From b328ae5871ec495723f21cb29764e212b18194c4 Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Sun, 21 Feb 2016 12:47:32 -0500
Subject: [PATCH 1/2] Updated git ignore.

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 6b72a7b..9451491 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@
 bin
 *.idea/*
 nexml.iml
+/target/

From 7ddf58b8a59b12202bbb98529cd876efa944e5a6 Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Sun, 21 Feb 2016 13:00:14 -0500
Subject: [PATCH 2/2] In progress implementation of reading character sets.
 Need to implement Mesquite translation.

---
 .../NexmlReaders/NexmlCharactersBlockReader.java          | 3 +++
 src/org/nexml/model/impl/CategoricalMatrixImpl.java       | 8 ++++++++
 2 files changed, 11 insertions(+)

diff --git a/src/mesquite/nexml/InterpretNEXML/NexmlReaders/NexmlCharactersBlockReader.java b/src/mesquite/nexml/InterpretNEXML/NexmlReaders/NexmlCharactersBlockReader.java
index e999ae0..a5bb882 100644
--- a/src/mesquite/nexml/InterpretNEXML/NexmlReaders/NexmlCharactersBlockReader.java
+++ b/src/mesquite/nexml/InterpretNEXML/NexmlReaders/NexmlCharactersBlockReader.java
@@ -144,6 +144,9 @@ private FileElement readMatrix(String mesDataType,Matrix<?> xmlMatrix,MesquiteFi
 				}
 				mesCharacter++;
 			}
+		}
+		for (String subset : xmlMatrix.getSubsetNames()) {
+			
 		}
 		mesMatrix.setUniqueID(xmlMatrix.getId());
 		mesMatrix.setName(xmlMatrix.getLabel());		
diff --git a/src/org/nexml/model/impl/CategoricalMatrixImpl.java b/src/org/nexml/model/impl/CategoricalMatrixImpl.java
index 5bc9996..dd183de 100644
--- a/src/org/nexml/model/impl/CategoricalMatrixImpl.java
+++ b/src/org/nexml/model/impl/CategoricalMatrixImpl.java
@@ -10,6 +10,7 @@
 import org.nexml.model.CharacterState;
 import org.nexml.model.CharacterStateSet;
 import org.nexml.model.OTU;
+import org.nexml.model.Subset;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
@@ -60,6 +61,13 @@ protected CategoricalMatrixImpl(Document document, Element element, OTUsImpl otu
 		for ( Element characterElement : getChildrenByTagName( getFormatElement(), CharacterImpl.getTagNameClass() ) ) {
 			createCharacter(characterElement);
 		}
+		
+		for (Element setElement : getChildrenByTagName(getFormatElement(), SubsetImpl.getTagNameClass())) {
+			String name = setElement.getAttribute("id");
+			for (String charID : setElement.getAttribute("char").split(getSplitString(), -1)) {
+				addToSubset(name, getThingById(charID));
+			}
+		}
 
 		for ( Element row : getChildrenByTagName( getMatrixElement(), "row") ) {
 			OTU otu = otus.getThingById(row.getAttribute("otu"));