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Matrix Science Mascot Parser toolkit
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Matrix Science Mascot Parser toolkit
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| ID | Title |
| 11568 | Remove references to Integra and Insight in Mascot Security. Mascot Insight is no longer available. |
| 12892 | Zero value for Observed in unassigned list for query whose only match is a chimeric duplicate |
| 13106 | Add new method ms_inputquery::getQueryNumber(). |
| 13447 | Add ms_inputquery::getPeakCharge() method |
| 13480 | get_ms_mascotresults_params() defaults to old protein grouping for sequence tag searches |
| 13531 | Reduce the time spent in caching search results |
| 13678 | Support new .msr file format |
| 14068 | Remove directory gnu/7.2.0 from Linux shipper image. The directory duplicated the contents of the gnu/lib directory. |
| 14109 | MascotFileProcessingThreads set to -1 should automatically use all possible threads. The default value is 4. |
| 14111 | Rename ms_mascotresfile to ms_mascotresfile_dat. Only the class name changes. The rest of the methods and class members are identical to Parser 2.8. Please see the migration instructions in Upgrading to Mascot Parser 3.0.x from 2.8.x. |
| 14121 | New API for .msr results files, and implement parsing and interpretation of MSR v0.9 files. Mascot Search Results (MSR) is a new format in Mascot Server 3.0. MSR v0.9 was an intermediate format leading up to MSR v1.0. |
| 14127 | Support for Visual Studio 2012 and 2013 has now been dropped. This change only affects the statically linked msparser.lib. If you are still using these compilers, please link dynamically against msparser.dll. |
| 14157 | Undefined behaviour in ms_fdr_query_processor::getThresholdForFDR() when comparing pointer address to integer zero. Fixed due to a compiler warning. The fault made no observable difference to the algorithm. |
| 14179 | MinGW instructions have been reviewed and tested using MinGW GCC 12.1. |
| 14192 | C++ shippers on Linux are now compiled width GCC 5.5.0, and MinGW on Windows with GCC 7.1.0. If you are using the Parser static C++ library, please upgrade your compiler to GCC 5.5 or newer (Linux) or GCC 7.1 or newer (MinGW). If you are using the shared library, earlier compiler versions may be compatible. |
| 14208 | ms_searchparams::getVarModsNeutralLosses() doesn't return satellite NLs. |
| 14217 | Failing to read query-level mods NL string, fault introduced in Parser 2.7.0. |
| 14240 | New mascot.dat option SearchSubmitOutputFormat. The setting is used by the Mascot Server web-based search form (search_form.pl). The setting defaults to 'msr', which is the new file format in Mascot Server 3.0. |
| 14247 | New mascot.dat option to diagnose MSR generation. |
| 14257 | Move Quantlib/Distiller time alignment code to Parser and save/load in cdb/xml |
| 14262 | TMTpro 16-plex and 18-plex mod groups should be required=false |
| 14274 | Methods and classes not wrapped properly by SWIG for Perl, Python, Java and C# |
| 14285 | Implement New Imputation Methods in Parser. ms_imputation is experimental in Parser 3.0 and may be changed in a future release. |
| 14293 | Further thread safety issues : matrix_science::ms_mascotresults::getPeptideThreshold. This method is now safe to call from multiple threads. |
| 14315 | Add getStage method to ms_http_client_search |
| 14320 | Update Doxygen to version 1.9.6. |
| 14323 | ms_ms1quantitation should allow a search without a quantitation method to load replicate or average results. |
| 14337 | Roll-up of changes to API doc and release notes for 3.0 |
| 14361 | ms_inputquery::getPeakMass(): Ions2 and Ions3 lines are missing the first peak. Ions2 and Ions3 lines in .dat format contain data entered with the rarely used ions(b-...) and ions(y-...) qualifiers. ms_inputquery::getPeakMass() and getPeakIntensity() accidentally skipped the first mass in the list. |
| 14377 | getQmatch() returns INT_MAX if called with non-existent query number, should return 0. |
| 14389 | Implement schema changes for MSR v0.99; implement MSR parsing/processing for v0.99; fix bugs in MSR parsing/processing; implement schema changes for SDB v0.99; implement SDB writing/processing for v0.99; fix bugs in SDB parsing/processing; rename headers |
| 14392 | Add MSR files to the Parser test harness |
| 14422 | Support MSR file download in new method ms_http_client_search::downloadResultsFileMSR() |
| 14432 | Add streaming decompression to ms_zip |
| 14433 | Parser should give a warning if reading a file from future version of Mascot |
| 14441 | New Parser class for retrieving MSR file in .dat format |
| 14445 | New option AlwaysCreateDat28ResultsFile. The setting is used by the Mascot Server search engine (nph-mascot.exe). The setting defaults to 0 (false) – Mascot Server 3.0 and later default to writing search results in MSR format. |
| 14481 | All methods of ms_inputquery should be const. |
| 14483 | Documentation for ms_inputquery::getNumUsed() was incorrect. This method always returns 0. |
| 14544 | Change ms_modfile private member std::auto_ptr<ms_masses> to std::unique_ptr |
| 14549 | Display emPAI in integrated error tolerant searches |
| 14551 | ms_searchparams::getLIBRARY_SEARCH() returns -1 when LIBRARY_SEARCH=1 in search params |
| 14553 | Remove ms_mascotoptions::getSeparateLockMem() |
| 14554 | Compile SWIG modules with GCC11 and VS2019 (Perl, Python, C#, Java) |
| 14558 | Update SWIG to 4.2.1 |
| 14571 | Unstable order of sameset accessions in integrated SL searches |
| 14577 | Add wrapper for Perl 5.36 on Linux |
| 14578 | Add new method ms_mascotresfilebase::getSLExecCommand() |
| 14588 | Add accessor method ms_ms2quantitation::getPeptideSummary() |
| 14590 | Update ms_ms1quantitation::mergeQuantitationResults() to support MSR |
| 14636 | ms_fileutilities::getLastModificationTime() fails on Windows if the file has been opened without shared read access |
| 14637 | Drop version-specific Python libraries and ship a single 'universal' library |
| 14647 | New argument to ms_mascotresfilebase::setPercolatorFeatures(): a vector of ML adapter parameters. The argument is optional and defaults to empty vector. A new argument is also introduced for ms_mascotresfilebase::staticGetPercolatorFileNames(). The new argument is not optional, so if you use staticGetPercolatorFileNames(), this is a breaking change. Please pass an empty vector as argument. |
| 14649 | ms_mascotresfilebase constructor, if XMLschemaDirectory is empty string, treat it the same as null pointer |
| 14665 | Add a ms_modification::getClassification() method |
| 14673 | ms_linker_site_vector fails to initialise alpha and beta peptide lengths to zero |
| 14674 | Add quantitation option to choose type of time alignment |
| 14692 | Internal shipper for Perl 5.38 built with VS2019 and GCC 11 |
| 14707 | ms_datfile::updateForInstaller(), replace ResultsCache with a default |
| 14748 | New methods ms_searchparams::getPERCOLATE() and ms_searchparams::getML_ADAPTER_PARAM() |
| 14749 | When setting Percolator flag in ms_mascotresfilebase::get_ms_mascotresults_params(), check the new search param PERCOLATE, then mascot.dat options |
| 14750 | ms_mascotresfilebase::get_ms_mascotresults_params() treats DECOY=-1 as DECOY=1 when deciding whether to set MSPEPSUM_PERCOLATOR |
| 14752 | ms_mascotresfilebase::get_ms_mascotresults_params() should not set MSPEPSUM_PERCOLATOR for error tolerant search |
| 14766 | Update unimod.xml and unimod_xl.xml to the latest versions for 3.0 |
| 14775 | Python msparser library cannot be used with xgboost or tensorflow libraries |
| 14776 | ms_datfile::updateForInstaller(), change SplitNumberOfQueries from 1000 to 2000 |
| 14777 | New option CreateLegacyModAndSubstitutionFiles |
| 14778 | New option AlwaysEnableAutoDecoySearch |
| 14785 | ms_datfile::updateForInstaller(), set PercolatorUseRT to 0 |
| 14789 | New mascot.dat option SearchSubmitAcceptedFileTypes |
| 14795 | ms_ms1quant_time_align::getRToffset() looks in wrong part of array in some cases |
| 14797 | LabelAll option is obsolete |
| 14811 | Quantitation method for TMT 32/35-plex |
| 14820 | Default to sequence FDR in ms_mascotresfilebase::get_ms_mascotresults_params() |
| 14821 | ms_ms1quant_time_align::getRToffset() code is not treating the "to" consensus and "from" consensus properly |
| 14833 | Change behavior of ms_mascotresfilebase::get_ms_mascotresults_params() to set the target FDR |
| 14844 | Add new method ms_masses::saveToString() |
| ID | Title |
| 13751 | Add shippers for Python 3.7, 3.8, 3.9 |
| 13766 | 502.2 - Bad Gateway on opening search results, caused by segfault while reading empty protein description |
| 13864 | Sorting unassigned list fails if filtering is active, caused by findPeptides() always returning results in query order |
| 13927 | Start and end of quantitation match range can be reversed causing out of memory |
| 13961 | Error message 539 lacks information - relevant taxonomy node files now added to error message |
| 13962 | Dodgy protein inference when two interlinked proteins have the same very short beta peptide |
| 13963 | Add TMTpro 18plex quant method |
| 13989 | Xml configuration files should not be written in place |
| 14000 | Increase limit of taxonomy choice include/exclude line length - new limit is 32kB |
| ID | Title |
| 12447 | Calculate an expect value for error tolerant matches. See Error tolerant searches. |
| 13357 | End of 32-bit Parser on Windows. Parser 2.8 and later are now 64-bit only on all platforms. |
| 13378 | Section title "Using STL classes" should mention vectord, vectori, VectorString |
