From ff4d23ffd75231d342cd0714bf906cda45b147b6 Mon Sep 17 00:00:00 2001
From: danielgeiszler <danny.geisz@gmail.com>
Date: Fri, 20 Aug 2021 12:17:51 -0700
Subject: [PATCH] Bump to v1.1.1

---
 build.gradle                                            | 2 +-
 src/edu/umich/andykong/ptmshepherd/PTMShepherd.java     | 2 +-
 src/edu/umich/andykong/ptmshepherd/core/MSFMGFFile.java | 9 +++++++--
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/build.gradle b/build.gradle
index ec9453f..1dd704a 100644
--- 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
index 6e04b77..bb5cad8 100644
--- 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
index 10e33e3..96d7f64 100644
--- 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);