{

/*

public void Ab3P(String Filename,String FilenameAbb,String TrainTest) throws XMLStreamException,IOException

{

/** Abbreviation*/

//BioC -> Abb input

String line="";

BufferedWriter FileAbb = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(FilenameAbb), "UTF-8"));

for (int i = 0; i < GNormPlus.BioCDocobj.PMIDs.size(); i++)

{

String Pmid = GNormPlus.BioCDocobj.PMIDs.get(i);

String Context="";

for (int j = 0; j < GNormPlus.BioCDocobj.PassageNames.get(i).size(); j++)

{

String PassageContext=GNormPlus.BioCDocobj.PassageContexts.get(i).get(j);

if(PassageContext.matches(".*\\([^\\(\\)]+,[^\\(\\)]+\\).*"))

{

PassageContext=PassageContext.replaceAll("\\([^\\(\\)]+,[^\\(\\)]+\\)", "");

}

if(PassageContext.contains("\\("))

{

Context = Context+PassageContext+" ";

}

}

FileAbb.write(Pmid+"\n"+Context+"\n\n");

}

FileAbb.close();

//Abb

File f = new File(FilenameAbb+".out");

BufferedWriter fr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(f), "UTF-8"));

Runtime runtime = Runtime.getRuntime();

String cmd ="./Ab3P "+FilenameAbb+".Abb "+FilenameAbb+".out";

String OS=System.getProperty("os.name").toLowerCase();

if(OS.contains("windows"))

{

cmd ="java -jar bioadi.jar "+FilenameAbb;

}

else //if(OS.contains("nux")||OS.contains("nix"))

{

cmd ="./Ab3P "+FilenameAbb+" "+FilenameAbb+".out";

//cmd ="java -jar bioadi.jar "+FilenameAbb+" > "+FilenameAbb+".out";

}

Process process = runtime.exec(cmd);

InputStream is = process.getInputStream();

InputStreamReader isr = new InputStreamReader(is, "UTF-8");

BufferedReader br = new BufferedReader(isr);

line="";

while ( (line = br.readLine()) != null)

{

fr.write(line);

fr.newLine();

fr.flush();

}

is.close();

isr.close();

br.close();

fr.close();

//Abb output -> Hash

BufferedReader inputfile = new BufferedReader(new InputStreamReader(new FileInputStream(FilenameAbb+".out"), "UTF-8"));

line="";

String pmid="";

while ((line = inputfile.readLine()) != null)

{

String patt="^ (.+)\\|(.+)\\|([0-9\\.]+)$";

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(line);

if(line.matches("^[0-9]+$"))

{

pmid=line;

}

if(mtmp.find())

{

String SF = mtmp.group(1);

String LF = mtmp.group(2);

double weight= Double.parseDouble(mtmp.group(3));

GNormPlus.Pmid2Abb_hash.put(pmid+"\t"+SF, "Abb:SF");

GNormPlus.Pmid2Abb_hash.put(pmid+"\t"+LF, "Abb:LF");

GNormPlus.PmidLF2Abb_lc_hash.put(pmid+"\t"+LF.toLowerCase(), SF.toLowerCase());

GNormPlus.PmidAbb2LF_lc_hash.put(pmid+"\t"+SF.toLowerCase(), LF.toLowerCase());

GNormPlus.PmidAbb2LF_hash.put(pmid+"\t"+SF, LF);

if(weight >= 0.9)

{

GNormPlus.PmidLF2Abb_hash.put(pmid+"\t"+LF, SF);

}

}

}

inputfile.close();

}

public void LoadInputFile(String Filename,String FilenameAbb,String TrainTest) throws XMLStreamException,IOException

{

/** Read BioC file */

//if(TrainTest.equals("Train"))

//{

GNormPlus.BioCDocobj.BioCReaderWithAnnotation(Filename);

//}

//else

//{

// GNormPlus.BioCDocobj.BioCReader(Filename);

//}

/** Abbreviation*/

//BioC -> Abb input

String line="";

BufferedWriter FileAbb = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(FilenameAbb), "UTF-8"));

for (int i = 0; i < GNormPlus.BioCDocobj.PMIDs.size(); i++)

{

String Pmid = GNormPlus.BioCDocobj.PMIDs.get(i);

String Context="Text:";

for (int j = 0; j < GNormPlus.BioCDocobj.PassageNames.get(i).size(); j++)

{

String PassageContext=GNormPlus.BioCDocobj.PassageContexts.get(i).get(j);

if(PassageContext.matches(".*\\([^\\(\\)]+,[^\\(\\)]+\\).*"))

{

PassageContext=PassageContext.replaceAll("\\([^\\(\\)]+,[^\\(\\)]+\\)", "");

}

if(PassageContext.contains("("))

{

Context = Context+PassageContext+" ";

}

}

FileAbb.write(Pmid+"\n"+Context+"\n\n");

}

FileAbb.close();

//Abb

File f = new File(FilenameAbb+".out");

BufferedWriter fr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(f), "UTF-8"));

Runtime runtime = Runtime.getRuntime();

String cmd ="./Ab3P "+FilenameAbb+".Abb "+FilenameAbb+".out";

