arrays_with_some_repeated_values' do
+    hits = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    decoys = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    num_hits_e = [1,2,4,5,6,7]
+    num_fps = [1,2,4,5,6,7]
+    _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+  end
+
+  ###################################################################
+
+  it 'gives pred_tps_ppv__leading_fps' do
+    ## leading fp's
+    hits = [1,2,3]
+    decoys = [0,0,1,2,3,4]
+    num_hits_e = [1,2,3]
+    num_fps = [3,4,5]
+    tps_e = make_tps_e(num_fps, num_hits_e)
+    ppv_e = make_ppv_e(tps_e, num_hits_e)
+    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+  end
+
+  it 'gives pred_tps_ppv__leading_tps' do
+    ## leading tp's
+    hits = [-1,2,3]
+    decoys = [0,4]
+    num_hits_e = [1,2,3]
+    num_fps = [0,1,1]
+    tps_e = make_tps_e(num_fps, num_hits_e)
+    ppv_e = make_ppv_e(tps_e, num_hits_e)
+    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+  end
+
+  it 'gives pred_tps_ppv__equal_tps_leading' do
+    hits = [0.0001,0.0001,0.0001,2]
+    decoys = [0.01,4.0]
+    num_hits_e = [3,4]
+    num_fps = [0,1]
+    tps_e = make_tps_e(num_fps, num_hits_e)
+    ppv_e = make_ppv_e(tps_e, num_hits_e)
+    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+  end
+
+  it 'gives pred_tps_ppv__equal_arrays_with_some_repeated_values' do
+    hits = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    decoys = %w(1 2 3 3 4 5 6 ).collect {|x| x.to_f } # 17 total
+    num_hits_e = [1,2,4,5,6,7]
+    num_fps = [1,2,4,5,6,7]
+    tps_e = make_tps_e(num_fps, num_hits_e)
+    ppv_e = make_ppv_e(tps_e, num_hits_e)
+    _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+  end
+
+  def  _test_pred_and_ppv(hits, decoys, num_hits_e, num_fps)
+    answer = DecoyROC.new.pred_and_ppv(hits, decoys)
+    precision = num_hits_e.zip(num_fps).map do |h,f|
+      (h - f).to_f / h
+    end
+    answer.should == [num_hits_e, precision]
+  end
+
+  def _test_pred_and_tps_and_ppv(hits, decoys, num_hits_e, tps_e, ppv_e)
+    answer = DecoyROC.new.pred_and_tps_and_ppv(hits, decoys)
+    expected = [num_hits_e, tps_e, ppv_e]
+    %w(num_hits num_tps ppv).each_with_index do |cat, i|
+      answer[i].should == expected[i]
+    end
+  end
+
+  def make_tps_e(num_fps, num_hits_e)
+    tps_e = []
+    num_hits_e.each_with_index do |v,i|
+      tps_e[i] = v - num_fps[i]
+    end
+    tps_e
+  end
+
+  def make_ppv_e(tps_e, num_hits_e)
+    ppv_e = []
+    tps_e.each_with_index {|v,i| ppv_e[i] = v.to_f/num_hits_e[i] }
+    ppv_e
+  end
+
+end
+

