Homec4science
Diffusion molecular_data_processing (master) Browse

mdp/project.dot
c516ecb4392emaster

Last Change
Raw File

project.dot
View Options

digraph "test"
{
edge [fontname="Helvetica",fontsize="10",
labelfontname="Helvetica", labelfontsize="10"];
node [fontname="Helvetica",fontsize="10",shape=record];
"Operator" [label="{Operator\n|+ Operator(institution)\l+ ~Operator()\l|+ string operatorname\l+ string institution\l}"];
"string" -> "Operator" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Sample" [label="{Sample\n|+ Sample()\l+ ~Sample()\l|+ string convert_date_to_days()\l+ int convert_date_to_days()\l|+ SludgeCaracteristics sample_sludge_caract\l+ Event recent_event\l+ clusterDictionary sample_clusters\l+ ReactorOperation sample_reactor_op\l+ Operator op_sequencing\l+ Performances sample_perf\l+ string sampleID\l+ Operator op_water_sampling\l+ Experiment sample_exp\l+ Operator op_reactor_run\l+ Reactor sample_reactor\l+ Operator op_biomass_sampling\l+ string sample_date\l+ string institution\l+ String sequencing_technology\l+ Operator op_molecular_extraction\l}"];
"clusterDictionary" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"string" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"ReactorOperation" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"String" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Experiment" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Performances" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Operator" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"SludgeCaracteristics" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Event" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Reactor" -> "Sample" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Event" [label="{Event\n|+ Event(description)\l+ ~Event()\l|+ string event_date\l+ string event_description\l}"];
"string" -> "Event" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Experiment" [label="{Experiment\n|+ string experiment_begin\l+ string experiment_description\l+ string experimentID\l}"];
"string" -> "Experiment" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"SequenceCollection" [label="{SequenceCollection\n|+ Sequence getSequence(seqID)\l+ int removeSequences(list_of_seqIDs)\l+ int actualizeLenght()\l+ int addSequence(new_sequence)\l+ int modifyClusterID(new_cluster_id)\l|+ int length\l+ SequenceDictionnary dict\l}"];
"SequenceDictionnary" -> "SequenceCollection" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Sequence" [label="{Sequence\n|+ Sequence(sequence)\l+ virtual ~Sequence()\l|+ void printSequence(cluster_info=False)\l|+ Cluster seq_cluster_id\l+ string seq\l+ Sample seq_sample\l+ String qual\l+ string seqID\l+ int seq_lenght\l}"];
"Sample" -> "Sequence" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Cluster" -> "Sequence" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"string" -> "Sequence" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"String" -> "Sequence" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"DNAsequence" [label="{DNAsequence\n|+ ProteinSequence translate()\l+ DNASequence(sequence)\l+ ~DNASequence()\l+ DNASequence reverse_complement()\l}"];
"Sequence" -> "DNAsequence" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"RNAsequence" [label="{RNAsequence\n|+ ~RNASequence()\l+ ProteinSequence translate()\l+ RNASequence(sequence)\l+ RNASequence reverse_complement()\l}"];
"Sequence" -> "RNAsequence" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"ProteinSequence" [label="{ProteinSequence\n|+ ProteinSequence(sequence)\l+ ~ProteinSequence()\l}"];
"Sequence" -> "ProteinSequence" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"Cluster" [label="{Cluster\n|+ Cluster(cluster_head_id,sequence=None)\l+ ~Cluster()\l|+ void attributeClusterHead(sequence)\l+ void printCluster(number_per_sample=False)\l|+ Float taxon_similarity\l+ Dictionnary d_abundance_per_sample\l+ String cluster_head_id\l+ Sequence seq\l+ Float similarity_threshold\l+ Taxonomy taxonomic_affiliation\l+ String best_match_ref_id\l+ int size\l}"];
"Dictionnary" -> "Cluster" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Float" -> "Cluster" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"String" -> "Cluster" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Taxonomy" -> "Cluster" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Sequence" -> "Cluster" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"ClusterCollection" [label="{ClusterCollection\n|+ ClusterCollection()\l+ ~ClusterCollection()\l|+ int addCluster(new_cluster)\l+ Cluster getCluster(cluster_head_id)\l+ int modifyClusterHead(new_cluster_head)\l+ int assignTaxonomy(blast_dictionnary,taxonomy_collection)\l+ buildClusterTables(min_cluster_size,list_sample_id,output_filename)\l+ int storeInDatabase(my_db_name)\l|+ ClusterDictionnary cluster_collection\l}"];
"ClusterDictionnary" -> "ClusterCollection" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Performances" [label="{Performances\n|+ Performances()\l+ ~Performances()\l|+ Float COD_removal\l+ Float NH4_removal\l+ Float N_removal\l+ Float P_removal\l}"];
"Float" -> "Performances" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Reactor" [label="{Reactor\n|+ Reactor(reactorID)\l+ ~Reactor()\l|+ string reactorID\l+ Float working_volume\l}"];
"Float" -> "Reactor" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"string" -> "Reactor" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"ReactorOperation" [label="{ReactorOperation\n|+ ReactorOperation()\l+ ~ReactorOperation()\l|+ int aerobic_mixing_length\l+ int anaerobic_mixing_length\l+ string reactor_operation_description\l+ int settling_time\l+ int feedingLenght\l+ boolean intermittent_aeration\l}"];
