#!/bin/bash
#**************************************************************************
#   Copyright (C) 2007 by Universidad Nacional de Colombia                *
#   http://www.unal.edu.co                                                *
#                                                                         *
#   This program is free software; you can redistribute it and/or modify  *
#   it under the terms of the GNU General Public License as published by  *
#   the Free Software Foundation; either version 2 of the License, or     *
#   (at your option) any later version.                                   *
#                                                                         *
#   This program is distributed in the hope that it will be useful,       *
#   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
#   GNU General Public License for more details.                          *
#                                                                         *
#   You should have received a copy of the GNU General Public License     *
#   along with this program; if not, write to the                         *
#   Free Software Foundation, Inc.,                                       *
#   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
#**************************************************************************

function header()
{
	echo "TARIS-Dendrogram (Apr 4 2008)                                     "
	echo "                                                                  "
	echo "Authors: Nestor F. Aguirre, Ray M. Marin and Edgar E. Daza C.     "
	echo "Universidad Nacional de Colombia                                  "
	echo "                                                                  "
}

function help()
{
	header
	echo "Build dendrograms, loading a similarity matrix previously         "
	echo "generated with TARIS-Matrices. The output file is an image        "
	echo "in PNG format                                                     "
	echo "                                                                  "
	echo "Depends:                                                          "
	echo "  1) R ( >= 2.4)                                                  "
	echo "     The R Project for Statistical Computing                      "
	echo "     http://www.r-project.org                                     "
	echo "  2) ade4 ( >= 1.4 )                                              "
	echo "     Analysis of Ecological Data :                                "
	echo "     Exploratory and Euclidean methods in Environmental sciences  "
	echo "     http://cran.r-project.org/web/packages/ade4/index.html       "
	echo "                                                                  "
	echo "For example:                                                      "
	echo "                                                                  "
	echo "\$ find . -name \"*.cube\" > list                                 "
	echo "\$ TARIS_Matrices -i list -m similarity -o matrix.dat             "
	echo "\$ dendrogram.sh matrix.dat output.png                            "
	echo "                                                                  "
	echo "Synopsis:                                                         "
	echo "     dendrogram.sh INPUT_FILE [OUPUT_FILE] [CLUSTERING_METHOD]    "
	echo "                                                                  "
	echo "Description:                                                      "
	echo "     INPUT_FILE: Text file that contains the simmilarity matrix   "
	echo "                 generated by TARIS.                              "
	echo "     OUPUT_FILE: Name of the PNG file with the resulting          "
	echo "                 dendrogram. Default = output.png                 "
	echo "     CLUSTERING_METHOD: The clustering method to be used for the  "
	echo "                 dendrogram construction. The available           "
	echo "                 clustering methods are: ward, single, complete,  "
	echo "                 average, mcquitty, median or centroid.           "
	echo "                 default = average                                "
	echo "                                                                  "
}

function run()
{
	header
	
	INPUT_FILE=$1
	OUTPUT_FILE=$2
	METHOD=$3
	
	gawk '{ if( $2 == ":" ) { printf( "%-8s ", $1 ) } } END{ printf("\n") }' $INPUT_FILE > header
	gawk '{ if( $2 == ":" ) { printf("%-8s ", $1); for( i=3; i<=NF; i++ ) printf("%7.6f ", 100.0-$i); print "" }}' $INPUT_FILE > dissimilarityTMP
	echo -n "labels       " > dissimilarity.csv
	cat header >> dissimilarity.csv
	cat dissimilarityTMP >> dissimilarity.csv
	
	rm header dissimilarityTMP
	
	# Making R script for build the dendrogram
	echo "require(ade4)" > dendrogram.r
	echo "require(foreign)" >> dendrogram.r
	
	echo "data <- as.dist(read.table(\"dissimilarity.csv\", header=TRUE, row.names=\"labels\"))" >> dendrogram.r
	echo "dend <- hclust(data, method=\"$METHOD\")" >> dendrogram.r
	echo "par(cex=0.1)" >> dendrogram.r
	echo "dend <- as.dendrogram(dend)" >> dendrogram.r
	echo "png(\"$OUTPUT_FILE\", width=800, height=600)" >> dendrogram.r
	echo "plot(dend, horiz=TRUE, xlab=\"Similarity\", frame.plot=FALSE, axes=TRUE)" >> dendrogram.r
	echo "dev.off()" >> dendrogram.r
	
	R --no-save < dendrogram.r
	
	rm dissimilarity.csv dendrogram.r
	
	return
}

if [ $1 ]
then
	if [ $2 ]
	then
		if [ $3 ]
		then
			run $1 $2 $3
		else
			run $1 $2 "average"
		fi
	else
		run $1 "output.png" "average"
	fi
else
	help
fi