Show warnings when scores are out of the expected range, but continue…

… searching
MSGFPlus · Sep 7, 2021 · 4fa1ed9 · 4fa1ed9
1 parent aec0ec5
commit 4fa1ed9
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Showing 3 changed files with 27 additions and 9 deletions.
diff --git a/src/main/java/edu/ucsd/msjava/msgf/FlexAminoAcidGraph.java b/src/main/java/edu/ucsd/msjava/msgf/FlexAminoAcidGraph.java
@@ -327,8 +327,13 @@ private void makeForwardEdges(NominalMass curNode, ArrayList<AminoAcid> aaList,
 //			if(aa.isModified())
 //				errorScore += MODIFIED_EDGE_PENALTY;
             if (errorScore < -100 || errorScore > 100) {
-                System.err.println("Invalid ErrorScore: " + errorScore);
-                System.exit(-1);
+                System.err.println("Warning, invalid ErrorScore: " + errorScore);
+
+                // Could abort the search
+                // System.exit(-1);
+
+                // Instead, use a score of -4
+                errorScore = -4;
             }
             edge.setErrorScore(errorScore);
             if (addCleavageScore) {

diff --git a/src/main/java/edu/ucsd/msjava/msgf/GeneratingFunction.java b/src/main/java/edu/ucsd/msjava/msgf/GeneratingFunction.java
@@ -413,11 +413,24 @@ private void setCurNode(T curNode, ScoreDistFactory scoreDistFactory) {
         if (curMinScore >= curMaxScore)
             return;
 
-        if (curMinScore < -10000 || curMaxScore > 10000) {
-            System.err.println("Error! MinScore: " + curMinScore + ", MaxScore: " + curMaxScore + ", "
-                    + "CurNode: " + curNode.getNominalMass()
-                    + ", CurNodeScore: " + curNodeScore);
-            System.exit(-1);
+        if (curMinScore < -10000) {
+            System.err.println("Warning, MinScore is abnormally low; "
+                    + "MinScore: " + curMinScore + ", MaxScore: " + curMaxScore + ", "
+                    + "CurNode: " + curNode.getNominalMass() + ", CurNodeScore: " + curNodeScore);
+            // Could abort processing
+            // System.exit(-1);
+            // Instead, skip this node
+            return;
+        }
+
+        if (curMaxScore > 10000) {
+            System.err.println("Warning, MaxScore is abnormally high; "
+                    + "MinScore: " + curMinScore + ", MaxScore: " + curMaxScore + ", "
+                    + "CurNode: " + curNode.getNominalMass() + ", CurNodeScore: " + curNodeScore);
+            // Could abort processing
+            // System.exit(-1);
+            // Instead, skip this node
+            return;
         }
 
         ScoreDist curDist = scoreDistFactory.getInstance(curMinScore, curMaxScore);

diff --git a/src/main/java/edu/ucsd/msjava/ui/MSGFPlus.java b/src/main/java/edu/ucsd/msjava/ui/MSGFPlus.java
@@ -22,8 +22,8 @@
 
 
 public class MSGFPlus {
-    public static final String VERSION = "Release (v2021.03.22)";
-    public static final String RELEASE_DATE = "22 March 2021";
+    public static final String VERSION = "Release (v2021.09.06)";
+    public static final String RELEASE_DATE = "06 September 2021";
 
     public static final String DECOY_DB_EXTENSION = ".revCat.fasta";
     public static final String DEFAULT_DECOY_PROTEIN_PREFIX = "XXX";