V1.6.743.rc1

 * new modification type - besides "fixed", "variable", and "known" one 
	can now define "linear" modification that are only to be found on 
	peptides matched as linear peptides 
 * some scores get the RunConfig as part of the initialisation
 * renamed "searchStoped" to searchStopped in SimpleXiProcess
 * when threads stop they report the reason they stop
 * reordered some initialisations in AbstractRunConfig
 * storeObject and retrieveObject are caseinsensetive if a String is 
	used as key
 * updated filter readout from config
 * new Filter "RemoveSinglePeaks" as an alternative denoising method
 * new Filter "ScanFilteredSpectrumAccess" to only search specific scans
	actally that filter already exists but was not selectable via the 
	config
 * new filter "Rebase": the main use is to write out the filtered 
	spectrum to the database by declaring the up to that point processed 
	spectrum as the "original" spectrum 
 * GenericTextPopUpMenu insalles now also a simple search function on 
	textareas
 * the peakfile table the database is now filed and referenced
 * peakFileName will be recorded for each spectrum.
 * CSVExportMatches can change the delimiter and quote charater that is 
	used 
 * CSVExportMatches automatically switches the delimiter to simicolon if 
	"," is found to be the decimal separator in the current local
 * saving the result-file as .txt, .txt.gz, .tsv, or .tsv.gz automatically 
	switches to a tab-separated output.
 * if for some reason CSVExportMatches is set to write out CSV with "," 
	as delimiter under a german local then all floating-point values get 
	surounded by quotes.
 * new "peaklist reader" that forwards a single spectrum from memory.
	mainly used in the annotator project
 * new supscores:
	CCPepFragmentCount : how many unique cross-linker stub modified 
		peptideIon fragments where found
	CCPepFragmentError: the smallest error for cross-linker stub modified 
		peptideIon fragments  
 * BugFix in crosslinkerrestrictedLoss
 * new setting "TransferLossToBase:true|false"
	if set to true and isotope cluster is matched to a loss xi will try 
	to find a isotope-cluster for the basic (non-lossy) fragment even
	if the isotope cluster is contained in another isotope cluster
 * BugFix in Spectra.cloneTopPeaksRolling to ensure the right number of 
	peaks are considered 
 * the origin of a spectrum can be overwriten (used in the rebase filter)

nbproject/genfiles.properties

@@ -4,5 +4,5 @@ build.xml.stylesheet.CRC32=8064a381@1.80.1.48
 # This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
 # Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
 nbproject/build-impl.xml.data.CRC32=be8a7bc0
-nbproject/build-impl.xml.script.CRC32=f54f9770
-nbproject/build-impl.xml.stylesheet.CRC32=830a3534@1.80.1.48
+nbproject/build-impl.xml.script.CRC32=31664875
+nbproject/build-impl.xml.stylesheet.CRC32=3a2fa800@1.89.1.48