String OS=System.getProperty("os.name").toLowerCase();

if(OS.contains("windows"))

{

cmd ="java -jar bioadi.jar "+FilenameAbb;

}

else //if(OS.contains("nux")||OS.contains("nix"))

{

cmd ="./Ab3P "+FilenameAbb+" "+FilenameAbb+".out";

//cmd ="java -jar bioadi.jar "+FilenameAbb+" > "+FilenameAbb+".out";

}

Process process = runtime.exec(cmd);

InputStream is = process.getInputStream();

InputStreamReader isr = new InputStreamReader(is, "UTF-8");

BufferedReader br = new BufferedReader(isr);

line="";

while ( (line = br.readLine()) != null)

{

fr.write(line);

fr.newLine();

fr.flush();

}

is.close();

isr.close();

br.close();

fr.close();

//Abb output -> Hash

BufferedReader inputfile = new BufferedReader(new InputStreamReader(new FileInputStream(FilenameAbb+".out"), "UTF-8"));

line="";

String pmid="";

while ((line = inputfile.readLine()) != null)

{

String patt="^ (.+)\\|(.+)\\|([0-9\\.]+)$";

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(line);

if(line.matches("^[0-9]+$"))

{

pmid=line;

}

if(mtmp.find())

{

String SF = mtmp.group(1);

String LF = mtmp.group(2);

double weight= Double.parseDouble(mtmp.group(3));

GNormPlus.Pmid2Abb_hash.put(pmid+"\t"+SF, "Abb:SF");

GNormPlus.Pmid2Abb_hash.put(pmid+"\t"+LF, "Abb:LF");

GNormPlus.PmidLF2Abb_lc_hash.put(pmid+"\t"+LF.toLowerCase(), SF.toLowerCase());

GNormPlus.PmidAbb2LF_lc_hash.put(pmid+"\t"+SF.toLowerCase(), LF.toLowerCase());

GNormPlus.PmidAbb2LF_hash.put(pmid+"\t"+SF, LF);

if(weight >= 0.9)

{

GNormPlus.PmidLF2Abb_hash.put(pmid+"\t"+LF, SF);

}

}

}

inputfile.close();

}

/*

public void FeatureExtraction(String FilenameData,String FilenameLoca,String TrainTest) throws XMLStreamException

{

try

{

/** output files */

BufferedWriter FileLocation = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(FilenameLoca), "UTF-8")); // .location

BufferedWriter FileData = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(FilenameData), "UTF-8")); // .data

//NLP modules

SnowballStemmer stemmer = new englishStemmer();

/** PMIDs : i */

for (int i = 0; i < GNormPlus.BioCDocobj.PMIDs.size(); i++)

{

String Pmid = GNormPlus.BioCDocobj.PMIDs.get(i);

/** Paragraphs : j */

for (int j = 0; j < GNormPlus.BioCDocobj.PassageNames.get(i).size(); j++)

{

String PassageName= GNormPlus.BioCDocobj.PassageNames.get(i).get(j); // Passage name

int PassageOffset = GNormPlus.BioCDocobj.PassageOffsets.get(i).get(j); // Passage offset

String PassageContext = GNormPlus.BioCDocobj.PassageContexts.get(i).get(j); // Passage context

ArrayList<String> Annotation = GNormPlus.BioCDocobj.Annotations.get(i).get(j); // Annotation

HashMap<Integer, String> CTDGene_hash = new HashMap<Integer, String>();

HashMap<Integer, String> FamilyName_hash = new HashMap<Integer, String>();

HashMap<Integer, String> character_hash = new HashMap<Integer, String>();

HashMap<Integer, String> Abbreviation_hash = new HashMap<Integer, String>();

String PassageContext_tmp=" "+PassageContext+" ";

/** Abbreviation */

HashMap<Integer, String> Abb_sortebylength = new HashMap<Integer, String>();

ArrayList<Integer> length_list = new ArrayList<Integer>();

int countn=0;

for (Object key : GNormPlus.Pmid2Abb_hash.keySet())

{

String pmid2abb[]=key.toString().split("\t");

if(Pmid.equals(pmid2abb[0]))

{

Abb_sortebylength.put(pmid2abb[1].length()*100+countn, pmid2abb[1]);

length_list.add(pmid2abb[1].length()*100+countn);

countn++;

}

}

Collections.sort(length_list);

for (int l=length_list.size()-1;l>=0;l--)

{

String AbbLF = Abb_sortebylength.get(length_list.get(l));

AbbLF=AbbLF.replaceAll("([^A-Za-z0-9@ ])", "\\\\$1");

AbbLF=AbbLF.replaceAll(" ", "\\[ \\]\\+");

Pattern ptmp = Pattern.compile("^(.*[^A-Za-z0-9]+)("+AbbLF+")([^A-Za-z0-9]+.*)$");

Matcher mtmp = ptmp.matcher(PassageContext_tmp);

while(mtmp.find())

{

String str1=mtmp.group(1);

String str2=mtmp.group(2);

String str3=mtmp.group(3);

for(int m=str1.length();m<=(str1.length()+str2.length());m++)

