spectra-cluster-cli 1.1.2

This tool requires Java (at least version 1.8) to be installed.

To cluster your MGF files, simply extract the files from this zip and execute (on the command line):

$ java -jar spectra-cluster-cli-1.1.2.jar -filter immonium_ions -output_path my_clustering_result.clustering C:\my_first_file.mgf C:\my_second_file.mgf

Version 1.1.2

• Fixed a bug that caused a crash when re-binning very small datasets
  with scarce m/z regions.

spectra-cluster-cli 1.1.1

This tool requires Java (at least version 1.8) to be installed.

To cluster your MGF files, simply extract the files from this zip and execute (on the command line):

$ java -jar spectra-cluster-cli-1.1.1.jar -filter immonium_ions -output_path my_clustering_result.clustering C:\my_first_file.mgf C:\my_second_file.mgf

Version 1.1.1

• Fixed a bug when running on systems with non-english locale
• Fixed a bug in the merging of adjacent bins: Spectra were not re-binned correctly
• Adapted binning procedure to create fewer files

spectra-cluster 1.1

This tool requires Java (at least version 1.8) to be installed.

To cluster your MGF files, simply extract the files from this zip and execute (on the command line):

$ java -jar spectra-cluster-cli-1.1.0.jar -filter immonium_ions -output_path my_clustering_result.clustering C:\my_first_file.mgf C:\my_second_file.mgf

Version 1.1.0

• Updated to spectra-cluster API version 1.1 Therefore, the following new features are available
  • Automatically detect the number of comparison to use. This no longer has to be
    set by the user.
  • A new command line option was added (-x_min_adapt_comparison) that sets a minimum number of
    comparisons that will always be used (as a correction factor) in case the number learned from the
    data is smaller. This feature is only recommended when clustering very small datasets.
• New command line option -add_scores was added. This then outputs additional scores to the generated
  .clustering file. These additional properties are stored as JSON encoded strings.
• Added command line options to only cluster identified or only cluster unidentified spectra.
• For a complete list of command line options, please refer to the output of the -help option

spectra-cluster-cli version 1.0.3 BETA

• Changed to spectra-cluster API version 1.0.10 which includes contaminant peak filters
• Added CLI options to remove contaminant peaks from spectra.

spectra-cluster-cli version 1.0.2 BETA

• Changed to spectra-cluster API version 1.0.9. This fixes issues caused
  by unknown charge states (as well as
  #2).

spectra-cluster-cli version 1.0.1 BETA

The new version comes with a few bug fixes and most importantly new features:

• updated to new .clustering format version
  • .clustering files now includes complete reference to original spectrum using the same indexing system
    as the PSI standard file formats
• added feature to learn the cumulative distribution function (CDF) from a given dataset and then use
  this newly learned CDF
• added a list of experimental / advanced parameters (all starting with "-x_"). For
  more information simply launch the application with the "-help" parameter
• fixed #3 see 1db57ae

spectra-cluster-cli version 1.0 BETA

First beta release of the spectra-cluster-cli

This is the first beta release of the spectra-cluster-cli. The statistics behind the clustering process were only tested for very large datasets (ie. all of the PRIDE repository as used in PRIDE Cluster.

The implementation of spectra-cluster-cli replicates the algorithm used for the PRIDE Cluster resource. Nevertheless, the spectra-cluster-cli uses a completely different approach for binning spectra. This will lead to slightly different results compared to the Hadoop settings.