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Commit 306af45c authored by valot's avatar valot
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Add equals function to group and subgroup 

Don't clear and addAll at each subgroup addition of groupList
Performed removed non informative sub-group after finish grouping.
Now, all work fine and are reproductibly.

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@301 b8ef2a07-7df7-436f-90b9-41648038564b
parent 917e6a16
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xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/Group.java
+ 167
− 143
View file @ 306af45c
package fr.inra.pappso.xtandempipeline.grouping;
import java.util.ArrayList;
import java.util.HashSet;
import org.apache.log4j.Logger;
......@@ -30,7 +31,13 @@ public class Group extends HashKey4GroupsSet implements Comparable<Group> {
groupStr = groupStr + sg.toString();
}
return groupStr;
}
@Override
public boolean equals(Object InCompare) {
if (this == InCompare)
return (true);
return false;
}
public boolean fusionWith(Group incomingGroup) throws Exception {
......@@ -58,7 +65,8 @@ public class Group extends HashKey4GroupsSet implements Comparable<Group> {
throw new Exception(message);
}
if (this.contains(hashPeptide)) {
logger.debug("launch fusion : this peptide was found in group "+hashPeptide.toString());
logger.debug("launch fusion : this peptide was found in group "
+ hashPeptide.toString());
return true;
} else {
// logger.debug(" hashPeptide " + hashPeptide +
......@@ -101,156 +109,172 @@ public class Group extends HashKey4GroupsSet implements Comparable<Group> {
}
}
@SuppressWarnings("unused")
private boolean removeNonInformativeConsideringGroup(Group incomingGroup)
throws Exception {
boolean changed = false;
HashSampleScanSet sampleScanSetOverall = new HashSampleScanSet();
sampleScanSetOverall.addAll(this.getHashSampleScanSet());
sampleScanSetOverall.addAll(incomingGroup.getHashSampleScanSet());
// remove in self
SubGroupSet newSubGroupListToKeepSelf = new SubGroupSet();
for (HashSampleScan SampleScan : sampleScanSetOverall) {
int nbPresence = 0;
SubGroup sgSpec = null;
for (SubGroup sg : this.subGroupList) {
if (sg.contains(SampleScan)) {
nbPresence++;
sgSpec = sg;
}
}
if (nbPresence == 1) {
newSubGroupListToKeepSelf.add(sgSpec);
}
}
if (this.subGroupList.size() > newSubGroupListToKeepSelf.size()) {
logger.debug((this.subGroupList.size() - newSubGroupListToKeepSelf
.size()) + " subgroups removed : non informative");
this.subGroupList.clear();
this.subGroupList.addAll(newSubGroupListToKeepSelf);
HashKey4GroupsSet newKeys = new HashKey4GroupsSet();
for (SubGroup sg : subGroupList) {
newKeys.addAll(sg.getHashKey4GroupsSet());
}
if (this.size() > newKeys.size()) {
logger.debug(" this group has changed : " + this.size() + " > "
+ newKeys.size());
this.clear();
this.addAll(newKeys);
changed = true;
logger.debug(" this group new size : " + this.size());
}
}
// remove in incoming
SubGroupSet newSubGroupListToKeepIncoming = new SubGroupSet();
for (HashSampleScan SampleScan : sampleScanSetOverall) {
int nbPresence = 0;
SubGroup sgSpec = null;
for (SubGroup sg : incomingGroup.subGroupList) {
if (sg.contains(SampleScan)) {
nbPresence++;
sgSpec = sg;
}
}
if (nbPresence == 1) {
newSubGroupListToKeepIncoming.add(sgSpec);
}
}
if (incomingGroup.subGroupList.size() > newSubGroupListToKeepIncoming
