From f2fedb42f84eb7ad8ac32f98174123cc0e54d733 Mon Sep 17 00:00:00 2001
From: langella <langella@b8ef2a07-7df7-436f-90b9-41648038564b>
Date: Thu, 24 May 2012 16:01:12 +0000
Subject: [PATCH] performance problem fixed using hashmap
git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@295 b8ef2a07-7df7-436f-90b9-41648038564b
---
.../grouping/HashPeptideSet.java | 18 ++++++---------
.../grouping/HashProteinSet.java | 23 ++++++++-----------
.../grouping/HashSampleScanSet.java | 17 ++++++--------
3 files changed, 24 insertions(+), 34 deletions(-)
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
index cea6378af..adede18de 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashPeptideSet.java
@@ -15,6 +15,9 @@ public class HashPeptideSet extends HashKey4GroupsSet {
*/
private static final Logger logger = Logger.getLogger(HashPeptideSet.class);
+ private HashMap<HashPeptide, HashPeptide> mapHashPeptide = new HashMap<HashPeptide, HashPeptide>(
+ 0);
+
public HashPeptideSet() {
// logger.debug("HashPeptideSet begin");
}
@@ -32,20 +35,13 @@ public class HashPeptideSet extends HashKey4GroupsSet {
HashPeptide temp = new HashPeptide(sampleScan, sequence);
if (this.add(temp)) {
- //this HashPeptide is new
+ // this HashPeptide is new
+ this.mapHashPeptide.put(temp, temp);
return (temp);
- }
- else {
+ } else {
// find the existing instance of the same peptide scan :
- for (HashKey4Groups toCompare:this) {
- HashPeptide hashPeptideToCompare = (HashPeptide) toCompare;
- if (temp.equals(hashPeptideToCompare)) {
- return hashPeptideToCompare;
- }
- }
+ return this.mapHashPeptide.get(temp);
}
- logger.error("ERROR this might not appear");
- return temp;
}
}
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
index dabf87b07..182d2e77b 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashProteinSet.java
@@ -1,5 +1,7 @@
package fr.inra.pappso.xtandempipeline.grouping;
+import java.util.HashMap;
+
import org.apache.log4j.Logger;
public class HashProteinSet extends HashKey4GroupsSet {
@@ -14,28 +16,23 @@ public class HashProteinSet extends HashKey4GroupsSet {
*/
private static final Logger logger = Logger.getLogger(HashProteinSet.class);
+ private HashMap<HashProtein, HashProtein> mapHashProtein = new HashMap<HashProtein, HashProtein>(
+ 0);
+
public HashProteinSet() {
// logger.debug("HashPeptideSet begin");
}
public HashProtein getInstance(String accession) {
HashProtein temp = new HashProtein(accession);
-
if (this.add(temp)) {
- //this HashProtein is new
+ // this HashProtein is new
+ this.mapHashProtein.put(temp, temp);
return (temp);
+ } else {
+ // find the existing instance of the same protein :
+ return this.mapHashProtein.get(temp);
}
- else {
- // find the existing instance of the same sample scan :
- for (HashKey4Groups toCompare:this) {
- HashProtein hashProtToCompare = (HashProtein) toCompare;
- if (temp.equals(hashProtToCompare)) {
- return hashProtToCompare;
- }
- }
- }
- logger.error("ERROR this might not appear");
- return temp;
}
@Override
diff --git a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
index a7abc9769..76bd0bb86 100644
--- a/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
+++ b/xtandempipeline/src/fr/inra/pappso/xtandempipeline/grouping/HashSampleScanSet.java
@@ -2,6 +2,7 @@ package fr.inra.pappso.xtandempipeline.grouping;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.HashMap;
import java.util.HashSet;
import org.apache.log4j.Logger;
@@ -16,6 +17,8 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
private static final long serialVersionUID = -9055338154900110371L;
private static final Logger logger = Logger
.getLogger(HashSampleScanSet.class);
+ private HashMap<HashSampleScan, HashSampleScan> mapHashSampleScan = new HashMap<HashSampleScan, HashSampleScan>(
+ 0);
public HashSampleScanSet() {
}
@@ -31,19 +34,13 @@ public class HashSampleScanSet extends HashSet<HashSampleScan> implements
HashSampleScan temp = new HashSampleScan(scan, msRun);
if (this.add(temp)) {
- //this hashSampleScan is new
+ // this HashSampleScan is new
+ this.mapHashSampleScan.put(temp, temp);
return (temp);
- }
- else {
+ } else {
// find the existing instance of the same sample scan :
- for (HashSampleScan toCompare:this) {
- if (temp.equals(toCompare)) {
- return toCompare;
- }
- }
+ return this.mapHashSampleScan.get(temp);
}
- logger.error("ERROR this might not appear");
- return temp;
}
public void loggerDebug() {
--
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