{

Abbreviation_hash.put((m-1),GNormPlus.Pmid2Abb_hash.get(Pmid+"\t"+Abb_sortebylength.get(length_list.get(l))));

}

String men="";

for(int m=0;m<str2.length();m++){men=men+"@";}

PassageContext_tmp=str1+men+str3;

mtmp = ptmp.matcher(PassageContext_tmp);

}

}

/** PT_CTDGene */

ArrayList<String> locations = GNormPlus.PT_CTDGene.SearchMentionLocation(PassageContext,"CTDGene");

for (int k = 0 ; k < locations.size() ; k++)

{

String anno[]=locations.get(k).split("\t");

int start= Integer.parseInt(anno[0]) + PassageOffset;

int last= Integer.parseInt(anno[1]) + PassageOffset;

String mention = anno[2];

String id = anno[3];

CTDGene_hash.put(start,"CTDGene_B");

CTDGene_hash.put(last,"CTDGene_E");

for(int s=start+1;s<last;s++)

{

CTDGene_hash.put(s,"CTDGene_I");

}

}

/** FamilyName */

ArrayList<String> locations_Fname = GNormPlus.PT_FamilyName.SearchMentionLocation(PassageContext,"FamilyName");

for (int k = 0 ; k < locations_Fname.size() ; k++)

{

String anno[]=locations_Fname.get(k).split("\t");

int start= Integer.parseInt(anno[0]) + PassageOffset;

int last= Integer.parseInt(anno[1]) + PassageOffset;

String mention = anno[2];

String id = anno[3];

if(!CTDGene_hash.containsKey(start))

{

FamilyName_hash.put(start,"famplex_B");

FamilyName_hash.put(last,"famplex_E");

for(int s=start+1;s<last;s++)

{

FamilyName_hash.put(s,"famplex_I");

}

}

}

/** Annotations : k

for (int k = 0; k < Annotation.size() ; k++) // k : Annotations

{

String anno[]=Annotation.get(k).split("\t");

int start= Integer.parseInt(anno[0]);

int last= Integer.parseInt(anno[1]);

String type = anno[3];

character_hash.put(start,type+"_B");

character_hash.put(last,type+"_E");

for(int s=start+1;s<last;s++)

{

character_hash.put(s,type+"_I");

}

}

String PassageContext_rev=PassageContext;

PassageContext_rev = PassageContext_rev.replaceAll("([A-Z][A-Z])([A-Z][0-9][0-9]+[A-Z][\\W\\-\\_])", "$1 $2"); //PTENK289E

PassageContext_rev = PassageContext_rev.replaceAll("([0-9])([A-Za-z])", "$1 $2");

PassageContext_rev = PassageContext_rev.replaceAll("([A-Za-z])([0-9])", "$1 $2");

//PassageContext_rev = PassageContext_rev.replaceAll("([A-Z])([a-z])", "$1 $2");

//PassageContext_rev = PassageContext_rev.replaceAll("([a-z])([A-Z])", "$1 $2");

PassageContext_rev = PassageContext_rev.replaceAll("([\\W])", " $1 ");

PassageContext_rev = PassageContext_rev.replaceAll("[ ]+", " ");

PassageContext_tmp = PassageContext;

int Offset=0;

String tokens[]=PassageContext_rev.split(" ");

for(int p=0;p<tokens.length;p++)

{

String WSB="WSB:NoGap"; //no gap to backward

String WSF="WSF:NoGap"; //no gap to forward

while(PassageContext_tmp.substring(0,1).equals(" "))

{

PassageContext_tmp=PassageContext_tmp.substring(1);

Offset++;

WSB="WSB:Gap";

}

if(PassageContext_tmp.length()>tokens[p].length() && PassageContext_tmp.substring(tokens[p].length(),tokens[p].length()+1).equals(" "))

{

WSF="WSF:Gap";

}

if(p==0)

{

WSB="WSB:1st";

}

else if(p==tokens.length-1)

{

WSF="WSF:last";

}

if(PassageContext_tmp.substring(0,tokens[p].length()).equals(tokens[p]))

{

if(tokens[p].length()>0)

{

/*

int start=Offset;

int last=Offset+tokens[p].length();

String State="";

if(!character_hash.containsKey(start) || !character_hash.containsKey(last)){}

else if(character_hash.get(start).matches(".*B$"))

{

State=character_hash.get(start);

}

else if(character_hash.get(last).matches(".*E$"))

{

State=character_hash.get(last);

}

else if(character_hash.get(start).matches(".*I$"))

{

State=character_hash.get(start);

}

if((!tokens[p].equals("\t")))

{

FileLocation.write(Pmid+"\t"+PassageName+"\t"+j+"\t"+tokens[p]+"\t"+(Offset+1)+"\t"+(Offset+tokens[p].length())+"\t"+State+"\n");

}

/*

//Abbreviation

String Abb_State="__nil__";

if(!Abbreviation_hash.containsKey(start) || !Abbreviation_hash.containsKey(last)){Abb_State="__nil__";}

else if(Abbreviation_hash.containsKey(start))

{

Abb_State=Abbreviation_hash.get(start);

}

//CTDGene

start=PassageOffset+Offset;

last=PassageOffset+Offset+tokens[p].length();