.size()) {
logger.debug("incoming group before : \n"
+ incomingGroup.toString());
logger.debug((incomingGroup.subGroupList.size() - newSubGroupListToKeepIncoming
.size())
+ " subgroups removed from incomingGroup : non informative");
incomingGroup.subGroupList.clear();
incomingGroup.subGroupList.addAll(newSubGroupListToKeepIncoming);
HashKey4GroupsSet newKeys = new HashKey4GroupsSet();
for (SubGroup sg : incomingGroup.subGroupList) {
newKeys.addAll(sg.getHashKey4GroupsSet());
}
if (incomingGroup.size() > newKeys.size()) {
logger.debug(" incoming group has changed : "
+ incomingGroup.size() + " > " + newKeys.size());
incomingGroup.clear();
incomingGroup.addAll(newKeys);
changed = true;
logger.debug(" incoming group new size : "
+ incomingGroup.size());
logger.debug("incoming group after : \n"
+ incomingGroup.toString());
}
}
return changed;
}
// @SuppressWarnings("unused")
// private boolean removeNonInformativeConsideringGroup(Group incomingGroup)
// throws Exception {
//
// boolean changed = false;
// HashSampleScanSet sampleScanSetOverall = new HashSampleScanSet();
// sampleScanSetOverall.addAll(this.getHashSampleScanSet());
// sampleScanSetOverall.addAll(incomingGroup.getHashSampleScanSet());
//
// // remove in self
// SubGroupSet newSubGroupListToKeepSelf = new SubGroupSet();
//
// for (HashSampleScan SampleScan : sampleScanSetOverall) {
// int nbPresence = 0;
// SubGroup sgSpec = null;
// for (SubGroup sg : this.subGroupList) {
// if (sg.contains(SampleScan)) {
// nbPresence++;
// sgSpec = sg;
// }
// }
// if (nbPresence == 1) {
// newSubGroupListToKeepSelf.add(sgSpec);
// }
// }
//
// if (this.subGroupList.size() > newSubGroupListToKeepSelf.size()) {
// logger.debug((this.subGroupList.size() - newSubGroupListToKeepSelf
// .size()) + " subgroups removed : non informative");
// this.subGroupList.clear();
// this.subGroupList.addAll(newSubGroupListToKeepSelf);
//
// HashKey4GroupsSet newKeys = new HashKey4GroupsSet();
// for (SubGroup sg : subGroupList) {
// newKeys.addAll(sg.getHashKey4GroupsSet());
// }
// if (this.size() > newKeys.size()) {
// logger.debug(" this group has changed : " + this.size() + " > "
// + newKeys.size());
// this.clear();
// this.addAll(newKeys);
// changed = true;
// logger.debug(" this group new size : " + this.size());
// }
// }
//
// // remove in incoming
//
// SubGroupSet newSubGroupListToKeepIncoming = new SubGroupSet();
//
// for (HashSampleScan SampleScan : sampleScanSetOverall) {
// int nbPresence = 0;
// SubGroup sgSpec = null;
// for (SubGroup sg : incomingGroup.subGroupList) {
// if (sg.contains(SampleScan)) {
// nbPresence++;
// sgSpec = sg;
// }
// }
// if (nbPresence == 1) {
// newSubGroupListToKeepIncoming.add(sgSpec);
// }
// }
//
// if (incomingGroup.subGroupList.size() > newSubGroupListToKeepIncoming
// .size()) {
// logger.debug("incoming group before : \n"
// + incomingGroup.toString());
// logger.debug((incomingGroup.subGroupList.size() - newSubGroupListToKeepIncoming
// .size())
// + " subgroups removed from incomingGroup : non informative");
// incomingGroup.subGroupList.clear();
// incomingGroup.subGroupList.addAll(newSubGroupListToKeepIncoming);
//
// HashKey4GroupsSet newKeys = new HashKey4GroupsSet();
// for (SubGroup sg : incomingGroup.subGroupList) {
// newKeys.addAll(sg.getHashKey4GroupsSet());
// }
