Merge pull request #121 from Rappsilber-Laboratory/1.8.7

Rappsilber-Laboratory · Nov 13, 2024 · 0a3ab2b · 0a3ab2b
2 parents 11af2ea + 2a71043
commit 0a3ab2b
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Showing 5 changed files with 19 additions and 7 deletions.
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>rappsilber</groupId>
     <artifactId>xiSEARCH</artifactId>
-    <version>1.8.6</version>
+    <version>1.8.7</version>
     <packaging>jar</packaging>
     <dependencies>
         <dependency>
@@ -112,5 +112,5 @@
             </plugin>          
         </plugins>    
     </build>
-    <name>xiSEARCH 1.8.6</name>
+    <name>xiSEARCH 1.8.7</name>
 </project>
diff --git a/src/main/java/rappsilber/gui/SimpleXiGui.java b/src/main/java/rappsilber/gui/SimpleXiGui.java
@@ -986,7 +986,7 @@ public void errorOutput(char[] output) {
                     sbErr.append(output);
                     String serr = sbErr.toString();
                     if (serr.contains(gctext)) {
-                        JOptionPane.showMessageDialog(SimpleXiGui.this, "xisearch is spending a lot of time in garbage collection!\n Probably running out of memmory soon.", "GC time", JOptionPane.WARNING_MESSAGE);
+                        JOptionPane.showMessageDialog(SimpleXiGui.this, "xisearch is spending a lot of time in garbage collection!\n Probably running out of memory soon.", "GC time", JOptionPane.WARNING_MESSAGE);
                     }
                     if (serr.contains(memexept)) {
                         JOptionPane.showMessageDialog(SimpleXiGui.this, "Out Of Memmory Error detected!!\n\nTry to run with more memory or less threads!", "Out Of Memmory Error", JOptionPane.ERROR_MESSAGE);

diff --git a/src/main/java/rappsilber/ms/dataAccess/output/PeakListWriter.java b/src/main/java/rappsilber/ms/dataAccess/output/PeakListWriter.java
@@ -65,7 +65,7 @@ public void run() {
     }
 
     public void writeHeader() {
-                m_out.println("Run\tScanNumber\tscore\tcrosslinker\tFastaHeader1\tPeptide1\tFastaHeader2\t" +
+                m_out.println("Run\tScanNumber\tprec charge\tprec mz\tscore\tcrosslinker\tFastaHeader1\tPeptide1\tFastaHeader2\t" +
                         "Peptide2\tMatchedPeptide\talpha/beta\tLinkerPosition1\tLinkerPostion2\t" +
                         "FragmentName\tFragment\tNeutralMass\tCharge\tCalcMZ\tExpMZ\tMS2Error\tIsotopPeak\tDescription\tvirtual\tBasePeak\tAbsoluteIntesity\tRelativeIntensity\tIsPrimaryMatch");
     }
@@ -125,7 +125,8 @@ public void writeResult(MatchedXlinkedPeptide match) {
             if (peak.getMatchedAnnotation().isEmpty()) {
                 try {
                 m_out.print(
-                        s.getRun() + "\t" + i2s(s.getScanNumber()) + "\t" + d2s(match.getScore()) +
+                        s.getRun() + "\t" + i2s(s.getScanNumber())  + "\t" + s.getPrecurserCharge() + "\t" +
+                        s.getPrecurserMZExp() + "\t" + d2s(match.getScore()) +
                         "\t" + (pep2!=null ? match.getCrosslinker().getName() : "") +
                         "\t" + pep1.getSequence().getFastaHeader() +
                         "\t" + pep1.toString() +
@@ -158,7 +159,8 @@ public void writeResult(MatchedXlinkedPeptide match) {
                         p = f.getPeptide();
                     }
                     m_out.print(
-                            s.getRun() + "\t" + i2s(s.getScanNumber()) +  "\t" + d2s(match.getScore()) +
+                            s.getRun() + "\t" + i2s(s.getScanNumber()) +  "\t" + s.getPrecurserCharge() + "\t" +
+                            s.getPrecurserMZExp() + "\t" + d2s(match.getScore()) +
                             "\t" + (pep2!=null ? match.getCrosslinker().getName() : "") +
                             "\t" + pep1.getSequence().getFastaHeader() +
                             "\t" + pep1.toString() +

diff --git a/src/main/java/rappsilber/ms/lookup/peptides/FUPeptideTree.java b/src/main/java/rappsilber/ms/lookup/peptides/FUPeptideTree.java
@@ -444,7 +444,7 @@ public void applyVariableModifications(RunConfig conf) {
         int c = 0;
         while (peps.hasNext()) {
             if (c++ % 10000 == 0) {
-                    conf.getStatusInterface().setStatus("Applying variable modification " +  Util.twoDigits.format(c*100.0/cm) + "%" );
+                conf.getStatusInterface().setStatus("Applying variable modification " +  Util.twoDigits.format(c*100.0/cm) + "%" );
             }
 
             Peptide pep = peps.next();

diff --git a/src/main/java/rappsilber/ms/sequence/digest/AAConstrainedDigestion.java b/src/main/java/rappsilber/ms/sequence/digest/AAConstrainedDigestion.java
@@ -22,6 +22,7 @@
 import rappsilber.config.RunConfig;
 import rappsilber.ms.sequence.AminoAcid;
 import rappsilber.ms.sequence.AminoAcidSequence;
+import rappsilber.ms.sequence.AminoModification;
 import rappsilber.ms.sequence.Peptide;
 import rappsilber.ms.sequence.Sequence;
 
@@ -132,6 +133,15 @@ public boolean isDigestedPeptide(Peptide p) {
         int next = p.getStart() + p.length();
         int end = next -1;
         AminoAcid endAA = p.aminoAcidAt(p.length() - 1);
+
+        if (endAA instanceof AminoModification && ((AminoModification)endAA).postDigest) {
+            endAA = ((AminoModification)endAA).BaseAminoAcid;
+        }
+        if (startAA instanceof AminoModification && ((AminoModification)startAA).postDigest) {
+            startAA = ((AminoModification)startAA).BaseAminoAcid;
+        }
+
+
         boolean nret = false;
 
         if (prev>=0) {