| 13406 | getThresholdForFDRAboveIdentity() doesn't always work when Percolator is enabled |
| 13514 | Parser 2.7.0 C# is built with VS2015, not VS2012 |
| 13604 | New setting for number of input file parsing threads |
| 13633 | updateForInstaller: replace PercolatorFeatures with new feature set |
| 13634 | New options PercolatorTargetRankScoreThreshold and PercolatorTargetRankRelativeThreshold |
| 13639 | Add static and shared libraries for VS2017. Parser 2.8 ships with libraries compiled for VS2012, VS2013, VS2015 and VS2017. |
| 13663 | ms_aahelper never returns internal ions over 700 Da |
| 13673 | ms_proteinsummary needs to check inference flags |
| 13696 | New parameter for ms-createpip.exe multithreading |
| 13715 | Only return false from getThresholdForFDRAboveHomology() if closest FDR is not within a factor of 2 of target FDR |
| 13716 | Make ms_searchparams thread safe and more efficient |
| 13726 | Logging and error handling documentation is mostly missing |
| 13730 | Allow zero child elements in mxm:accessions, mxm:filters, mxm:scope, mxm:settings |
| 13746 | Remove ICC2016 shippers. The GCC 4.8.5 static and shared libraries now shipped with Parser can be used with both GCC 4.8.5 and later, and Intel® Compiler 2016 and later. See C++ toolkit installation on Unix. |
| 13759 | New ms_peptidesummary parameters: target FDR and FDR type. See Target-decoy searches and false discovery rate. |
| 13763 | Add willCreateCache methods which take a ms_mascotresults_params argument |
| 13769 | Update unimod.xml and unimod_xl.xml for 2.8.0 |
| 13806 | Target FDR algorithm: maximise the number of target matches if FDR is 0% |
| 13808 | Update element descriptions in crosslinking schema for the crosslinking configuration editor |
| 13818 | If alpha and beta are in different proteins, one of them is not assigned to any protein |
| 13848 | Add Parser targets for Perl 5.32 and 5.34 (Linux) and Perl 5.32 (Windows). |
| ID | Title |
| 11666 | Add MS1 quantitation result reading to msparser |
| 12409 | ms_ms1quantitation needs to handle normalisation |
| 13548 | ms_http_client_session::submitSearch should be able to use -batch option |
| 13556 | Schema changes required for Mascot Distiller 2.8 |
| 13607 | Multiple issues with ms_quant_helper::isPeptideQuantifiable for MS1 based quantitation |
| 13614 | MS1 quantitation, XML output, Hit ratio set to invalid when it should be valid |
| 13667 | ms_quant_helper VarModStringToVector doesn't handle letters correctly |
| 13686 | ms_xic is not thread safe |
| 13702 | Memory leak in mshandle |
| 13725 | HTTP authentication fails if POST request redirects to GET (e.g. search with -batch mode) |
| 13743 | More problems with ms_quant_helper |
| 13760 | Missing and additional protein ratios for Precursor quantitation when mass-time-match is enabled |
| ID | Title |
| 10427 | ms_aahelper needs argument to generate mass values for all neutral losses |
| 10714 | Parser error handling is not thread safe |
| 10752 | Satellite ions should not be restricted to fragments containing R |
| 10793 | findPeptides() with FT_PEPTIDE_EXP_MZ and FC_SEARCH_ALL_RANKS returns all ranks with no match |
| 11802 | Python example script emits "query out of range" errors and crashes |
| 12100 | single underscore character identifier is #defined in des.h |
| 12326 | Add switch to mascot.dat to over-ride asynchronous search submission (batch mode) |
| 12493 | Add an internal interface for fast conversions between strings and numbers |
| 12496 | Disallow creating a database whose name differs from an existing one only by case |
| 12624 | Use cache files from 2.4 and 2.5 in test harness to ensure backwards compatibility won't break |
| 12672 | ms_mascotoptions setters should check the limits or be removed |
| 12753 | ms_tinycdb openIndexFile uses string comparison on gmt timestamps to check file dates |
| 12808 | ms_umod_configfile::findModification should be optimised with a lookup table |
| 12820 | Add a clear() method to ms_progress_info |
| 12832 | Expand parser test harness with files combining, mod search and ambiguity groups |
| 12857 | Potential crash when sorting peptides |
| 12860 | willCreateCache adds errors to the ms_mascotresfile object, resulting in duplicates |
| 12863 | Search modification by name with findPeptides returns only one value on Windows |
| 12888 | Add a documentation page for the FDR procedure |
| 12891 | Test harness scripts should be converted to python |
| 12895 | Add a utility function to compare XML files |
| 12902 | Modification statistics for error tolerant search can be highly misleading |
| 12913 | Revert to just saving rank 1 in percolator pip file |
| 12921 | Add PSM and sequences used for ID to proteinHit element of quant XML export |
| 12924 | Peptide summary cache file name is different between master_results and ms-searchcontrol |
| 12932 | Support for Visual Studio 2005, 2008 and 2010 has now been dropped. |
| 12959 | Added XML export to ms_ms2quantitation and cdb file export and import to record user protein-peptide ratio selections. The following methods have been renamed and moved to ms_quantitation from ms_ms1quantitation: addHeaderInfo renamed to addHeaderField, addRawFileInfo renamed to addRawFileField, clearHeaderInfo renamed to clearHeaderFields and clearRawFileInfo renamed to clearRawFileFields. For examples, see: ms_ms2quantitation::saveXmlFile, ms_ms2quantitation::saveCdbFile, ms_ms2quantitation::loadCdbFile, ms_ms2quantitation::loadCdbFiles, ms_quantitation::addHeaderField, ms_quantitation::clearHeaderFields, ms_quantitation::addRawFileField and ms_quantitation::clearRawFileFields |
| 12936 | Report of Error tolerant search does not display all matches when None is selected |
| 12937 | Update from SWIG 2.0.12 to SWIG 3.0.12 for ALL languages supported by Parser |
| 12950 | Compile Parser with GCC 4.8.5 |
| 12951 | Support for GCC 4.1 and Intel Parallel Studio XE 2013 has now been dropped. Static libraries on Linux are compiled with GCC 4.8.5 and Intel Parallel Studio XE 2016. Support for 32-bit Linux has been dropped. |
| 12977 | Support for Perl 5.8 to Perl 5.14 has been dropped on Linux. Support for Perl 5.28 and 5.30 has been added on Linux. Support for Perl 5.8 to Perl 5.16 has been dropped on Windows. Support for Perl 5.24, 5.26, 5.28 and 5.30 has been added on Windows. |
| 12990 | Logging: Improvements for ms_loggingmonitor required including better documentation |
| 13020 | I don't believe PSM and PepSeq counts for Percolated results |
| 13029 | Add ActivePerl 5.24, 5.26, 5.28, 5.30 build targets on Linux |
| 13033 | .MSP File Format Issues (Was Error message text for ERR_MSP_NIST_MSP_NO_SPECTRA is misleading) |
| 13047 | Crosslinking changes for protein inference and Parser results file API |
| 13048 | Why are a third of the tests slower on Windows compared to Linux? |
| 13101 | Add support for Python 3.6 |
| 13108 | .MSP File Format Issues #2 |
| 13122 | Mascot Server reporters error with ms-ms data when variable reporter ion modifications are selected |
| 13124 | Segfault when caching an iTRAQ 4-plex file with variable mod group |
| 13200 | New ms_peptidesummary constructor parameter: minimum number of significant unique sequences |
| 13203 | Make ms_mascotresfile more const |
| 13230 | ms_mascotresfile::appendResfile() generates lots of XML errors unless used on Mascot Server |
| 13234 | Crosslinking method definition API and class structure |
| 13241 | Description of getMaxPepModArrangements method in the documentation is confusing |
| 13243 | Update unimod.xml to the latest one |
| 13268 | ms_peptidesummary::isDataCached() returns false for BUGFIX_12740 |
| 13276 | ms_mascotresfile::getMasses() sets electron mass to 0.0 for results files from 1.9 and earlier |
| 13278 | ms_aahelper must support ET and library mods |
| 13284 | DEFAULT_MINPEPLENINPEPSUMMARY should be 7 |
| 13288 | ms_fragment needs a constructor for precursor NL peaks |
| 13294 | Replace Numerical Recipes code with ALGLIB |
| 13301 | Add flanking residues to the distiller xml MS1 quantitation results export |
| 13310 | Peptide without required fixed mod for Reporter quant incorrectly has quant ratios |
| 13312 | Add new option in ms_mascotoptions for suppressing PIP file creation during the search |
| 13315 | Review default crosslinking methods in crosslinking.xml |
| 13324 | New method ms_mascotresults::getDiscoveredLocalModDeltas(), and output order of getDiscoveredErrTolModDeltas() is ambiguous |
| 13409 | ms_peptide::getIonsScore() and ms_mascoresults::getIonsScore() return different values with same args. |
| 13437 | Add Options: DechargeFragmentPeaks |
| ID | Title |
| 10731 | ms_processors produces bogus results for more than 64 logical CPUs |
| 12944 | Last pretty rank 2 peptide incorrectly assigned to a protein in ms_peptidesummary cache file, caused by dangerous map deletion during iteration. Occasional exception thrown in debug mode. |
| 13064 | New option UseHTTPProxyForHTTPS available from ms_mascotoptions::isUseHTTPProxyForHTTPS and ms_connection_settings::isUseHTTPProxyForHTTPS |
| ID | Title |
| 12276 | Documentation changes for schema paths with spaces. See, for example: ms_distiller_data::loadXmlFile . |
| 12538 | Performance improvements when expanding proteins etc. in a 3GB results file. Used to take several minutes with some files. |
| 12606 | The rank argument of ms_mascotresults::getHomologyThreshold has been changed from an int to an enum. |
| 12642 | Add functionality to allow a specified range of spectra in an MSP file to be exported/saved. Additional parameters for ms_spectral_lib_file::saveAs. |
