Version 1.3.35

BugFix for ambiguous peptides
lutzfischer · Sep 5, 2019 · da23db1 · da23db1
1 parent e3640b6
commit da23db1
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Showing 6 changed files with 42 additions and 32 deletions.
diff --git a/nb-configuration.xml b/nb-configuration.xml
@@ -11,6 +11,9 @@ Without this configuration present, some functionality in the IDE may be limited
             <configuration id="csv commandline" profiles=""/>
         </configurations>
     </config-data>
+    <spellchecker-wordlist xmlns="http://www.netbeans.org/ns/spellchecker-wordlist/1">
+        <word>psms</word>
+    </spellchecker-wordlist>
     <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
         <!--
 Properties that influence various parts of the IDE, especially code formatting and the like. 
@@ -20,8 +23,6 @@ Any value defined here will override the pom.xml file value but is only applicab
 -->
         <netbeans.hint.license>apache20</netbeans.hint.license>
         <org-netbeans-modules-javascript2-requirejs.enabled>false</org-netbeans-modules-javascript2-requirejs.enabled>
+        <netbeans.hint.jdkPlatform>JDK_1.8</netbeans.hint.jdkPlatform>
     </properties>
-    <spellchecker-wordlist xmlns="http://www.netbeans.org/ns/spellchecker-wordlist/1">
-        <word>psms</word>
-    </spellchecker-wordlist>
 </project-shared-configuration>
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.rappsilberlab</groupId>
     <artifactId>xiFDR</artifactId>
-    <version>1.3.34</version>
+    <version>1.3.35</version>
     <packaging>jar</packaging>
     <dependencies>
         <dependency>
@@ -35,11 +35,6 @@
             <artifactId>RUtils</artifactId>
             <version>1.0-SNAPSHOT</version>
         </dependency>
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>CSV</artifactId>
-            <version>1.0-SNAPSHOT</version>
-        </dependency>
         <dependency>
             <groupId>rappsilber</groupId>
             <artifactId>XiSearch</artifactId>
@@ -103,6 +98,11 @@
             <artifactId>fastutil</artifactId>
             <version>7.2.1</version>
         </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>CSV</artifactId>
+            <version>1.0-SNAPSHOT</version>
+        </dependency>
     </dependencies>
     <build>
 	<plugins>
@@ -145,5 +145,5 @@
     </properties>
     <description>Application for FDR estimation cross-linking massspectrometry data
 </description>
-    <name>xiFDR-1.3.34</name>
+    <name>xiFDR-1.3.35</name>
 </project>
diff --git a/src/main/java/org/rappsilber/fdr/CSVinFDR.java b/src/main/java/org/rappsilber/fdr/CSVinFDR.java
@@ -359,26 +359,27 @@ public void readCSV(CsvParser csv, CsvCondition filter) throws FileNotFoundExcep
                     ipeppos2[i] = Integer.parseInt(pepPositions2[i]);
                 }
 
+                String run = crun == null ? "":csv.getValue(crun);
+                String scan = cscan == null ? "":csv.getValue(cscan);
+                String crosslinker = cCrosslinker == null ? "":csv.getValue(cCrosslinker);
+                double crosslinkerMass = cCrosslinkerMass == null ? -1:csv.getDouble(cCrosslinkerMass);
+                String negativeCase = null;
+                String poisitiveCase = null;
+                if (cNegativeGrouping != null && cNegativeGrouping >=0) {
+                    negativeCase = csv.getValue(cNegativeGrouping);
+                    if (negativeCase.isEmpty())
+                        negativeCase=null;
+                }
+                if (cPositiveGrouping != null && cPositiveGrouping >=0) {
+                    poisitiveCase = csv.getValue(cPositiveGrouping);
+                    if (poisitiveCase.isEmpty())
+                        poisitiveCase=null;
+                }
+
 
