#format ruby
# psi.rb 
# 
# Psi Blast Query 
# by destine  2005-04-14 
# 사용 방법
# ruby psi.rb rhodopsin.txt visible             => precise result
# ruby psi.rb rhodopsin.txt visible /r    => redundant result
# ruby psi.rb rhodopsin.txt visible /i    => informative result
# 
# 입력 파일
# rhodopsin.txt : FASTA format으로 되어 있습니다.
#

require 'win32ole'
def wait(ie) 
   while ie.busy 
   end 
   until ie.readyState == 4 # READYSTATE_COMPLETE 
	end 
end 

class PsiBlastResult
	attr_reader :id, :sequence
	def initialize(id, sequence)
		@id = id
		@sequence = sequence
	end
	
	def addsequence(sequence)
		@sequence += sequence
	end
end

class PsiBlastQuery
	attr_reader :comment, :sequence, :rawResult, :blastResults
	attr_writer :rawResult
	def initialize(comment, sequence)
		@comment = comment
		@sequence = sequence
		@rawResult = ""
		@blastResults = []
	end
	
	def printout(mode)
		blastResults.each do |aResult|
			print ">#{aResult.id}\n"
			print "#{aResult.sequence}\n"
		end
	end
	
	def process( manager, visible )
		manager.connect(visible)
		#query = PsiBlastQuery.new("comment", 
		#"MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA")
		manager.input("QUERY",self)
		manager.submit()
		
		# Format 얻는 방법
		# 1.  자동을 업데이트 될때까지 기다린다.
		#manager.submit()
		#manager.waiting(false)
		
		# Format  얻는 방법
		# 2. 수동으로  refresh  시킨다.
		#rid = "1113539432-3598-127383550938.BLASTQ4"
		   rid = manager.getRID()
		#http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?RID=1113540862-28790-25293121580.BLASTQ2&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&MASK_CHAR=0&MASK_COLOR=0&DESCRIPTIONS=100&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&I_THRESH=0.001&FORMAT_ENTREZ_QUERY=&FORMAT_ENTREZ_QUERY=All+organisms&EXPECT_LOW=&EXPECT_HIGH=&RID=1113540862-28790-25293121580.BLASTQ2&RTOE=13&CLIENT=web&FORMAT_OBJECT=Alignment&CMD=Get&PAGE=Proteins&_PGR=0&PID=28790&LAYOUT=OneWindow&FORMAT_BLOCK_ON_RESPAGE=None&STEP_NUMBER=1&EXPECT=10&HITLIST_SIZE=100&DESCRIPTIONS=100&ALIGNMENTS=50&AUTO_FORMAT=Off	
		   url = "http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?RID=" +
		   	rid +
		   	"&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&MASK_CHAR=0&MASK_COLOR=0&DESCRIPTIONS=100&ALIGNMENTS=50&ALIGNMENT_VIEW=QueryAnchoredNoIdentities&I_THRESH=0.001&FORMAT_ENTREZ_QUERY=&FORMAT_ENTREZ_QUERY=All+organisms&EXPECT_LOW=&EXPECT_HIGH="+
		   	"&RTOE=13&CLIENT=web&FORMAT_OBJECT=Alignment&CMD=Get&PAGE=Proteins&_PGR=0&PID=28790&LAYOUT=OneWindow&FORMAT_BLOCK_ON_RESPAGE=None&STEP_NUMBER=1&EXPECT=10&HITLIST_SIZE=100&DESCRIPTIONS=100&ALIGNMENTS=50&AUTO_FORMAT=Off"
		   manager.browse( url )
		   manager.waiting(true)
		
		# 결과를 얻어온다.
		@rawResult = manager.gettext()
		#print @rawResult	
		purification()
	end	
	
	def purification()
		bAlignments = false
		nEnterCount = 0
		hash = {}
		r = Regexp.new("([_0-9A-Z]+)[' ']+([0-9]+)[' ']+([A-Z\-]+)[' ']+([0-9]+)")
		id = ""
		sequence = ""
		
		results = rawResult
		results.each do |line|
			if ( line.strip == "Alignments" )
				bAlignments = true
			end
			if ( bAlignments == true )
				if ( r =~ line )
					id = r.match(line)[1]
					sequence = r.match(line)[3]
					if ( hash[ id ] == nil )
						result = PsiBlastResult.new( id, sequence )
						hash.store( id, result )
					else
						hash[id].addsequence( sequence )
					end
					nEnterCount = 0
					# print  r.match(line)[0]
					# 1_29407      1   MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY 60
					# print r.match(line)[1]
					# 1_29407
					# print r.match(line)[2]
					# 1
					# print r.match(line)[3]
					# MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
					# print r.match(line)[4]
					# 60
					
				end
				#print r.match(line)
				#print r.match(line)
				#print r.match(line)
			end
			if ( bAlignments == true && line.strip.empty? )
				nEnterCount = nEnterCount + 1
			end
			if ( nEnterCount >= 2 )
				bAlignments = false
			end
		end
		
