GNormPluslib.SR Maven / Gradle / Ivy
/**
* Project: GNormPlus
* Function: Species recognition and Species assignment
*/
package GNormPluslib;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.text.BreakIterator;
import java.time.LocalDate;
import java.time.ZoneId;
import javax.xml.stream.XMLStreamException;
import org.tartarus.snowball.SnowballStemmer;
import org.tartarus.snowball.ext.englishStemmer;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
public class SR
{
private GNPProcessingData data;
public SR(GNPProcessingData data) {
this.data = data;
}
public void SpeciesRecognition(String Filename, String FilenameBioC, String StrainFilename, String FilterAntibody) throws IOException, XMLStreamException
{
/** Recognizing Species Names: SP */
for (int i = 0; i < data.getBioCDocobj().PMIDs.size(); i++) /** PMIDs : i */
{
String Pmid = data.getBioCDocobj().PMIDs.get(i);
PrefixTree PT_Genus = new PrefixTree();
HashMap SPID_hash = new HashMap();
ArrayList TargetedLocation = new ArrayList();
HashMap GenusNames = new HashMap();
HashMap Mention2ID_lc = new HashMap();
ArrayList IDset = new ArrayList();
for (int j = 0; j < data.getBioCDocobj().PassageNames.get(i).size(); j++) /** Paragraphs : j */
{
String PassageContext = data.getBioCDocobj().PassageContexts.get(i).get(j); // Passage context
/** Species recognition */
ArrayList 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="";
try {
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());
}
} catch (Exception e) {
throw new InconsistentDataException("Exception in document " + Pmid + " in paragraph with offset " + data.getBioCDocobj().PassageOffsets.get(i).get(j) + " and length " + PassageContext.length() + " beginning with " + PassageContext.substring(0, Math.min(PassageContext.length(), 80)), e);
}
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(data.getBioCDocobj().Annotations.size()>i && data.getBioCDocobj().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;
}
data.getBioCDocobj().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");
data.getFiltering_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 PassageContext.length()) {
// Erik Faessler: We had offset issues with texts that contain non-ASCII characters
continue;
}
String mention = anno[2];
String id = anno[3];
if(data.getBioCDocobj().Annotations.size()>i && data.getBioCDocobj().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;
}
data.getBioCDocobj().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");
data.getFiltering_hash().put(mentions_tmp,"");
IDset.add(id);
for(int s=start;s=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 < data.getBioCDocobj().PassageNames.get(i).size(); j++) /** Paragraphs : j */
{
if(data.getBioCDocobj().PassageContexts.size()>i &&
data.getBioCDocobj().PassageContexts.get(i).size()>j &&
data.getBioCDocobj().Annotations.size()>i &&
data.getBioCDocobj().Annotations.get(i).size()>j
)
{
String PassageContext = data.getBioCDocobj().PassageContexts.get(i).get(j);
ArrayList 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;
}
data.getBioCDocobj().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");
data.getFiltering_hash().put(mentions_tmp,"");
IDset.add(id);
for(int s=Integer.parseInt(start);s StrainID_hash = new HashMap();
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 StrainNames = new HashMap();
for(String ID: StrainID_hash.keySet())
{
StrainNames.put(ID,StrainID_hash.get(ID));
}
PT_Strain.Hash2Tree(StrainNames);
/** Strain recognition */
for (int j = 0; j < data.getBioCDocobj().PassageNames.get(i).size(); j++) /** Paragraphs : j */
{
if(data.getBioCDocobj().PassageContexts.size()>i &&
data.getBioCDocobj().PassageContexts.get(i).size()>j &&
data.getBioCDocobj().Annotations.size()>i &&
data.getBioCDocobj().Annotations.get(i).size()>j
)
{
String PassageContext = data.getBioCDocobj().PassageContexts.get(i).get(j); // Passage context
ArrayList 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;
}
data.getBioCDocobj().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");
data.getFiltering_hash().put(mentions_tmp,"");
IDset.add(id);
for(int s=Integer.parseInt(start);s OtherNames = new HashMap();
for(String men : Mention2ID_lc.keySet())
{
String men_id= Mention2ID_lc.get(men);
