### CHSalign
##  Compile and run this program in an NJIT AFS (Linux) account.

### Introduction
##  This package contains the executable CHSalign.jar file, and 
##  the source code placed in the sub-folder "chsalign".
##  To run the program, Java SE Development Kit 7u51 
##  (jdk-7u51) or a later version must already be installed on
##  your computer. If not, please first download it from 
##  the ORACLE website.

### Required external data:
##  Scoring matrix file: RIBOSUM85_60 file
##  Sample input files: RNA1.txt, RNA2.txt, RNA3.txt, RNA4.txt

### Compile and run the CHSalign source code:
##  Our program has already been compiled and the executable code is
##  included in the package.
##  In case you want to make up the executable file again by yourself,
##  please follow these steps:
#   (1) Put all the files in the CHSalign.zip package 
#       in a folder named "CHSalign".
#   (2) Go to the sub-folder "chsalign" and compile all the .java files
#       using this command:
#          javac *.java
#   (3) Go back to the main folder "CHSalign".
#   (4) Run the program using the java command.
##  The above steps can be executed as follows:
#   	$ cd chsalign
#   	$ javac *.java
#   	$ cd ..
#   	$ java chsalign/CHSalign -a [algorithm] [options] -i RNA1.txt RNA2.txt

### Run the CHSalign executable code:
##  Put all the files in the CHSalign.zip package 
##  in a folder named "CHSalign".
##  Run the executable CHSalign.jar file:
#	java -jar CHSalign.jar -a [algorithm] [options] -i RNA1.txt RNA2.txt

### Description:
##  There are two algorithms offered in this package:
#   `c' refers to the constrained algorithm, with the constraint
#   that a junction of RNA1 can be aligned with a junction of
#   RNA2 only if they have the same number of branches and
#   the same coaxial helical stacking status.
#   `r' refers to the more relaxed algorithm, which relaxes the constraint;
#   it can align two junctions with different numbers of branches 
#   by requiring that coaxially stacked helices be aligned with 
#   coaxially stacked helices when matching a p-way junction with a
#   q-way junction for p different than q.  
##  General options:
#     -o (output format; default: s):
#        `s' uses the SETTER output format.
#        `d' uses the Dynalign output format.
#     -g (gap penalty; default: -1):
#        This option is used to specify the gap penalty value.
#   The CHSalign program automatically writes the output into a file named
#   result.txt.

### Usage examples:
##    java -jar CHSalign.jar -a r -o d -g -1 -i RNA1.txt RNA2.txt
##    (RNA1 and RNA2 have the same junction pattern and 
##     output is shown in result_RNA1_RNA2_r_d.txt file)
##
##    java -jar CHSalign.jar -a r -o s -g -1 -i RNA3.txt RNA4.txt
##    (RNA3 and RNA4 have different junction patterns and 
##     output is shown in result_RNA3_RNA4_r_s.txt file)
##
##    java chsalign/CHSalign -a c -o d -g -1 -i RNA1.txt RNA2.txt
##    (RNA1 and RNA2 have the same junction pattern and
##     output is shown in result_RNA1_RNA2_c_d.txt file)
##
##    java chsalign/CHSalign -a c -o s -g -1 -i RNA3.txt RNA4.txt
##    (RNA3 and RNA4 have different junction patterns and
##     output is shown in result_RNA3_RNA4_c_s.txt file)