{

@SuppressWarnings("null")

public void SpeciesRecognition(String Filename,String FilenameBioC,String StrainFilename,String FilterAntibody) throws IOException, XMLStreamException

{

/** Recognizing Species Names: SP */

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

{

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

PrefixTree PT_Genus = new PrefixTree();

HashMap<String, String> SPID_hash = new HashMap<String, String>();

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

HashMap<String, String> GenusNames = new HashMap<String, String>();

HashMap<String, String> Mention2ID_lc = new HashMap<String, String>();

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

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

{

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

/** Species recognition */

ArrayList<String> locations = GNormPlus.PT_Species.SearchMentionLocation(PassageContext,"Species"); /** PT_Species */

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

{

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

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

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

// For anti-serum filtering

String ForwardSTR="";

String BackwardSTR="";

if(start>21)

{

ForwardSTR = (PassageContext+"ZZZZZZZZZZZZZZZZZZZZZZZZZZZ").substring(start-21,last);

}

else

{

ForwardSTR = (PassageContext+"ZZZZZZZZZZZZZZZZZZZZZZZZZZZ").substring(0,last);

}

if(PassageContext.length()>last+21)

{

BackwardSTR = PassageContext.substring(start,last+21);

}

else

{

BackwardSTR = PassageContext.substring(start,PassageContext.length());

}

String mention = anno[2];

String id = anno[3];

String mention_tmp=mention.toLowerCase();

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

String antibody="";

if(ForwardSTR.toLowerCase().matches(".*(anti|antibody|antibodies|serum|polyclonal|monoclonal|igg)[\\W\\-\\_]+"+mention_tmp)) {antibody="(anti)";}//filtering : antibody

else if(BackwardSTR.toLowerCase().matches(mention_tmp+"[\\W\\-\\_]+(anti|antibody|antibodies|serum|polyclonal|monoclonal|igg).*")){antibody="(anti)";} //filtering : antibody

else if(BackwardSTR.toLowerCase().matches(mention_tmp+"[\\W\\-\\_]+[A-Za-z0-9]+[\\W\\-\\_]+(anti|antibody|antibodies|serum|polyclonal|monoclonal|igg).*")){antibody="(anti)";} //filtering : antibody

if(mention.matches(".*[\\(\\[\\{].*") && BackwardSTR.toLowerCase().matches(mention_tmp+"\\).*") )

{

last=last+1;

mention=mention+")";

}

if(BackwardSTR.toLowerCase().matches(mention_tmp+"[0-9].*")){} // filtered: Bee1p

else if((mention.matches(".*[;:,].*")) && mention.length()<=10){} // filtered : x, XXX

else if(mention.matches("to[\\W\\-\\_]+[0-9]+")){} // to 7

else if(mention.matches("[a-z][\\)\\]\\}].*") && (!mention.matches(".*[\\(\\[\\{].*")) && mention.length()<=10){} // s). Major

else if(mention.matches(".*[\\(\\[\\{].*") && (!mention.matches(".*[\\)\\]\\}].*")) && mention.length()<=10){} // s). Major

else if(!id.equals("NA"))

{

if(GNormPlus.BioCDocobj.Annotations.size()>i && GNormPlus.BioCDocobj.Annotations.get(i).size()>j)

{

if((!mention.matches("^[A-Za-z] [A-Za-z0-9]+$")) && (mention.length()>=3)) // invalid species: "a group/a GAL4/a strain"

{

if(FilterAntibody.equals("False") || (!antibody.equals("(anti)")))

{

String patt="^(.+?) [sS]train";

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(mention);

if(mtmp.find())

{

mention=mtmp.group(1);

last=last-7;

}

GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(start+"\t"+last+"\t"+mention+"\tSpecies\t"+id); //+antibody

String mentions_tmp=mention.toLowerCase();

mentions_tmp=mentions_tmp.replaceAll("[\\W\\-\\_]","");

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

GNormPlus.Filtering_hash.put(mentions_tmp,"");

Mention2ID_lc.put(mention.toLowerCase(), id); //+antibody

String mention_genus = "";

patt="^([A-Za-z]+) ";

ptmp = Pattern.compile(patt);

mtmp = ptmp.matcher(mention);

if(mtmp.find())

{

mention_genus=mtmp.group(1); // get genus

}

IDset.add(id);