| 12643 | Add Parameter in the options section of mascot.dat to specify max number of spectra in a block. See ms_mascotoptions::getSpectraPerLibraryBlock. |
| 12656 | Segmentation fault if you pass null as filename to ms_mascotresfile has been fixed. |
| 12657 | New parameter in options section: number of peaks per 100 Da to choose from observed spectrum when creating library spectrum. See ms_mascotoptions::getCrawlerNumPeaksPer100Da. |
| 12683 | User entered sensitivity count or significance threshold not working as expected for low scores in library-only search. |
| 12689 | Fixed small memory leaks in ms_datfile, ms_mascotoptions and ms_processors. |
| 12695 | Supply additional schema files to support reading of Distiller xml files:
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| 12704 | New functions, ms_mascotresfile::getSLFragmentTolerance and ms_mascotresfile::getSLFragmentToleranceUnit for reading spectral library fragment tolerance. |
| 12717 | Minor peptide sorting changes for duplicate peptides from spectral libraries. |
| 12721 | Calling the function willCreateCache used to create the directory if it didn't exist. |
| 12724 | Change default value for ms_mascotoptions::getPepSearchTool |
| 12729 | When searching two or more spectral libraries mapped to the same reference, all the proteins reported are to the same SL in master_results_2 |
| 12731 | Added a new methods for annotating an MSP spectrum : ms_spectral_lib_entry::annotatePeaks and ms_spectral_lib_peak_list::annotatePeaks. |
| 12737 | Fixed a segmentation fault if you call setReferenceFasta() before setToleranceInDa() or setToleranceInPPM() |
| 12740 | With Percolator enabled get "Protein: KLH40_HUMAN has 1 cached, but 0 from the re-load" |
| 12749 | Added support for std::wstring in C# |
| ID | Title |
| 11481 | Improvements to ms_peptidesummary::getThresholdForFDRAboveHomology and ms_peptidesummary::getThresholdForFDRAboveIdentity |
| 12026 | More progress reports when building cache files for ms_peptidesummary with hundreds of thousands of protein hits. |
| 12036 | Changes to ms_peptidesummary::findPeptides to support finding error tolerant modifications |
| 12037 | Added ms_mascotoptions::getSpectrumViewerColourSchemeString |
| 12053 | Improved examples for using ms_peptidesummary |
| 12101 | Support for C# under Windows. See C# toolkit installation and Using the toolkit from Perl, Java, Python and C# |
| 12121 | Mascot security doesn't allow multiple Fasta files to be specified in multiple groups. The ms_security_tasks::addTask function was just adding the first item in the array. |
| 12172 | Implement protein inference for both database and library matches. See Spectral libraries |
| 12173 | New mascot.dat configuration values for spectral libraries. Primarily adding a new DATABASE_TYPE |
| 12174 | New mascot.dat Options for library search and compression tool configuration. See ms_mascotoptions::getCompressToolSL |
| 12212 | Fixed index error in ms_mascotoptions::isDefaultTargetFDRPercentage |
| 12222 | The module for HTTP Communication to a Mascot Server could not be used from Perl and the documentation needed improving. |
| 12244 | Occasional failure to write session files in cases where the authentication type was IP address or computer name |
| 12331 | Support for Perl 5.20 and 5.22 on Linux |
| 12232 | Chimeric duplicate peptide matches missing from some queries in merged results |
| 12244 | Occasional failure to write session files for IP address and computer name |
| 12265 | matrix_science::ms_http_helper class needs to support https |
| 12291 | Added a new matrix_science::ms_loggingmonitor class |
| 12349 | Extend Percolator calculations to all ranks |
| 12364 | Some Error tolerant search reports junk matches and average threshold score of 0 |
| 12391 | Added ms_mascotresults_params |
| 12405 | mzIdentML export of fragment matches fails if ITOL is ppm |
| 12408 | Add XML_SCHEMA_DIRECTORY option to ms_mascotresfile::getXMLschemaFilePath |
| 12414 | Support Python 3 |
| 12428 | Create Python scripts for the Parser Documentation |
| 12430 | Score distribution does not include ET matches and the values look wrong |
| 12431 | Support Visual Studio 2015 |
| 12433 | matrix_science::ms_http_client now works properly on Linux |
| 12438 | Supply Perl, Python and Java modules built using VS2012 rather VS2005/VS2008. See Installation on Windows, Python toolkit installation, Installation on Windows for details of Visual Studio Runtime Library requirements. |
| 12448 | Cache file with missing quantitation if errors due to missing xsd file causes missing quantitation information |
| 12456 | Added an additional bool parameter (addMissingResidueMasses)to the matrix_science::ms_masses constructor that takes a ms_umod_configfile parameter. |
| 12458 | Inconsistent handling of whitespace in user parameters between cache and non-cache mode |
| 12468 | Add ms_umod_modification::isSameAs comparison method and ms_umod_modification::getSpecificityBySiteAndPosition |
| 12497 | New overloaded method ms_inputquery::getRetentionTimes for reading all rtinseconds values |
| 12508 | New mascot.dat setting for ions score cutoff checkbox / edit box ms_mascotoptions::getDisplayNonSignificantMatches |
| 12578 | Changes to updateForInstaller for Mascot Server 2.6 |
| 12604 | ms_inputquery fails to parse a peak list if it contains no colons |
| ID | Title |
| 11333 | The default value returned by ms_mascotoptions::getPercolatorMinQueries is 100 and this is too low for when there are 15 features. Increased the value to 750. |
| 11806 | Make getProteinRatio() return negative standard deviation, standard error and p-values when protein ratio type is weighted, and add a new interface to ms_protein_quant_ratio for querying the reason why the values are unavailable. |
| 11825 | Performance improvements for ms_inputquery. |
| 11856 | The function getNumDiscoveredErrTolMods filters peptides based on Ions score below a significance threshold. This was also being applied to the Error Tolerant peptides as well and so erroneously filtered out some error tolerant peptides and their modifications. |
| 11858 | The Mascot Server Windows installer should now always set ForkForUnixApache to 0. If the IFLG_UPDATEAPACHEFORKOPT flag is set when calling updateForInstaller then the value passed in wst is ignored and setForkForUnixApache is always called with 'false'. This change is for Windows only. |
| 11862 | Support filtering of peptides using decimal mass values as doubles rather than strings. See ms_mascotresults::findPeptides. |
| 11863 | Use correct Xerces encoding transcoder when loading and saving xml files. Supports UTF-8 correctly now so that some latin characters are parsed correctly. |
| 11883 | Add support to ms_ms2quantitation::normaliseIntensities to allow for normalisation to selected peptides or proteins when using summed intensities. |
| 11884 | ms_ms2quantitation::getCombinedReportRatioNames now returns unique ratio names in file order rather than alphabetical order. |
| 11885 | Warning message : Attempting to call function matrix_science::ms_peptidesummary::getPeptide before createSummary() has completed with some files where _ignoreiosscorebelow is non-zero and it is an error tolerant search. |
| 11888 | Support for Visual Studio 2013, Update 3. |
| 11892 | Specificity visibility class was not allowing for multiple sites of the same name that differ by position. |
| 11899 | ms_umod_modification::findSpecGroup sorts modification sites incorrectly. For example, it does not find the correct spec group for Phospho (ST) if the input string is "Phospho (ST)" and the T specificity preceeds S in in the list of specificities. This is because the method doesn't sort the sites, so its internal string ends up as "Phospho (TS)", which is of course different from "Phospho (ST)". |
| 11907 | ms_peptidesummary::getQuantitationComponentForPeptide, should exclude a peptide if it matches more than one component. Added code to identify ambiguous components. |
| 11937 | Implementation of willCreateCache function that doesn't require a ms_mascotresfile object and checks both cache files. |
| 11959 | Performance improvements for ms_mascotresfile::getRepeatSearchString. |
| 11960 | Open cache files for writing as soon as possible to reduce potential problems with multiple processes trying to create at the same time |
| ID | Title |
| 6930 | Error tolerant match with exactly the 'same' score as a standard match is not discarded. |
| 10671 | New function: ms_mascotresults::getQuantitationComponentForPeptide |
| 11467 | Add a new MSPEPSUM flag to specify using homology threshold for ignore ions score below. See: matrix_science::ms_peptidesummary::MSPEPSUM_USE_HOMOLOGY_THRESH |
| 11486 | Support Perl 5.16 under Windows and Linux, and Perl 5.18 under Linux. |
| 11545 | Cron and ExecAfterSearch in mascot.dat cannot cope with spaces in paths. |
| 11547 | matrix_science::ms_peptidesummary::getProtein() fails to return null when dbIdx is incorrect |
| 11622 | A residue mass of zero is not permitted in mod_file. It is allowed in a unimod file. |
| 11634 | Report standard error as well as standard deviation. Added function: matrix_science::ms_protein_quant_ratio::getStandardError |
| 11686 | Added support for global and per-group modification visibility for matrix_science::ms_umod_configfile |
| 11705 | Improved behaviour for chimeric spectra. New flag: matrix_science::ms_peptidesummary::MSPEPSUM_REMOVE_CHIMERIC_DUPES |
| 11708 | ms_peptide::getAnyMatch was broken and always returned true in version 2.4.4 and version 2.5.0 |