src/rappsilber/applications/SimpleXiProcess.java

@@ -66,6 +66,7 @@
 import rappsilber.ms.score.SpectraCoverage;
 import rappsilber.ms.score.SpectraCoverageConservative;
 import rappsilber.ms.sequence.AminoAcid;
+import rappsilber.ms.sequence.ModificationType;
 import rappsilber.ms.sequence.Peptide;
 import rappsilber.ms.sequence.SequenceList;
 import rappsilber.ms.sequence.digest.AASpecificity;
@@ -609,9 +610,9 @@ protected void setupScores() {
         //        } catch (IOException ex) {
         //            Logger.getLogger(this.getClass().getName()).log(Level.WARNING, "Error reading statistics", ex);
         //        }
-        Logger.getLogger(this.getClass().getName()).log(Level.INFO, "FragmentLibrary Coverage");
+//        Logger.getLogger(this.getClass().getName()).log(Level.INFO, "FragmentLibrary Coverage");
         getConfig().getScores().add(new FragmentLibraryScore(m_Fragments, m_sequences.getCountPeptides()));
-        Logger.getLogger(this.getClass().getName()).log(Level.INFO, "Spectar Coverage");
+//        Logger.getLogger(this.getClass().getName()).log(Level.INFO, "Spectar Coverage");
         getConfig().getScores().add(new SpectraCoverage());
         getConfig().getScores().add(new FragmentChargeState());
         getConfig().getScores().add(new SpectraCoverageConservative(minConservativeLosses));
@@ -620,7 +621,7 @@ protected void setupScores() {
         getConfig().getScores().add(new BS3ReporterIonScore());
 //        getConfig().getScores().add(new Normalizer());
         //getConfig().getScores().add(new LinkSiteDelta());
-        getConfig().getScores().add(new NormalizerML());
+        getConfig().getScores().add(new NormalizerML(getConfig()));
         // add dummy score for feeding in the delta score
         getConfig().getScores().add(m_deltaScore);
     }
@@ -632,6 +633,16 @@ protected void variableModifications() {
         m_peptidesLinear.applyVariableModificationsLinear(m_config,m_peptides);
         m_config.getStatusInterface().setStatus("Applying variable modification to cross-linkable peptides");
         m_peptides.applyVariableModifications(m_config, m_peptidesLinear);
+        m_config.getStatusInterface().setStatus("Applying linear modification to cross-linkable peptides");
+        ArrayList<Peptide> linearMods =  new ArrayList<>();
+        for (Peptide p: m_peptides) {
+            linearMods.addAll(p.modify(m_config,ModificationType.linear));
+        }
+        for (Peptide p: m_peptidesLinear) {
+            linearMods.addAll(p.modify(m_config,ModificationType.linear));
+        }
+
+        linearMods.addAll(linearMods);
         //        m_sequences.applyVariableModifications(getConfig(),m_peptides, m_Crosslinker, digest);
         //        m_sequences.applyVariableModifications(getConfig(),m_peptidesLinear, m_Crosslinker, digest);
 
@@ -823,7 +834,7 @@ public void sendPing() {
         watchdog.scheduleAtFixedRate(watchdogTask, 10, 60000);
 
 
-        while (running && !m_config.searchStoped()) {
+        while (running && !m_config.searchStopped()) {
             for (int i = 0; i < getSearchThreads().length; i++) {
                 if (getSearchThreads()[i].isAlive()) {
                     try {
@@ -917,14 +928,26 @@ public void sendPing() {
 
         long proc = getProcessedSpectra();
         if (m_msmInput.getSpectraCount() >0) {
-            int procPerc = (int)(getProcessedSpectra()*100/m_msmInput.getSpectraCount());
-            m_config.getStatusInterface().setStatus(procPerc +"% processed (" + proc + ") " + m_msmInput.countReadSpectra() + " read of " + m_msmInput.getSpectraCount());
-        } else {
+            long filteredOut = m_msmInput.getDiscardedSpectra();
+            long procTotal = proc+m_msmInput.getDiscardedSpectra();
+            int procPerc = (int)(procTotal*100/m_msmInput.getSpectraCount());
+            if (filteredOut >0)
+                m_config.getStatusInterface().setStatus(procPerc +"% processed (" + proc + " + " + filteredOut + " fitlered out" + ") " + m_msmInput.countReadSpectra() + " read of " + m_msmInput.getSpectraCount());
+            else
+                m_config.getStatusInterface().setStatus(procPerc +"% processed (" + proc + ") " + m_msmInput.countReadSpectra() + " read of " + m_msmInput.getSpectraCount());
+//            int procPerc = (int)(getProcessedSpectra()*100/m_msmInput.getSpectraCount());
+//            m_config.getStatusInterface().setStatus(procPerc +"% processed (" + proc + ") " + m_msmInput.countReadSpectra() + " read of " + m_msmInput.getSpectraCount());
+        } else if (proc==0) {
+            m_config.getStatusInterface().setStatus("Error: no Spectra found to process");
+            Logger.getLogger(this.getClass().getName()).log(Level.SEVERE,"Error: no Spectra found to process");
+
+            System.exit(-1);
+        }else {
             m_config.getStatusInterface().setStatus(proc + " spectra processed " + m_msmInput.countReadSpectra() + " read of " + m_msmInput.getSpectraCount());
         }
 
 
-        if (m_msmInput.hasNext() && !m_config.searchStoped()) {
+        if (m_msmInput.hasNext() && !m_config.searchStopped()) {
             emptyBufferedWriters();
             for (BufferedResultWriter brw : (LinkedList<BufferedResultWriter>)BufferedResultWriter.allActiveWriters.clone()) {
                 if (brw.getInnerWriter() instanceof BufferedResultWriter) {
@@ -981,7 +1004,7 @@ public void sendPing() {
             Logger.getLogger(this.getClass().getName()).log(Level.FINE, "It should be save to say good by now." );
         }
 