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

{

TargetedLocation.add(j+"\t"+s);

}

String ids[]=id.split(";");

for(int x=0;x<ids.length;x++)

{

patt="^\\**([0-9]+)";

ptmp = Pattern.compile(patt);

mtmp = ptmp.matcher(ids[x]);

if(mtmp.find())

{

SPID_hash.put(mtmp.group(1), mention_genus);

}

}

}

}

}

}

}

/** Cell Line recognition */

locations = GNormPlus.PT_Cell.SearchMentionLocation(PassageContext,"Cell"); /** PT_Cell */

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

{

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

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

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

String mention = anno[2];

String id = anno[3];

if(GNormPlus.BioCDocobj.Annotations.size()>i && GNormPlus.BioCDocobj.Annotations.get(i).size()>j)

{

if(!TargetedLocation.contains(j+"\t"+start)) //already exists

{

int last40=0;

if(PassageContext.length()>=last+40)

{

last40=last+40;

}

else

{

last40=PassageContext.length();

}

// For anti-serum filtering

String ForwardSTR="";

String BackwardSTR="";

if(start>21)

{

ForwardSTR = PassageContext.substring(start-21,last);

}

else

{

ForwardSTR = PassageContext.substring(0,last);

}

if(PassageContext.length()>last+21)

{

BackwardSTR = PassageContext.substring(start,last+21);

}

else

{

BackwardSTR = PassageContext.substring(start,PassageContext.length());

}

String mention_tmp=mention.toLowerCase();

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

if(mention_tmp.matches(".*[\\[\\]\\(\\)\\{\\}].*")){}

else if(BackwardSTR.toLowerCase().matches(mention_tmp+"[0-9\\-\\_].*")){} // filtered: Bee1p

else if(ForwardSTR.toLowerCase().matches(".*[0-9\\-\\_]"+mention_tmp)){} // filtered: IL-22RA1

else

{

String patt="[\\W\\-]cell([\\- ]*line|)[s]*[\\W\\-]";

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(PassageContext.substring(last, last40).toLowerCase());

if(mtmp.find())

{

if(GNormPlus.taxid4gene.contains(id)) // for gene

{

id="*"+id;

}

GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(start+"\t"+last+"\t"+mention+"\tCell\t"+id);

String mentions_tmp=mention.toLowerCase();

mentions_tmp=mentions_tmp.replaceAll("[\\W\\-\\_]","");

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

GNormPlus.Filtering_hash.put(mentions_tmp,"");

IDset.add(id);

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

{

TargetedLocation.add(j+"\t"+s);

}

}

}

}

}

}

/** Genus names*/

for(String ID: SPID_hash.keySet())

{

if(GNormPlus.GenusID_hash.containsKey(ID))

{

GenusNames.put(ID,GNormPlus.GenusID_hash.get(ID));

}

if(SPID_hash.get(ID).length()>=7)

{

GenusNames.put(ID,SPID_hash.get(ID));

}

}

}

GenusNames.put("3702", "arabidopsis");

GenusNames.put("4932", "saccharomyces");

GenusNames.put("562", "escherichia");

GenusNames.put("7227", "drosophila");

GenusNames.put("8355", "xenopus");

PT_Genus.Hash2Tree(GenusNames);

/** Genus recognition */

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

{

if(GNormPlus.BioCDocobj.PassageContexts.size()>i &&

GNormPlus.BioCDocobj.PassageContexts.get(i).size()>j &&

GNormPlus.BioCDocobj.Annotations.size()>i &&

GNormPlus.BioCDocobj.Annotations.get(i).size()>j

)

{

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

ArrayList<String> locations_Genus = PT_Genus.SearchMentionLocation(PassageContext,"Genus"); /** PT_Genus*/

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

{

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

String start= anno[0];

String last= anno[1];

String mention = anno[2];

String id = anno[3];

if(!TargetedLocation.contains(j+"\t"+start)) //already exists

{

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

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(id);

if(mtmp.find())

{

id = mtmp.group(1);

}

if(GNormPlus.taxid4gene.contains(id)) // for gene

{

id="*"+id;

}

GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(start+"\t"+last+"\t"+mention+"\tGenus\t"+id);

String mentions_tmp=mention.toLowerCase();

mentions_tmp=mentions_tmp.replaceAll("[\\W\\-\\_]","");