		hash.each do |key,value|
			#print ">#{value.id}\n"
			#print "#{value.sequence}\n"
			if ( finder( @blastResults, sequence ) )
				@blastResults << value
			end
		end
	end
end

class PsiBlastQueryManager
	attr_reader :list, :web
	def initialize(visible)
		@visible = visible
		@list = []
		@web = WIN32OLE.new('InternetExplorer.Application')
	end
	
	def add( query )
		@list << query
	end
	
	def openfile( filename )
		comment = ">no_comment"
		sequence = ""
	
		f = File.open(filename)
		f.each do |line|
			if (line =~ />/) != nil
				if ( sequence.empty? == false )
					add( PsiBlastQuery.new( comment, sequence ) )
					comment = ">no_comment"
					sequence = ""
				end
				comment = line.chop #delete carriage return			
			elsif line.strip.size > 0
				sequence += line.strip
			end
		end
		if ( sequence.empty? == false )
			add( PsiBlastQuery.new( comment, sequence ) )
			comment = ">no_comment"
			sequence = ""
		end	
	end	
	
	def getResult()
		list.each do |data|
			data.process(self, @visible)
		end	
	end
	
	def printout(mode)
		list.each do |data|
			print "\n=================#{data.comment}====================\n"
			data.printout(mode)
		end
	end
	
	def finalize()
		web.quit
	end
	
	def connect(visible)
		web.navigate('http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&LAYOUT=OneWindow&AUTO_FORMAT=Semiauto&ALIGNMENTS=250&ALIGNMENT_VIEW=QueryAnchoredNoIdentities&CLIENT=web&COMPOSITION_BASED_STATISTICS=on&DATABASE=nr&CDD_SEARCH=on&DESCRIPTIONS=500&ENTREZ_QUERY=%28none%29&EXPECT=10&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&I_THRESH=0.005&MATRIX_NAME=BLOSUM62&NCBI_GI=on&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on&SERVICE=plain&SET_DEFAULTS.x=36&SET_DEFAULTS.y=5&SHOW_OVERVIEW=on&END_OF_HTTPGET=Yes&SHOW_LINKOUT=yes&GET_SEQUENCE=yes') 
		wait(web) 		
		web.visible =visible
	end
	
	def input(name, query)
		doc = web.document 
		if doc != nil 
			begin 
			   doc.all(name).value = query.sequence
			   wait(web) 
			rescue 
			end
		end		
	end
	
	def submit()
		doc = web.document 
		if doc != nil
			doc.forms(0).submit() 
			wait(web) 	
		end
	end
	
	def gettext()
		doc = web.document 
		if doc != nil
			wait(web) 	
			return doc.body.innerText
		end
	end
	
	def getRID()
		doc = web.document 
		if doc != nil
			wait(web) 	
			r = doc.all('RID')
			r0 = r.item(0)
			return r0.value
		end		
	end
	
	def browse(url)
		web.navigate(url)
		wait(web)
	end
	
	def waiting(refresh)
		text = gettext()
		while ( text =~ /WAITING/ )
			if ( refresh == true )
				web.refresh()
			end
			text = gettext()
			sleep(3)
		end
	end
end

def testPsiWeb
	manager = PsiBlastQueryManager.new()
	manager.connect(true)
end

def testPsiQueryInput
	manager = PsiBlastQueryManager.new()
	manager.connect(true)
	query = PsiBlastQuery.new("comment", "input")
	manager.input("QUERY",query)
end

def testPsiSubmit
	manager = PsiBlastQueryManager.new()
	manager.connect(true)
	query = PsiBlastQuery.new("comment", 
	"MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA")
	manager.input("QUERY",query)
	manager.submit()
end

def testPsiGetFormat
	manager = PsiBlastQueryManager.new()
	manager.connect(true)
	query = PsiBlastQuery.new("comment", 
	"MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA")
	manager.input("QUERY",query)
	manager.submit()
	# f = doc.forms(0)
	# f.METHOD = "get"
	# f.submit()
	#http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?QUERY=MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA&QUERY_FROM=&QUERY_TO=&DATABASE=nr&CDD_SEARCH=on&ENTREZ_QUERY=&ENTREZ_QUERY=All+organisms&COMPOSITION_BASED_STATISTICS=on&EXPECT=10&WORD_SIZE=3&MATRIX_NAME=BLOSUM62&GAPCOSTS=11+1&PSSM=&OTHER_ADVANCED=&PHI_PATTERN=&SHOW_OVERVIEW=on&SHOW_LINKOUT=on&GET_SEQUENCE=on&NCBI_GI=on&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&MASK_CHAR=0&MASK_COLOR=0&DESCRIPTIONS=500&ALIGNMENTS=250&ALIGNMENT_VIEW=Pairwise&RUN_PSIBLAST=on&I_THRESH=0.005&FORMAT_ENTREZ_QUERY=&FORMAT_ENTREZ_QUERY=All+organisms&EXPECT_LOW=&EXPECT_HIGH=&LAYOUT=TwoWindows&FORMAT_BLOCK_ON_RESPAGE=None&AUTO_FORMAT=Semiauto&PROGRAM=blastp&CLIENT=web&SERVICE=plain&PAGE=Proteins&CMD=Put
	manager.submit()
end

def testPsiGetResult
	manager = PsiBlastQueryManager.new()
	manager.connect(false)
	query = PsiBlastQuery.new("comment", 
	"MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA")
	manager.input("QUERY",query)
	manager.submit()
	
