Alifold results are now parsed and stored in a ScoreManager object

[jabaws.git] / datamodel / compbio / data / sequence / RNAstruct.java

diff --git a/datamodel/compbio/data/sequence/RNAstruct.java b/datamodel/compbio/data/sequence/RNAstruct.java
deleted file mode 100644 (file)
index 1e36064..0000000
--- a/datamodel/compbio/data/sequence/RNAstruct.java
+++ /dev/null
@@ -1,76 +0,0 @@
-package compbio.data.sequence;
-
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-
-import compbio.util.annotation.Immutable;
-
-/*
- * RNA secondary structure
- */
-
-@XmlAccessorType(XmlAccessType.FIELD)
-public final class RNAstruct {
-       
-       private String sequence;
-       private String structure; // needs to be array to deal with all output
-       private Float minEnergy;
-       private Float energySum1; private Float energySum2;
-       
-       
-       public RNAstruct() {
-               // default JaxB Constructor
-       }
-       
-       public RNAstruct(String sequence, String structure, Float minEnergy
-                       , Float energySum1, Float energySum2) {
-               this.sequence = sequence;
-               this.structure = structure;
-               this.minEnergy = minEnergy;
-               this.energySum1 = energySum1;
-               this.energySum2 = energySum2;
-       }
-       
-       public String getSequence() {
-               return sequence;
-       }
-       
-       public String getStructure() {
-               return structure;
-       }
-       
-       public Float getEnergy() {
-               return minEnergy;
-       }
-       
-       
-       @Override
-       public String toString() {
-               String newLine = System.getProperty("line.separator",".");
-               return sequence + newLine + structure + " (" + minEnergy.toString() 
-                               + " = " + energySum1.toString() + " +  " + energySum2.toString()
-                               + ")"; 
-       }
-       
-       @Override 
-       public boolean equals(Object obj) {
-               if (obj == null) {
-                       return false;
-               }
-               if (!(obj instanceof RNAstruct)) {
-                       return false;
-               }
-               RNAstruct st = (RNAstruct) obj;
-               if (!(this.getSequence() == st.getSequence() &&
-                               this.getStructure() == st.getStructure() &&
-                               this.getEnergy() == st.getEnergy())) {
-                       return false;
-               }
-               
-               return true;
-       }
-}
-
-