String CTDGene_State="__nil__";

if(!CTDGene_hash.containsKey(start) || !CTDGene_hash.containsKey(last)){CTDGene_State="__nil__";}

else if(CTDGene_hash.get(start).matches(".*B$"))

{

CTDGene_State=CTDGene_hash.get(start);

}

else if(CTDGene_hash.get(last).matches(".*E$"))

{

CTDGene_State=CTDGene_hash.get(last);

}

else if(CTDGene_hash.get(start).matches(".*I$"))

{

CTDGene_State=CTDGene_hash.get(start);

}

//FamilyName

if(CTDGene_State.equals("__nil__"))

{

start=PassageOffset+Offset;

last=PassageOffset+Offset+tokens[p].length();

if(!FamilyName_hash.containsKey(start) || !FamilyName_hash.containsKey(last)){}

else if(FamilyName_hash.get(start).matches(".*B$"))

{

CTDGene_State=FamilyName_hash.get(start);

}

else if(FamilyName_hash.get(last).matches(".*E$"))

{

CTDGene_State=FamilyName_hash.get(last);

}

else if(FamilyName_hash.get(start).matches(".*I$"))

{

CTDGene_State=FamilyName_hash.get(start);

}

}

//stemming

stemmer.setCurrent(tokens[p].toLowerCase());

stemmer.stem();

String stem=stemmer.getCurrent();

//Number of Numbers [0-9]

String Num_num="";

String tmp=tokens[p];

tmp=tmp.replaceAll("[^0-9]","");

if(tmp.length()>3){Num_num="N:4+";}else{Num_num="N:"+ tmp.length();}

//Number of Uppercase [A-Z]

String Num_Uc="";

tmp=tokens[p];

tmp=tmp.replaceAll("[^A-Z]","");

if(tmp.length()>3){Num_Uc="U:4+";}else{Num_Uc="U:"+ tmp.length();}

//Number of Lowercase [a-z]

String Num_lc="";

tmp=tokens[p];

tmp=tmp.replaceAll("[^a-z]","");

if(tmp.length()>3){Num_lc="L:4+";}else{Num_lc="L:"+ tmp.length();}

//Number of ALL char

String Num_All="";

if(tokens[p].length()>3){Num_All="A:4+";}else{Num_All="A:"+ tokens[p].length();}

//specific character (;:,.->+_)

String SpecificC="__nil__";

if(tokens[p].equals(";") || tokens[p].equals(":") || tokens[p].equals(",") || tokens[p].equals(".") || tokens[p].equals("-") || tokens[p].equals(">") || tokens[p].equals("+") || tokens[p].equals("_"))

{

SpecificC="-SpecificC1-";

}

else if(tokens[p].equals("(") || tokens[p].equals(")"))

{

SpecificC="-SpecificC2-";

}

else if(tokens[p].equals("{") || tokens[p].equals("}"))

{

SpecificC="-SpecificC3-";

}

else if(tokens[p].equals("[") || tokens[p].equals("]"))

{

SpecificC="-SpecificC4-";

}

else if(tokens[p].equals("\\") || tokens[p].equals("/"))

{

SpecificC="-SpecificC5-";

}

//Chemical Prefix/Suffix

String ChemPreSuf="__nil__";

if(tokens[p].matches(".*(yl|ylidyne|oyl|sulfonyl)")){ChemPreSuf="-CHEMinlineSuffix-";}

else if(tokens[p].matches("(meth|eth|prop|tetracos).*")){ChemPreSuf="-CHEMalkaneStem-";}

else if(tokens[p].matches("(di|tri|tetra).*")){ChemPreSuf="-CHEMsimpleMultiplier-";}

else if(tokens[p].matches("(benzen|pyridin|toluen).*")){ChemPreSuf="-CHEMtrivialRing-";}

else if(tokens[p].matches(".*(one|ol|carboxylic|amide|ate|acid|ium|ylium|ide|uide|iran|olan|inan|pyrid|acrid|amid|keten|formazan|fydrazin)(s|)")){ChemPreSuf="-CHEMsuffix-";}

//Mention Type

String MentionType="__nil__";

/*

if(tokens[p].matches("(ytochrome|cytochrome)")){MentionType="-Type_cytochrome-";}

else if(tokens[p].matches(".*target") ){MentionType="-Type_target-";}

else if(tokens[p].matches(".*(irradiation|hybrid|fusion|experiment|gst|est|gap|antigen)") ){MentionType="-Type_ExperimentNoun-";}

else if(tokens[p].matches(".*(disease|disorder|dystrophy|deficiency|syndrome|dysgenesis|cancer|injury|neoplasm|diabetes|diabete)") ){MentionType="-Type_Disease-";}

else if(tokens[p].matches(".*(motif|domain|omain|binding|site|region|sequence|frameshift|finger|box).*") ){MentionType="-Type_DomainMotif-";}

else if(tokens[p].equals("-") && (p<tokens.length-1 && tokens[p+1].matches(".*(motif|domain|omain|binding|site|region|sequence|frameshift|finger|box).*")) ){MentionType="-Type_DomainMotif-";}

