Bump to v1.1.1

Nesvilab · Aug 20, 2021 · ff4d23f · ff4d23f
1 parent 42dfec2
commit ff4d23f
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/build.gradle b/build.gradle
@@ -27,7 +27,7 @@ repositories {
 
 sourceCompatibility = '1.8'
 targetCompatibility = '1.8'
-version = '1.1.0'
+version = '1.1.1'
 
 application {
     // Define the main class for the application

diff --git a/src/edu/umich/andykong/ptmshepherd/PTMShepherd.java b/src/edu/umich/andykong/ptmshepherd/PTMShepherd.java
@@ -26,7 +26,7 @@
 public class PTMShepherd {
 
 	public static final String name = "PTM-Shepherd";
- 	public static final String version = "1.1.0";
+ 	public static final String version = "1.1.1";
 
 	static HashMap<String,String> params;
 	static TreeMap<String,ArrayList<String []>> datasets;

diff --git a/src/edu/umich/andykong/ptmshepherd/core/MSFMGFFile.java b/src/edu/umich/andykong/ptmshepherd/core/MSFMGFFile.java
@@ -137,11 +137,12 @@ else if (cline.equals("END IONS"))
             int iend = (i + 1) * BLOCKSIZE; //end scan 500
             int ilinestart = scanStarts[istart]; //start at line corresponding to line 0 (0)
             int ilineend;
-            if (iend > scanC) {
+            //System.out.println(istart + "\t" + iend + "\t" + i + "\t" + scanC);
+            if (iend >= scanC) {
                 iend = scanC;
                 ilineend = fileLines.size(); //last line
             } else
-                ilineend = scanStarts[iend + 1] - 1; //end at line corresponding to line before scan 501
+                ilineend = scanStarts[iend]; //end at line corresponding to line before scan 501
 
             futureList.add(executorService.submit(() -> processMSFMGFSpectraBlock(fileLines, ilinestart, ilineend)));
         }
@@ -150,6 +151,8 @@ else if (cline.equals("END IONS"))
         for (Future future : futureList) { //checks to make sure all threads are done
             future.get();
         }
+
+        //TEST TODO
         //System.out.println("Time: " + Long.toString(System.currentTimeMillis() - t1));
         //todo
     }
@@ -165,6 +168,8 @@ private void processMSFMGFSpectraBlock(ArrayList<String> lines, int istart, int
         ArrayList<String> cspecLines = new ArrayList<>();
         String line;
 
+        int nScans = 0;
+
         for (int i = istart; i < iend; i++) {
             line = lines.get(i);
             cspecLines.add(line);