GenDBWiki/DeveloperDocumentation/UseTheSource

Working with the GenDB Sources (Where to find what!)

The list below briefly describes the structure of the GenDB repository and the content of each directory. If you are programming within the GenDB environment please respect the existing directory structure.

The GenDB Core Sources

`gendb/bin/`	only binaries and executable shell scripts like the GenDB start up wrapper
`gendb/share/`	directory for most of the GenDB sources
`gendb/share/exec/`	executable Perl scripts etc
`gendb/share/data/`	default directory for all kinds of data files, e.g. the GenDB logo and splash screen images
`gendb/share/doc/`	directory that contains the GenDB documentation
`gendb/share/perl/`	all Perl sources of the GenDB system
`gendb/share/perl/GENDB/`	the GenDB core library
`gendb/share/perl/GENDB/Common/`	the GenDB core library
`gendb/share/perl/GENDB/DB/`	a `.pod` file for each class of the database schema automatically created by O2DBI
`gendb/share/perl/GENDB/DB_Server/`	the GenDB core server library; here you can find the manually implemented extensions for each class of the database schema (in several other subdirectories where subclasses exist)
`gendb/share/perl/GENDB/Exporter/`	some exporter modules written for the GenDB system, e.g. a FASTA or EMBL export library
`gendb/share/perl/GENDB/Importer/`	some importer modules written for the GenDB system, e.g. a FASTA or EMBL import library
`gendb/share/perl/GENDB/Tools`	some common library functions implemented for frequently used tools like Blast which are utilized by several classes
`gendb/share/perl/GENDB/Wizard`	some wizards that were implemented for more complex tasks, e.g. tool creation or job submission
`gendb/src`	contains only some raw sources
`gendb/src/dbschema`	the GenDB O2DBI database schema

The GenDB Web Sources

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The GenDB GUI Sources

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List of GenDB Server Modules

Completed: + / Incomplete: - / All methods in Perldoc: = / Requires cleanup: !!!

• DB_Server/
  • - Annotation.pm =
  • + Annotator.pm =
  • + AssemblyInfo.pm =
  • + FunCat.pm =
  • - Job.pm
  • - Library.pm tbekel
  • - MTP.pm tbekel
  • - Observation.pm
  • + Organism.pm =
  • + Persistent.pm =
  • - Region.pm !!!
  • + Sequence.pm =
  • + Strain.pm =
  • - Tool.pm bl
  • + TrainingSeq.pm =
  • + Tree.pm = !!!
• DB_Server/Annotation/
  • - Function.pm !!!
  • - Region.pm =
• DB_Server/Annotation/Function/
  • - CDS.pm =
  • + rRNA.pm =
  • - tRNA.pm =
• DB_Server/Annotation/Region/
  • + Repeat_Region.pm =
• DB_Server/Annotator/
  • + Human.pm =
  • - Machine.pm =
• DB_Server/Annotator/Machine/
  • - Blast.pm =
  • + CoBias.pm =
  • + Metanor.pm =
  • + TMHMM.pm =
• DB_Server/Observation/
  • + External.pm =
  • - Function.pm =
  • + Pattern.pm =
  • - Region.pm =
• DB_Server/Observation/Function/
  • - Blast.pm !!!
  • + CoBias.pm =
  • + HMMPfam.pm =
  • + HTH.pm =
  • + InterPRO.pm =
  • + iPSORT.pm =
  • + PFScan.pm =
  • + SAPS.pm =
  • + SignalP.pm =
  • + TMHMM.pm =
• DB_Server/Observation/Function/Blast/
  • + COG.pm =
• DB_Server/Observation/Pattern/
  • + PSSM.pm =
• DB_Server/Observation/Region/
  • + Assembly.pm = tbekel
  • + CAG.pm =
  • + CDS.pm =
  • + ContigUpdate.pm =
  • + Feature.pm =
  • + FrameShift.pm =
  • + Operon.pm =
  • + RBS.pm =
  • + Signal.pm =
  • + Transcript.pm =
• DB_Server/Observation/Region/CDS/
  • + Critica.pm =
  • + Gismo.pm =
  • + Glimmer.pm =
• DB_Server/Observation/Region/RBS/
  • + Critica.pm =
  • + RBSfinder.pm =
• DB_Server/Observation/Region/Signal/
  • + Dyad.pm =
• DB_Server/Observation/Region/Transcript/
  • + rRNA.pm =
  • - tRNA.pm =
• DB_Server/Persistent/
  • + File.pm =
  • + FileStorage.pm =
• DB_Server/Persistent/File/
  • + Source.pm =
• DB_Server/Region/
  • + Binding_Site.pm =
  • + CAG.pm =
  • + CDS_Feature.pm =
  • - CDS.pm !!!
  • + Gene.pm =
  • + Mutation.pm =
  • + Oligomere.pm =
  • + Operon.pm =
  • + ORF.pm =
  • + Partial_Region.pm =
  • + PCR_Fragment.pm =
  • + Primer_Bind.pm =
  • + Pseudo.pm =
  • - Read_Feature.pm = tbekel
  • + Repeat_Unit.pm =
  • + Signal.pm =
  • - Source.pm !!!
  • + Transcript.pm =
• DB_Server/Region/CDS_Feature/
  • + Domain.pm =
  • + HTH_Motif.pm =
  • + Mature_Peptide.pm =
  • + Modification_Site.pm =
  • + Motif.pm =
  • + Signal_Peptide.pm =
  • + TMH.pm =
  • + Transit_Peptide.pm =
• DB_Server/Region/Group/
  • + IS_Element.pm =
  • - Random.pm tbekel
  • + Regulon.pm =
  • + Repeat.pm =
• DB_Server/Region/Mutation/
  • + Deletion_Insertion.pm =
  • + Deletion.pm =
  • + Insertion.pm =
• DB_Server/Region/Mutation/Deletion_Insertion/
  • + Interposon.pm =
  • + Plasmid.pm =
  • + Transposable_Element.pm =
• DB_Server/Region/Mutation/Insertion/
  • + Interposon.pm =
  • + Plasmid.pm =
  • + Transposable_Element.pm =
• DB_Server/Region/Read_Feature/
  • - QC.pm tbekel
  • - VC.pm tbekel
• DB_Server/Region/Signal/
  • + Attenuator.pm =
  • + Enhancer.pm =
  • + PolyA_Signal.pm =
  • + Promotor.pm =
  • + Protein_bind.pm =
  • + RBS.pm =
  • + Rep_origin.pm =
  • + Terminator.pm =
• DB_Server/Region/Signal/Promotor/
  • + CAAT_Signal.pm =
  • + GC_Signal.pm =
  • + TATA_Signal.pm =
• DB_Server/Region/Signal/Protein_bind/
  • + Dyad.pm =
• DB_Server/Region/Source/
  • - Contig.pm = !!!
  • + Fragment.pm =
  • + Inserted_Fragment.pm =
  • - Read.pm tbekel
  • + TC.pm =
• DB_Server/Region/Transcript/
  • + mRNA.pm =
  • + rRNA.pm =
  • + tRNA.pm =