if(data.getPmidLF2Abb_lc_hash().containsKey(Pmid+"\t"+men))
{
String Abb = data.getPmidLF2Abb_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);
/**
*
* Others:
* 1) Abbreviation
* 2) no space
*
* */
for (int j = 0; j < data.getBioCDocobj().PassageNames.get(i).size(); j++) /** Paragraphs : j */
{
if(data.getBioCDocobj().PassageContexts.size()>i &&
data.getBioCDocobj().PassageContexts.get(i).size()>j &&
data.getBioCDocobj().Annotations.size()>i &&
data.getBioCDocobj().Annotations.get(i).size()>j
)
{
String PassageContext = data.getBioCDocobj().PassageContexts.get(i).get(j); // Passage context
ArrayList 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;
}
data.getBioCDocobj().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");
data.getFiltering_hash().put(mentions_tmp,"");
Mention2ID_lc.put(mention.toLowerCase(), id);
IDset.add(id);
for(int s=Integer.parseInt(start);si && data.getBioCDocobj().PassageContexts.get(i).size()>j && data.getBioCDocobj().Annotations.size()>i && data.getBioCDocobj().Annotations.get(i).size()>j)
{
for (int a = 0; a < data.getBioCDocobj().Annotations.get(i).get(j).size(); a++) /** Annotations : a */
{
String SpAnno[]=data.getBioCDocobj().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];
/** Abbreviation solution */
if(data.getPmidAbb2LF_lc_hash().containsKey(Pmid+"\t"+mention.toLowerCase()) && Mention2ID_lc.containsKey(data.getPmidAbb2LF_lc_hash().containsKey(Pmid+"\t"+mention.toLowerCase())))
{
String LF_lc=data.getPmidAbb2LF_lc_hash().get(Pmid+"\t"+mention.toLowerCase());
if(Mention2ID_lc.containsKey(LF_lc))
{
String LF_ID=Mention2ID_lc.get(LF_lc);
data.getBioCDocobj().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");
data.getFiltering_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 PrefixIDTarget_hash = new HashMap();
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 SP2Num_hash = new HashMap();
for (int j = 0; j < data.getBioCDocobj().Annotations.get(i).size(); j++) /** Paragraphs : j */
{
for (int k = 0; k < data.getBioCDocobj().Annotations.get(i).get(j).size(); k++) // Annotation : k
{
String anno[] = data.getBioCDocobj().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))
{
if(SP2Num_hash.containsKey("9606"))
{
SP2Num_hash.put("9606", SP2Num_hash.get("9606")+2);
}
else
{
SP2Num_hash.put("9606", 2 + GNormPlus.TaxFreq_hash.get("9606")+1);
}
}*/
}
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))
{
if(SP2Num_hash.containsKey("9606"))
{
SP2Num_hash.put("9606", SP2Num_hash.get("9606")+1);
}
else
{
SP2Num_hash.put("9606", GNormPlus.TaxFreq_hash.get("9606")+1);
}
}*/
}
}
}
}
}
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 < data.getBioCDocobj().PassageContexts.get(i).size(); j++) /** Paragraphs : j */
{
String PassageContext = data.getBioCDocobj().PassageContexts.get(i).get(j); // Passage context
//int PassageOffset = data.getBioCDocobj().PassageOffsets.get(i).get(j); // Passage offset
iterator.setText(PassageContext);
ArrayList Sentence_offsets = new ArrayList();
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 Annotations_Gene_hash = new HashMap();
ArrayList Annotations_Species = new ArrayList();
if(data.getBioCDocobj().Annotations.get(i).size()>j)
{
for (int k = 0; k < data.getBioCDocobj().Annotations.get(i).get(j).size(); k++) // Annotation : k
{
String anno[] = data.getBioCDocobj().Annotations.get(i).get(j).get(k).split("\t");
if(anno.length==5) //Species
{
Annotations_Species.add(data.getBioCDocobj().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,data.getBioCDocobj().Annotations.get(i).get(j).get(k)); // k -> Gene Annotation
}
}
//Gene --> Species Inference (PMID:28777492)
HashMap> mention2Location2Species_hash = new HashMap>();
HashMap Location2Species_hash = new HashMap();
for (int k : Annotations_Gene_hash.keySet()) // k is the index of data.getBioCDocobj().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];
/**
* 2. Co-occurring word
* boundary :
* Sentence Start: Sentence_offsets.get(Target_Sentence)
* Sentence Last: Sentence_offsets.get(Target_Sentence+1)
*/
//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 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= 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= 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 data.getBioCDocobj().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("\\|");
