| 1 | package nl.tno.metagenomics |
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| 2 | |
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| 3 | /** |
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| 4 | * Represents a samples that is used in an assay. |
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| 5 | * |
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| 6 | * @author Robert Horlings (robert@isdat.nl) |
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| 7 | * |
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| 8 | */ |
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| 9 | class AssaySample { |
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| 10 | // To be computed in run time |
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| 11 | private long _numSequences = -1; |
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| 12 | private float _averageQuality = -1.0; |
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| 13 | |
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| 14 | Integer numUniqueSequences // Number of unique sequences / OTUs. Is only available after preprocessing |
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| 15 | |
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| 16 | String oligoNumber // Oligonumber used to identify the sample |
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| 17 | String tagSequence // Tag originally used to identify the sample |
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| 18 | |
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| 19 | static belongsTo = [ assay: Assay, sample: Sample ] |
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| 20 | static hasMany = [ sequenceData: SequenceData ] |
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| 21 | |
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| 22 | static constraints = { |
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| 23 | numUniqueSequences(nullable: true) |
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| 24 | oligoNumber(nullable: true) |
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| 25 | tagSequence(nullable: true) |
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| 26 | } |
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| 27 | |
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| 28 | static mapping = { |
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| 29 | columns { |
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| 30 | numSequences index:'numsequences_idx' |
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| 31 | } |
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| 32 | } |
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| 33 | |
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| 34 | /** |
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| 35 | * Returns the number of files in the system, belonging to this |
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| 36 | * assay-sample combination. |
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| 37 | * |
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| 38 | * @return |
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| 39 | */ |
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| 40 | public int numFiles() { |
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| 41 | if( !sequenceData ) |
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| 42 | return 0 |
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| 43 | |
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| 44 | int numFiles = 0; |
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| 45 | sequenceData.each { numFiles += it.numFiles() } |
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| 46 | |
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| 47 | return numFiles; |
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| 48 | } |
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| 49 | |
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| 50 | /** |
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| 51 | * Returns the number of sequences in the files on the system, belonging to this |
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| 52 | * assay-sample combination. |
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| 53 | * |
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| 54 | * @return |
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| 55 | */ |
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| 56 | public long numSequences() { |
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| 57 | if( _numSequences > -1 ) |
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| 58 | return _numSequences; |
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| 59 | |
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| 60 | if( !sequenceData ) |
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| 61 | return 0 |
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| 62 | |
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| 63 | long numSequences = 0; |
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| 64 | sequenceData.each { numSequences += it.numSequences } |
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| 65 | |
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| 66 | // Save as cache |
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| 67 | _numSequences = numSequences; |
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| 68 | |
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| 69 | return numSequences; |
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| 70 | } |
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| 71 | |
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| 72 | /** |
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| 73 | * Returns the average quality of the sequences in the files on the system, |
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| 74 | * belonging to this assay-sample combination. |
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| 75 | * |
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| 76 | * @return |
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| 77 | */ |
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| 78 | public float averageQuality() { |
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| 79 | if( _averageQuality > -1 ) |
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| 80 | return _averageQuality; |
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| 81 | |
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| 82 | if( !sequenceData ) |
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| 83 | return 0.0 |
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| 84 | |
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| 85 | int numSequences = 0; |
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| 86 | float averageQuality = 0.0; |
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| 87 | |
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| 88 | sequenceData.each { |
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| 89 | numSequences += it.numSequences |
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| 90 | averageQuality = averageQuality + ( it.averageQuality - averageQuality ) / numSequences * it.numSequences; |
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| 91 | } |
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| 92 | |
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| 93 | // Save as cache |
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| 94 | _averageQuality = averageQuality; |
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| 95 | |
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| 96 | return averageQuality; |
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| 97 | } |
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| 98 | } |
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