else if(tokens[p].matches("[rmc]") && (p<tokens.length-1 && (tokens[p+1].equals("DNA") || tokens[p+1].equals("RNA")) ) ){MentionType="-Type_DomainMotif-";}

else if(tokens[p].matches(".*(famil|complex|cluster|proteins|genes|factors|transporter|proteinase|membrane|ligand|enzyme|channels|tors$|ase$|ases$)") ){MentionType="-Type_Family-";}

else if(tokens[p].toLowerCase().matches("^marker") ){MentionType="-Type_Marker-";}

else if(tokens[p].equals(".*cell.*") || (p<tokens.length-1 && tokens[p+1].equals("cell") && tokens[p].matches("^(T|B|monocytic|cancer|tumor|myeloma|epithelial|crypt)$") ) ){MentionType="-Type_Cell-";}

else if(tokens[p].equals(".*chromosome.*") ){MentionType="-Type_Chromosome-";}

else if(tokens[p].matches("[pq]") && ( (p<tokens.length-1 && tokens[p+1].matches("^[0-9]+$")) || (p>0 && tokens[p-1].matches("^[0-9]+$")) ) ){MentionType="-Type_ChromosomeStrain-";}

else if(tokens[p].matches(".*(related|regulated|associated|correlated|reactive).*")){MentionType="-Type_relation-";}

else if(tokens[p].toLowerCase().matches(".*(polymorphism|mutation|deletion|insertion|duplication|genotype|genotypes).*") ){MentionType="-Type_VariationTerms-";}

else if(tokens[p].matches(".*(oxidase|transferase|transferases|kinase|kinese|subunit|unit|receptor|adrenoceptor|transporter|regulator|transcription|antigen|protein|gene|factor|member|molecule|channel|deaminase|spectrin).*") ){MentionType="-Type_suffix-";}

else if(tokens[p].matches("[\\(\\-\\_]") && (p<tokens.length-1 && tokens[p+1].toLowerCase().matches(".*(alpha|beta|gamma|delta|theta|kappa|zeta|sigma|omega|i|ii|iii|iv|v|vi|[abcdefgyr])")) ){MentionType="-Type_strain-";}

else if(tokens[p].matches("(alpha|beta|gamma|delta|theta|kappa|zeta|sigma|omega|i|ii|iii|iv|v|vi|[abcdefgyr])") ){MentionType="-Type_strain-";}

//Protein symbols

String ProteinSym="__nil__";

if(tokens[p].matches(".*(glutamine|glutamic|leucine|valine|isoleucine|lysine|alanine|glycine|aspartate|methionine|threonine|histidine|aspartic|asparticacid|arginine|asparagine|tryptophan|proline|phenylalanine|cysteine|serine|glutamate|tyrosine|stop|frameshift).*")){ProteinSym="-ProteinSymFull-";}

else if(tokens[p].matches("(cys|ile|ser|gln|met|asn|pro|lys|asp|thr|phe|ala|gly|his|leu|arg|trp|val|glu|tyr|fs|fsx)")){ProteinSym="-ProteinSymTri-";}

else if(tokens[p].matches("[CISQMNPKDTFAGHLRWVEYX]")){ProteinSym="-ProteinSymChar-";}

//prefix

String prefix="";

tmp=tokens[p];

if(tmp.length()>=1){ prefix=tmp.substring(0, 1);}else{prefix="__nil__";}

if(tmp.length()>=2){ prefix=prefix+" "+tmp.substring(0, 2);}else{prefix=prefix+" __nil__";}

if(tmp.length()>=3){ prefix=prefix+" "+tmp.substring(0, 3);}else{prefix=prefix+" __nil__";}

if(tmp.length()>=4){ prefix=prefix+" "+tmp.substring(0, 4);}else{prefix=prefix+" __nil__";}

if(tmp.length()>=5){ prefix=prefix+" "+tmp.substring(0, 5);}else{prefix=prefix+" __nil__";}

//suffix

String suffix="";

tmp=tokens[p];

if(tmp.length()>=1){ suffix=tmp.substring(tmp.length()-1, tmp.length());}else{suffix="__nil__";}

if(tmp.length()>=2){ suffix=suffix+" "+tmp.substring(tmp.length()-2, tmp.length());}else{suffix=suffix+" __nil__";}

if(tmp.length()>=3){ suffix=suffix+" "+tmp.substring(tmp.length()-3, tmp.length());}else{suffix=suffix+" __nil__";}

if(tmp.length()>=4){ suffix=suffix+" "+tmp.substring(tmp.length()-4, tmp.length());}else{suffix=suffix+" __nil__";}

if(tmp.length()>=5){ suffix=suffix+" "+tmp.substring(tmp.length()-5, tmp.length());}else{suffix=suffix+" __nil__";}

if(State.equals(""))

{

State="O";

}

if((!tokens[p].equals("\t")))

{

if(TrainTest.equals("Train"))

{

FileData.write(tokens[p]+" "+stem+" "+WSB+" "+WSF+" "+Num_num+" "+Num_Uc+" "+Num_lc+" "+Num_All+" "+SpecificC+" "+ChemPreSuf+" "+MentionType+" "+ProteinSym+" "+prefix+" "+suffix+" "+CTDGene_State+" "+Abb_State+" "+State+"\n");

