| 1 | package nl.tno.massSequencing |
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| 2 | |
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| 3 | import org.codehaus.groovy.grails.commons.ConfigurationHolder |
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| 4 | |
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| 5 | class SequenceData { |
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| 6 | def fileService |
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| 7 | |
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| 8 | String sequenceFile = '' |
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| 9 | String qualityFile = '' |
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| 10 | Long numSequences = 0L |
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| 11 | Float averageQuality = 0.0 |
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| 12 | |
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| 13 | static belongsTo = [sample: AssaySample] |
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| 14 | static constraints = { |
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| 15 | qualityFile(nullable: true) |
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| 16 | numSequences(nullable: true) |
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| 17 | averageQuality(nullable: true) |
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| 18 | } |
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| 19 | |
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| 20 | /** |
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| 21 | * Returns the number of files in this data object. |
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| 22 | * @return |
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| 23 | */ |
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| 24 | public int numFiles() { |
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| 25 | int number = 0; |
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| 26 | if( sequenceFile != null && sequenceFile != "" ) |
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| 27 | number++; |
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| 28 | |
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| 29 | if( qualityFile != null && qualityFile != "" ) |
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| 30 | number++; |
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| 31 | |
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| 32 | return number; |
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| 33 | } |
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| 34 | |
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| 35 | |
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| 36 | /** |
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| 37 | * Returns the number of quality scores in this data object. This equals |
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| 38 | * the number of sequences iff a quality score is attached to this object |
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| 39 | * |
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| 40 | * @return Number of quality scores in this object |
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| 41 | */ |
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| 42 | public int numQualScores() { |
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| 43 | if( qualityFile != null ) |
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| 44 | return numSequences |
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| 45 | else |
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| 46 | return 0; |
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| 47 | } |
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| 48 | |
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| 49 | def beforeDelete = { |
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| 50 | def permanentDir = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir.toString() ) |
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| 51 | if( sequenceFile ) { |
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| 52 | fileService.delete( sequenceFile, permanentDir ) |
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| 53 | } |
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| 54 | |
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| 55 | if( qualityFile ) |
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| 56 | fileService.delete( qualityFile, permanentDir ) |
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| 57 | |
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| 58 | // Reset statistics of the assay sample, to ensure the deleted files are removed from statistics |
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| 59 | sample?.resetStats(); |
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| 60 | |
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| 61 | return true; |
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| 62 | } |
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| 63 | |
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| 64 | public SequenceData clone() { |
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| 65 | // Copy the files to a new name |
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| 66 | def permanentDir = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir.toString() ) |
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| 67 | |
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| 68 | def newSequenceFileName = sequenceFile; |
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| 69 | if( this.sequenceFile ) { |
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| 70 | newSequenceFileName = fileService.getUniqueFilename( this.sequenceFile, permanentDir ); |
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| 71 | fileService.copy( sequenceFile, newSequenceFileName, permanentDir ); |
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| 72 | } |
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| 73 | |
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| 74 | def newQualityFileName = qualityFile; |
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| 75 | if( this.qualityFile ) { |
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| 76 | newQualityFileName = fileService.getUniqueFilename( this.qualityFile, permanentDir ); |
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| 77 | fileService.copy( qualityFile, newQualityFileName, permanentDir ); |
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| 78 | } |
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| 79 | |
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| 80 | def sd = new SequenceData( |
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| 81 | sequenceFile: newSequenceFileName, |
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| 82 | qualityFile: newQualityFileName, |
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| 83 | numSequences: this.numSequences, |
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| 84 | averageQuality: this.averageQuality |
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| 85 | ); |
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| 86 | |
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| 87 | if( this.sample ) |
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| 88 | this.sample.addToSequenceData( sd ); |
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| 89 | |
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| 90 | return sd; |
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| 91 | } |
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| 92 | } |
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