                 PSM psm = null;
                 for (int p1 = 0; p1< accessions1.length; p1++) {
                     for (int p2 = 0; p2< accessions2.length; p2++) {
-                        String run = crun == null ? "":csv.getValue(crun);
-                        String scan = cscan == null ? "":csv.getValue(cscan);
-                        String crosslinker = cCrosslinker == null ? "":csv.getValue(cCrosslinker);
-                        double crosslinkerMass = cCrosslinkerMass == null ? -1:csv.getDouble(cCrosslinkerMass);
-                        String negativeCase = null;
-                        String poisitiveCase = null;
-                        if (cNegativeGrouping != null && cNegativeGrouping >=0) {
-                            negativeCase = csv.getValue(cNegativeGrouping);
-                            if (negativeCase.isEmpty())
-                                negativeCase=null;
-                        }
-                        if (cPositiveGrouping != null && cPositiveGrouping >=0) {
-                            poisitiveCase = csv.getValue(cPositiveGrouping);
-                            if (poisitiveCase.isEmpty())
-                                poisitiveCase=null;
-                        }
 
                         psm = addMatch(psmID, pepSeq1, pepSeq2, peplen1, peplen2, 
                                 site1, site2, isDecoy1, isDecoy2, charge, score, 
@@ -407,9 +408,6 @@ public void readCSV(CsvParser csv, CsvCondition filter) throws FileNotFoundExcep
                             }
                         }
 
-
-
-
                         if (cInfo != null) {
                             psm.setInfo(csv.getValue(cInfo));
                         }

diff --git a/src/main/java/org/rappsilber/fdr/OfflineFDR.java b/src/main/java/org/rappsilber/fdr/OfflineFDR.java
@@ -759,7 +759,7 @@ public PSM addMatch(String psmID, Peptide peptide1, Peptide peptide2, int peplen
             score = 10 - (10 * score);
         }
 
-        PSM psm = new PSM(psmID, npepid1, npepid2, (byte) nsite1, (byte) nsite2, proteinId1.isDecoy(), proteinId2.isDecoy(), (byte) charge, score, peptide1Score, peptide2Score);
+        PSM psm = new PSM(psmID, npepid1, npepid2, (byte) nsite1, (byte) nsite2, nproteinId1.isDecoy(), nproteinId2.isDecoy(), (byte) charge, score, npeptide1Score, npeptide2Score);
         psm.setNegativeGrouping(isSpecialCase);
 
         psm.setRun(registerRun(run));

diff --git a/src/main/java/org/rappsilber/fdr/entities/PSM.java b/src/main/java/org/rappsilber/fdr/entities/PSM.java
@@ -316,9 +316,18 @@ public boolean equals(Object l) {
         PSM c = (PSM) l;
         if (isNonCovalent != c.isNonCovalent)
             return false;
+        if (this.origScore != c.origScore)
+            return false;
+        if (this.crosslinker != c.crosslinker)
+            return false; 
+        if (this.charge != c.charge)
+            return false;
+
+        if (!this.psmID.contentEquals(c.psmID))
+            return false;
+
 //        return this.score == c.score && this.charge == c.charge &&  this.psmID.contentEquals(c.psmID);
-        return this.origScore == c.origScore && this.crosslinker == c.crosslinker && this.charge == c.charge &&  this.psmID.contentEquals(c.psmID) &&
-                ((((c.peptide1Score == this.peptide1Score &&c.peptide2Score == this.peptide2Score)) && c.peptide1.equals(this.peptide1) && c.peptide2.equals(this.peptide2) && c.pepsite1 == pepsite1 && c.pepsite2 == pepsite2) 
+        return ((((c.peptide1Score == this.peptide1Score &&c.peptide2Score == this.peptide2Score)) && c.peptide1.equals(this.peptide1) && c.peptide2.equals(this.peptide2) && c.pepsite1 == pepsite1 && c.pepsite2 == pepsite2) 
                 || /* to be safe from binary inaccuracy we make an integer-comparison*/
                 ((c.peptide1Score == this.peptide2Score &&c.peptide2Score == this.peptide1Score) && c.peptide2.equals(this.peptide1) && c.peptide1.equals(this.peptide2) && c.pepsite2 == pepsite1 && c.pepsite1 == pepsite2));
     }

diff --git a/src/main/resources/xifdrproject.properties b/src/main/resources/xifdrproject.properties
@@ -1,6 +1,8 @@
 xifdr.version=${project.version}
 xifdr.artifactId=${project.artifactId}
 xifdr.changelog=\
+1.3.35\n\
+* BugFix for ambiguous peptides\n\
 1.3.34\n\
 * support for local FDR (PEP)\n\
 * will read in and try to boost on delta score and peptide coverage\n\