| 11718 | Added new functions: getNumDistinctPeptideRepeats and getDistinctPeptide |
| 11797 | ms_datfile::updateForInstaller shouldn't update parse rules if Database Manager is being used. |
| ID | Title |
| 11679 | ms_ms2quantitation is not taking uniquePepseq value from the passed quantitation method |
| 11717 | If peptide ratios are manually excluded from a protein ratio then values from duplicate same query are used |
| ID | Title |
| 10290 | Added support for HTTP Communication to a Mascot Server |
| 11234 | Move quantitation support from the perl cgi scripts to Mascot Parser. See Peptide and protein quantitation |
| 11235 | Added a new function: ms_mascotresults::getProteinEmPAI |
| 11358 | When combining results files, need to check that quantitation methods match rather than just comparing names. Added a new function isMethodCompatible |
| 11392 | Need to be able to return std::string & parameters in Java. SWIG supports returning references to native types in Java by passing a single element array of, for example an int. However, it doesn't support this for std::string. Where a parameter is a std::string & it is now necessary to supply a StringBuffer object which will be modified by Parser. Note that const std::string & parameters are unaffected, and still expect a Java String |
| 11399 | Simplify the requirements for specifying the location of the unimod and quantitation schema files when using ms_mascotresfile. See Specifying xml schema file locations |
| 11409 | Temporary cdb file created even when MSPEPSUM_DISCARD_RELOADABLE not specified. Minor performance issue, but no other side effects. |
| 11411 | Save qmatch and qploghole in the cdb file to improve performance. |
| 11415 | ms_mascotresfile now inherits from the ms_errors class. See ms_mascotresfile now inherits from ms_errors |
| 11422 | Under Windows, file sizes stored in cdb files are limited to 32 bits. Larger files had 'wrapped around' values and cdb files will be rebuilt automatically for these files. |
| 11425 | New function ms_mascotresults::getIonsScore to return an ions score more rapidly than calling ms_mascotresults::getPeptide and then ms_peptide::getIonsScore |
| 11438 | The functions ms_mascotresfile::getObservedCharge and ms_mascotresfile::getObservedMrValue need an optional parameter for specifying the summary or decoy summary section |
| 11513 | Save the values returned by ms_protein::getCoverage in the cache |
| 11568 | Remove support for Mascot Integra |
| 11631 | Sign the msparser.jar file using a CA trusted certificate |
| ID | Title |
| 10873 | Support Python 2.7 |
| 11559 | Add MISECTASK_ flags for Mascot Insight to the security_tasks.xml file |
| 11560 | MSPEPSUM_DISCARD_RELOADABLE and MSRES_INTEGRATED_ERR_TOL are incompatible. |
| ID | Title |
| 11115 | Provide interface to the tree/hierarchical cluster method of the C Clustering library: ms_treecluster. |
| 11266 | New function: ms_mascotresfile::getNumEtSeqsSearched(). |
| 11190 | The function getProteinTaxonomyIDs() now also returns taxonomy IDs for PMF results where they are available for Mascot 2.4.1 and later. In version 2.4.0, it only returned values from the proteins section (for ms-ms searches). |
| 11269 | Incorrect return value for getObservedCharge() when the charge state is greater than 8+. |
| 11275 | Additional return values for getThresholdForFDRAboveIdentity() and getThresholdForFDRAboveHomology() |
| 11305 | Get error: "Requested query 1, hit -64 in function ms_proteinsummary::getPeptide" with some PMF mixture results when creating a ms_proteinsummary |
| ID | Title |
| 11182 | Support streaming of compression date using ms_zip |
| 11185 | Support for multiple modifications on one site in ms_aahelper. See: Multiple modifications for the same site for details. |
| 11201 | ms_aahelper constructor using a results file needs path(s) to unimod schema and needs to report errors when the schema cannot be found. |
| ID | Title |
| 10471 | Load and save mascot.dat using matrix_science::ms_datfile can move comments around. Also added functions: matrix_science::ms_datfile::getHeaderComments matrix_science::ms_datfile::setHeaderComments matrix_science::ms_customproperty::getPreceedingComments matrix_science::ms_customproperty::setPreceedingComments |
| 10797 | Added functions to save and load custom parameters for ms_group and ms_user. See: matrix_science::ms_group::saveStringParam and matrix_science::ms_user::saveStringParam |
| 10798 | New functions matrix_science::ms_mascotoptions::getReportBuilderColumnArrangement and matrix_science::ms_mascotoptions::setReportBuilderColumnArrangement |
| 10823 | New function matrix_science::ms_peptide::getSummedModsStr for improved support in Mascot 2.4 for modifications on labelled residues. See also Multiple modifications for the same site |
| 10874 | New function matrix_science::ms_taxonomyrules::getSpeciesFormatRegex() for additional regular expression in the Taxonomy_n section to read speclist.txt |
| 10906 | New function matrix_science::ms_mascotresults::getThresholdForFDRAboveIdentity returns false and fails to find reasonable values for some Percolator files |
| 10943 | Cron emulator improvements including new ms_cronoptions functions: getLoggingLevel(), setLoggingLevel(), getLogFileName() , setLogFileName() , deleteCronJob() and setCronJob() and new ms_cronjob functions: isEnabled() and setEnabled() |
| 10979 | Add support for RAWFILE and LOCUS to matrix_science::ms_inputquery |
| 10991 | ms_mascotresfile::versionGreaterOrEqual returns incorrect value. |
| 10995 | Internal change to allowed values for identity threshold. |
| 11002 | Change minPepLenInPepSummary functionality. Don't show proteins in which the only significant peptides have length < MinPepLenInPepSummary. |
| 11018 | matrix_science::ms_mascotresults::getThresholdForFDRAboveIdentity and matrix_science::ms_mascotresults::getThresholdForFDRAboveHomology can fail to get the best values. |
| 11042 | ms_mascotresfile doesn't fail safely if a cache file cannot be created due to incorrect permissions. Issue was introduced when Bug 10745 was fixed in version 2.4.0. |
| 11041 | On 64 bit Linux only, the function matrix_science::int ms_mascotresults::getQmatch() can return a 'wrapped' negative number in the extremely rare case of the qmatch_x= value being > INT_MAX. In such cases, it now returns INT_MAX on all platforms. |
| 11094 | Using matrix_science::ms_peptidesummary::MSPEPSUM_NO_PROTEIN_GROUPING can cause a crash when creating a ms_peptidesummary object. |
| ID | Title |
| 10536 | IgnoreIonsScoreBelow is converted to a score and rounded to an integer internally. First fixed as bug #567 in version 2.3, but this minor issue was re-introduced in version 2.3.1 |
| 10610 | "Possible duplicate accession string" errors caused by two accessions that only differ in upper/lower case. |
| 10611 | Memory efficient mode for large search results. See matrix_science::ms_peptidesummary::freeHit and matrix_science::ms_peptidesummary::MSPEPSUM_DISCARD_RELOADABLE |
| 10621 | Added new class: matrix_science::ms_taxonomytree and function: matrix_science::ms_mascotresults::getProteinTaxonomyIDs to support additional taxonomy information available in Mascot 2.4 and later. |
| 10622 | Added functions matrix_science::ms_mascotresults::createSummary, matrix_science::ms_mascotresults::getCreateSummaryProgress and matrix_science::ms_mascotresults::cancelCreateSummary to enable an application to cancel creating an ms_peptidesummary object. |
| 10623 | Confusing error messages if ExecAfterSearch logging level set incorrectly. |
| 10624 | Increase 2Gb CDB file size limit to 4Gb for 32 bit applications. |
| 10626 | Font size in chm (help) file is too large. |
| 10627 | On Windows, NTFS, cache files get re-created when going to/from daylight savings. Cache directory names also change. |
| 10628 | New function: ms_mascotresfile::resetKeepAlive and added a %f tag for displaying the filename, which is useful with Combining multiple results files |
| 10629 | Small memory leak in protein family grouping. |
| 10630 | New function: matrix_science::ms_connection_settings::setUserAgent() and matrix_science::ms_connection_settings::getUserAgent() |
| 10631 | Rare crash when using results cache with family summary and minPepLenInSearch < minPepLenInPepSummary. |
| 10632 | ms_protein copy constructor is not reliable when using the results cache |
| 10634 | ms_protein copy constructor is not reliable when using the results cache |
| 10652 | Cannot load protein description line from ms_mascotresfile when protein accessions contain an = sign. |
| 10657 | matrix_science::ms_peptide::getProteins() can return incomplete list when lead protein in a family is not the highest scoring. |
| 10668 | Added function ms_mascotresfile::getMultiFileQueryNumber useful with Combining multiple results files |
| 10673 | Added function matrix_science::ms_mascotresults::findProteins and added flags for searching for modifications. |
| 10682 | Added functions: matrix_science::ms_mascotoptions::setIgnoreDupeAccession() and matrix_science::ms_mascotoptions::setReportNumberChoice() |
| 10704 | Add support for a taxonomy rule where TaxID explicitly given. |
| 10711 | Make matrix_science::ms_tinycdb thread safe. |
| 10712 | Add a method to matrix_science::ms_session to return the timeout value. |
| 10716 | New functions matrix_science::ms_mascotresults::getThresholdForFDRAboveIdentity and matrix_science::ms_mascotresults::getThresholdForFDRAboveHomology. |
| 10734 | Use only the filename part of result files when constructing the cache filename for a multi-file peptide summary. |