data/specs/rspec_autotest.rb

@@ -0,0 +1,149 @@
+# (c) Copyright 2006-2007 Nick Sieger <nicksieger@gmail.com>
+# 
+# Permission is hereby granted, free of charge, to any person
+# obtaining a copy of this software and associated documentation files
+# (the "Software"), to deal in the Software without restriction,
+# including without limitation the rights to use, copy, modify, merge,
+# publish, distribute, sublicense, and/or sell copies of the Software,
+# and to permit persons to whom the Software is furnished to do so,
+# subject to the following conditions:
+# 
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+# 
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+require 'rubygems'
+gem 'ZenTest'
+require 'autotest'
+
+class RspecAutotest < Autotest
+  attr_accessor :spec_command
+  def initialize # :nodoc:
+    @spec_command = "spec --diff unified"
+    super
+    @exceptions = %r%^\./(?:coverage|doc)%
+  end
+
+  def tests_for_file(filename)
+    case filename
+    when /^lib\/.*\.rb$/ then
+      impl = File.basename(filename).gsub('_', '_?').sub(/\.rb$/, '')
+      @files.keys.select do |k|
+        k =~ %r%^spec/.*#{impl}_spec\.rb$%
+      end
+    when %r%^spec/spec_helper.rb% then
+      @files.keys.select do |f|
+        f =~ %r%^spec/.*_spec\.rb$%
+      end
+    when /^spec\/.*_spec\.rb$/ then
+      [filename]
+    when /#{Regexp.quote(File.basename(__FILE__))}/
+      # Don't respond to changes to this file
+      []
+    else
+      @output.puts "Dunno! #{filename}" if $TESTING
+      []
+    end
+  end
+
+  def handle_results(results)
+    failed = results.scan(/^\d+\)\n(?:\e\[\d*m)?(?:.*?Error in )?'([^\n]*)'(?: FAILED)?(?:\e\[\d*m)?\n(.*?)\n\n/m)
+    @files_to_test = consolidate_failures failed
+    unless @files_to_test.empty? then
+      hook :red
+    else
+      hook :green
+    end unless $TESTING
+    @tainted = true unless @files_to_test.empty?
+  end
+
+  def consolidate_failures(failed)
+    filters = Hash.new { |h,k| h[k] = [] }
+    failed.each do |spec, failed_trace|
+      @files.keys.select{|f| f =~ /spec\//}.each do |f|
+        if failed_trace =~ Regexp.new(f)
+          filters[f] << spec 
+          break
+        end
+      end
+    end
+    return filters
+  end
+
+  def make_test_cmd(files_to_test)
+    cmds = []
+    full, partial = files_to_test.partition { |k,v| v.empty? }
+
+    unless full.empty? then
+      classes = full.map {|k,v| k}.flatten.join(' ')
+      cmds << "#{spec_command} #{classes}"
+    end
+
+    partial.each do |klass, methods|
+      methods.each { |meth| cmds << "#{spec_command} -s #{meth.inspect} #{klass}" }
+    end
+
+    return cmds.join('; ')
+  end
+end
+
+class RspecOnRailsAutotest < RspecAutotest
+  def initialize # :nodoc:
+    super
+    @exceptions = %r%^\./(?:coverage|db|doc|log|public|script|vendor)%
+  end
+
+  def tests_for_file(filename)
+    case filename
+    when %r%^spec/fixtures/(.*)s.yml% then
+      ["spec/models/#{$1}_spec.rb",
+       "spec/controllers/#{$1}_controller_spec.rb"]
+    when %r%^spec/models/.*rb$% then
+      [filename]
+    when %r%^spec/controllers/.*\.rb$% then
+      [filename]
+    when %r%^spec/views/.*\.rb$% then
+      [filename]
+    when %r%^spec/helpers/.*\.rb$% then
+      [filename]
+    when %r%^app/models/(.*)\.rb$% then
+      ["spec/models/#{$1}_spec.rb"]
+    when %r%^app/helpers/application_helper.rb% then
+      @files.keys.select { |f|
+        f =~ %r%^spec/controllers/.*_spec\.rb$%
+      }
+    when %r%^app/helpers/(.*)_helper.rb% then
+      ["spec/controllers/#{$1}_controller_spec.rb", "spec/helpers/#{$1}_spec.rb"]
+    when %r%^app/controllers/application.rb$% then
+      @files.keys.select { |f|
+        f =~ %r%^spec/controllers/.*_spec\.rb$%
+      }
+    when %r%^app/controllers/(.*)\.rb$% then
+      ["spec/controllers/#{$1}_spec.rb"]
+    when %r%^app/views/layouts/% then
+      []
+    when %r%^app/views/(.*)/% then
+      ["spec/controllers/#{$1}_controller_spec.rb", "spec/views/#{$1}_spec.rb"]
+    when %r%^config/routes.rb$% then
+      @files.keys.select do |f|
+        f =~ %r%^spec/controllers/.*_spec\.rb$%
+      end
+    when %r%^spec/spec_helper.rb%,
+         %r%^config/((boot|environment(s/test)?).rb|database.yml)% then
+      @files.keys.select do |f|
+        f =~ %r%^spec/(models|controllers)/.*_spec\.rb$%
+      end
+    else
+      @output.puts "Dunno! #{filename}" if $TESTING
+      []
+    end.uniq.select { |f| @files.has_key? f }
+  end
+end

