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mdp/project.classes
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project.classes
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class Operator
public String operatorname;
public String institution;
public Operator(String name, String institution);
public ~Operator();
class Sample
public String sampleID;
public String sample_date;
public Experiment sample_exp;
public String institution;
public Event recent_event;
public Performances sample_perf;
public SludgeCaracteristics sample_sludge_caract;
public Reactor sample_reactor;
public ReactorOperation sample_reactor_op;
public clusterDictionary sample_clusters;
public Int convert_date_to_days();
public Operator op_reactor_run;
public Operator op_biomass_sampling;
public Operator op_water_sampling;
public Operator op_molecular_extraction;
public Operator op_sequencing;
public String sequencing_technology;
public String convert_date_to_days();
public Sample();
public ~Sample();
class Event
public String event_date;
public String event_description;
public Event(String date, String description);
public ~Event();
class Experiment
public String experimentID;
public String experiment_begin;
public String experiment_description;
class SequenceCollection
public SequenceDictionnary dict;
public Int length;
public Int addSequence(Sequenc new_sequence);
public Int removeSequences(list list_of_seqIDs);
public Sequence getSequence(String seqID);
public Int modifyClusterID(String previous_cluster_id, String new_cluster_id):
public Int actualizeLenght();
class Sequence
public String seqID;
public String seq;
public Int seq_lenght;
public Cluster seq_cluster_id;
public Sample seq_sample;
public String qual
public void printSequence(bool cluster_info=False)
public Sequence(String ID, String sample, String sequence);
public virtual ~Sequence()
class DNAsequence(Sequence)
public DNASequence reverse_complement()
public ProteinSequence translate();
public DNASequence(String ID, String sample, String sequence);
public ~DNASequence();
class RNAsequence(Sequence)
public ProteinSequence translate();
public RNASequence reverse_complement()
public RNASequence(String ID, String sample, String sequence);
public ~RNASequence();
class ProteinSequence(Sequence)
public ProteinSequence(String ID, String sample, String sequence);
public ~ProteinSequence();
class Cluster
public String best_match_ref_id;
public Int size;
public String cluster_head_id;
public Sequence seq
public Float similarity_threshold;
public Taxonomy taxonomic_affiliation;
public Float taxon_similarity;
public Dictionnary d_abundance_per_sample;
public void attributeClusterHead(Sequence sequence);
public void printCluster(bool number_per_sample=False);
public Cluster(String cluster_head_id, Sequence sequence=None);
public ~Cluster();
class ClusterCollection
public ClusterDictionnary cluster_collection;
public Int addCluster(Cluster new_cluster);
public Cluster getCluster(String cluster_head_id);
public Int modifyClusterHead(String previous_cluster_head_id, String new_cluster_head);
public Int assignTaxonomy(Dictionnary blast_Dictionnary, TaxonomyCollection taxonomy_collection);
public buildClusterTables(self,list list_sample_id,String output_filename,Int min_cluster_size);
public Int storeInDatabase(String my_db_name)
public ClusterCollection();
public ~ClusterCollection();
class Performances
public Float N_removal;
public Float P_removal;
public Float COD_removal;
public Float NH4_removal;
public Performances();
public ~Performances();
class Reactor
public String reactorID;
public Float working_volume;
public Reactor(String reactorID);
public ~Reactor();
class ReactorOperation
public Int feedingLenght;
public Int anaerobic_mixing_length;
public Int aerobic_mixing_length;
public boolean intermittent_aeration
public Int settling_time
public String reactor_operation_description;
public ReactorOperation();
public ~ReactorOperation();
class TaxonomyCollection
public Taxonomy_Dictionnary dict;
public Int addTaxonomy(String, Taxonomy);
public Taxonomy getTaxonomy(String)
public TaxonomyCollection();
public ~TaxonomyCollection();
class Taxonomy
public String kingdom;
public String phylum;
public String classe;
public String order;
public String family;
public String genus;
public String species;
public Taxonomy(String taxonomic_information);
public virtual ~Taxonomy();
class SludgeCaracteristics
public float bed_heigth;
public float VSS;
public float TSS;
public float SVI3;
public float SVI8;
public SludgeCaracteristics();
public virtual ~SludgeCaracteristics();
class FilterBuilder
public Filter build_filter_from_request(String request);
public FilterBuilder();
public virtual ~FilterBuilder();
class Filter
public list list_of_seqname;
public Filter();
public virtual ~Filter();
class FileReader
public virtual void read(Filter filter,String key_String=None);
public Reader(String filename);
public ~Reader();
class TaxReader(FileReader)
public TaxonomyCollection read(Filter filter,String key_String=None);
public databaseReader(String filename);
public ~databaseReader();
class TaxonomicDatabaseReader(FileReader)
public SequenceCollection sequence_collection;
public String reference_tax_file;
public TaxonomyCollection taxonomy_collection;
public Int read(Filter filter, String key_String=None);
public Taxonomy getReferenceTaxonomy(String ref_id);
public Sequence getReferenceSequence(String ref_id);
public TaxonomicDatabaseReader(String filename);
public ~TaxonomicDatabaseReader();
class fastaReader(FileReader)
public SequenceCollection new_sequence_collection;
public Int read(Filter filter,String key_String=None);
public Int build_fasta(String new_fasta_filename,SequenceCollection sequence_collection=None);
public fastaReader(String filename);
public ~fastaReader();
class BlastFileReader(FileReader)
public Dictionnary dict;
public Int read(Filter filter,String key_String=None);
public blastFileReader(String filename);
public ~blastFileReader();
class databaseReader
public void read();
public databaseReader(String filename);
public virtual ~databaseReader();
class ConfigFileReader
public String filename;
public Dictionnary dict;
public Dictionnary conversion_dict;
public Dictionnary args;
public Int read();
public add_argument(String arg_short, String arg_long, String help, boolean required);
public Dictionnary parse_args();
public ConfigFileReader(String filename);
public ~ConfigFileReader();
class metadataReader
public String filename;
public Dictionnary current_item;
public String database_name;
public void read(Filter filter,String key_String);
public void store(String table_name, String item_to_store);
public metadataReader(String filename,String database_name);
public ~metadataReader();
class ClusterFileReader
public String filename;
public Stringlist list_sample_id;
public SequenceCollection sequence_collection;
public void virtual read(String key_String,Int min_size=200);
public incrementAbundancePerSample(Cluster cluster,String sampleID);
public clusterFileReader(String filename);
public ~clusterFileReader();
class cdHitClusterFileReader(ClusterFileReader)
public ClusterCollection read(String key_String,Int min_size=200);
public cdHitClusterFileReader(String filename);
public ~cdHitClusterFileReader();
class dbcClusterFileReader(ClusterFileReader)
public ClusterCollection read(String key_String,Int min_size=200);
public String getClusterHeads(String num_clust);
public Int incrementTempDictionary(String num_clust, String sequence);
public dbcClusterFileReader(String filename);
public ~dbcClusterFileReader();
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