| 10745 | Creating an ms_mascotresfile object with a 'junk' file when specifying RESFILE_USE_CACHE creates a (tiny) cache file. The second time the ms_mascotresfile object is created with the same parameters, it reads the tiny cache file but fails to set the INVALID_RESFILE error. |
| 10749 | ms_mascotresfile::getNumQueries() incorrectly returned -1 for the last file in a multi-file result set. |
| 10780 | Change definition of matrix_science::ms_mascotresults::isPeptideUnique to be unique per family member rather than per family. |
| 10804 | Change matrix_science::ms_mascotresults::getPeptideThreshold() to allow return of either homology or identity threshold as double. |
| ID | Title |
| 461 | matrix_science::ms_umod_configfile::getElementByName() hangs if called with null argument. Now just returns NULL. |
| 596 | Documentation improvements and restructuring of some of the help. |
| 614 | matrix_science::ms_aahelper::createPeptide now supports more than 9 variable modifications. |
| 629 | Added matrix_science::ms_peptidesummary::FC_SEARCH_ALL_RANKS for use with matrix_science::ms_peptidesummary::findPeptides |
| 630 | Accession strings with spaces in are truncated when loading proteins from cache. |
| 632 | Added new function matrix_science::ms_peptidesummary::getFlags2() |
| 633 | MinPepLenInPepSummary not used for family gouping. Also added function matrix_science::ms_peptide::getPeptideLength. |
| 634 | matrix_science::ms_datfile error message says that 'mascot.dat. file does not exist even when opening file with different name, for example 'not.mascot.dat'. Change message to output the name of the file. |
| 635 | Added support for Combining multiple results files |
| 638 | ms_mascotresfile::getRepeatSearchString does not include scans, rawscans, rtinseconds and index |
| 639 | Added ms_mascotresfile::enumerateQuerySectionKeys |
| 641 | Unigene reports too slow. A cache file is now created and used automatically. See matrix_science::ms_unigene |
| 644 | Added tags to pass through session_id and task_id in matrix_science::ms_mascotoptions::getExecAfterSearch |
| 645 | Can't load family report for an ET search with ignoreIonsScoreBelow >0 and < 1 |
| 647 | Add Support for Python under Linux. See Python toolkit installation |
| 649 | Performance improvements for matrix_science::ms_mascotresults::getProteinDescription and matrix_science::ms_mascotresults::getProteinMass |
| 653 | Very slow to create cache files when > 100k potential proteins in the results file. |
| 654 | Concurrency issue on Windows when using matrix_science::ms_session |
| 655 | matrix_science::ms_fragment::getLabel returns an string with a truncated rather than a rounded neutral loss. For MetOx, this reports -63 rather than -64. |
| 656 | Concurrency issue: if two processes try to create a directory using matrix_science::ms_fileutilities::createDirectory at the same time, one process may fail. |
| ID | Title |
| 624 | Family grouping no longer requires that the top scoring protein for a group appears as a lead protein. There are cases where more compact grouping can be obtained by making the highest scoring protein a subset/intersection. |
| 626 | In rare cases, a protein could be marked as a subset when it should have been another family member. This is because the algorithm defined a protein as a subset when all of the peptides were found in any other protein, rather than any other family member protein. |
| 627 | Change to matrix_science::ms_aahelper::ms_aahelper constructor when creating from a ms_mascotresfile. Added an additional optional parameter to pass a quantitation schema that will be used before calling ms_mascotresfile::getQuantitation |
| 628 | Functions matrix_science::ms_protein::getNumDisplayPeptides and matrix_science::ms_protein::getNumDistinctPeptides return incorrect values for an error tolerant search when the flag for aboveThreshold is set to true. Error tolerant matches are now ignored in this case. |
See Upgrading to Mascot Parser 2.3.x from 2.2.x For a summary of changes required to scripts using Mascot Parser 2.2,
| ID | Title |
| 17 | Would like to collapse peptides that only differ with Isoleucine <-> Leucine. For the new protein grouping, peptides with the same same score and same query are considered to be the same, so, for example, Q <-> K will also collapse if the tolerances are wide enough. |
| 117 | matrix_science::ms_mascotresults::getNextSubsetProtein is now significantly faster. |
| 511 | Increase maximum number of enzyme cutters from 5 to 20 and improve error message and documentation. |
| 523 | Mascot security doesn't work when specifying user_type=computer_name on Apache. This was because the session file names are case sensitive under unix. |
| 531 | Allowed p value for significance threshold has been changed from 0 < p < 0.1 to 1E-18 < p < 1. |
| 569 | Change homology threshold reporting. Can now report a homology threshold value where the qmatch value is less than 100 and the version is Mascot 2.3 or later. |
| 575 | Session timeout fails to give an error if the session file has been deleted and guest is enabled. |
| 582 | Support 64 bit Java for Windows. |
| 583 | Better support for AMD processors. |
| 584 | Added a flag to matrix_science::ms_umod_configfile::save_buffer() for whether to validate. |
| 585 | Added matrix_science::ms_tinycdb for giving access to tinycdb files. |
| 586 | Cache the ms_peptidesummary results. See Caching Mascot Results |
| 587 | matrix_science::ms_mascotresults::isNA() should look in peptide matches and not protein matches. It used to return incorrect results in cases where there were no significant protein matches. |
| 588 | Add a function to return a 'histogram' for all ions scores. Added: matrix_science::ms_mascotresults::getIonsScoreHistogram() |
| 589 | matrix_science::ms_aahelper::calcFragmentsEx() used to not take fixed modifications into account for searches where a quantitation method was specified. |
| 590 | Added functions: Added additional parameter to: |
| 593 | Add a function: matrix_science::ms_protein::getNumUniquePeptides() |
| 594 | Add a function: matrix_science::ms_umod_modification::getRecordID() |
| 595 | Add functions to find accessions, descriptions, masses, sequences: |
| 598 | Add Using Percolator scores |
| 600 | Add function to retrieve flags and other parameters required for creating an ms_peptidesummary or ms_proteinsummary. |
| 601 | Quantitation: Support Multiplex with multiple ions series (e.g. for IPTL) Deprecated functions: New funtions:
|
| 606 | matrix_science::ms_protein::isShowSubsets() does not read the value from mascot.dat because it is looking for ShowSubsets rather than ShowSubSets |
| 607 | Call to delete should be delete [] in ms_mascotresfile destructor. Will show up in valgrind as Mismatched free() / delete / delete []
at 0x4C20A6E: operator delete(void*) (vg_replace_malloc.c:346)
by 0x5B89ACB: matrix_science::ms_mascotresfile::~ms_mascotresfile() |
| 613 | The only way to be able to get an ms_peptide object is to have an ms_mascotresults object which can be slow, so add a new flag to create an ms_peptidesummary object with no proteins. New flag added: matrix_science::ms_peptidesummary::MSPEPSUM_NO_PROTEIN_GROUPING |
| 615 | Support for EMBL EST Taxonomy and Unigene. New enumeration: matrix_science::TAX_SPECIES_ACC2TAXID |
| ID | Title |
| 198 | Added matrix_science::ms_protein::getPepNumber() function, for when you're working bottom to top |
| 456 | Added ms_mascotresfile::getMasses() function to create an ms_masses object from ms_mascotresfile. |
| 465 | Additional function for PMF iteration: matrix_science::ms_protein::getMasses |
| 471 | Added the function matrix_science::ms_peptidesummary::getQueryList(QL_FLAG flag) for an easier repeat search. Requires Mascot 2.3 |
| 474 | In security, add parameter to restrict spoofing. Additional security task: matrix_science::ms_security_tasks::SECTASK_SPOOFNAMEDGROUPSONLY and function matrix_science::ms_session::getSpoofableUsers() that is used in Mascot 2.3 ms-status.exe for the Show=MS_USERS command. |
| 497 | matrix_science::ms_umod_element::setMonoMass and setAvgMass now check input parameters correctly |
| 514 | Added a new matrix_science::ms_aahelper::ms_aahelper constructor to create an object based on the masses and modifications in a results file. Makes it easier to produce the tables found, for example in the peptide view table. |
| 530 | Initial implementation of new protein grouping for Mascot 2.3. Warning: This code is experimental and there may be further changes before Mascot 2.3 is released Additional flag: matrix_science::ms_peptidesummary::MSRES_CLUSTER_PROTEINS and additional function: matrix_science::ms_peptidesummary::getNextFamilyProtein Added matrix_science::ms_mascotresults::getTreeClusterNodes which is used to provide values for producing the dendrograms in the Mascot 2.3 reports. Note that new license C Clustering library needs to be included in applications that use Mascot Parser |
| 536 | Added a function: matrix_science::ms_peptidesummary::getAllProteinsWithThisPepMatch |
| 538 | Added ms_mascotresfile::getFastaPath to retrieve the path to the fasta file(s) used in a search |
| 540 | Support Perl 5.10. See Perl toolkit installation for details of which versions of Perl are supported on which platforms |
| 542 | h1_q1_et_mods_pep and reqpep were not retrieved properly. This only affected protein summary, where they are are not used in the standard Mascot protein summary reports which don't show error tolerant matches |
| 545 | Added support for searches against multiple databases (introduced in Mascot 2.3). Existing functions just have an added optional parameter.