// if (incomingGroup.size() > newKeys.size()) {
// logger.debug(" incoming group has changed : "
// + incomingGroup.size() + " > " + newKeys.size());
// incomingGroup.clear();
// incomingGroup.addAll(newKeys);
// changed = true;
// logger.debug(" incoming group new size : "
// + incomingGroup.size());
// logger.debug("incoming group after : \n"
// + incomingGroup.toString());
// }
// }
// return changed;
// }
protected boolean removeNonInformative() throws Exception {
boolean changed = false;
HashSampleScanSet sampleScanSetOverall = this.getHashSampleScanSet();
SubGroupSet newSubGroupListToKeep = new SubGroupSet();
for (HashSampleScan SampleScan : sampleScanSetOverall) {
int nbPresence = 0;
SubGroup sgSpec = null;
for (SubGroup sg : this.subGroupList) {
if (sg.contains(SampleScan)) {
nbPresence++;
sgSpec = sg;
}
}
if (nbPresence == 1) {
newSubGroupListToKeep.add(sgSpec);
}
}
int deltaSize = this.subGroupList.size()- newSubGroupListToKeep.size();
if (deltaSize == 0) {
changed = false;
}
else if (deltaSize == 1) {
logger.debug((this.subGroupList.size() - newSubGroupListToKeep
.size()) + " subgroups removed : non informative");
this.subGroupList.clear();
this.subGroupList.addAll(newSubGroupListToKeep);
changed = true;
}
else {
//Plusieurs sous-groupe à enlever ???
SubGroupSet sgListToRemove = new SubGroupSet();
sgListToRemove.addAll(subGroupList);
sgListToRemove.removeAll(newSubGroupListToKeep);
SubGroup sgToRemove = null;
int sgToRemoveSize = 1000000;
for (SubGroup sg : sgListToRemove) {
logger.debug("Remove non informative : "
+ sg.getHashSampleScanSetProtList().get(0)
ArrayList<SubGroup> sgList = this.subGroupList.getSubGroupList();
for (int i = sgList.size() - 1; i >= 0; i--) {
HashSampleScanSetProt hashProt = sgList.get(i)
.getHashSampleScanSetProtList().get(0);
int count = this.getNumberOfSpecificPeptideInSubGroup(hashProt);
if (count == 0) {
this.subGroupList.remove(sgList.get(i));
logger.debug("Remove non informative subgroup "
+ sgList.get(i).getHashSampleScanSetProtList().get(0)
.getMatch().get_protein_match()
.get_cle_accession());
if (sg.size() < sgToRemoveSize) {
sgToRemove = sg;
sgToRemoveSize = sg.size();
}
return(true);
}
this.subGroupList.remove(sgToRemove);
this.removeNonInformative();
changed=true;
}
return changed;
return(false);
}
// protected boolean removeNonInformative() throws Exception {
// boolean changed = false;
// HashSampleScanSet sampleScanSetOverall = this.getHashSampleScanSet();
// SubGroupSet newSubGroupListToKeep = new SubGroupSet();
// for (HashSampleScan SampleScan : sampleScanSetOverall) {
// int nbPresence = 0;
// SubGroup sgSpec = null;
// for (SubGroup sg : this.subGroupList) {
// if (sg.contains(SampleScan)) {
// nbPresence++;
// sgSpec = sg;
// }
// }
// if (nbPresence == 1) {
// newSubGroupListToKeep.add(sgSpec);
// }
// }
// int deltaSize = this.subGroupList.size() - newSubGroupListToKeep.size();
// if (deltaSize == 0) {
// changed = false;
// } else if (deltaSize == 1) {
// logger.debug((this.subGroupList.size() - newSubGroupListToKeep
// .size()) + " subgroups removed : non informative");
// this.subGroupList.clear();
// this.subGroupList.addAll(newSubGroupListToKeep);
// changed = true;
// } else {
// logger.debug((this.subGroupList.size() - newSubGroupListToKeep
// .size()) + " subgroups removed : non informative");
// // Plusieurs sous-groupe à enlever ???
