Separated contaminants database filter on separated class

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@214 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java

@@ -6,6 +6,7 @@ import java.util.Collections;
 import org.apache.log4j.Logger;
 
 import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+import fr.inra.pappso.xtandempipeline.filter_print.FilterGroupFromFastaDatabase;
 import fr.inra.pappso.xtandempipeline.filter_print.filter_base;
 import fr.inra.pappso.xtandempipeline.filter_print.print_base;
 import fr.inra.pappso.xtandempipeline.filter_print.swt_table_base;
@@ -118,7 +119,7 @@ public class Identification {
 
 	public void remove_contaminant_submatch(File database) {
 		//TODO Remove group containing prot from this database
-		grouping.removeGroupFromDatabase(database);
+		new FilterGroupFromFastaDatabase(database).filter(grouping);
 	}
 
 	public void setProteinListValideToGroupeSet() {

xtandempipeline/src/fr/inra/pappso/xtandempipeline/filter_print/FilterGroupFromFastaDatabase.java

+package fr.inra.pappso.xtandempipeline.filter_print;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
+import java.util.HashSet;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.pappso.xtandempipeline.grouping.Group;
+import fr.inra.pappso.xtandempipeline.grouping.GroupSet;
+import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
+import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
+
+public class FilterGroupFromFastaDatabase {
+	
+	private static final Logger logger = Logger.getLogger(FilterGroupFromFastaDatabase.class);
+	
+	private File database;
+	
+	public FilterGroupFromFastaDatabase(File database) {
+		logger.info("Remove Group from Fasta Database "+ database.getName());
+		this.database=database;
+	}
+	
+	public void filter (GroupSet grouping) {
+		//Read fasta file to get accession list
+		if(database.exists()){
+			logger.info("Read fasta file : "+database.getName());
+			HashSet<String> access = new HashSet<String>();
+			try{
+				FileInputStream is = new FileInputStream(database);
+				InputStreamReader isr = new InputStreamReader(is);
+				BufferedReader br = new BufferedReader(isr);
+				
+				String line;
+				while((line= br.readLine())!=null){
+					line.trim();
+					if(line.length()>0){
+						if(line.startsWith(">")){
+							access.add(line.split(" ")[0].replaceFirst(">", ""));
+						}
+					}
+				}
+			}catch (Exception e) {
+				logger.error(e);
+			}
+			//Search contaminants proteins
+			logger.info("Remove Group in new mode");
+			for (Group group : grouping.getGroupList()) {
+				boolean isconta = false;
+				for (SubGroup sg : group.getSubGroupSet()) {
+					for (HashSampleScanSetProt hashProt : sg
+							.getHashSampleScanSetProtSet()) {
+						if (access.contains(hashProt.getMatch().get_protein_match().get_cle_accession())) {
+							isconta = true;
+						}
+					}
+				}
+				if (isconta)
+					grouping.getHashSetOfGroups().remove(group);
+			}
+		}else{
+			logger.error("fasta file doesnt not exist: " + database.getAbsolutePath());
+			logger.info("Remove Group from Database in old mode");
+			for (Group group : grouping.getGroupList()) {
+				boolean isconta = false;
+				for (SubGroup sg : group.getSubGroupSet()) {
+					for (HashSampleScanSetProt hashProt : sg
+							.getHashSampleScanSetProtSet()) {
+						if (hashProt.getMatch().get_protein_match().getDatabase().getDatabasePath()
+								.contains(database.getName())) {
+							isconta = true;
+						}
+					}
+				}
+				if (isconta)
+					grouping.getHashSetOfGroups().remove(group);
+			}
+		}
+		
+		//Numbering after contaminant removing
+		grouping.numbering();
+	}
+
+}

xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java

 package fr.inra.pappso.xtandempipeline.grouping;
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
@@ -31,7 +27,7 @@ public class GroupSet {
 		this.numbering();
 	}
 
-	private void numbering() {
+	public void numbering() {
 		// numerotation
 		ArrayList<Group> orderedGroupList = new ArrayList<Group>(groupList);
 
@@ -86,67 +82,7 @@ public class GroupSet {
 		return orderedGroupList;
 	}
 
-	public void removeGroupFromDatabase(File database) {
-		//Read fasta file to get accession list
-		if(database.exists()){
-			logger.info("Read fasta file : "+database.getName());
-			HashSet<String> access = new HashSet<String>();
-			try{
-				FileInputStream is = new FileInputStream(database);
-				InputStreamReader isr = new InputStreamReader(is);
-				BufferedReader br = new BufferedReader(isr);
-				
-				String line;
-				while((line= br.readLine())!=null){
-					line.trim();
-					if(line.length()>0){
-						if(line.startsWith(">")){
-							access.add(line.split(" ")[0].replaceFirst(">", ""));
-						}
-					}
-				}
-			}catch (Exception e) {
-				logger.error(e);
-			}
-			//Search contaminants proteins
-			logger.info("Remove Group from Database in new mode: " + database.getName());
-			for (Group group : this.getGroupList()) {
-				boolean isconta = false;
-				for (SubGroup sg : group.getSubGroupSet()) {
-					for (HashSampleScanSetProt hashProt : sg
-							.getHashSampleScanSetProtSet()) {
-						if (access.contains(hashProt.getMatch().get_protein_match().get_cle_accession())) {
-							isconta = true;
-						}
-					}
-				}
-				if (isconta)
-					this.groupList.remove(group);
-			}
-		}else{
-			logger.error("fasta file doesnt not exist: " + database.getAbsolutePath());
-			logger.info("Remove Group from Database in old mode: " + database.getName());
-			for (Group group : this.getGroupList()) {
-				boolean isconta = false;
-				for (SubGroup sg : group.getSubGroupSet()) {
-					for (HashSampleScanSetProt hashProt : sg
-							.getHashSampleScanSetProtSet()) {
-						if (hashProt.getMatch().get_protein_match().getDatabase().getDatabasePath()
-								.contains(database.getName())) {
-							isconta = true;
-						}
-					}
-				}
-				if (isconta)
-					this.groupList.remove(group);
-			}
-		}
-		
-		//Numbering after contaminant removing
-		this.numbering();
-	}
-
-	protected HashSet<Group> getHashSetOfGroups() {
+	public HashSet<Group> getHashSetOfGroups() {
 		return this.groupList;
 	}