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

GNormPlus.Filtering_hash.put(mentions_tmp,"");

IDset.add(id);

for(int s=Integer.parseInt(start);s<Integer.parseInt(last);s++)

{

TargetedLocation.add(j+"\t"+s);

}

}

}

}

}

/** Strain Tree */

PrefixTree PT_Strain = new PrefixTree();

HashMap<String, String> StrainID_hash = new HashMap<String, String>();

BufferedReader br = new BufferedReader(new FileReader(StrainFilename));

String line="";

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

{

String l[]=line.split("\t");

String ancestor = l[0];

String tax_id = l[1];

String tax_names = l[2];

if(SPID_hash.containsKey(ancestor))

{

StrainID_hash.put(tax_id, tax_names); // tax id -> strain

}

else if(SPID_hash.containsKey(tax_id))

{

StrainID_hash.put(tax_id, tax_names); // tax id -> strain

}

}

br.close();

HashMap<String, String> StrainNames = new HashMap<String, String>();

for(String ID: StrainID_hash.keySet())

{

StrainNames.put(ID,StrainID_hash.get(ID));

}

PT_Strain.Hash2Tree(StrainNames);

/** Strain recognition */

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

{

if(GNormPlus.BioCDocobj.PassageContexts.size()>i &&

GNormPlus.BioCDocobj.PassageContexts.get(i).size()>j &&

GNormPlus.BioCDocobj.Annotations.size()>i &&

GNormPlus.BioCDocobj.Annotations.get(i).size()>j

)

{

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

ArrayList<String> locations_Strain = PT_Strain.SearchMentionLocation(PassageContext,"Strain"); /** PT_Strain*/

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

{

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

String start= anno[0];

String last= anno[1];

String mention = anno[2];

String id = anno[3];

if(!TargetedLocation.contains(j+"\t"+start)) //already exists

{

if((!mention.matches(".*[;,\\{\\}\\(\\)\\[\\]].*")) && !mention.matches("[a-z]{1,4} [0-9]{1,3}"))

{

if(GNormPlus.taxid4gene.contains(id)) // for gene

{

id="*"+id;

}

GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(start+"\t"+last+"\t"+mention+"\tStrain\t"+id);

String mentions_tmp=mention.toLowerCase();

mentions_tmp=mentions_tmp.replaceAll("[\\W\\-\\_]","");

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

GNormPlus.Filtering_hash.put(mentions_tmp,"");

IDset.add(id);

for(int s=Integer.parseInt(start);s<Integer.parseInt(last);s++)

{

TargetedLocation.add(j+"\t"+s);

}

}

}

}

}

}

HashMap<String, String> OtherNames = new HashMap<String, String>();

for(String men : Mention2ID_lc.keySet())

{

String men_id= Mention2ID_lc.get(men);

if(GNormPlus.PmidLF2Abb_lc_hash.containsKey(Pmid+"\t"+men))

{

String Abb = GNormPlus.PmidLF2Abb_lc_hash.get(Pmid+"\t"+men);

// Abbreviation

if(OtherNames.containsKey(men_id))

{

OtherNames.put(men_id, OtherNames.get(men_id)+"|"+Abb);

}

else

{

OtherNames.put(men_id,Abb);

}

}

String men_nospace=men.replaceAll(" ", "");

// no space

if(OtherNames.containsKey(men_id))

{

OtherNames.put(men_id, OtherNames.get(men_id)+"|"+men_nospace);

}

else

{

OtherNames.put(men_id,men_nospace);

}

}

PrefixTree PT_Others = new PrefixTree();

PT_Others.Hash2Tree(OtherNames);

/**

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

{

if(GNormPlus.BioCDocobj.PassageContexts.size()>i &&

GNormPlus.BioCDocobj.PassageContexts.get(i).size()>j &&

GNormPlus.BioCDocobj.Annotations.size()>i &&

GNormPlus.BioCDocobj.Annotations.get(i).size()>j

)

{

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

ArrayList<String> locations_Abb = PT_Others.SearchMentionLocation(PassageContext,"Species"); /** PT_Abb*/

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

{

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

String start= anno[0];

String last= anno[1];

String mention = anno[2];

String id = anno[3];

if(!TargetedLocation.contains(j+"\t"+start)) //already exists

{

if(GNormPlus.taxid4gene.contains(id)) // for gene

{

id="*"+id;