|
| 551 | Added functions matrix_science::ms_umod_configfile::getMajorVersion() and matrix_science::ms_umod_configfile::getMinorVersion(). |
| 552 | Added matrix_science::ms_mascotoptions::getMinEtagMassDelta and matrix_science::ms_mascotoptions::getMaxEtagMassDelta . |
| 556 | Memoryleak in ms_modfile fixed |
| 557 | Added matrix_science::ms_mascotoptions::getMaxDatabases function. |
| 558 | Support for Quantitation version 2 schema. A number of functions have been added and some deprecated:
|
| 559 | Added Caching Mascot Results |
| 560 | Add basic support for ontology files in the .obo format. See matrix_science::ms_obofile . |
| 561 | Added a function matrix_science::ms_mascotresults::getQmatch to retrieve the the qmatch value from the results file. |
| 564 | The default value for matrix_science::ms_mascotoptions::getInterFileBasePath was C:/InetPub/Mascot/data for Linux and Unix platforms. |
| 565 | For Java, throw an exception if out of memory |
| 566 | Added a security task matrix_science::ms_security_tasks::SECTASK_MAXNOENZQUERIES that enforces a separate query limit for no enzyme searches |
| 567 | IgnoreIonsScoreBelow was converted to a score and rounded to an integer internally. No internal rounding performed now. |
| 568 | Add simple_ratio to integration in quantitation_2 |
| 573 | Quantitation reporter protocol: need to be able to specify a mod as required. Added functions: |
| 574 | Added matrix_science::ms_peptidesummary::isPeptideUnique for quantitation support |
| 577 | Finer control over progress reports. See ms_mascotresfile::outputKeepAlive |
| 578 | Experimentatl support for Python. Windows only for now. See Python toolkit installation |
| 579 | More security tasks: matrix_science::ms_security_tasks::SECTASK_MAXFASTAFILES and matrix_science::ms_security_tasks::SECTASK_DENYQUANT |
| ID | Title |
| 581 | Patch for Dunnington, i7 and Nehalem processors for Linux. (Bug #562 only supported Windows) |
| ID | Title |
| 562 | Support for Dunnington and Intel i7 processors. |
| 563 | Support for Power5+ processors. |
| 458 | matrix_science::ms_processors class may give incorrect information about number of cores per cpu in 64 bit Windows. (Linux and 32 bit Windows unaffected). |
| ID | Title |
| 546 | The function matrix_science::ms_masses.copyFrom leaves a dangling pointer. |
| 550 | Added statistical algroithm for use by Distiller to the Mascot utilities and tools module. |
| ID | Title |
| 509 | matrix_science::ms_mascotresults::createUnassignedList did not free some memory when the ms_mascot_results object was deleted. |
| 539 | Add support for UltraSPARC T1 and T2, and IV+ processors |
| 543 | Corrupt text could be caused by unicode characters in reference fields in unimod.xml. Error returns from Windows functions are now handled properly. |
| ID | Title |
| 532 | Support mingw and a more recent version of gcc. See Using the MinGW compiler |
| 526 | Performance improvements in calls to getHomologyThreshold() |
| 522 | The example code, create_mgf.pl misses last peak |
| 520 | Add matrix_science::ms_peptide::getNum13C function |
| 519 | Support Java 6. Previous releases would occasionally crash with Java 6 on Windows |
| 518 | Need to escape spaces in schema file paths that are passed to Xerces. |
| 493 | ms_proteinsummary is wrong for NA searches where there are hits from different frames. Instead of reporting a separate protein hit for each frame, the results are merged into one hit. |
The following items were fixed in this release which was shipped with Mascot Server 2.2.02
| ID | Title |
| 512 | Calls to matrix_science::ms_fileutilities::setAccessRights can result in security tokens being repeated multiple times. (Only visible using command line cacls) |
| 508 | matrix_science::ms_modification::setNeutralLoss could not be called from java or perl |
| 507 | Trailing tabs in database definition line caused problems for some 3rd party software |
The following items were fixed in this release which was shipped with Mascot Distiller 2.1.1
| ID | Title |
| 504 | Failed to retrieve a remote configuration file when using an https Mascot server |
| 502 | Failed to retrieve a remote configuration file when a proxy server requires a username and password to be specified |
The following items were fixed in this release which was shipped with Mascot 2.2.1
| ID | Title |
| 482 489 | Changes to matrix_science::ms_datfile::updateForInstaller for Windows installer |
The following items were fixed in this release which was shipped with Mascot 2.2
| ID | Title |
| 485 | Change matrix_science::ms_databases::findDatabase to allow searching of inactive databases |
| 473 | The limit of 64 databases should only count active databases |
| 481 | Added a function for Mascot installers to perform all required changes to mascot.dat. See matrix_science::ms_datfile::updateForInstaller() |
| 480 | ms_license fails to report an error message in some cases |
| 476 | Add support for a feature string in the mascot license file (required for BigMascot) |
| 470 | standalone="no" is now omitted in xml-documents |
| 466 | Add new function: matrix_science::ms_processors::getNumCores() |
| 462 | Bugs in plpa library for 64 bit Linux fixed. |
| 460 | Increase limit on number of parse rules from 64 to 256 |
| 449 | Homology threshold now uses the significance threshold value |
| 447 | Mudpit score now decreases when the significance threshold is decreased |
| 453 | Added matrix_science::ms_mascotoptions::getMaxVarMods() and matrix_science::ms_mascotoptions::getMaxEtVarMods() |
| 451 | Errors now detected while saving config files |
| 448 | Issue with leading space in comments when modifying mascot.dat fixed |
| 446 | There are no longer and unicode versions of the Parser library for Windows. Applications that are compiled with unicode support should still be able to link against the non-unicode versions of Parser |
| 444 | If modification is missing from ms_modvector, ms_aahelper crashes and burns |
| 370 | Download of unimod.xml (0.5Mb) will be too slow over the internet. Parser now downloads the compressed unimod.xml, using the matrix_science::ms_zip class |
| 442 | Curl support has never worked on 64 bit AIX and possibly other platforms |
| 441 | Unigene support has never worked properly on 64 bit AIX release, (and possibly SGI/Sun/Tru64). The 64 bit Linux versions were not affected by this issue |
| 440 | Add a new option to mascot.dat - access through matrix_science::ms_mascotoptions::getMaxPepNumVarMods |
| 439 | ShowSubSets is now a double rather than a boolean. Add matrix_science::ms_mascotoptions::getShowSubsets and allow matrix_science::ms_mascotoptions::setShowSubsets to take a double as well as a boolean value |
| 414 | 64 Bit Windows in now supported using Visual Studio 2005, service pack 1. This is available as a separate package |
| 320 | Support for files > 2Gb introduced a file handle leak bug when accessing parameters in the query sections. |
| 438 | Add matrix_science::ms_mascotresults::MSRES_MAXHITS_OVERRIDES_MINPROB. See matrix_science::ms_peptidesummary::ms_peptidesummary for details. |
| 437 | Add security task matrix_science::ms_security_tasks::SECTASK_SEESEARCHINANYGROUP for the right to view searches for all users in all groups belonged to. Shouldn't require any changes to any third party applications that call matrix_science::ms_session::canResultsFileBeViewed |
| 436 | File Handle Leak in ms_mascotresfile with a zero byte file |
| 435 | Spaces at the start of all configuration files are now stripped. |
| 434 | A database name that starts with End is treated as the end of the database section. |
| 433 | Preliminary support for UniGene section in mascot.dat: See matrix_science::ms_unigeneoptions. The main aim purpose of this change is to get the mascot.dat file to save correctly for the installation program. |
| 427 | matrix_science::ms_enzyme::verifyEnzyme doesn't complain about numbers in restrict and and also allows lower case letters. |
| 423 | Integrated error tolerant - numerous further changes, but may be complete now? |
| 424 | ms_fragmentationrules::verifyRule - further additions to rules |
| 427 | verifyEnzyme doesn't complain about numbers in restrict and and also allows lower case letters. |
| 430 | Added z+2 series |
| 154 | Sort order for peptide summary with single etag - now sorted by delta. |
| 253 | Integra session files now get deleted properly. They now use the default timeout period. |
| 293 | When logging in using the 'guest' username, guest session files, such as guest_12312312313 session no longer get created. |
| 295 | Show Sub-sets is now a fraction, not boolean. See Grouping proteins together |
| 298 | matrix_science::ms_aahelper::createPeptide documentation improved. |
| 320 | File larger than 2Gb can now be read on 32bit parser. |
| 335 | Calling matrix_science::ms_mascotresults::createUnassignedList for a protein summary when there is no protein summary no longer gives errors, but just creates an empty list. |
| 337 | Mascot Integra users can no longer log in through Mascot - they must login through Integra. |
| 343 | Taxonomy strings can now contains commas. |
| 391 | Add method to ms_umod_modification to generate ms_modification objects. |
| 393 | Threshold cut-offs have changed. Old behaviour was to suppress the homology threshold if there were less than 1000 sequences in the search. New behaviour is to supress the threshold if qmatch is less than 100. There is also now a minimum for identity threshold of 13. |
| 409 | Verify enzyme used to return false if Restrict was empty |
| 420 | matrix_science::ms_mascotresults::getIonsScoreCorrected was incorrect if ITOL units were mmu rather than Da |
| 421 | Added matrix_science::ms_mascotoptions::getMudpitSwitch() and matrix_science::ms_mascotoptions::getSelectSwitch() |
| 415 | Support for minInternalMass and maxInternalMass. See matrix_science::ms_fragmentationrules::getMinInternalMass() matrix_science::ms_searchparams::getMinInternalMass() and matrix_science::ms_inputquery::getMinInternalMass() |
| 413 | New security params - varmods, varmods ET, num accessions. See matrix_science::ms_security_tasks::SECTASK_MAXVARMODS matrix_science::ms_security_tasks::SECTASK_MAXETVARMODS matrix_science::ms_security_tasks::SECTASK_MAXETACCESSIONS |
| 410 | Add PSI_MS_Name ( ex_code_name) and maybe Approved. See matrix_science::ms_umod_modification::getExCodeName() and matrix_science::ms_umod_modification::isApproved |
| 408 | Remove limit of 1024 mods - make it unlimited |
| 407 | msparser class ms_umod_xref needs to have url-property |
| 397 | Speed up ms_inputquery |
| 396 | Output keep alives in matrix_science::ms_peptidesummary::createUnassignedList() |
| 394 | Example C++ projects have the wrong compiler options for debug DLL versions |
| 385 | Added matrix_science::ms_inputquery::getScanNumbers() and matrix_science::ms_inputquery::getRetentionTimes() |
| 384 | mascot.dat Options functions missing: SortUnassigned etc. |
| 358 | getTagStart, getTagEnd, getTagSeries stuck in infinite loop |
