From ac160b3302008d5449da5b40248f18bf06563679 Mon Sep 17 00:00:00 2001
From: Daniel Barton <daluke.barton@gmail.com>
Date: Wed, 21 Aug 2013 11:57:21 +0100
Subject: [PATCH] A third commit where there should have been one....
 Everything is here now I hope.

---
 .../data/sequence/RNAStructScoreManager.java       |    2 +-
 datamodel/compbio/data/sequence/ScoreManager.java  |   42 ++------------------
 2 files changed, 5 insertions(+), 39 deletions(-)

diff --git a/datamodel/compbio/data/sequence/RNAStructScoreManager.java b/datamodel/compbio/data/sequence/RNAStructScoreManager.java
index 3fb856c..e792969 100644
--- a/datamodel/compbio/data/sequence/RNAStructScoreManager.java
+++ b/datamodel/compbio/data/sequence/RNAStructScoreManager.java
@@ -38,7 +38,7 @@ public class RNAStructScoreManager extends ScoreManager {
 		this.seqScores = seqScores;
 	}
 	
-	// I put this in purely because it mirrors a method in ScoreManager, not because I need it :/
+	// I put this in purely because it mirrors a method in ScoreManager, not because I need it 
 	public static RNAStructScoreManager newInstance(List<String> structs, List<TreeSet<Score>> data) {
 		return new RNAStructScoreManager(structs, data);
 	}
diff --git a/datamodel/compbio/data/sequence/ScoreManager.java b/datamodel/compbio/data/sequence/ScoreManager.java
index c3b6a85..9b1803d 100644
--- a/datamodel/compbio/data/sequence/ScoreManager.java
+++ b/datamodel/compbio/data/sequence/ScoreManager.java
@@ -36,9 +36,10 @@ public class ScoreManager {
 	@XmlTransient
 	public static final String SINGLE_ENTRY_KEY = "Alignment";
 
-	private List<ScoreHolder> seqScores;
+	protected List<ScoreHolder> seqScores;
 
-	private ScoreManager() {
+	// Do I have to change this to protected?
+	protected ScoreManager() {
 		// Default JAXB constructor
 	}
 
@@ -56,27 +57,6 @@ public class ScoreManager {
 		this.seqScores = seqScores;
 	}
 
-	/*
-	 *  Next constructor added by Daniel
-	 *  a constructor for using ScoreManager to represent RNAalifold output
-	    
-	 */
-	
-	public ScoreManager(RNAStruct rnaStruct) {
-		assert(rnaStruct.getStructs().size() == rnaStruct.getData().size());
-		// This had better be used to create a RNAalifold output structure
-		assert(java.util.regex.Pattern.matches(
-				"^[\\.)(]*$", rnaStruct.getStructs().get(1)));
-		List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();
-		
-		for (int i = 0; i < rnaStruct.getStructs().size(); i++) {
-			seqScores.add(new ScoreHolder(rnaStruct.getStructs().get(i),
-					rnaStruct.getData().get(i)));
-		}
-		this.seqScores = seqScores;
-	}
-	
-	
 	public static ScoreManager newInstance(Map<String, Set<Score>> data) {
 		return new ScoreManager(data);
 	}
@@ -96,19 +76,6 @@ public class ScoreManager {
 		return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,
 				new TreeSet(data));
 	}
-
-	// Also Daniel's. Check this with Jim to make sure that I am not compromising
-	// the security of this class
-		public RNAStruct asRNAStruct() {
-			List<String> structs = new ArrayList<String>();
-			List<TreeSet<Score>> data = new ArrayList<TreeSet<Score>>();
-			for (ScoreHolder sch : this.seqScores) {
-				structs.add(sch.id);
-				data.add(sch.scores);
-			}
-			return new RNAStruct(structs, data);
-		}
-		 
 	
 	public Map<String, TreeSet<Score>> asMap() {
 		Map<String, TreeSet<Score>> seqScoresMap = new TreeMap<String, TreeSet<Score>>();
@@ -199,8 +166,7 @@ public class ScoreManager {
 
 		ScoreHolder(String id, Set<Score> scores) {
 			this.id = id;
-			this.scores = new TreeSet<Score>(scores);
-		}
+			this.scores = new TreeSet<Score>(scores);		}
 
 		public void writeOut(Writer writer) throws IOException {
 			writer.write(">" + id + "\n");
-- 
1.7.10.2