}

GNormPlus.BioCDocobj.Annotations.get(i).get(j).add(start+"\t"+last+"\t"+mention+"\tSpecies\t"+id);

String mentions_tmp=mention.toLowerCase();

mentions_tmp=mentions_tmp.replaceAll("[\\W\\-\\_]","");

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

GNormPlus.Filtering_hash.put(mentions_tmp,"");

Mention2ID_lc.put(mention.toLowerCase(), id);

IDset.add(id);

for(int s=Integer.parseInt(start);s<Integer.parseInt(last);s++)

{

TargetedLocation.add(j+"\t"+s);

}

}

}

}

}

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

{

if(GNormPlus.BioCDocobj.PassageContexts.size()>i && GNormPlus.BioCDocobj.PassageContexts.get(i).size()>j && GNormPlus.BioCDocobj.Annotations.size()>i && GNormPlus.BioCDocobj.Annotations.get(i).size()>j)

{

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

for (int a = 0; a < GNormPlus.BioCDocobj.Annotations.get(i).get(j).size(); a++) /** Annotations : a */

{

String SpAnno[]=GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(a).split("\t");

String start= SpAnno[0];

String last= SpAnno[1];

String mention = SpAnno[2];

String type = SpAnno[3];

if(type.matches("Gene|FamilyName|GENERIF"))

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(a,start+"\t"+last+"\t"+mention+"\t"+type);

}

else if(type.matches("Species|Genus|Strain|Cell") && SpAnno.length==5)

{

//System.out.println(GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(a));

/** Abbreviation solution */

if(GNormPlus.PmidAbb2LF_lc_hash.containsKey(Pmid+"\t"+mention.toLowerCase()) && Mention2ID_lc.containsKey(GNormPlus.PmidAbb2LF_lc_hash.containsKey(Pmid+"\t"+mention.toLowerCase())))

{

String LF_lc=GNormPlus.PmidAbb2LF_lc_hash.get(Pmid+"\t"+mention.toLowerCase());

if(Mention2ID_lc.containsKey(LF_lc))

{

String LF_ID=Mention2ID_lc.get(LF_lc);

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(a, start+"\t"+last+"\t"+mention+"\t"+type+"\t"+LF_ID);

String mentions_tmp=mention.toLowerCase();

mentions_tmp=mentions_tmp.replaceAll("[\\W\\-\\_]","");

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

GNormPlus.Filtering_hash.put(mentions_tmp,"");

}

}

else if (SpAnno.length>4)

{

String id = SpAnno[4];

String id_split[]=id.split(";");

if(id_split.length>=2)

{

/** Smallest set of tax ids */

boolean found=false;

for(int x=0;x<IDset.size();x++)

{

String id_tmp= IDset.get(x);

for(int y=0;y<id_split.length;y++) // if any other id is a component of the target id

{

if(id_split[y].equals(id_tmp))

{

found=true;

}

}

if(found == true)

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(a, start+"\t"+last+"\t"+mention+"\t"+type+"\t"+id_tmp);

String mentions_tmp=mention.toLowerCase();

mentions_tmp=mentions_tmp.replaceAll("[\\W\\-\\_]","");

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

GNormPlus.Filtering_hash.put(mentions_tmp,"");

x=1000000;

}

}

/** smallest tax id number */

if(found == false)

{

int min=10000000;

String min_id="";

for(int y=0;y<id_split.length;y++) // if any other id is a component of the target id

{

String id_tmp = id_split[y];

String patt="^\\**([0-9]+)";

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(id_tmp);

if(mtmp.find())

{

id_tmp = mtmp.group(1);

}

if(y==0)

{

min_id=id_split[y];

min=Integer.parseInt(id_tmp);

}

else if(Integer.parseInt(id_tmp)<min)

{

min=Integer.parseInt(id_tmp);

min_id=id_tmp;

}

}

if(GNormPlus.taxid4gene.contains(min_id)) // for gene

{

min_id="*"+min_id;

}

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(a,start+"\t"+last+"\t"+mention+"\tSpecies\t"+min_id);

String mentions_tmp=mention.toLowerCase();

mentions_tmp=mentions_tmp.replaceAll("[\\W\\-\\_]","");

