Update readme

README.md

@@ -24,54 +24,21 @@ your sample preparation protocols etc.
 This is where this program comes into play.
 
 ## Running
-Download the **jar** from [Releases](https://github.com/chhh/deltamass/releases/) section.
-
-##### *Command line*
-Run `java -jar okde-x.x.jar` to see the help.
-There are quite a few options there and it might seem overwhelming at
-first, so you might want to try the GUI version first.
+Download the **jar** file from the [Releases](https://github.com/chhh/deltamass/releases) section.
 
 ##### *GUI*
-Run `java -jar okde-x.x.jar --gui` to launch the GUI. You might want to
+- On Windows you can just start the `.exe` file from the [Downloads](https://github.com/chhh/deltamass/releases).
+- Run `java -jar deltamass-x.x.jar gui` to launch the GUI. You might want to
 include a JVM switch `-Xmx2G` (change the number to the amount of gigabytes of
 memory you'll allow the process to consume), so the command becomes:  
-`java -Xmx2G -jar okde-x.x.jar --gui`
+`java -jar -Xmx2G deltamass-x.x.jar gui`
 
-## Input
-The program takes **.pep.xml** files as input. It can accept whole directories
-and traverse them recursively as well. See `-i` command line option.  
-If your _.pep.xml_ files are named differently, use `-ip` or `--in_pattern` to
-change the regular expression used for matching file paths.  
-**Note**: the regular expression is matched against the whole absolute path for
-each file, so you almost always want to start the regex with `.*`. Use double
-backslash to escape characters, e.g. `\\.` to match a literal dot.
-
-## Most important settings
- * `-g` or `--gui` - run in GUI mode.
- * `-i` or `--in` input paths, can be a comma separated list (don't use spaces).
- If one of the files is a directory, then it will be traversed recursively and
- all files within will be matched against a regular expression provided in
- the `-ip` option (which defaults to _*.\\\\.pep\\\\.xml_).
- * `-ip` or `--in_pattern` - a regular expression for matching files found in
- paths of `-i`. The default is `.*\\.pep\\.xml`.
- * `-k` or `--kernel` - the kernel to be used in KDE. Default is *EPANECHNIKOV*,
- which is very fast, but the shape of the peaks might suffer a bit depending on
- your sample size. If you want smoother curves try *GAUSS_FAST* instead.
- * `-b` or `--bandwidth` - list of bandwidths to be used for generating KDEs.
- You can think of bandwidth as of the area of influence of each input data
- point. E.g. `-b 0.1,0.001,0.0001` will plot three KDEs in the same plot using
- these three bandwidths.
- * `-hd` or `--h_dynamic` - will automatically estimate the best bandwidth
- at each nominal mass separately. Thus, the are under the whole KDE might not
- be unity anymore, but the plot might be a lot nicer. It also takes more time,
- as the estimation requires looping through data.
- * `-p` or `--peaks` - if peaks should be detected. If KDE is being plotted
- (using `--plot` which is on by default), then peaks will be overlaid over the
- plot. **Note**: peak picking is very parameter dependent. In general it will
- depend on the number of data points (affected by the total data range and the
- sampling rate `-ms`) and most of all on the denoising, specified in
- `--denoise` and `denoisingParams` options. See help for corresponding options
- and just try different parameters for yourself.
+##### *Command line*
+Run `java -jar deltamass-x.x.jar` to see the help, it will print available *commands*.  
+To print help/usage for a specific command add `command -h`, e.g. 
+`java -jar deltamass-x.x.jar peaks -h`
+There are quite a few options there and it might seem overwhelming at
+first, so you might want to try the GUI version first.
 
 ## Plot navigation
  * Left Mouse Button = __LMB__, Right Mouse Button = __RMB__.
@@ -90,57 +57,4 @@ backslash to escape characters, e.g. `\\.` to match a literal dot.
  results that fall into this range.
  * `RMB click` - options for the plot (__Preferences__), you can also save the
  plot from here (prefer saving to _PNG_) and change how zooming works.
-
-
-## Starting tips
- * First do a preliminary run with low mass step (e.g. `-ms 0.01`) and low
- bandwidth (e.g. `-b 0.01` or `List of bandwidths` in GUI) to get a bird's eye
- view of your data.
- * Typically you'd want to look at the data using `-ms 0.0001 -b 0.001` to
- see individual peaks better.
- * The peak at zero is always the largest one, and the situation to the left
- (negative mass shifts) and right (positive) of it are quite different, so it's
- better to view them separately and avoid the zero peak at all.
- * Most of your data points will be concentrated in the zero peak,
- calculating KDE for it is relatively expensive and there is little merit to it.
- You can easily avoid the peak at zero at all by adding e.g. `-ml 0.75` option
- (`Mass Lo` in GUI), which will only plot mass differences above mass of 0.75.
- * Similarly for negative massses, use `-mh -0.75` (`Mass Hi` in GUI) to plot
- everything from negative infinity up to -0.75.
- * Use `-ml` and `-mh` options simultaneously to limit the view and increase
- plot's responsiveness.
- * You can output the detected peaks to a file using `-o` option and skip
- plotting completely by providing `--plot false`, however you'll likely
- want to do the other thing around most of the time.
-
-## Filtering data
-Input data can be filtered according to the scores in _pep.xml_ files. All then
-input files must have this corr in order for it to work. E.g. if you want
-to filter based on _peptideprophet_ probability, all the files must have between
-processed with PeptideProphet.  
-
-* Filters are provided using `-s` or `--corr` option. The GUI provides a
-builder for the filter strings.  
-* The names of the scores are exactly as they appear  _pep.xml_ (e.g. `expect`,
-`hyperscore`, `interprophet`, etc). The GUI has a dropdown menu for the most
-common ones.  
-* Filters can be combined using commas.  
-* Supported operators are `>`, `>=`, `==`, `<=`, `<`.
-
-Example: `-s "expect<=0.001,peptideprophet>0.95"`
-
-## Caching
-The input data are _.pep.xml_ files, which are typically large, the included
-parser for them is not very fast, so if you want to play around with parameters
-it makes a lot of sense to cache the parsing results. The option to cache
-.pep.xml contents is on by default in both GUI and command line versions.
-##### *Disabling*
-The cache files are stored nearby your original files. If for some reason you
-don't want those extra files to be created use `--cache false` option or untick
-`Use cache` checkbox in GUI.
-##### *Deleting*
-If you've already run the program with cache option and now want to get rid of
-those extra files, run the program with `-x` or `--delete_cache` switch, This
-won't trigger any processing and will only look for cache files in the input
-paths (`-i`) and delete them. The GUI has a `Delete cache` checkbox in *Files &
-Cache* section.
+