| 313 | Unigene file parsing not quite right. File format change in unigene files now processed properly |
| 402 | add validation precedures to fragrules and enzymes |
| 395 | Keep alives need to be flushed. On Linux, the keep alive html comments are kept in a buffer and not flushed. This means, assuming that the standard text and default time of 5 seconds is used, that it takes 20 minutes for something to appear. |
| 386 | Support for mulitple neutral losses. The function matrix_science::ms_searchparams::getVarModsNeutralLosses which returns an array of neutral losses has been added. matrix_science::ms_searchparams::getVarModsPepNeutralLoss and matrix_science::ms_searchparams::getVarModsReqPepNeutralLoss have also been added. |
| 387 | The functions: matrix_science::ms_searchparams::getFixedModsName matrix_science::ms_searchparams::getFixedModsDelta matrix_science::ms_searchparams::getFixedModsNeutralLoss matrix_science::ms_searchparams::getFixedModsResidues have been added. |
| 329 | Return the new parts of the results file required for quantitation |
| 332 | Support decoy search results |
| 338 | New option ResultsFileFormatVersion in mascot.dat |
| 339 | ICAT mods mapping accepts only modnames without spaces |
| 355 | Need to escape text in ms_inputquery::getINSTRUMENT() and ms_inputquery::getIT_MODS() |
| 356 | Need to read enzyme and taxonomy sections of resfile |
| 373 | getSeriesName returns empty string for ion series 19,20 |
| 376 | setDelta() for unimod modification disables mod delta |
| 326 | If an old ICAT search is repeated with Mascot 2.2 or later, then the ICAT=ON should be translated to QUANTITATION=ICAT. The name 'ICAT' is retrieved from the options section of mascot.dat using getICATQuantitationMethod() |
| 327 | If the require bold red flag is set, then the wrong protein number used to appear in the yellow popup. The protein accession string was correct. |
| 328 | Further changes to quantitation.xml design. [Remove from 2.2 changes list] |
| 330 | Support MODS and INSTRUMENT at the query level. See getINSTRUMENT(), getRULES() and getIT_MODS(). Needed for instruments that, for example, can switch between ETD and CID. |
| 329 | Support more than 9 variable mods. See Increase in the number of variable modifications for details on the impact of this to existing clients using Mascot Parser. |
| 333 | Add 3 new search parameters: getQUANTITATION() , getPEP_ISOTOPE_ERROR() and getDECOY() |
| 248 | Support for new PMF iterations introduced in Mascot 2.2 See: ms_proteinsummary::isPmfQueryUsed() |
| 297 | A Java or Perl application calling matrix_science::ms_aahelper::calcFragments can now access the fragments array. |
The following items were fixed in this release which was shipped with Mascot 2.1.04
| ID | Title |
| 300 | Support high charge state fragments in aa_helper. Mascot only matches singly and doubly charged fragments, and there are no plans to change this. However, if someone wants to label peaks with higher charge states in Mascot Distiller or any other product that uses Mascot Parser, they can now do this. |
| 301 | aa_helper used to give a negative peptide mz value for negative charge. |
| 302 | calcPeptideMz() now gives correct mz values for higher charges. |
| 307 | A dual core Xeon system with HT disabled in the bios was not detected correctly. The work-around was to enable HT in the bios. |
| 310 | Process Affinity was not working on some 2.6 kernels (Linux). This has been fixed by using the PLPA library from Open-MPI. |
The following items were fixed in this release which was shipped with Mascot 2.1.02
| ID | Title |
| 263 | If a search was run using 'MONOISOTOPIC' rather than 'Monoisotopic', then a repeat search using search_form.pl would submit the second search using average masses because it doesn't recognise MONOISOTOPIC. This has been fixed in this parser release. |
| 270 | The Tru64 release of parser 1.x sometimes gives a different sort order for the concise protein summary due to a bug in the Tru64 compiler. This problem has been fixed in this release by using a patched Tru64 compiler. |
| 276 | Advanced topic! MSRES_DUPE_REMOVE_A will always be set which causes incorrect filtering when modifying these advanced flags. This does not affect any standard reports. |
| 280 | getNextSubsetProtein() now always returns false unless MSRES_SHOW_SUBSETS is set. This makes coding for the client a little easier and more transparent. |
| 281 | In cases where the highest scoring protein has no bold red peptides, selecting REQUIRE_BOLD_RED used to return no hits. Obviously, it is very rare for the highest scoring protein to not have any rank 1 peptide hits. |
| 282 | Add SECTASK_BIOTOOLSBATCH in preparation for next Bruker Biotools release. Added this task to the PowerUsers group. |
| 283 | Some customers still have systems with the electron mass being incorrect from the Mascot 1.9 installation. 'Fudge' the code by returning the correct value (0.000549) if the value in the file is 0.00549. If, so some bizarre reason, you really want the electron mass to be 0.00549, then specify it as 0.005490 in the masses file. |
| 285 | The matrix_science::ms_processors class now supports dual core AMD Opteron and reports that process affinity is available on Linux 2.6 kernels. Additional functions are now available to determine the name of the processor manufacturer and a description of the hyperthreading/multi-core/SMT functionality on the processor. |
| 286 | matrix_science::ms_protein::getFrame used to return -1 for protein database if the search was PMF. It now returns 0 as specified in the documentation. |
| 287 and 290 | Using the require bold red flag, it was possible to get occasional matches to proteins without any bold red peptides. |
The following items were fixed in this release which was shipped with Mascot 2.1.01
| ID | Title |
| 261 | Java version of ms_aahelper fails. C++ and Perl worked OK. |
| 262 | Passing a directory name rather than a file name caused a crash. |
| 266 | ms_searchparams::getUSERID returns -1 for old searches - meaning that it is impossible to see old searches unless the view all searches token is set. |
| 267 | In rare circumstances, a single peptide match generates multiple protein hits. Only happens at the random matching level and if minPepLenInPepSummary is non-zero. |
| 267 | getErrTolModMasterNeutralLoss() returned an incorrect value. |
| 272 | Java Parser on Linux fails to run. |
| 273 | Performance improvement for results files with matches to a large number of ambiguous residues |
The following items were fixed in this release which was shipped with Mascot 2.1
| ID | Title |
| 2 | Read and parse the Mascot configuration files. See Mascot configuration files module |
| 122 | Ambiguous residues coped with transparently. matrix_science::ms_peptide::getPeptideStr now takes an optional argument to specify whether ambiguous residues are reported with the substituted value |
| 126 | Documentation - ms_searchparams class reference had multiple references to MASS= |
| 142 | ms_protein::getFrame() is now a const function |
| 143 | Documentation - now specifies that oneInXProb has lower limit of 10 |
| 144 | Documentation - now specifies that 0 is returned for auto in matrix_science::ms_searchparams::getREPORT() |
| 145 | Documentation - matrix_science::ms_peptide::getIonsIntensity() is now clearer |
| 146 | Documentation - matrix_science::ms_peptide::getNumIonsMatched() is now clearer |
| 151 | Provide functions to calculate peptide and fragment masses. See Mascot utilities and tools module |
| 162 | Example perl script for protein summary and peptide summary have incorrect tag calls. |
| 164 | C++ test harness: peptide_list.cpp only builds on Windows. |
| 173 | Performing a search in the Windows msparser help no longer gives the same 'Title' for all pages. |
| 175 | Documentation - Ions series are now correct in matrix_science::ms_searchparams::getRULES() |
| 183 | Peptides with and without ambigious residues are now split into two entries. When decides whether to check if one protein is a sub-set of another it now compares the substituted peptide strings instead of original. |
| 186 | Mascot User authentication and login. See Mascot security and authentication module |
| 187 | Re-organise the help into separate modules, and provide example code in the examples directory as well as the online help. |
| 199 | Huge results files loaded and parsed using less memory. |
| 200 | AutoSelectCharge is a new parameter in the options section of mascot.dat See: matrix_science::ms_mascotoptions::getAutoSelectCharge() |
| 206 | Before loading whole results file, check it really is a Mascot result file. |
| 218 | Support for negative charge state. |
| 221 | In the help, remove the class and class hierachy menu in the tree. These are now grouped together under the separate modules. |
The following items were fixed in this release which was shipped with Mascot 2.0:
| ID | Title |
| 134 | Support non-threaded build of Perl on Linux. Perl supplied with RedHat Linux is normally built with threads support. The default build of Perl (and therefore the one supplied with most other Linux distributions) has thread support disabled. See Installation on Linux platforms for details of which version of msparser.so is required for your system |
| 135 | If a query contains a tag or an etag, then the homology threshold is now suppressed. |
| 137 | New protein scoring for MudPIT type searches. See matrix_science::ms_mascotresults::MSRES_MUDPIT_PROTEIN_SCORE |
| 139 | Version string format in msparser.pm changed from, for example: $VERSION = "1.2.1"to $VERSION = 1.002001; for more reliable version checking with different versions of perl. |
| 140 | Add matrix_science::ms_mascotresults::getProteinExpectationValue() and matrix_science::ms_mascotresults::getPeptideExpectationValue() |
The following items were fixed in this release:
| ID | Title |
| 121 | Support for tag and etag additions in Mascot 2.0 result files has been added. See for example, matrix_science::ms_peptidesummary::getTagString() , matrix_science::ms_peptidesummary::getTagDeltaRangeStart() and matrix_science::ms_peptidesummary::getTagDeltaRangeEnd() |
| 125 | The C++ documentation referred to msparser.h where it should have been 'msparser.hpp' |
| 127 | DLLMain is no longer defined in the Windows static C++ libraries. |
| 128 | Added ms_mascotresfile::getUniqueTaskID() to support taskid's used by Mascot Daemon in Mascot 2.0 |
| 129 | Fixed a crash for a faulty results file with the incorrect number of queries. |
| 130 | Sort order for proteins with identical scores used to be incorrect with .NET 2003 compiler, and Linux Intel compiler. Code generated by all other compilers was working properly. |
| 132 | getAvePeptideIdentityThreshold used to be incorrect for a search that has queries with no matches. Also, added matrix_science::ms_mascotresults::getMaxPeptideIdentityThreshold() as a safer option to display above the histogram on the Mascot 2.0 reports. |
Support for Java has now been added. See Java toolkit installation for details.