-        if (m_msmInput.hasNext()) {
+        if (m_msmInput.hasNext() && !m_config.searchStopped()) {
             startSearch();
             waitEnd();
             return;
@@ -1021,6 +1044,8 @@ public void sendPing() {
             m_debugFrame.dispose();
         }
         watchdog.cancel();
+
+        m_config.getStatusInterface().setStatus("completed");
 
         if (countActiveThreads()>1){
             int delay = 60000;
@@ -1035,6 +1060,7 @@ public void run() {
                         for (Handler h : Logger.getGlobal().getHandlers()) {
                             h.flush();
                         }
+                        m_config.getStatusInterface().setStatus("completed");
                         System.exit(-1);
                     } else {
                         Logger.getLogger(this.getClass().getName()).log(Level.WARNING,"No Warning: Threads did shut down by themself"  );

src/rappsilber/applications/SimpleXiProcessLinearIncluded.java

@@ -367,7 +367,7 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
             int countSpectra = 0;
             int processed = 0;
             // go through each spectra
-            while (delayedHasNext(input, unbufInput) && ! m_config.searchStoped()) {
+            while (delayedHasNext(input, unbufInput) && ! m_config.searchStopped()) {
 
                 if (input.countReadSpectra() % 100 ==  0) {
                     System.err.println("("+Thread.currentThread().getName()+")Spectra Read " + unbufInput.countReadSpectra() + "\n");
@@ -684,7 +684,9 @@ protected boolean delayedHasNext(SpectraAccess input, SpectraAccess unbufInput)
             } catch (InterruptedException ex) {
                 Logger.getLogger(SimpleXiProcessLinearIncluded.class.getName()).log(Level.SEVERE, null, ex);
             }
-            Logger.getLogger(this.getClass().getName()).log(Level.WARNING,"({0}) Oddety here: input finished but not finished",Thread.currentThread().getName());
+            if ((input.hasNext() || unbufInput.hasNext())) {
+                Logger.getLogger(this.getClass().getName()).log(Level.WARNING,"({0}) Oddety here: input finished but not finished",Thread.currentThread().getName());
+            }
         }
         return input.hasNext() || unbufInput.hasNext();
     }

src/rappsilber/applications/SimpleXiProcessMultipleCandidates.java

@@ -93,6 +93,7 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
 //        input = bsa;
         BufferedResultWriter brw = new BufferedResultWriter(output, 100);
         output = brw;
+        String quitReason="";
 
 
         try {
@@ -122,13 +123,23 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
             int countSpectra = 0;
             int processed = 0;
             // go through each spectra
-            while (delayedHasNext(input, unbufInput) && ! m_config.searchStoped()) {
+            while (true) {
+                if (m_config.searchStopped()) {
+                    quitReason="Search got stoped through config";
+                    break;
+                }
+                if (!(delayedHasNext(input, unbufInput) && ! m_config.searchStopped())) {
+                    quitReason="no new spectra";
+                    break;
+                }
                 if (input.countReadSpectra() % 100 ==  0) {
                     System.err.println("("+Thread.currentThread().getName()+")Spectra Read " + unbufInput.countReadSpectra() + "\n");
                 }
 
-                if (m_doStop)
+                if (m_doStop) {
+                    quitReason="search got stop";
                     break;
+                }
                 // ScoredLinkedList<Peptide,Double> scoredPeptides = new ScoredLinkedList<Peptide, Double>();
                 Spectra spectraAllchargeStatess = input.next();
 //                int sn = spectraAllchargeStatess.getScanNumber();
@@ -538,6 +549,7 @@ public int compare(Peptide o1, Peptide o2) {
                     processed=0;
                 }
                 if (threadStop.get()) {
+                    quitReason="thread stop";
                     System.err.println("Closing down search thread " + Thread.currentThread().getName());
                     break;
                 }
@@ -551,7 +563,7 @@ public int compare(Peptide o1, Peptide o2) {
             e.printStackTrace(System.err);
             System.exit(1);
         }
-        Logger.getLogger(this.getClass().getName()).log(Level.INFO, "Search Thread {0} finished", Thread.currentThread().getName());
+        Logger.getLogger(this.getClass().getName()).log(Level.INFO, "Search Thread {0} finished ("+quitReason +")", Thread.currentThread().getName());
 
