From 006b3d7c631e42fbf5b333e04e09bf14ff9c1fc1 Mon Sep 17 00:00:00 2001
From: langella <langella@b8ef2a07-7df7-436f-90b9-41648038564b>
Date: Mon, 11 Feb 2013 20:54:18 +0000
Subject: [PATCH] AlgoGrouping created
git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@338 b8ef2a07-7df7-436f-90b9-41648038564b
---
.../class_msms/Identification.java | 48 +++++++------------
.../grouping/AlgoGrouping.java | 36 ++++++++++++++
.../grouping/AlgoGroupingPhospho.java | 39 +++++++++++++++
3 files changed, 92 insertions(+), 31 deletions(-)
create mode 100644 xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGrouping.java
create mode 100644 xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingPhospho.java
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java
index 6881af988..ce07dffb4 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/class_msms/Identification.java
@@ -11,12 +11,12 @@ 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;
+import fr.inra.pappso.xtandempipeline.grouping.AlgoGrouping;
+import fr.inra.pappso.xtandempipeline.grouping.AlgoGroupingPhospho;
import fr.inra.pappso.xtandempipeline.grouping.Group;
import fr.inra.pappso.xtandempipeline.grouping.GroupSet;
-import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetPhospho;
import fr.inra.pappso.xtandempipeline.grouping.HashSampleScanSetProt;
import fr.inra.pappso.xtandempipeline.grouping.SubGroup;
-import fr.inra.pappso.xtandempipeline.grouping.SubGroupSet;
public class Identification {
@@ -31,7 +31,7 @@ public class Identification {
private ModifsList mods;
private MsRunSet msRunSet = new MsRunSet();
-
+
private DatabaseSet databaseSet = new DatabaseSet();
public Identification() {
@@ -40,12 +40,12 @@ public class Identification {
this.grouping = null;
this.mods = new ModifsList();
}
-
+
@Override
protected void finalize() throws Throwable {
logger.debug("finalize identification");
- logger.debug("Match : "+protein_liste.size());
- logger.debug("Peptide : "+peptide_liste.size());
+ logger.debug("Match : " + protein_liste.size());
+ logger.debug("Peptide : " + peptide_liste.size());
}
public void add_peptide(PeptideId P) {
@@ -92,7 +92,7 @@ public class Identification {
public MsRunSet getMsRunSet() {
return this.msRunSet;
}
-
+
public Match get_match(Protein P) {
if (this.protein_liste.containsKey(P.getAccession()))
return (this.protein_liste.get(P.getAccession()));
@@ -115,7 +115,7 @@ public class Identification {
}
public void remove_contaminant_submatch(File database) {
- //TODO Remove group containing prot from this database
+ // TODO Remove group containing prot from this database
new FilterGroupFromFastaDatabase(database).filter(grouping);
}
@@ -139,40 +139,26 @@ public class Identification {
public void performedGroupSet() throws Exception {
logger.info("Performed grouping");
- GroupSet resultGroupSet = new GroupSet();
-
- SubGroupSet subGroupSet = new SubGroupSet();
+ AlgoGrouping groupingAlgo = new AlgoGrouping();
for (Match m : protein_liste.values()) {
if (m.isIsvalidate()) {
- subGroupSet.addHashSampleScanSetProt(new HashSampleScanSetProt(
- m));
+ groupingAlgo
+ .addHashSampleScanSetProt(new HashSampleScanSetProt(m));
}
}
- logger.info("Number of subgroup before group creation : "+subGroupSet.size());
-
- resultGroupSet.groupingSubGroupSet(subGroupSet);
- grouping = resultGroupSet;
+
+ grouping = groupingAlgo.getGroupSet();
}
public void performedPhosphoGroupSet() throws Exception {
- GroupSet resultGroupSet = new GroupSet();
-
- SubGroupSet subGroupSet = new SubGroupSet();
+ AlgoGroupingPhospho groupingAlgoPhospho = new AlgoGroupingPhospho();
for (Match m : protein_liste.values()) {
if (m.isIsvalidate()) {
- ArrayList<HashSampleScanSetPhospho> phosphoSites = m
- .getHashSampleScanSetPhosphoList();
- for (HashSampleScanSetPhospho phospho : phosphoSites) {
- subGroupSet.addHashSampleScanSetProt(phospho);
- }
+ groupingAlgoPhospho.addAllHashSampleScanSetPhospho(m
+ .getHashSampleScanSetPhosphoList());
}
}
-
- /*
- * for (SubGroup sg:subGroupSet) { sg.loggerDebug(); }
- */
- resultGroupSet.groupingSubGroupSet(subGroupSet);
- this.grouping = resultGroupSet;
+ grouping = groupingAlgoPhospho.getGroupSet();
}
public ArrayList<Database> get_database_list() {
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGrouping.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGrouping.java
new file mode 100644
index 000000000..e8bf0a8e2
--- /dev/null
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGrouping.java
@@ -0,0 +1,36 @@
+package fr.inra.pappso.xtandempipeline.grouping;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+
+public class AlgoGrouping {
+ private static final Logger logger = Logger.getLogger(AlgoGrouping.class);
+
+ SubGroupSet subGroupSet = new SubGroupSet();
+
+ public void addHashSampleScanSetProt(HashSampleScanSetProt hashSampleScanSetProt) {
+ subGroupSet.addHashSampleScanSetProt(hashSampleScanSetProt);
+ }
+
+ public GroupSet getGroupSet() throws Exception {
+ if (subGroupSet.size() == 0) {
+ String message = "There is nothing to group, please use the addHashSampleScanSetProt function";
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ try {
+ logger.info("Perform grouping");
+
+ logger.info("Number of subgroup before group creation : "
+ + subGroupSet.size());
+ GroupSet resultGroupSet = new GroupSet();
+ resultGroupSet.groupingSubGroupSet(subGroupSet);
+ return resultGroupSet;
+ } catch (Exception e) {
+ String message = "ERROR in AlgoGrouping : " + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ }
+}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingPhospho.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingPhospho.java
new file mode 100644
index 000000000..f89031457
--- /dev/null
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/AlgoGroupingPhospho.java
@@ -0,0 +1,39 @@
+package fr.inra.pappso.xtandempipeline.grouping;
+
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+
+import fr.inra.pappso.xtandempipeline.MsException.MSMSException;
+
+public class AlgoGroupingPhospho {
+ private static final Logger logger = Logger
+ .getLogger(AlgoGroupingPhospho.class);
+ SubGroupSet subGroupSet = new SubGroupSet();
+
+ public void addAllHashSampleScanSetPhospho(
+ Collection<HashSampleScanSetPhospho> arrHashSampleScanSetPhospho) {
+ for (HashSampleScanSetPhospho HashSampleScanSetPhospho : arrHashSampleScanSetPhospho) {
+ subGroupSet.addHashSampleScanSetProt(HashSampleScanSetPhospho);
+ }
+ }
+
+ public GroupSet getGroupSet() throws Exception {
+ if (subGroupSet.size() == 0) {
+ String message = "There is nothing to group, please use the addArrHashSampleScanSetPhospho function";
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ try {
+ logger.info("Perform phospho grouping");
+ GroupSet resultGroupSet = new GroupSet();
+ resultGroupSet.groupingSubGroupSet(subGroupSet);
+ return resultGroupSet;
+ } catch (Exception e) {
+ String message = "ERROR in AlgoGroupingPhospho : " + e.getMessage();
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ }
+
+}
--
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