data/specs/sample_enzyme_spec.rb

@@ -0,0 +1,41 @@
+
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
+require 'sample_enzyme'
+require 'set'
+
+describe SampleEnzyme, "digesting sequences" do
+  it 'can digest with no missed cleavages' do
+    st = "CRGATKKTAGRPMEK"
+    SampleEnzyme.tryptic(st).should == %w(CR GATK K TAGRPMEK)
+    st = "CATRP"
+    SampleEnzyme.tryptic(st).should == %w(CATRP)
+    st = "RCATRP"
+    SampleEnzyme.tryptic(st).should == %w(R CATRP)
+    st = ""
+    SampleEnzyme.tryptic(st).should == []
+    st = "R"
+    SampleEnzyme.tryptic(st).should == %w(R)
+  end
+
+  it 'can digest with missed cleavages' do
+    st = "CRGATKKTAGRPMEKLLLERTKY"
+    zero = %w(CR GATK K TAGRPMEK LLLER TK Y)
+    SampleEnzyme.tryptic(st,0).to_set.should == zero.to_set
+    one = %w(CRGATK GATKK KTAGRPMEK TAGRPMEKLLLER LLLERTK TKY)
+    SampleEnzyme.tryptic(st,1).to_set.should == (zero+one).to_set
+    two = %w(CRGATKK GATKKTAGRPMEK KTAGRPMEKLLLER TAGRPMEKLLLERTK LLLERTKY)
+    all = zero + one + two
+    SampleEnzyme.tryptic(st,2).to_set.should == all.to_set
+  end
+
+  it 'contains duplicates IF there are duplicate tryptic sequences' do
+    st = "AAAAKCCCCKDDDDKCCCCK"
+    peps = SampleEnzyme.new('trypsin').digest(st, 2)
+    peps.select {|aaseq| aaseq == 'CCCCK'}.size.should == 2
+  end
+
+  
+end
+
+
+

data/specs/spec_helper.rb

@@ -0,0 +1,133 @@
+gem 'rspec'
+
+
+# a global flag that lets me know what format we're dealing with for output
+$specdoc = false
+ObjectSpace.each_object do |obj|
+  case obj
+  when Spec::Runner::Formatter::SpecdocFormatter
+    $specdoc = true
+  end
+end
+
+# Set up some global testing variables:
+#silent {
+  ROOT_DIR = File.dirname(__FILE__) + '/..'
+  SPEC_DIR = File.dirname(__FILE__)
+
+  Tfiles = File.dirname(__FILE__) + '/../test_files'
+  Tfiles_l = File.dirname(__FILE__) + '/../test_files_large'
+  Tfiles_large = Tfiles_l
+#}
+
+# this variable is for large files!
+if ENV['SPEC_LARGE']
+  $spec_large = true
+else
+  #[NOTE: NOT testing with large test files]"
+  # ** run with env var: SPEC_LARGE and ensure tfiles_large dir"
+  $spec_large = false
+end
+
+def spec_large(&block)
+  if $spec_large
+    block.call
+  else
+    # Requires SPEC_LARGE=true and tfiles_large dir for testing large test files
+    it 'SKIPPING (not testing large files)' do
+    end
+  end
+end
+
+# returns all output to stdout as a string
+# will respond to is_a? File -> false is_a? IO true even though it is really a
+# file
+def capture_stdout(&block)
+  capture_file = Tfiles + '/capture_stdout.tmp'
+  def capture_file.is_a?(klass)
+    case klass.to_s
+    when 'IO'
+      true
+    when 'File'
+      false
+    else
+      false
+    end
+  end
+  $stdout = File.open(capture_file, 'w')
+  block.call
+  $stdout.close
+  $stdout = STDOUT
+  string = IO.read(capture_file)
+  File.unlink capture_file
+  string
+end
+
+require 'ostruct'
+# class for using a ruby-ish initializer
+class MyOpenStruct < OpenStruct
+  def initialize(*args) 
+    super(*args)
+    if block_given?
+      yield(self)
+    end
+  end
+end
+
+
+def xdescribe(*args)
+  puts "describe: #{args.join(' ')}"
+  puts "**SKIPPING**"
+end
+
+def Xdescribe(*args)
+  xdescribe(*args)
+end
+
+def xit(*args)
+  puts "\n- SKIPPING: #{args.join(' ')}"
+end
+
+def it_should(*args)
+  string = "- WRITE TEST: #{args.join(' ')}"
+  if $specdoc
+    puts(string)
+  else
+    puts("\n" + string)
+  end
+end
+
+def silent(&block)
+  tmp = $VERBOSE ; $VERBOSE = nil
+  block.call
+  $VERBOSE = tmp
+end
+
+
+require SPEC_DIR + '/load_bin_path'
+
+class String
+  #alias_method :exist?, exist_as_a_file?
+  #alias_method exist_as_a_file?, exist?
+  def exist?
+    File.exist? self
+  end
+  def exist_as_a_file?
+    File.exist? self
+  end
+end
+
+describe "a cmdline program", :shared => true do
+  before(:all) do
+    testdir = File.dirname(__FILE__)
+    libdir = testdir + '/../lib'
+    bindir = testdir +  '/../bin'
+    @cmd = "ruby -I #{libdir} #{bindir}/#{@progname} "
+  end
+
+  it 'gives usage when called with no args' do
+    reply = `#{@cmd}`
+    reply.should =~ /usage/i
+  end
+
+end