     }
 

src/rappsilber/applications/SimpleXiProcessOpenModification.java

@@ -210,7 +210,7 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
 
             int countSpectra = 0;
             // go through each spectra
-            while (delayedHasNext(input, input) && ! m_config.searchStoped()) {
+            while (delayedHasNext(input, input) && ! m_config.searchStopped()) {
 
                 if (input.countReadSpectra() % 100 ==  0) {
                     System.err.println("Spectra Read " + input.countReadSpectra() + "\n");

src/rappsilber/applications/SimpleXiProcessOpenModificationSiteProb.java

@@ -211,7 +211,7 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
 
             int countSpectra = 0;
             // go through each spectra
-            while (input.hasNext() && ! m_config.searchStoped()) {
+            while (input.hasNext() && ! m_config.searchStopped()) {
 
                 if (input.countReadSpectra() % 100 ==  0) {
                     System.err.println("Spectra Read " + input.countReadSpectra() + "\n");

src/rappsilber/applications/SimpleXiProcessOpenModificationXlink.java

@@ -261,7 +261,7 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
             int countSpectra = 0;
             int processed = 0;
             // go through each spectra
-            while (input.hasNext() && ! m_config.searchStoped()) {
+            while (input.hasNext() && ! m_config.searchStopped()) {
                 processed ++;
 
                 if (input.countReadSpectra() % 100 ==  0) {

src/rappsilber/applications/SimpleXiProcessOpenTargetedModification.java

@@ -272,7 +272,7 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
 
             int countSpectra = 0;
             // go through each spectra
-            while (input.hasNext()&& ! m_config.searchStoped()) {
+            while (input.hasNext()&& ! m_config.searchStopped()) {
 
                 if (input.countReadSpectra() % 100 ==  0) {
                     System.err.println("Spectra Read " + input.countReadSpectra() + "\n");

src/rappsilber/applications/SimpleXiProcessTargetModificationXlink.java

@@ -296,7 +296,7 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
             int countSpectra = 0;
             int processed = 0;
             // go through each spectra
-            while (input.hasNext()&& ! m_config.searchStoped()) {
+            while (input.hasNext()&& ! m_config.searchStopped()) {
                 processed ++;
 
                 if (input.countReadSpectra() % 100 ==  0) {

src/rappsilber/applications/SimpleXiProcessTargetModificationXlinkMulti.java

@@ -295,7 +295,7 @@ public void process(SpectraAccess input, ResultWriter output, AtomicBoolean thre
             int countSpectra = 0;
             int processed = 0;
             // go through each spectra
-            while (input.hasNext()&& ! m_config.searchStoped()) {
+            while (input.hasNext()&& ! m_config.searchStopped()) {
                 processed ++;
 
                 if (input.countReadSpectra() % 100 ==  0) {

src/rappsilber/applications/Xi.java

@@ -258,14 +258,25 @@ public void setupMSMIterator() {
     public void setupOutput() {
         for (String out : outputArgs) {
             try {
+                boolean gzip = false;
+                boolean tabSep=false;
+                if (out.endsWith(".gz")) {
+                    gzip=true;
+                }
+                if (out.endsWith("txt.gz")||out.endsWith("tsv.gz")||out.endsWith("txt")||out.endsWith("tsv")) {
+                    tabSep=true;
+                }
+
+                CSVExportMatches CSVOut = null;
                 if (out.contentEquals("-")) {
-                    result_multiplexer.addResultWriter(new CSVExportMatches(System.out, xiconfig));
+                    CSVOut = new CSVExportMatches(System.out, xiconfig,gzip);
                 } else {
-                    if (out.endsWith(".gz")) {
-                        result_multiplexer.addResultWriter(new CSVExportMatches(new FileOutputStream(out), xiconfig,true));
-                    } else
-                        result_multiplexer.addResultWriter(new CSVExportMatches(new FileOutputStream(out), xiconfig,false));
+                    CSVOut = new CSVExportMatches(new FileOutputStream(out), xiconfig,gzip);
+                }
+                if (tabSep) {
+                    CSVOut.setDelimChar("\t");
                 }
+                result_multiplexer.addResultWriter(CSVOut);
             } catch (IOException ex) {
                 Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, "could not open ouput file:" + out, ex);
                 System.exit(1);