if (G_mention_list.length == 0) {
InconsistentDataException e = new InconsistentDataException("There is no gene mention but at least one was expected in document with ID " + data.getBioCDocobj().PMIDs.get(i) + " in paragraph with offset " + data.getBioCDocobj().PassageOffsets.get(i).get(j) + " and length " + PassageContext.length() + " beginning with " + PassageContext.substring(0, Math.min(PassageContext.length(), 80)));
e.setDocId(data.getBioCDocobj().PMIDs.get(i));
throw e;
}
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);
data.getBioCDocobj().Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+anno[2]+"|"+MentionWoPrefix+"\t"+anno[3]+"\tPrefix:"+taxid);
SPfound=true;
break;
}
}
}
/**
* 2. Co-occurring word
* boundary :
* Sentence Start: Sentence_offsets.get(Target_Sentence)
* Sentence Last: Sentence_offsets.get(Target_Sentence+1)
*/
//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 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= Sentence_Start && Sp_Start >closet_Sp_Start)
{
closet_Sp_Start=Sp_Start;
if(GNormPlus.SP_Virus2Human_hash.containsKey(taxid))
{
data.getBioCDocobj().Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tLeft:"+taxid+"&9606");
}
else
{
data.getBioCDocobj().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= G_Last && Sp_Last <= Sentence_Last && Sp_Last < closet_Sp_Last)
{
closet_Sp_Last=Sp_Last;
if(GNormPlus.SP_Virus2Human_hash.containsKey(taxid))
{
data.getBioCDocobj().Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tRight:"+taxid+"&9606");
}
else
{
data.getBioCDocobj().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_startclosed_loca)
{
closed_loca=loca_start;
}
}
}
if(closed_loca>0)
{
if(GNormPlus.SP_Virus2Human_hash.containsKey(Location2Species_hash.get(closed_loca)))
{
data.getBioCDocobj().Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+Location2Species_hash.get(closed_loca)+"&9606");
}
else
{
data.getBioCDocobj().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))
{
data.getBioCDocobj().Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+MajorSP+"&9606");
}
else
{
data.getBioCDocobj().Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+MajorSP);
}
}
}
else
{
if(GNormPlus.SP_Virus2Human_hash.containsKey(MajorSP))
{
data.getBioCDocobj().Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+MajorSP+"&9606");
}
else
{
data.getBioCDocobj().Annotations.get(i).get(j).set(k, Annotations_Gene_hash.get(k)+"\tFocus:"+MajorSP);
}
}
}
}
}
}
}
data.getBioCDocobj().BioCOutput(Filename,FilenameBioC,data.getBioCDocobj().Annotations,false,true);
}
public void SpeciesAssignment(String Filename,String FilenameBioC,String FocusSpecies) throws IOException, XMLStreamException
{
for (int i = 0; i < data.getBioCDocobj().Annotations.size(); i++) /** PMIDs : i */
{
for (int j = 0; j < data.getBioCDocobj().Annotations.get(i).size(); j++) /** Paragraphs : j */
{
for (int k = 0; k < data.getBioCDocobj().Annotations.get(i).get(j).size(); k++) // Annotation : k
{
String anno[] = data.getBioCDocobj().Annotations.get(i).get(j).get(k).split("\t");
if(anno.length==5) //Species
{
String id=anno[4].replaceAll("\\*", "");
data.getBioCDocobj().Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+anno[2]+"\t"+anno[3]+"\t"+id);
}
else //Gene : if(anno.length==3)
{
/** 1. prefix */
boolean SPfound = false;
if(GNormPlus.GeneWithoutSPPrefix_hash.containsKey(anno[2].toLowerCase()))
{
//special case, and no need for prefix - SA
}
else
{
Pattern ptmp = Pattern.compile("^("+GNormPlus.PrefixID_hash.get(FocusSpecies)+")([A-Z].*)$");
Matcher mtmp = ptmp.matcher(anno[2]);
if(mtmp.find())
{
String MentionWoPrefix=mtmp.group(2);
data.getBioCDocobj().Annotations.get(i).get(j).set(k, anno[0]+"\t"+anno[1]+"\t"+anno[2]+"|"+MentionWoPrefix+"\t"+anno[3]+"\tPrefix:"+FocusSpecies);
SPfound=true;
}
}
if(SPfound == false)
{
data.getBioCDocobj().Annotations.get(i).get(j).set(k, data.getBioCDocobj().Annotations.get(i).get(j).get(k)+"\tFocus:"+FocusSpecies);
}
}
}
}
}
data.getBioCDocobj().BioCOutput(Filename,FilenameBioC,data.getBioCDocobj().Annotations,false,true);
}
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