// SubGroupSet sgListToRemove = new SubGroupSet();
// sgListToRemove.addAll(subGroupList);
// sgListToRemove.removeAll(newSubGroupListToKeep);
//
// SubGroup sgToRemove = null;
// int sgToRemoveSize = 1000000;
//
// for (SubGroup sg : sgListToRemove) {
// logger.debug("Remove non informative : "
// + sg.getHashSampleScanSetProtList().get(0).getMatch()
// .get_protein_match().get_cle_accession());
// if (sg.size() < sgToRemoveSize) {
// sgToRemove = sg;
// sgToRemoveSize = sg.size();
// }
// }
// this.subGroupList.remove(sgToRemove);
// this.removeNonInformative();
//
// changed = true;
//
// }
// return changed;
// }
public SubGroupSet getSubGroupSet() {
return this.subGroupList;
}
......
xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/GroupSet.java
+ 32
− 21
View file @ 306af45c
......@@ -21,9 +21,11 @@ public class GroupSet {
for (SubGroup subGroup : subGroupSet) {
this.addSubGroup(subGroup);
}
/*
* for (Group group : this.groupList) { group.removeNonInformative(); }
*/
logger.debug("Removing Non Informative Sub-Group");
this.removingNonIformativeGroup();
logger.debug("Numbering group");
this.numbering();
}
......@@ -40,41 +42,50 @@ public class GroupSet {
}
}
private void removingNonIformativeGroup() throws Exception {
HashSet<Group> toRemove = new HashSet<Group>(0);
HashSet<Group> toAdd = new HashSet<Group>(0);
for (Group group : this.groupList) {
boolean remove = false;
//remove sequentially sub-group to
while(group.removeNonInformative()){
remove=true;
}
//There is removed Sub-grouped, check it
if(remove){
toAdd.addAll(group.reGroup());
toRemove.add(group);
}
}
this.groupList.removeAll(toRemove);
this.groupList.addAll(toAdd);
}
protected void addSubGroup(SubGroup subGroup) throws Exception {
logger.debug("addSubGroup "+subGroup.getHashSampleScanSetProtList().get(0).toString());
logger.debug("addSubGroup "
+ subGroup.getHashSampleScanSetProtList().get(0).toString());
Group group = new Group(subGroup);
this.add(group);
}
private boolean add(Group groupToAdd) throws Exception {
HashSet<Group> newGroupList = new HashSet<Group>(0);
HashSet<Group> removeGroupList = new HashSet<Group>(0);
boolean fusion = false;
for (Group group : groupList) {
if (groupToAdd.fusionWith(group)) {
fusion = true;
} else {
newGroupList.add(group);
removeGroupList.add(group);
}
}
if (fusion) {
logger.debug("fusioning");
if (groupToAdd.removeNonInformative()) {
logger.debug("fusioning, deleting new non informative info");
newGroupList.addAll(groupToAdd.reGroup());
}
else {
logger.debug("fusioning, no removal of non informative");
newGroupList.add(groupToAdd);
}
this.groupList.add(groupToAdd);
this.groupList.removeAll(removeGroupList);
} else {
this.groupList.add(groupToAdd);
}
else {
newGroupList.add(groupToAdd);
}
this.groupList.clear();
this.groupList.addAll(newGroupList);
return true;
}
......
xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/SubGroup.java
+ 8
− 5
View file @ 306af45c
......@@ -36,6 +36,14 @@ public class SubGroup extends HashSampleScanSet {
return subGroupStr;
}
@Override
public boolean equals(Object toCompar) {
if(this==toCompar){
return(true);
}
return(false);
}
// @Override
public boolean addHashSampleScanSetProt(HashSampleScanSetProt incomingProt) {
......@@ -90,11 +98,6 @@ public class SubGroup extends HashSampleScanSet {
public void loggerDebug() {
super.loggerDebug();
/*logger.debug(" int this subgroup:" );
for (HashSampleScanSetProt scanProt :this.peptideSetProtList) {
logger.debug(" scanProt "+scanProt.getMatch().get_protein_match().get_cle_accession()+" "+ scanProt.size());
}
logger.debug(" end of subgroup:" ); */
}
}
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