input stringlengths 10 828 | output stringlengths 5 107 |
|---|---|
public string get process id throws exception string id string run name management factory get runtime mxbean get name string tokens run name split if tokens length 2 throw new exception get process id failed because process name could not be parsed run name else id tokens 0 return id | assuming we are on a nix style system |
public string record to file record r string output dir string descriptor string extention string outfile output dir get unique file name descriptor extention try print writer out new print writer new file writer outfile out println r get out close catch ioexception e e print stack trace return outfile | input a record |
protected boolean skip string current record string if header keyword null return current record string matches i header keyword current record string matches i well current record string matches i template else return current record string matches i well current record string matches i template | indicates that the current record should be skipped |
public linked list set string indxs linked list ll new linked list set positions indxs ll return ll | set assumes an embl style string 12345 |
public void set header keyword string header keyword this header keyword header keyword | sets a keyword search pattern that will indicate a row contains a header |
public int check order if start end return 0 else return 1 | return 0 if out of order |
public string get header keyword return this header keyword | get the current file header keyword |
public string format final line string last bit string line string spaces return line last bit spaces substring last bit length spaces length format number this sequence length n | format final line actually just backfills the spaces needed |
public hash map hash string string super string int l hash map hm new hash map for int i 0 i super string length i hm put super string substring i i l i return hm | this implementation uses a hash to only search super string once so |
public string get return this file name | return the filename |
public void set string r throws illegal argument exception try parse r catch illegal argument exception ex logger get logger fasta record class get name log level severe null ex throw new illegal argument exception could not parse r ex | calls parse to establish valid fasta record |
override public string to string return this get end to string | provide a to string implementation that will return the content of this object |
public string get attribute return attribute | gets the value of the attribute property |
public void set attribute string value this attribute value | sets the value of the attribute property |
public evidence type create evidence type return new evidence type | create an instance of |
public assembly location type create assembly location type return new assembly location type | create an instance of |
public position type create position type return new position type | create an instance of |
public emblservices create emblservices return new emblservices | create an instance of |
public feature type create feature type return new feature type | create an instance of |
public citation type create citation type return new citation type | create an instance of |
public void set citation reference type citation value this citation value | sets the value of the citation property |
public location element type create location element type return new location element type | create an instance of |
public void set contig emblservices entry contig value this contig value | sets the value of the contig property |
public big integer get begin return begin | gets the value of the begin property |
public entry type create entry type return new entry type | create an instance of |
public db reference type create db reference type return new db reference type | create an instance of |
public void set begin big integer value this begin value | sets the value of the begin property |
public location type create location type return new location type | create an instance of |
public big integer get end return end | gets the value of the end property |
public base type create base type return new base type | create an instance of |
public void set sequence emblservices entry sequence value this sequence value | sets the value of the sequence property |
public void set end big integer value this end value | sets the value of the end property |
public assembly location element type create assembly location element type return new assembly location element type | create an instance of |
public big integer get position return position | gets the value of the position property |
public void set version big integer value this version value | sets the value of the version property |
public void set position big integer value this position value | sets the value of the position property |
public boolean is complement return complement | gets the value of the complement property |
public void set complement boolean value this complement value | sets the value of the complement property |
public void set organism feature type organism value this organism value | sets the value of the organism property |
public void set primary string value this primary value | sets the value of the primary property |
public location type get location return location | gets the value of the location property |
public big integer get primary begin return primary begin | gets the value of the primary begin property |
public void set primary begin big integer value this primary begin value | sets the value of the primary begin property |
public void set location location type value this location value | sets the value of the location property |
public big integer get primary end return primary end | gets the value of the primary end property |
public void set primary end big integer value this primary end value | sets the value of the primary end property |
public string get scientific name return scientific name | gets the value of the scientific name property |
public void set scientific name string value this scientific name value | sets the value of the scientific name property |
public assembly location type get assembly return assembly | gets the value of the assembly property |