Blinke cares for all tools ;-)

==========================

• DB_Server/Tool/ bl, heiko
  • + BRIDGE.pm
  • - Function.pm
  • - Generic.pm bl
  • - Pipeline.pm
  • - Region.pm
  • - Reporter.pm
• DB_Server/Tool/Function/ bl, clex
  • + Bidirectional.pm
  • + Blast.pm
  • + CoBias.pm
  • + Coils.pm
  • + Garnier.pm
  • + MMPfam_ORF_Search.pm
  • + HMMPfam.pm
  • + HTH.pm
  • + InterPRO.pm
  • + iPSORT.pm
  • + PatScan.pm
  • + PFScan.pm
  • + Predator.pm
  • + Prof.pm
  • + ProtFun.pm
  • - SAPS.pm
  • - SignalP.pm
  • - TMHMM.pm
  • + Toppred.pm
• DB_Server/Tool/Function/Bidirectional/
  • - Blast.pm Oli
  • + HMMSearch.pm
• DB_Server/Tool/Function/Blast/ Malte
  • - CDD.pm
  • - COG.pm
  • + Genome.pm
  • - KEGG.pm
  • - Self.pm
  • - SwissProt.pm
  • + TransportDB.pm
• DB_Server/Tool/Pipline/ Oli
  • - Metanor.pm
  • - Retanor.pm
• DB_Server/Tool/Region/ Lutz, Sebastian K.
  • - AMORF.pm
  • - Assembly.pm
  • - BioProspector.pm
  • - Blast.pm
  • + CAG.pm
  • - CDS_to_ORF.pm
  • + ContigUpdate.pm
  • - Critica.pm
  • - Genepred_SVM.pm
  • - Getorf.pm
  • - Gismo.pm
  • - Glimmer.pm
  • + INFERNAL.pm
  • + MAST.pm bl
  • + METAMEME.pm
  • - qRNA.pm !!!
  • - RBSfinder.pm
  • - SearchForRNAs.pm
  • - tRNAscan.pm = bl !!!
• DB_Server/Tool/Region/Blast/
  • - Chunk.pm Malte
  • - Intergenic.pm Malte
  • - Vector_clipper.pm tbekel
• DB_Server/TrainingSeq/
  • + External.pm =
  • + Internal.pm =