}

else

{

FileData.write(tokens[p]+" "+stem+" "+WSB+" "+WSF+" "+Num_num+" "+Num_Uc+" "+Num_lc+" "+Num_All+" "+SpecificC+" "+ChemPreSuf+" "+MentionType+" "+ProteinSym+" "+prefix+" "+suffix+" "+CTDGene_State+" "+Abb_State+"\n");

}

}

PassageContext_tmp=PassageContext_tmp.substring(tokens[p].length()); // remove the token for the context

Offset=Offset+tokens[p].length();

}

}

}

if(tokens.length>0)

{

FileLocation.write("\n");

FileData.write("\n");

}

}

}

FileLocation.close();

FileData.close();

}

catch(IOException e1){ System.out.println("[MR]: Input file is not exist.");}

}

/*

public void CRF_test(String model, String FilenameData, String FilenameOutput) throws IOException

{

File f = new File(FilenameOutput);

BufferedWriter fr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(f), "UTF-8"));

Runtime runtime = Runtime.getRuntime();

String OS=System.getProperty("os.name").toLowerCase();

String cmd="./CRF/crf_test -m "+model+" -o "+FilenameOutput+" "+FilenameData;

if(OS.contains("windows"))

{

cmd ="CRF/crf_test -m "+model+" -o "+FilenameOutput+" "+FilenameData;

}

else //if(OS.contains("nux")||OS.contains("nix"))

{

cmd ="./CRF/crf_test -m "+model+" -o "+FilenameOutput+" "+FilenameData;

}

try {

Process process = runtime.exec(cmd);

InputStream is = process.getInputStream();

InputStreamReader isr = new InputStreamReader(is, "UTF-8");

BufferedReader br = new BufferedReader(isr);

String line="";

while ( (line = br.readLine()) != null)

{

fr.write(line);

fr.newLine();

fr.flush();

}

is.close();

isr.close();

br.close();

fr.close();

}

catch (IOException e) {

System.out.println(e);

runtime.exit(0);

}

}

public void CRF_test(String model,String FilenameData,String FilenameOutput,String top3) throws IOException

{

File f = new File(FilenameOutput);

BufferedWriter fr = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(f), "UTF-8"));

Runtime runtime = Runtime.getRuntime();

String OS=System.getProperty("os.name").toLowerCase();

String cmd="./CRF/crf_test -n 3 -m "+model+" -o "+FilenameOutput+" "+FilenameData;

if(OS.contains("windows"))

{

cmd ="CRF/crf_test -n 3 -m "+model+" -o "+FilenameOutput+" "+FilenameData;

}

else //if(OS.contains("nux")||OS.contains("nix"))

{

cmd ="./CRF/crf_test -n 3 -m "+model+" -o "+FilenameOutput+" "+FilenameData;

}

try {

Process process = runtime.exec(cmd);

InputStream is = process.getInputStream();

InputStreamReader isr = new InputStreamReader(is, "UTF-8");

BufferedReader br = new BufferedReader(isr);

String line="";

while ( (line = br.readLine()) != null)

{

fr.write(line);

fr.newLine();

fr.flush();

}

is.close();

isr.close();

br.close();

fr.close();

}

catch (IOException e) {

System.out.println(e);

runtime.exit(0);

}

}

/*

public void CRF_learn(String model, String FilenameData) throws IOException

{

Runtime runtime = Runtime.getRuntime();

Process process = null;

String line = null;

InputStream is = null;

InputStreamReader isr = null;

BufferedReader br = null;

String OS=System.getProperty("os.name").toLowerCase();

String cmd="./CRF/crf_learn -f 3 -c 4.0 CRF/template_UB "+FilenameData+" "+model;

if(OS.contains("windows"))

{

cmd ="CRF/crf_learn -f 3 -c 4.0 CRF/template_UB "+FilenameData+" "+model;

}

else //if(OS.contains("nux")||OS.contains("nix"))

{

cmd ="./CRF/crf_learn -f 3 -c 4.0 CRF/template_UB "+FilenameData+" "+model;

}

try {

process = runtime.exec(cmd);

is = process.getInputStream();

isr = new InputStreamReader(is, "UTF-8");

br = new BufferedReader(isr);

while ( (line = br.readLine()) != null)

{

System.out.println(line);

System.out.flush();

}

is.close();

isr.close();

br.close();

}

catch (IOException e) {

System.out.println(e);

runtime.exit(0);

}

}

public void ReadCRFresult(String Filename,String FilenameLoca,String FilenameOutput,String FilenameBioC) throws XMLStreamException, IOException

{

/** load CRF output */

ArrayList<String> outputArr = new ArrayList<String>();

BufferedReader inputfile = new BufferedReader(new InputStreamReader(new FileInputStream(FilenameOutput), "UTF-8"));

String line;

while ((line = inputfile.readLine()) != null)

{

outputArr.add(line);

}

inputfile.close();

/** load location */

ArrayList<String> locationArr = new ArrayList<String>();

inputfile = new BufferedReader(new InputStreamReader(new FileInputStream(FilenameLoca), "UTF-8"));

while ((line = inputfile.readLine()) != null)

