v0.3.5

fixed linux bug
added custom modlist param

src/edu/umich/andykong/ptmshepherd/PTMShepherd.java

@@ -42,10 +42,22 @@ public static synchronized void print(String s) {
 	}
 
 	public static void parseParamFile(String fn) throws Exception {
-		File f = new File(fn);
-		if(!f.exists()) 
-			die(String.format("Parameter file %s does not exist",fn));
-		BufferedReader in = new BufferedReader(new FileReader(f));
+		Path path = null;
+		//String fn2 = fn.replaceAll("\"", "");
+		//for (int i = 0; i < fn2.length(); i++) {
+		//	System.out.println(fn.charAt(i) + "*");
+		//}
+		try {
+			path = Paths.get(fn.replaceAll("['\"]", ""));
+		} catch (Exception e) {
+			System.out.println(e);
+			die(String.format("Malformed parameter path string: [%s]", fn));
+		}
+		if (path == null || !Files.exists(path)) {
+			die(String.format("Parameter file does not exist: [%s]", fn));
+		}
+
+		BufferedReader in = new BufferedReader(new FileReader(path.toFile()));
 		String cline;
 		while((cline = in.readLine())!= null) {
 			int comments = cline.indexOf("//");
@@ -65,7 +77,7 @@ public static void parseParamFile(String fn) throws Exception {
 					datasets.put(dsName, new ArrayList<>());
 				datasets.get(dsName).add(new String[] {tsvTxt,mzPath});
 			} else {
-				params.put(key, value);
+				params.put(key, value.trim());
 			}
 		}
 		in.close();
@@ -119,7 +131,7 @@ public static void init(String [] args) throws Exception {
 				overrides.put(args[i].substring(2),args[i+1]);
 				i++;
 			} else
-				parseParamFile(args[i]);
+				parseParamFile(args[i].trim());
 		}
 		params.put("peakpicking_background", Double.toString(2.5*Double.parseDouble(params.get("peakpicking_width"))));
 		//replace overrides

src/edu/umich/andykong/ptmshepherd/glyco/GlycoAnalysis.java

@@ -1,10 +1,15 @@
 package edu.umich.andykong.ptmshepherd.glyco;
 
+import edu.umich.andykong.ptmshepherd.PSMFile;
+import edu.umich.andykong.ptmshepherd.PTMShepherd;
 import edu.umich.andykong.ptmshepherd.core.MXMLReader;
+import edu.umich.andykong.ptmshepherd.core.Spectrum;
+
 import java.io.File;
 import java.io.FileWriter;
 import java.io.PrintWriter;
 import java.io.RandomAccessFile;
+import java.util.ArrayList;
 import java.util.HashMap;
 
 public class GlycoAnalysis {
@@ -14,13 +19,78 @@ public class GlycoAnalysis {
     HashMap<String, MXMLReader> multiMr;
     double ppmTol, condRatio, peakTol;
     int condPeaks;
-    int specCol, pepCol, modpepCol, chargecol, deltaCol, rtCol, intCol;
+    int specCol, pepCol, modpepCol, chargecol, deltaCol, rtCol, intCol, pmassCol;
 
     public GlycoAnalysis(String dsName) {
         this.dsName = dsName;
         glycoFile = new File(dsName+".rawglyco");
     }
 
+    public void glycoPSMs(PSMFile pf, HashMap<String, File> mzMappings) throws Exception {
+        //open up output file
+        HashMap<String, ArrayList<Integer>> mappings = new HashMap<>();
+        PrintWriter out = new PrintWriter(new FileWriter(glycoFile, true));
+        //write header
+        out.printf("%s\t%s\t%s\t%s\t%s\n", "Spectrum", "Peptide", "Mod_Peptide", "Mass_Shift", "Pep_Mass");
+        //get necessary col indices
+        specCol = pf.getColumn("Spectrum");
+        pepCol = pf.getColumn("Peptide");
+        modpepCol = pf.getColumn("Modified Peptide");
+        //chargeCol = pf.getColumn("Charge");
+        deltaCol = pf.dMassCol;
+        rtCol = pf.getColumn("Retention");
+        intCol = pf.getColumn("Intensity");
+
+        //map PSMs to file
+        for (int i = 0; i < pf.data.size(); i++) {
+            String[] sp = pf.data.get(i).split("\t");
+            String bn = sp[specCol].substring(0, sp[specCol].indexOf(".")); //fraction
+            if (!mappings.containsKey(bn))
+                mappings.put(bn, new ArrayList<>());
+        }
+        for (int i = 0; i < pf.data.size(); i++) {
+            for (String fraction : mappings.keySet())
+                mappings.get(fraction).add(i);
+        }
+
+        for (String cf : mappings.keySet()) { //for file in relevant spectral files
+            long t1 = System.currentTimeMillis();
+            mr = new MXMLReader(mzMappings.get(cf), Integer.parseInt(PTMShepherd.getParam("threads")));
+            mr.readFully();
+            ArrayList<Integer> clines = mappings.get(cf); //lines corr to curr spec file
+            for (int i = 0; i < clines.size(); i++) {//for relevant line in curr spec file
+                try {
+                    //out.println(processLine());
+                } catch (Exception e) {
+                    e.printStackTrace();
+                    System.out.println("Error in: " + pf.data.get(clines.get(i)));
+                }
+            }
+        }
+    }
+
+    public void processLine(String line) {
+        StringBuffer sb = new StringBuffer();
+        String [] sp = line.split("\\t");
+        String seq = sp[pepCol];
+        float dmass = Float.parseFloat(sp[deltaCol]);
+
+        String specName = sp[specCol];
+        //String [] smods = sp[modCol].split(",");
+
+        //sb.append(String.format("%s\t%s\t%s\t%.4f", specName,seq,sp[modCol],dmass));
+
+        //StringBuffer sb = new StringBuffer();
+        String [] s = line.split("\\t");
+        //Spectrum spec = mr.getSpectrum(reNormName(specName))
+        //findIonMasses();
+        //localizeRemainderFragments();
+    }
+
+    public void findIonMasses(float pepMass) {
+
+    }
+
     public String reNormName(String s) {
         String[] sp = s.split("\\.");
         int sn = Integer.parseInt(sp[1]);