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

GNormPlus.Filtering_hash.put(mentions_tmp,"");

}

}

}

}

else //disease, and other concepts

{

remove_anno.add(a);

}

}

Collections.sort(remove_anno);

for (int counter = remove_anno.size()-1; counter >= 0 ; counter--)

{

int ai=remove_anno.get(counter);

//System.out.println("\n"+ai+"\t"+GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(ai));

GNormPlus.BioCDocobj.Annotations.get(i).get(j).remove(ai);

}

}

}

}

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

}

public void SpeciesAssignment(String Filename,String FilenameBioC) throws IOException, XMLStreamException

{

GNormPlus.BioCDocobj.Annotations = new ArrayList();

GNormPlus.BioCDocobj.BioCReaderWithAnnotation(Filename);

BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.US);

for (int i = 0; i < GNormPlus.BioCDocobj.Annotations.size(); i++) /** PMIDs : i */

{

HashMap<String, String> PrefixIDTarget_hash = new HashMap<String, String>();

PrefixIDTarget_hash.put("9606", "h");

PrefixIDTarget_hash.put("10090", "m");

PrefixIDTarget_hash.put("10116", "r");

PrefixIDTarget_hash.put("4932", "y");

PrefixIDTarget_hash.put("7227", "d");

PrefixIDTarget_hash.put("7955", "z|zf|Zf|dr|Dr");

PrefixIDTarget_hash.put("3702", "at|At");

HashMap<String, Double> SP2Num_hash = new HashMap<String, Double>();

for (int j = 0; j < GNormPlus.BioCDocobj.Annotations.get(i).size(); j++) /** Paragraphs : j */

{

for (int k = 0; k < GNormPlus.BioCDocobj.Annotations.get(i).get(j).size(); k++) // Annotation : k

{

String anno[] = GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k).split("\t");

if(anno.length==5) //Species

{

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

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(anno[4]);

if(mtmp.find())

{

String id = mtmp.group(1);

if(!PrefixIDTarget_hash.containsKey(id))

{

PrefixIDTarget_hash.put(id,GNormPlus.PrefixID_hash.get(id)); // taxid -> prefix

}

if(j == 0)//title

{

if(SP2Num_hash.containsKey(id))

{

SP2Num_hash.put(id, SP2Num_hash.get(id)+2);

}

else

{

if(GNormPlus.TaxFreq_hash.containsKey(id))

{

SP2Num_hash.put(id, GNormPlus.TaxFreq_hash.get(id)+2);

}

else

{

SP2Num_hash.put(id, 2.0);

}

}

// Virus -> Human (not to double weight human to virus)

/*if(GNormPlus.SP_Virus2Human_hash.containsKey(id))

}

else

{

if(SP2Num_hash.containsKey(id))

{

SP2Num_hash.put(id, SP2Num_hash.get(id)+1);

}

else

{

if(GNormPlus.TaxFreq_hash.containsKey(id))

{

SP2Num_hash.put(id, 1 + GNormPlus.TaxFreq_hash.get(id));

}

else

{

SP2Num_hash.put(id, 1.0);

}

}

// Virus -> Human

/*if(GNormPlus.SP_Virus2Human_hash.containsKey(id))

}

}

}

}

}

String MajorSP="9606";

double MaxSP=0;

for(String tid : SP2Num_hash.keySet())

{

if(SP2Num_hash.get(tid)>MaxSP)

{

MajorSP=tid;

MaxSP=SP2Num_hash.get(tid);

}

}

for (int j = 0; j < GNormPlus.BioCDocobj.PassageContexts.get(i).size(); j++) /** Paragraphs : j */

{

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

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

iterator.setText(PassageContext);

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

int Sent_start = iterator.first();

for (int Sent_last = iterator.next(); Sent_last != BreakIterator.DONE; Sent_start = Sent_last, Sent_last = iterator.next())

{

Sentence_offsets.add(Sent_start);

}

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

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

if(GNormPlus.BioCDocobj.Annotations.get(i).size()>j)

{

for (int k = 0; k < GNormPlus.BioCDocobj.Annotations.get(i).get(j).size(); k++) // Annotation : k

{

String anno[] = GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k).split("\t");

if(anno.length==5) //Species

{

Annotations_Species.add(GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k));

}

else //Gene : if(anno.length==3)