public string get preferred common name return preferred common name | gets the value of the preferred common name property |
public string get consortium return consortium | gets the value of the consortium property |
public big integer get length return length | gets the value of the length property |
public void set assembly assembly location type value this assembly value | sets the value of the assembly property |
public void set consortium string value this consortium value | sets the value of the consortium property |
public void set preferred common name string value this preferred common name value | sets the value of the preferred common name property |
public void set length big integer value this length value | sets the value of the length property |
public long get tax id return tax id | gets the value of the tax id property |
public string get topology return topology | gets the value of the topology property |
public void set tax id long value this tax id value | sets the value of the tax id property |
public void set topology string value this topology value | sets the value of the topology property |
public void set lineage feature type organism lineage value this lineage value | sets the value of the lineage property |
public void set version long value this version value | sets the value of the version property |
public big integer get id return id | gets the value of the id property |
public void set id big integer value this id value | sets the value of the id property |
public evidence type get evidence return evidence | gets the value of the evidence property |
public void set evidence evidence type value this evidence value | sets the value of the evidence property |
public string get data class return data class | gets the value of the data class property |
public void set data class string value this data class value | sets the value of the data class property |
public void init setup features setup qualifiers obj factory new object factory alet obj factory create assembly location element type alt obj factory create assembly location type bt obj factory create base type ct obj factory create citation type drt obj factory create db reference type embls obj factory create emblservices et obj factory create entry type evt obj factory create evidence type ft obj factory create feature type let obj factory create location element type lt obj factory create location type pt obj factory create position type rt obj factory create reference type return | setup the data objects that will be used for data transformations |
public string get issue return issue | gets the value of the issue property |
public string get taxonomic division return taxonomic division | gets the value of the taxonomic division property |
public void set issue string value this issue value | sets the value of the issue property |
public string get first return first | gets the value of the first property |
public void set taxonomic division string value this taxonomic division value | sets the value of the taxonomic division property |
public void set first string value this first value | sets the value of the first property |
public xmlgregorian calendar get created return created | gets the value of the created property |
public string get last return last | gets the value of the last property |
public void set last string value this last value | sets the value of the last property |
public void set created xmlgregorian calendar value this created value | sets the value of the created property |
public string deparse throws null pointer exception this record don t call deparse if you don t intend to reset the contents of the record if this embls null throw new null pointer exception this record does not contain any information emblservices is null string buffer sb new string buffer sb append this get id this record sb to string return this record | deparse converts the object representation of a embl file into a embl record |
public big integer get release created return release created | gets the value of the release created property |
public string get accession number return accession number | gets the value of the accession number property |
public string get patent number return patent number | gets the value of the patent number property |
public void set release created big integer value this release created value | sets the value of the release created property |
public void set patent number string value this patent number value | sets the value of the patent number property |
public void set accession number string value this accession number value | sets the value of the accession number property |
public string get institute return institute | gets the value of the institute property |
public xmlgregorian calendar get last updated return last updated | gets the value of the last updated property |
public void set institute string value this institute value | sets the value of the institute property |
public xmlgregorian calendar get year return year | gets the value of the year property |
public void set last updated xmlgregorian calendar value this last updated value | sets the value of the last updated property |
public void set year xmlgregorian calendar value this year value | sets the value of the year property |
public big integer get release last updated return release last updated | gets the value of the release last updated property |
public void set release last updated big integer value this release last updated value | sets the value of the release last updated property |
public string get submitter accession return submitter accession | gets the value of the submitter accession property |
public void set submitter accession string value this submitter accession value | sets the value of the submitter accession property |
public big integer get submitter version return submitter version | gets the value of the submitter version property |
public void set submitter version big integer value this submitter version value | sets the value of the submitter version property |
public big integer get submitter wgs version return submitter wgs version | gets the value of the submitter wgs version property |
public void set submitter wgs version big integer value this submitter wgs version value | sets the value of the submitter wgs version property |
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