{

locationArr.add(line);

}

inputfile.close();

/** output -> mentions */

String pmid_last="";

String paragraph_num_last="";

String pmid="";

String paragraph="";

String paragraph_num="";

Pattern pat_B = Pattern.compile("((FamilyName|DomainMotif|Gene)_[B])$");

Pattern pat_IE = Pattern.compile("((FamilyName|DomainMotif|Gene)_[IE])$");

ArrayList<ArrayList<String>> AnnotationInPMID = new ArrayList(); // array of Annotations in the PMIDs

ArrayList<String> AnnotationInPassage= new ArrayList<String>(); // array of Annotations in the Passage

GNormPlus.BioCDocobj.Annotations = new ArrayList();

int countPMID=0;

int countPassage=0;

/** outputArr */

for(int i=0;i<outputArr.size();i++)

{

String outputsRow[]=outputArr.get(i).split("\\t");

String locationRow[]=locationArr.get(i).split("\\t");

int start=100000;

int last=0;

String MentionType="";

if(locationRow.length>3)

{

pmid=locationRow[0];

paragraph=locationRow[1];

paragraph_num=locationRow[2];

}

if( (!paragraph_num_last.equals("")) && (!paragraph_num.equals(paragraph_num_last)) )

{

AnnotationInPMID.add(AnnotationInPassage);

AnnotationInPassage = new ArrayList<String>();

countPassage++;

}

if( (!pmid_last.equals("")) && (!pmid.equals(pmid_last)) )

{

GNormPlus.BioCDocobj.Annotations.add(AnnotationInPMID);

AnnotationInPMID = new ArrayList();

countPMID++;

countPassage=0;

}

boolean F = false; //Flag of Finding

if(locationRow.length>2)

{

Matcher mat = pat_B.matcher(outputsRow[outputsRow.length-1]); // last column : Status

while(mat.find() && locationRow.length==6)

{

MentionType=mat.group(2);

pmid=locationRow[0];

paragraph_num=locationRow[2];

int start_tmp=Integer.parseInt(locationRow[4])-1;

int last_tmp=Integer.parseInt(locationRow[5]);

if(start_tmp<start){start=start_tmp;}

if(last_tmp>last){last=last_tmp;}

i++;

F = true;

if(locationArr.get(i).length()>0)

{

outputsRow=outputArr.get(i).split("\\t");

locationRow=locationArr.get(i).split("\\t");

mat = pat_IE.matcher(outputsRow[outputsRow.length-1]);

}

else

{

break;

}

}

}

if(F == true)

{

String PassageContext = GNormPlus.BioCDocobj.PassageContexts.get(countPMID).get(countPassage); // Passage context

String Mention = PassageContext.substring(start, last);

String Mention_nospace = Mention.replaceAll("[\\W\\-\\_]", "");

if(Mention.toLowerCase().matches("(figure|tables|fig|tab|exp\\. [0-9]+).*")){}

else if(Mention.matches("[A-Z][A-Z]s")){}

else if(Mention.matches(".*\\|.*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\;\\,\\'\\/\\\\].*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\(].*") && !Mention.matches(".*[\\)].*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\[].*") && !Mention.matches(".*[\\]].*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\)].*") && !Mention.matches(".*[\\(].*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\]].*") && !Mention.matches(".*[\\[].*")){}

else

{

AnnotationInPassage.add(start+"\t"+last+"\t"+Mention+"\t"+MentionType);

}

i--;

}

paragraph_num_last=paragraph_num;

pmid_last=pmid;

}// outputArr1

AnnotationInPMID.add(AnnotationInPassage);

GNormPlus.BioCDocobj.Annotations.add(AnnotationInPMID);

//GNormPlus.BioCDocobj.BioCOutput(Filename,FilenameBioC,GNormPlus.BioCDocobj.Annotations,false,false); //save in BioC file

}

public void ReadCRFresult(String Filename,String FilenameLoca,String FilenameOutput,String FilenameBioC,double threshold,double threshold_GeneType) throws XMLStreamException, IOException

{

/** load CRF output */

ArrayList<String> outputArr1 = new ArrayList<String>();

ArrayList<String> outputArr2 = new ArrayList<String>();

ArrayList<String> outputArr3 = new ArrayList<String>();

ArrayList<String> outputArr1_score = new ArrayList<String>();

ArrayList<String> outputArr2_score = new ArrayList<String>();

ArrayList<String> outputArr3_score = new ArrayList<String>();

BufferedReader inputfile = new BufferedReader(new InputStreamReader(new FileInputStream(FilenameOutput), "UTF-8"));

String line;

int rank=0;

String score="";

Pattern pat_Rank = Pattern.compile("^# ([0-2]) ([0-9\\.]+)$");

while ((line = inputfile.readLine()) != null)

{

Matcher mat = pat_Rank.matcher(line); // last column : Status

if(mat.find())

{

rank = Integer.parseInt(mat.group(1));

score = mat.group(2);

}

else if(rank == 0)

{

outputArr1.add(line);

outputArr1_score.add(score);

}

else if(rank == 1)

{

outputArr2.add(line);

outputArr2_score.add(score);

