From 166f59bd9586bb2e82c3fe698eebd07735d9ba1e Mon Sep 17 00:00:00 2001
From: Kevin Mader <kevinmader@gmail.com>
Date: Fri, 5 Dec 2014 16:41:35 +0100
Subject: [PATCH 1/2] changed to concurrent supported map

---
 .../java/org/scijava/annotations/AbstractIndexWriter.java    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/scijava/annotations/AbstractIndexWriter.java b/src/main/java/org/scijava/annotations/AbstractIndexWriter.java
index 9266d6d26..836c1a25b 100644
--- a/src/main/java/org/scijava/annotations/AbstractIndexWriter.java
+++ b/src/main/java/org/scijava/annotations/AbstractIndexWriter.java
@@ -44,6 +44,7 @@
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.TreeMap;
+import java.util.concurrent.ConcurrentSkipListMap;
 
 /**
  * Writes annotations as JSON-formatted files.
@@ -58,7 +59,7 @@
 public abstract class AbstractIndexWriter {
 
 	private final Map<String, Map<String, Object>> map =
-		new TreeMap<String, Map<String, Object>>();
+		new ConcurrentSkipListMap<String, Map<String, Object>>();
 
 	protected synchronized boolean foundAnnotations() {
 		return !map.isEmpty();
@@ -135,7 +136,7 @@ protected synchronized void merge(final String annotationName,
 		int changedCount = map.size();
 		boolean hasObsoletes = false;
 
-		final IndexReader reader = new IndexReader(in);
+		final IndexReader reader = new IndexReader(in,annotationName+" from "+in);
 		try {
 			for (;;) {
 				@SuppressWarnings("unchecked")

From 91829d081b7f8c155d8996c4f5d64095c71aacdf Mon Sep 17 00:00:00 2001
From: Kevin Mader <kevinmader@gmail.com>
Date: Wed, 21 Jan 2015 15:44:16 +0100
Subject: [PATCH 2/2] added new code to make debugging problems with the
 annotation processor easier

---
 .../org/scijava/annotations/IndexReader.java     | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/scijava/annotations/IndexReader.java b/src/main/java/org/scijava/annotations/IndexReader.java
index 3121bf4c1..5440ccde3 100644
--- a/src/main/java/org/scijava/annotations/IndexReader.java
+++ b/src/main/java/org/scijava/annotations/IndexReader.java
@@ -64,13 +64,23 @@
 class IndexReader {
 
 	private final PushbackInputStream in;
+	private final String originalISName;
 
 	IndexReader(final InputStream in) {
 		this.in =
 			in instanceof PushbackInputStream ? (PushbackInputStream) in
 				: new PushbackInputStream(new BufferedInputStream(in));
+		this.originalISName="";
 	}
 
+	IndexReader(final InputStream in,final String isName) {
+		this.in =
+				in instanceof PushbackInputStream ? (PushbackInputStream) in
+						: new PushbackInputStream(new BufferedInputStream(in));
+		this.originalISName=isName;
+	}
+
+
 	public Object next() throws IOException {
 		int c = in.read();
 		while (Character.isWhitespace(c)) c = in.read();
@@ -155,7 +165,8 @@ else if (c < '0' || c > '9') {
 		if (c == '"') {
 			return readString();
 		}
-		throw new IOException("Unexpected char: '" + (char) c + "'");
+		throw new IOException("Unexpected char: '" + (char) c + "'"+
+				((originalISName.length()>0) ? " from "+originalISName : ""));
 	}
 
 	public void close() throws IOException {
@@ -206,7 +217,7 @@ private int expect(char a, char b) throws IOException {
 			return 1;
 		}
 		throw new IOException("Expected '" + a + "' or '" + b + "', got '" +
-			(char) c + "'");
+			(char) c + "'"+((originalISName.length()>0) ? " from "+originalISName : ""));
 	}
 
 	private void expect(String match) throws IOException {
@@ -217,6 +228,7 @@ private void expect(String match) throws IOException {
 
 	private IndexReader() {
 		this.in = null;
+		this.originalISName="";
 	}
 
 	static IndexReader getLegacyReader(final InputStream in) throws IOException {