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AimeeD90 · Jul 11, 2018 · 66f1db9 · 66f1db9
1 parent e6aa7c8
commit 66f1db9
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Showing 4 changed files with 56 additions and 74 deletions.
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
diff --git a/out/artifacts/pClean_jar/pClean.jar b/out/artifacts/pClean_jar/pClean.jar
diff --git a/src/main/java/Preprocessing/pCleanMainClass.java b/src/main/java/Preprocessing/pCleanMainClass.java
@@ -47,8 +47,7 @@ public static void main(String[] args) throws ParseException, IOException, MzMLU
         options.addOption("ionsMerge", false, "merge two adjacent peaks within a mass tolerance of 20ppm");
         options.addOption("largerThanPrecursor", false, "remove peaks larger than precursor");
         options.addOption("a2", false, "Consider gap masses of two amino acids");
-        options.addOption("mzid", true, "mzIdentML file");
-        options.addOption("dat", true, "dat file");
+        options.addOption("idres", true, "Identification result");
         options.addOption("h", false, "Help info");
 
         CommandLineParser parser = new DefaultParser();
@@ -99,22 +98,24 @@ public static void main(String[] args) throws ParseException, IOException, MzMLU
         }
 
         String outlog = outdir+"/spectrumInfor.txt";
-        if (cmd.hasOption("mzid")) {
-            String mzid = cmd.getOptionValue("mzid");
-            if (labelMethod != null) {
-                doParseMzid123(mgf, outdir, outlog, imonFilter, labelMethod, repFilter, labelFilter, lowWinFilter, highWinFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, mzid);
-            } else {
-                doParseMzid23(mgf, outdir, outlog, imonFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, mzid);
-            }
-            //doParseMzid(mgf, outdir, outlog, imonFilter, labelMethod, repFilter, labelFilter, lowWinFilter, highWinFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, mzid);
-        } else if (cmd.hasOption("dat")) {
-            String dat = cmd.getOptionValue("dat");
-            if (labelMethod != null) {
-                doParseDat123(mgf, outdir, outlog, imonFilter, labelMethod, repFilter, labelFilter, lowWinFilter, highWinFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, dat);
-            } else {
-                doParseDat23(mgf, outdir, outlog, imonFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, dat);
+        if (cmd.hasOption("idres")) {
+            String idres = cmd.getOptionValue("idres");
+            if (idres.endsWith(".mzid")) {
+                String mzid = cmd.getOptionValue("mzid");
+                if (labelMethod != null) {
+                    doParseMzid123(mgf, outdir, outlog, imonFilter, labelMethod, repFilter, labelFilter, lowWinFilter, highWinFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, idres);
+                } else {
+                    doParseMzid23(mgf, outdir, outlog, imonFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, idres);
+                }
+                //doParseMzid(mgf, outdir, outlog, imonFilter, labelMethod, repFilter, labelFilter, lowWinFilter, highWinFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, idres);
+            } else if (idres.endsWith(".dat")) {
+                String dat = cmd.getOptionValue("dat");
+                if (labelMethod != null) {
+                    doParseDat123(mgf, outdir, outlog, imonFilter, labelMethod, repFilter, labelFilter, lowWinFilter, highWinFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, idres);
+                } else {
+                    doParseDat23(mgf, outdir, outlog, imonFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor, idres);
+                }
             }
-
         } else {
             if (labelMethod != null) {
                 //System.out.println(mgf + "\n" + outdir + "\n" + outlog + "\n" + imonFilter + "\n" + labelMethod + "\n" + repFilter + "\n" + labelFilter + "\n" + lowWinFilter + "\n" + highWinFilter + "\n" + isoReduction + "\n" + chargeDeconv + "\n" + ionsMarge + "\n" + largerThanPrecursor);
@@ -130,6 +131,8 @@ public static void main(String[] args) throws ParseException, IOException, MzMLU
                 doPreprocessing23(mgf, outdir, outlog, imonFilter, isoReduction, chargeDeconv, ionsMerge, largerThanPrecursor);
             }
         }
+
+
     }
 
     private static void doParseMzid123(String mgf, String outdir, String outlog, Boolean imonFilter, String labelMethod, Boolean repFilter, Boolean labelFilter, Boolean lowWinFilter, Boolean highWinFilter, Boolean isoReduction, Boolean chargeDeconv, Boolean ionsMerge, Boolean largerThanPrecursor, String mzid) throws IOException, MzMLUnmarshallerException, JAXBException, ClassNotFoundException, SQLException, MathException, InterruptedException {

diff --git a/target/classes/Preprocessing/pCleanMainClass.class b/target/classes/Preprocessing/pCleanMainClass.class