Merge remote-tracking branch 'origin/master'

README.md

@@ -2,10 +2,53 @@
 
 [![Build Status](https://travis-ci.org/wingardium/spc-reader-java.svg?branch=master)](https://travis-ci.org/wingardium/spc-reader-java)
 
-This java library provides functions that read and convert SPC files.
+This java library provides functions that read and convert SPC files to TSV files.
 
 ## Usage
 
+```
+gradle clean jar fatJar
+```
+This will build and create two jar files in the `build/libs` directory: `spc-reader-java-1.0.0-ALPHA.jar` and `spc-reader-java-dist-1.0.0-ALPHA.jar`.
+
+`spc-reader-java-1.0.0-ALPHA.jar` only contains the spc-reader-java classes, thus it requires external libraries to work properly.
+
+`spc-reader-java-dist-1.0.0-ALPHA.jar` is the standalone library, which includes all the dependency libraries.
+
+### Command Line Options
+`spc-reader-java-dist-1.0.0-ALPHA.jar` is also runnable in the command line. Below are available options:
+
+```
+-h  --help      list all available command line options
+-i  --input     input file path
+-o  --output    [optional] output file path, if not set then output will be the same directory as input
+-d  --decimals  [optional] number of decimals in converted tsv file, default value: 2
+-p  --peak      [optional] enable peak group mode, format: true/false, default value: false
+-s  --pstart    [required if -p is set to true] peak group range start value, inclusive
+-e  --pend      [required if -p is set to true] peak group range end value, inclusive
+```
+
+### Dependency libraries
+`spc-reader-java-1.0.0-ALPHA.jar` requires the following libraries:
+- commons-lang3, version: 3.5
+- commons-math3, version: 3.6.1
+- commons-io, version: 2.5
+- commons-cli, version: 1.3.1
+
+### Peak Group Mode
+The original data is exported if peak group mode is disabled.
+
+The peak group mode sums values within a certain range of the peak point. Normally the peak point should be an integer number, and the range start/end value should be integer multiples of the scanning resolution.
+
+The range start/end value must be greater than 0 and less than 1.
+
+The sum of range start and end values must be less than 1 to avoid overlapped peak group range.
+
+For example, if the scanning resolution is 0.05, and the peak range start/end values are set to 0.4/0.35, then for peak point 7, it sums values from 6.60 to 7.35, which equals to 8 data points before peak point, 7 data points after peak point, plus peak point itself.
+
+## TODO
+- Add header information into exported tsv file comment section
+- Add range start/end values validation before process
 
 ## SPC File Format