"boolean" -> "ReactorOperation" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"string" -> "ReactorOperation" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"TaxonomyCollection" [label="{TaxonomyCollection\n|+ TaxonomyCollection()\l+ ~TaxonomyCollection()\l|+ int addTaxonomy()\l+ Taxonomy getTaxonomy()\l|+ Taxonomy_dictionnary dict\l}"];
"Taxonomy_dictionnary" -> "TaxonomyCollection" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Taxonomy" [label="{Taxonomy\n|+ Taxonomy(taxonomic_information)\l+ virtual ~Taxonomy()\l|+ string kingdom\l+ string family\l+ string classe\l+ string species\l+ string phylum\l+ string genus\l+ string order\l}"];
"string" -> "Taxonomy" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"SludgeCaracteristics" [label="{SludgeCaracteristics\n|+ SludgeCaracteristics()\l+ virtual ~SludgeCaracteristics()\l|+ float SVI8\l+ float bed_heigth\l+ float SVI3\l+ float TSS\l+ float VSS\l}"];
"FilterBuilder" [label="{FilterBuilder\n|+ FilterBuilder()\l+ virtual ~FilterBuilder()\l|+ Filter build_filter_from_request(request)\l}"];
"Filter" [label="{Filter\n|+ Filter()\l+ virtual ~Filter()\l|+ list list_of_seqname\l}"];
"list" -> "Filter" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Reader" [label="{Reader\n|+ Reader(URI)\l+ virtual ~Reader()\l|+ virtual void read(filter,key_string)\l}"];
"databaseReader" [label="{databaseReader\n|+ databaseReader()\l+ virtual ~databaseReader()\l|+ void read(filter,URI,key_string)\l}"];
"Reader" -> "databaseReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"TaxReader" [label="{TaxReader\n|+ void read(filter,key_string)\l+ databaseReader()\l+ virtual ~databaseReader()\l|+ string tax_filename\l}"];
"Reader" -> "TaxReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"string" -> "TaxReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"TaxonomicDatabaseReader" [label="{TaxonomicDatabaseReader\n|+ TaxonomicDatabaseReader(folder_name)\l+ virtual ~TaxonomicDatabaseReader()\l|+ tupple read(filter,key_string=None)\l+ Sequence getReferenceSequence(ref_id)\l+ Taxonomy getReferenceTaxonomy(ref_id)\l|+ String reference_tax_file\l+ SequenceCollection sequence_collection\l+ TaxonomyCollection taxonomy_collection\l+ String reference_fasta_filename\l}"];
"SequenceCollection" -> "TaxonomicDatabaseReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"TaxonomyCollection" -> "TaxonomicDatabaseReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"String" -> "TaxonomicDatabaseReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"metadataReader" [label="{metadataReader\n|+ metadataReader(database_name)\l+ virtual ~metadataReader()\l|+ void read(filter,URI,key_string)\l+ void store(item_to_store)\l|+ string database_name\l+ dictionnary current_item\l+ string filename\l}"];
"Reader" -> "metadataReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"dictionnary" -> "metadataReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"string" -> "metadataReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"fastaReader" [label="{fastaReader\n|+ fastaReader(filename)\l+ virtual ~fastaReader()\l|+ SequenceCollection read(filter,URI,key_string)\l+ int build_fasta(sequence_collection=None,new_fasta_filename)\l|+ SequenceCollection new_sequence_collection\l+ string fasta_filename\l}"];
"Reader" -> "fastaReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"SequenceCollection" -> "fastaReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"string" -> "fastaReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"ClusterFileReader" [label="{ClusterFileReader\n|+ void virtual read(filter,min_size=200,key_string)\l+ clusterFileReader(filename)\l+ incrementAbundancePerSample(cluster,sampleID)\l+ virtual ~clusterFileReader()\l|+ Stringlist list_sample_id\l+ SequenceCollection sequence_collection\l+ String filename\l}"];
"Reader" -> "ClusterFileReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"SequenceCollection" -> "ClusterFileReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"Stringlist" -> "ClusterFileReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"String" -> "ClusterFileReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"cdHitClusterFileReader" [label="{cdHitClusterFileReader\n|+ cdHitClusterFileReader(filename)\l+ virtual ~cdHitClusterFileReader()\l|+ ClusterCollection read(min_size=200,key_string)\l}"];
"ClusterFileReader" -> "cdHitClusterFileReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"dbcClusterFileReader" [label="{dbcClusterFileReader\n|+ dbcClusterFileReader(filename)\l+ virtual ~dbcClusterFileReader()\l|+ ClusterCollection read(min_size=200,key_string)\l+ int incrementTempDictionary(sequence)\l+ String getClusterHeads(num_clust)\l}"];
"ClusterFileReader" -> "dbcClusterFileReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"BlastFileReader" [label="{BlastFileReader\n|+ void read(filter,key_string)\l+ blastFileReader(filename)\l+ virtual ~blastFileReader()\l|+ dictionnary dict\l+ String filename\l}"];
"Reader" -> "BlastFileReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"dictionnary" -> "BlastFileReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"String" -> "BlastFileReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"ConfigFileReader" [label="{ConfigFileReader\n|+ ConfigFileReader(filename)\l+ virtual ~ConfigFileReader()\l|+ int read(filter,key_string)\l+ add_argument(required,help,arg_long)\l+ dictionnary parse_args()\l|+ dictionnary conversion_dict\l+ dictionnary args\l+ dictionnary dict\l+ string filename\l}"];
"Reader" -> "ConfigFileReader" [style="solid",color="midnightblue",fontname="Helvetica",arrowtail="onormal",fontsize="10",dir="back"];
"dictionnary" -> "ConfigFileReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
"string" -> "ConfigFileReader" [style="dashed",color="midnightblue",fontname="Helvetica",arrowtail="odiamond",fontsize="10",dir="back"];
}
c4science · Help