}

else if(rank == 2)

{

outputArr3.add(line);

outputArr3_score.add(score);

}

}

inputfile.close();

/** load location */

ArrayList<String> locationArr = new ArrayList<String>();

inputfile = new BufferedReader(new InputStreamReader(new FileInputStream(FilenameLoca), "UTF-8"));

while ((line = inputfile.readLine()) != null)

{

locationArr.add(line);

}

inputfile.close();

/** output -> mentions */

String pmid_last="";

String paragraph_num_last="";

String pmid="";

String paragraph="";

String paragraph_num="";

Pattern pat_B = Pattern.compile("((FamilyName|DomainMotif|Gene)_[B])$");

Pattern pat_IE = Pattern.compile("((FamilyName|DomainMotif|Gene)_[IE])$");

ArrayList<ArrayList<String>> AnnotationInPMID = new ArrayList(); // array of Annotations in the PMIDs

ArrayList<String> AnnotationInPassage= new ArrayList<String>(); // array of Annotations in the Passage

GNormPlus.BioCDocobj.Annotations = new ArrayList();

int countPMID=0;

int countPassage=0;

/** outputArr1 */

int size_Arr=outputArr1.size();

if(locationArr.size()<outputArr1.size())

{

size_Arr=locationArr.size();

}

for(int i=0;i<size_Arr;i++)

{

String outputsRow[]=outputArr1.get(i).split("\\t");

String locationRow[]=locationArr.get(i).split("\\t");

int start=100000;

int last=0;

String MentionType="";

if(locationRow.length>3)

{

pmid=locationRow[0];

paragraph=locationRow[1];

paragraph_num=locationRow[2];

}

boolean F = false; //Flag of Finding

if(outputsRow.length>=1)

{

Matcher mat = pat_B.matcher(outputsRow[outputsRow.length-1]); // last column : Status

while(mat.find() && locationRow.length==6)

{

MentionType=mat.group(2);

pmid=locationRow[0];

int start_tmp=Integer.parseInt(locationRow[4])-1;

int last_tmp=Integer.parseInt(locationRow[5]);

if(start_tmp<start){start=start_tmp;}

if(last_tmp>last){last=last_tmp;}

i++;

outputsRow=outputArr1.get(i).split("\\t");

locationRow=locationArr.get(i).split("\\t");

mat = pat_IE.matcher(outputsRow[outputsRow.length-1]);

F = true;

}

}

if( (!paragraph_num_last.equals("")) && (!paragraph_num.equals(paragraph_num_last)) ) // paragraph change

{

AnnotationInPMID.add(AnnotationInPassage);

AnnotationInPassage = new ArrayList<String>();

countPassage++;

}

if( !pmid.equals(pmid_last) && paragraph_num.equals("0") && paragraph_num_last.equals("0") ) // pmid change (special case : the article only has one paragrpah)

{

AnnotationInPMID.add(AnnotationInPassage);

AnnotationInPassage = new ArrayList<String>();

GNormPlus.BioCDocobj.Annotations.add(AnnotationInPMID);

AnnotationInPMID = new ArrayList();

countPMID++;

countPassage=0;

}

else if( (!pmid_last.equals("")) && (!pmid.equals(pmid_last)) ) // pmid change

{

GNormPlus.BioCDocobj.Annotations.add(AnnotationInPMID);

AnnotationInPMID = new ArrayList();

countPMID++;

countPassage=0;

}

if(F == true)

{

if(GNormPlus.BioCDocobj.PassageContexts.size()>countPMID && GNormPlus.BioCDocobj.PassageContexts.get(countPMID).size()>countPassage && GNormPlus.BioCDocobj.PassageContexts.get(countPMID).get(countPassage).length()>=last && (last-start)<1000)

{

String PassageContext = GNormPlus.BioCDocobj.PassageContexts.get(countPMID).get(countPassage); // Passage context

String Mention = PassageContext.substring(start, last);

String Mention_nospace = Mention.replaceAll("[\\W\\-\\_]", "");

if(Mention.toLowerCase().matches("(figure|tables|fig|tab|exp\\. [0-9]+).*")){}

else if(Mention.matches("[A-Z][A-Z]s")){}

else if(Mention.matches(".*\\|.*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\;\\,\\'\\/\\\\].*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\(].*") && !Mention.matches(".*[\\)].*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\[].*") && !Mention.matches(".*[\\]].*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\)].*") && !Mention.matches(".*[\\(].*")){}

else if(Mention_nospace.length()<=3 && Mention.matches(".*[0-9].*") && Mention.matches(".*[\\]].*") && !Mention.matches(".*[\\[].*")){}

else if((GNormPlus.Abb2Longformtok_hash.containsKey(Mention_nospace.toLowerCase())) && (PassageContext.toLowerCase().matches(".*[\\W\\-\\-]("+GNormPlus.Abb2Longformtok_hash.get(Mention_nospace.toLowerCase())+")[\\W\\-\\-].*")))

{

//System.out.println(Mention_nospace.toLowerCase()+"\t"+GNormPlus.Abb2Longformtok_hash.get(Mention_nospace.toLowerCase()));

}

else

{