Changeset 12 for trunk/grails-app/domain/nl

Timestamp:

Feb 9, 2011, 9:04:29 AM (12 years ago)

Author:

robert@…

Message:

Implemented basic exporting functionality

Location:

trunk/grails-app/domain/nl/tno/metagenomics

Files:

• AssaySample.groovy (modified) (3 diffs)
• SequenceData.groovy (modified) (1 diff)

trunk/grails-app/domain/nl/tno/metagenomics/AssaySample.groovy

@@ -11 +11 @@
         private long _numSequences = -1;
         private float _averageQuality = -1.0;
+        private long _numQualScores = -1;
 
         Integer numUniqueSequences      // Number of unique sequences / OTUs. Is only available after preprocessing
@@ -137 +138 @@
                 return numSequences;
         }
-
+        
+        /**
+         * Returns the number of quality scores in the files on the system, belonging to this
+         * assay-sample combination.
+         *
+         * @return
+         */
+        public long numQualScores() {
+                if( _numQualScores > -1 )
+                        return _numQualScores;
+
+                if( !sequenceData )
+                        return 0
+
+                long numQualScores = 0;
+                sequenceData.each { numQualScores += it.numQualScores() }
+
+                // Save as cache
+                _numQualScores = numQualScores;
+
+                return numQualScores;
+        }
         /**
          * Returns the average quality of the sequences in the files on the system, 
@@ -170 +192 @@
         public void resetStats() {
                 _numSequences = -1;
+                _numQualScores = -1;
                 _averageQuality = -1;
         }

trunk/grails-app/domain/nl/tno/metagenomics/SequenceData.groovy

@@ -33 +33 @@
         }
         
+        
+        /**
+         * Returns the number of quality scores in this data object. This equals
+         * the number of sequences iff a quality score is attached to this object
+         * 
+         * @return      Number of quality scores in this object
+         */
+        public int numQualScores() {
+                if( qualityFile != null )
+                        return numSequences
+                else
+                        return 0;
+        }
+        
         def beforeDelete = {
                 def permanentDir = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir.toString() )