{

//String mention = PassageContext.substring(Integer.parseInt(anno[0]), Integer.parseInt(anno[1]));

Annotations_Gene_hash.put(k,GNormPlus.BioCDocobj.Annotations.get(i).get(j).get(k)); // k -> Gene Annotation

}

}

//Gene --> Species Inference (PMID:28777492)

HashMap<String,HashMap<Integer,String>> mention2Location2Species_hash = new HashMap<String,HashMap<Integer,String>>();

HashMap<Integer,String> Location2Species_hash = new HashMap<Integer,String>();

for (int k : Annotations_Gene_hash.keySet()) // k is the index of GNormPlus.BioCDocobj.Annotations.get(i).get(j)

{

boolean SPfound = false;

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

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

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

String G_mentions = anno[2];

/**

//Find the target sentence

int Target_Sentence=0;

if(SPfound == false) // 1. left : Closed to start of the gene mention

{

for(int s=0;s<Sentence_offsets.size();s++)

{

int Sentence_last=1000000;

if(s<Sentence_offsets.size()-1)

{

Sentence_last=Sentence_offsets.get(s+1);

}

if(G_Start<Sentence_last)

{

Target_Sentence=s;

break;

}

}

}

int Sentence_Start = Sentence_offsets.get(Target_Sentence);

int Sentence_Last = 1000000;

if(Sentence_offsets.size() > Target_Sentence+1){ Sentence_Last = Sentence_offsets.get(Target_Sentence+1); }

if(SPfound == false) // 1. left : Closed to start of the gene mention

{

int closet_Sp_Start=0;

for(int sp=0;sp<Annotations_Species.size();sp++) // Find the closet species

{

String AnnoSp[]=Annotations_Species.get(sp).split("\t");

int Sp_Start = Integer.parseInt(AnnoSp[0]);

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

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(AnnoSp[4]);

if(mtmp.find())

{

String taxid = mtmp.group(1);

Location2Species_hash.put(Sp_Start,taxid);

if(Sp_Start <= G_Start && Sp_Start >= Sentence_Start && Sp_Start >closet_Sp_Start)

{

closet_Sp_Start=Sp_Start;

Location2Species_hash.put(Integer.parseInt(anno[0]), taxid);

if(mention2Location2Species_hash.containsKey(G_mentions.toLowerCase()))

{

mention2Location2Species_hash.get(G_mentions.toLowerCase()).put(Integer.parseInt(anno[0]), taxid);

}

else

{

mention2Location2Species_hash.put(G_mentions.toLowerCase(),Location2Species_hash);

}

SPfound=true;

}

}

}

}

if(SPfound == false) // 2. right : Closed to last of the gene mention

{

int closet_Sp_Last=1000000;

for(int sp=0;sp<Annotations_Species.size();sp++) // Find the closet species

{

String AnnoSp[]=Annotations_Species.get(sp).split("\t");

int Sp_Last = Integer.parseInt(AnnoSp[1]);

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

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(AnnoSp[4]);

if(mtmp.find())

{

String taxid = mtmp.group(1);

if(Sp_Last >= G_Last && Sp_Last <= Sentence_Last && Sp_Last < closet_Sp_Last)

{

closet_Sp_Last=Sp_Last;

Location2Species_hash.put(Integer.parseInt(anno[0]), taxid);

if(mention2Location2Species_hash.containsKey(G_mentions.toLowerCase()))

{

mention2Location2Species_hash.get(G_mentions.toLowerCase()).put(Integer.parseInt(anno[0]), taxid);

}

else

{

mention2Location2Species_hash.put(G_mentions.toLowerCase(),Location2Species_hash);

}

SPfound=true;

}

}

}

}

}

for (int k : Annotations_Gene_hash.keySet()) // k is the index of GNormPlus.BioCDocobj.Annotations.get(i).get(j)

{

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

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

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

String G_mentions = anno[2];

String G_type = anno[3];

String G_mention_list[]=G_mentions.split("\\|");

String G_mention=G_mention_list[0]; // only use the first term to detect species ; should be updated after SimConcept

/** 1. prefix */

boolean SPfound = false;

for(String taxid: PrefixIDTarget_hash.keySet())

{

if(GNormPlus.GeneWithoutSPPrefix_hash.containsKey(G_mention.toLowerCase()))