	# Format 얻는 방법
	# 1.  자동을 업데이트 될때까지 기다린다.
	#manager.submit()
	#manager.waiting(false)
	
	# Format  얻는 방법
	# 2. 수동으로  refresh  시킨다.
	#rid = "1113539432-3598-127383550938.BLASTQ4"
	rid = manager.getRID()
	#http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?RID=1113540862-28790-25293121580.BLASTQ2&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&MASK_CHAR=0&MASK_COLOR=0&DESCRIPTIONS=100&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&I_THRESH=0.001&FORMAT_ENTREZ_QUERY=&FORMAT_ENTREZ_QUERY=All+organisms&EXPECT_LOW=&EXPECT_HIGH=&RID=1113540862-28790-25293121580.BLASTQ2&RTOE=13&CLIENT=web&FORMAT_OBJECT=Alignment&CMD=Get&PAGE=Proteins&_PGR=0&PID=28790&LAYOUT=OneWindow&FORMAT_BLOCK_ON_RESPAGE=None&STEP_NUMBER=1&EXPECT=10&HITLIST_SIZE=100&DESCRIPTIONS=100&ALIGNMENTS=50&AUTO_FORMAT=Off	
	url = "http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?RID=" +
		rid +
		"&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&MASK_CHAR=0&MASK_COLOR=0&DESCRIPTIONS=100&ALIGNMENTS=50&ALIGNMENT_VIEW=QueryAnchoredNoIdentities&I_THRESH=0.001&FORMAT_ENTREZ_QUERY=&FORMAT_ENTREZ_QUERY=All+organisms&EXPECT_LOW=&EXPECT_HIGH="+
		"&RTOE=13&CLIENT=web&FORMAT_OBJECT=Alignment&CMD=Get&PAGE=Proteins&_PGR=0&PID=28790&LAYOUT=OneWindow&FORMAT_BLOCK_ON_RESPAGE=None&STEP_NUMBER=1&EXPECT=10&HITLIST_SIZE=100&DESCRIPTIONS=100&ALIGNMENTS=50&AUTO_FORMAT=Off"
	manager.browse( url )
	manager.waiting(true)
	
	# 결과를 얻어온다.
	text = manager.gettext()
	print text
end

def finder(set, sequence)
	for aResult in set
		if ( aResult.sequence == sequence )
			return false
		end
	end
	return true
end

def testPurification(filename)
	bAlignments = false
	nEnterCount = 0
	hash = {}
	r = Regexp.new("([_0-9A-Z]+)[' ']+([0-9]+)[' ']+([A-Z]+)[' ']+([0-9]+)")
	f = File.open(filename)
	id = ""
	sequence = ""
	f.each do |line|
		#print line
		if ( line.strip == "Alignments" )
			bAlignments = true
		end
		if ( bAlignments == true )
			if ( r =~ line )
				id = r.match(line)[1]
				sequence = r.match(line)[3]
				if ( hash[ id ] == nil )
					result = PsiBlastResult.new( id, sequence )
					hash.store( id, result )
				else
					hash[id].addsequence( sequence )
				end
				nEnterCount = 0
				# print  r.match(line)[0]
				# 1_29407      1   MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY 60
				# print r.match(line)[1]
				# 1_29407
				# print r.match(line)[2]
				# 1
				# print r.match(line)[3]
				# MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
				# print r.match(line)[4]
				# 60
				
			end
			#print r.match(line)
			#print r.match(line)
			#print r.match(line)
		end
		if ( bAlignments == true && line.strip.empty? )
			nEnterCount = nEnterCount + 1
		end
		if ( nEnterCount >= 2 )
			bAlignments = false
		end
	end
	
	uniqueArray = []
	
	hash.each do |key,value|
		#print ">#{value.id}\n"
		#print "#{value.sequence}\n"
		if ( finder( uniqueArray, sequence ) )
			uniqueArray << value
		end
	end
	
	uniqueArray.each do |aResult|
		print ">#{aResult.id}\n"
		print "#{aResult.sequence}\n"
	end
end

if ( $*.size >= 1 )
	filename = $*[0]
	visible = $*[1]
	if visible == 'visible'
		visible = true
	else 
		visible = false
	end

	mode = $*[2]
	
	manager = PsiBlastQueryManager.new(visible)
	manager.openfile( filename )
	manager.getResult()
	manager.printout(mode)
	manager.finalize()
else
	#testPsiWeb()
	#testPsiQueryInput()
	#testPsiSubmit()
	#testPsiGetFormat()
	#testPsiGetResult()     # psi-raw.txt
	#testPurification("psi-raw.txt")    # clw-data.txt
	#testPurification("test.txt")    # clw-data.txt
end