X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=datamodel%2Fcompbio%2Fdata%2Fsequence%2FRNAStructScoreManager.java;fp=datamodel%2Fcompbio%2Fdata%2Fsequence%2FRNAStructScoreManager.java;h=3fb856c183a02eed9f62c112f8669258e5d7fcdb;hb=191ed00f52901ed7ee6d1137637e66c999913be8;hp=0000000000000000000000000000000000000000;hpb=711409a4b2322afb918d091fb602379f3b36d311;p=jabaws.git

diff --git a/datamodel/compbio/data/sequence/RNAStructScoreManager.java b/datamodel/compbio/data/sequence/RNAStructScoreManager.java
new file mode 100644
index 0000000..3fb856c
--- /dev/null
+++ b/datamodel/compbio/data/sequence/RNAStructScoreManager.java
@@ -0,0 +1,131 @@
+package compbio.data.sequence;
+
+
+import java.io.IOException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlTransient;
+
+import compbio.data.sequence.ScoreManager.ScoreHolder;
+import compbio.util.SysPrefs;
+
+@XmlAccessorType(XmlAccessType.FIELD)
+public class RNAStructScoreManager extends ScoreManager {
+
+	
+	private RNAStructScoreManager() {
+		//Default JAXB constructor
+	}
+	
+
+	public RNAStructScoreManager(List<String> structs, List<TreeSet<Score>> data) {
+		assert(structs.size() == data.size());
+		
+		List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();
+		
+		for (int i = 0; i < structs.size(); i++) {
+			seqScores.add(new ScoreHolder(structs.get(i), data.get(i)));
+		}
+		this.seqScores = seqScores;
+	}
+	
+	// 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);
+	}
+	
+	public List<String> getStructs() {
+		List<String> structs = new ArrayList<String>();
+		for (ScoreHolder sch : this.seqScores) {
+			structs.add(sch.id);
+		}
+		return structs;
+	}
+	
+	public List<TreeSet<Score>> getData() {
+		List<TreeSet<Score>> data = new ArrayList<TreeSet<Score>>();
+		for (ScoreHolder sch : this.seqScores) {
+			data.add(sch.scores);
+		}
+		return data;
+	}
+
+	// Send this data Structure back to something approximating the stdoutFile
+	// with extra information from alifold.out
+	@Override
+	public String toString() {
+		String out = "";
+		// The first objects hold the Consensus Alignment and the alifold.out info
+		out += this.getStructs().get(0) + SysPrefs.newlinechar;
+
+		// Now the rest of the structures with energies/frequencies
+		for (int i = 1; i < this.getStructs().size(); i++) {
+			out = out + this.getStructs().get(i).toString();
+
+			if (this.getData().get(i).first().getScores().size() > 0) {
+				List<Float> scores = this.getData().get(i).first().getScores();
+				if (scores.size() >= 3) {
+					out = out + " (" + scores.get(0).toString() + " = " 
+							+ scores.get(1).toString() + " + " + scores.get(2).toString()
+							+ ")" + SysPrefs.newlinechar;
+				}
+				else if (this.getData().get(i).first().getMethod().equals("alifoldMEA")) {
+					out = out + " { " + scores.get(0).toString() + " MEA=" 
+							+ scores.get(1).toString() + "}" + SysPrefs.newlinechar;
+				}
+				else if (scores.size() >= 2) {
+					out = out + " [" + scores.get(0).toString() + ", " 
+							+ scores.get(1).toString() + "]" + SysPrefs.newlinechar;
+
+				}
+			} else out += SysPrefs.newlinechar; 
+		}
+		if (this.getData().get(0).first().getScores().size() > 0) {
+			Iterator<Score> iScores = this.getData().get(0).iterator();
+			out += "Base Pairings followed by probability" + SysPrefs.newlinechar;
+			for (int i = 0; i < this.getData().get(0).size(); i++) {
+				Score s = iScores.next();
+				Range r = s.getRanges().first();
+				Float score = s.getScores().get(0);
+				out += String.format("%4d  %4d    %.1f%n", r.getFrom(), r.getTo(),
+						score);
+			}
+		}
+
+
+		return out;
+	}
+
+	@Override 
+	public boolean equals(Object obj) {
+		if (obj == null) {
+			return false;
+		}
+		if (!(obj instanceof RNAStructScoreManager)) {
+			return false;
+		}
+		RNAStructScoreManager other = (RNAStructScoreManager) obj;
+		if (this.getStructs() == null) {
+			if (other.getStructs() != null) {
+				return false;
+			}
+		} else if (!this.getStructs().equals(other.getStructs()))
+			return false;
+		if (this.getData() == null) {
+			if (other.getData() != null)
+				return false;
+		} else if (!this.getData().equals(other.getData()))
+			return false;
+
+		return true;
+	}
+}