{

//special case, and no need for prefix - SA

}

else

{

Pattern ptmp = Pattern.compile("^("+PrefixIDTarget_hash.get(taxid)+")([A-Z].*)$");

Matcher mtmp = ptmp.matcher(G_mention);

if(mtmp.find())

{

String MentionWoPrefix=mtmp.group(2);

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+anno[2]+"|"+MentionWoPrefix+"\t"+anno[3]+"\tPrefix:"+taxid);

SPfound=true;

break;

}

}

}

/**

//Find the target sentence

int Target_Sentence=0;

if(SPfound == false) // 1. left : Closed to start of the gene mention

{

for(int s=0;s<Sentence_offsets.size();s++)

{

int Sentence_last=1000000;

if(s<Sentence_offsets.size()-1)

{

Sentence_last=Sentence_offsets.get(s+1);

}

if(G_Start<Sentence_last)

{

Target_Sentence=s;

break;

}

}

}

int Sentence_Start = Sentence_offsets.get(Target_Sentence);

int Sentence_Last = 1000000;

if(Sentence_offsets.size() > Target_Sentence+1){ Sentence_Last = Sentence_offsets.get(Target_Sentence+1); }

if(SPfound == false) // 1. left : Closed to start of the gene mention

{

int closet_Sp_Start=0;

for(int sp=0;sp<Annotations_Species.size();sp++) // Find the closet species

{

String AnnoSp[]=Annotations_Species.get(sp).split("\t");

int Sp_Start = Integer.parseInt(AnnoSp[0]);

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

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(AnnoSp[4]);

if(mtmp.find())

{

String taxid = mtmp.group(1);

if(Sp_Start <= G_Start && Sp_Start >= Sentence_Start && Sp_Start >closet_Sp_Start)

{

closet_Sp_Start=Sp_Start;

if(GNormPlus.SP_Virus2Human_hash.containsKey(taxid))

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tLeft:"+taxid+"&9606");

}

else

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tLeft:"+taxid);

}

SPfound=true;

}

}

}

}

if(SPfound == false) // 2. right : Closed to last of the gene mention

{

int closet_Sp_Last=1000000;

for(int sp=0;sp<Annotations_Species.size();sp++) // Find the closet species

{

String AnnoSp[]=Annotations_Species.get(sp).split("\t");

int Sp_Last = Integer.parseInt(AnnoSp[1]);

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

Pattern ptmp = Pattern.compile(patt);

Matcher mtmp = ptmp.matcher(AnnoSp[4]);

if(mtmp.find())

{

String taxid = mtmp.group(1);

if(Sp_Last >= G_Last && Sp_Last <= Sentence_Last && Sp_Last < closet_Sp_Last)

{

closet_Sp_Last=Sp_Last;

if(GNormPlus.SP_Virus2Human_hash.containsKey(taxid))

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tRight:"+taxid+"&9606");

}

else

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tRight:"+taxid);

}

SPfound=true;

}

}

}

}

/** 3. Focus species */

if(SPfound == false) // 2. right : Closed to last of the gene mention

{

// 1. only the mentions appeared earlier are inferred

//

if(mention2Location2Species_hash.containsKey(G_mentions.toLowerCase()))

{

int closed_loca=0;

for (int loca_start : mention2Location2Species_hash.get(G_mentions.toLowerCase()).keySet())

{

if(loca_start<G_Start)

{

if(loca_start>closed_loca)

{

closed_loca=loca_start;

}

}

}

if(closed_loca>0)

{

if(GNormPlus.SP_Virus2Human_hash.containsKey(Location2Species_hash.get(closed_loca)))

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+Location2Species_hash.get(closed_loca)+"&9606");

}

else

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+Location2Species_hash.get(closed_loca));

}

}

else

{

if(GNormPlus.SP_Virus2Human_hash.containsKey(MajorSP))

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+MajorSP+"&9606");

}

else

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+MajorSP);

}

}

}

else

{

if(GNormPlus.SP_Virus2Human_hash.containsKey(MajorSP))

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+MajorSP+"&9606");

}

else

{

GNormPlus.BioCDocobj.Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+MajorSP);

}

}

}

}

}

}

}

GNormPlus.BioCDocobj.BioCOutput(Filename,FilenameBioC,GNormPlus.BioCDocobj.Annotations,false,true);

}