Windows Visual C++ .NET 2003 is now supported along with Visual C++ 6.0. Separate directories are provided for each compiler. The DLLs no longer require Perl to be installed on the computer.
Important Windows Perl users please note that the msparser.dll file is now located in a perl56 or perl58 directory. Do not use the one in the lib directory as this no longer provides any perl support.
The following items were fixed in this release:
| ID | Title |
| 5 | Proteins with identical scores are now sorted by accesion number. If the accessions contain numbers (e.g. gi numbers), then the sorting is by the actual number. Otherwise, it sorts lexicographically. See also issue #48 below. |
| 15 | A warning message is now provided for duplicate accessions. Duplicate accessions are normally an indication of a faulty database, or incorrect parse rules, and should be investigated by the Mascot Administrator. |
| 16 | A new function matrix_science::ms_mascotresults::isNA can be called to determine if the search was against a protein database or a nucleic acid database. |
| 36 | Peptide mass fingerprint mixture mode is now supported. See Peptide mass fingerprint mixtures |
| 40 and 102 | Version information can now be found using the standard perl and java interfaces. Further information can be found at: ms_mascotresfile::getMSParserVersion() |
| 42 | Added a function to find number of proteins in the results. see matrix_science::ms_mascotresults::getNumberOfHits() |
| 43 | Added two new functions: ms_mascotresfile::enumerateSectionKeys matrix_science::ms_searchparams::getAllUSERParams to get 'user' parameters. |
| 48 | For a full protein summary report, the sort order now has a one to one correspondence with the entries in the results file. See also issue #5 above, which affects concise summary and peptide summaries. |
| 49 | Added a new function matrix_science::ms_mascotresults::getProteinScoreForHistogram to return the top 50 scores. |
| 50 | Issue with symbol log10: referenced symbol not found on some Solaris systems has been resolved. |
| 54 | A number of minor problems with the unassigned list have been resolved |
| 56 | Added two new functions: matrix_science::ms_inputquery::getPepTol() matrix_science::ms_inputquery::getPepTolUnits() |
| 57 | Changed matrix_science::ms_peptidesummary::getProteinsWithThisPepMatch to have an extra default parameter that returns quotes around the accession strings. This is required to allow accessions with spaces. |
| 58 | Add matrix_science::ms_protein::getUnmatchedMasses to get the list of observed mass values that failed to get a match to a protein hit in a PMF (listed at end of each hit in a protein summary report). |
| 59 | For a peptide summary, the probability cutoff calculation was not the same as in the Mascot 1.9 results reports, which use the average peptide probability. This is always a very minor difference. |
| 60 | Calculation for protein score in peptide summary is now exactly the same as in the Mascot 1.9 results reports. This resulted in very rare minor differences. |
| 61 | Error handler changes. IsValid() no longer returns false if there are only warning messages. Messages are now classified by severity. The test harness shows new code to print out warnings if the file is valid. Messages no longer have the file name at the beginning. |
| 62 | Added new function: matrix_science::ms_searchparams::getElectronMass(). |
| 71 | Changes to the output of matrix_science::ms_mascotresults::getReadableVarMods for error tolerant search results. |
| 72 | Calling getProteinMass used to fail for hit number 50. |
| 74 | Option to 'leak bytes' to keep browser connection alive when a report is taking a long time to produce. See: ms_mascotresfile::ms_mascotresfile and ms_mascotresfile::outputKeepAlive() |
| 76 | Added a method for getting a protein or peptide summary for single hit very quickly. A parameter 'singleHit' has been added to both matrix_science::ms_peptidesummary::ms_peptidesummary and matrix_science::ms_proteinsummary::ms_proteinsummary. |
| 77 | Any SQ always used to return false - even for a sequence query. |
| 78 | Added matrix_science::ms_protein::getRMSDeltas to return RMS error for a protein. |
| 79 | Proteins in a protein summary are now collapsed by query number rather than peptide string. See Grouping proteins together for further information. This should give compatible results with Mascot 1.9 reports. |
| 81 | Key names in the results files are now always matched case insensitively. |
| 82 | Sample code for repeating a search is now provided in Perl, Java and C++ in the relevant 'test_' directory. See also Automated repeating of searches |
| 83 | Trying to read a result files from Mascot versions earlier than 1.02.00 will now produce an error. These files are not supported. |
| 84 and 85 | ms_mascotresfile::getRepeatSearchString used to fail to return the peptol() parameter in cases where an override peptide tolerance had been specified. It also returned seq() instead of comp() for a composition query. |
| 86 | Minor differences in the output for an error tolerant search have been fixed. |
| 91 | Changed matrix_science::ms_peptidesummary::getProteinsWithThisPepMatch() is now considerably faster |
| 92 | Added matrix_science::ms_inputquery::getPepTolString() |
| 93 | The parameter minPepLenInPepSummary now behaves in the same way as the Mascot 1.9 reports. In the previous version, peptides shorter than this were totally ignored. Now, they are just ignored for Grouping proteins together purposes. |
| 103 | OneInXprobRnd is now a a double rather than an int - it was previously possible to overflow this value. |
| 104 | Added a new function: matrix_science::ms_mascotresults::getSequenceMass to calculate the relative mass of a sequence. |
| 110 | The function: matrix_science::ms_peptide::getPrettyRank has changed. The ordering of the numbers is now slightly different and is consistent with the original Mascot reports. |
| 113 and 116 | A bug in: matrix_science::ms_protein::getCoverage that caused to large a value to be reported (particularly with error tolerant searches) has been fixed. The getCoverage function is not supported for Mixture mode and Unigene - and will return 0 for these results. |
Known bugs in Version 1.2.0
39 - Installer required for installing the perl package
The following items were fixed in this release
| ID | Title |
| 1 | Unigene indexes are now fully supported. Simply pass the name of the Unigene index file when creating a results object. |
| 28 | ms_mascotresfile::anyMSMS() always used to return false if there was just one query. It now functions properly. |
| 29 | ms_mascotresfile::getRepeatSearchString used to have a line feed at the end of the string, making it inconvenient to use. |
| 30 | matrix_science::ms_peptide::getMrExperimental() can return 0. This is "by design", since it is calculated from getMrCalc() + getDelta(). It is generally recommended that ms_mascotresfile::getObservedMrValue() is used, since this will always return the relative mass, even for no match. Documentation has been updated. |
| 31 | matrix_science::ms_mascotresults::MSRES_REQUIRE_BOLD_RED now functions properly. In version 1.0, supplying the flag had no effect. |
| 32 | The C++ test harness now (optionally) loads parameters from a configuration file. This functionality is solely designed to help in-house testing of the library. |
| 35 | Error messages: ERR_UNASSIGNED_??? were all reported incorrectly. (Message numbers were all out by one). |
| 37 | The documentation is no longer supplied as a pdf file. This help is only available in html format now. |
| 38 | "Corrupt" title strings could sometimes be returned by matrix_science::ms_inputquery::getStringTitle(true). Spaces were treated correctly, but other characters such as a parenthesis were not handled correctly. The unescaped string was always returned correctly. |
| – | Solaris and Linux versions now available. |
Known bugs in Version 1.01
39 - Installer required for installing the perl package
The following items were fixed in this release
| ID | Title |
| 22 | Duplicate accession strings in database or repeated peptides in a protein cause confusion. Added matrix_science::ms_protein::getNumDisplayPeptides() |
| 23 | Add function to get the string for a repeat search. See: ms_mascotresfile::getRepeatSearchString() |
| 24 | Documentation addition. Added requirement for #define _MATRIX_USE_STATIC_LIB when compiling under Windows using static library. See Compiler Options |
| 25 | Add "summary" example C++ test file. This outputs a list of of the top matching proteins. C++ example only. |
| 26 | Failure to get protein mass from proteins section. If a protein was in the proteins section, but not in the summary section, then the protein mass was not returned when calling matrix_science::ms_mascotresults::getProteinMass() |
| 27 | Added ms_mascotresfile::getMSParserVersion() to return the Mascot Parser version. |
Known bugs in Version 1.0
Bug 1 - Unigene support. Interfaces available, but not yet implemented.
The following items were fixed in this release
| ID | Title |
| 14 | Supply all (or nearly all!) combinations of C++ static and DLL libraries for Microsoft Windows. |
| 21 | Update the C++ example code documentation. |
| 18 | Infinite loop in perl test harness. |
The following items were fixed in this release
| ID | Title |
| 4 | Backward compatibility - need to know if there is a peptides block. Two new functions should enable this: |
| 6 | Need MinPepLenInPepSummary. There is a new parameter to matrix_science::ms_peptidesummary::ms_peptidesummary. |
| 7 | How to do AUTO. Improved documentation. See the examples. |
| 9 | Null accessions now create an error. See ms_mascotresfile::ERR_NULL_ACC_PEP_SUM and ms_mascotresfile::ERR_NULL_ACC_PROT_SUM. |
| 10 | Error reporting - instead of just keeping one error, have a list of errors. See Error Handling for details. |
| 11 | There is now a way of getting the list of unassigned peptides. See Unassigned peptides list for details. |
| 12 | Need an IsBold function. |
| 13 | Need a IsDisplayCheckBox function See matrix_science::ms_protein::getPeptideIsBold() |
First release with these help pages.
1.9.6