datamodel/compbio/data/sequence/RNAStruct.java

   1 package compbio.data.sequence;
   2
   3 import java.util.List;
   4 import java.util.Iterator;
   5 import java.util.Set;
   6 import java.util.TreeSet;
   7 import java.util.List;
   8 import java.util.ArrayList;
   9
  10 import javax.xml.bind.annotation.XmlAccessType;
  11 import javax.xml.bind.annotation.XmlAccessorType;
  12
  13 import compbio.util.annotation.Immutable;
  14 import compbio.util.SysPrefs;
  15 import compbio.data.sequence.Score;
  16
  17 /*
  18  * RNA secondary structure
  19  * A class which is essentially just a Pair(List<String>, List<Set<Score>>)
  20  * For the purpose of creating and retrieving data from ScoreManager Objects
  21  * which are being used to store RNA folding output
  22  */
  23
  24 @XmlAccessorType(XmlAccessType.FIELD)
  25 public final class RNAStruct {
  26
  27         private List<String> structs = new ArrayList<String>();
  28         private List<TreeSet<Score>> data = new ArrayList<TreeSet<Score>>();
  29
  30
  31         public RNAStruct() {
  32                 // default JaxB Constructor
  33         }
  34
  35         public RNAStruct(List<String> structs, List<TreeSet<Score>> data) {
  36                 assert(structs.size() == data.size());
  37                 this.structs = structs;
  38                 this.data = data;
  39         }
  40
  41         public List<String> getStructs() {
  42                 return structs;
  43         }
  44
  45         public List<TreeSet<Score>> getData() {
  46                 return data;
  47         }
  48
  49         // Send this data Structure back to something approximating the stdoutFile
  50         // with extra information from alifold.out
  51         @Override
  52         public String toString() {
  53                 String out = "";
  54                 // The first objects hold the Consensus Alignment and the alifold.out info
  55                 out += structs.get(0) + SysPrefs.newlinechar;
  56
  57                 // Now the rest of the structures with energies/frequencies
  58                 for (int i = 1; i < structs.size(); i++) {
  59                         out = out + structs.get(i).toString();
  60
  61                         if (data.get(i).first().getScores().size() > 0) {
  62                                 List<Float> scores = data.get(i).first().getScores();
  63                                 if (scores.size() >= 3) {
  64                                         out = out + " (" + scores.get(0).toString() + " = "
  65                                                         + scores.get(1).toString() + " + " + scores.get(2).toString()
  66                                                         + ")" + SysPrefs.newlinechar;
  67                                 }
  68                                 else if (data.get(i).first().getMethod().equals("alifoldMEA")) {
  69                                         out = out + " { " + scores.get(0).toString() + " MEA="
  70                                                         + scores.get(1).toString() + "}" + SysPrefs.newlinechar;
  71                                 }
  72                                 else if (scores.size() >= 2) {
  73                                         out = out + " [" + scores.get(0).toString() + ", "
  74                                                         + scores.get(1).toString() + "]" + SysPrefs.newlinechar;
  75
  76                                 }
  77                         } else out += SysPrefs.newlinechar;
  78                 }
  79                 if (data.get(0).first().getScores().size() > 0) {
  80                         Iterator<Score> iScores = data.get(0).iterator();
  81                         out += "Base Pairings followed by probability" + SysPrefs.newlinechar;
  82                         for (int i = 0; i < data.get(0).size(); i++) {
  83                                 Score s = iScores.next();
  84                                 Range r = s.getRanges().first();
  85                                 Float score = s.getScores().get(0);
  86                                 out += String.format("%4d  %4d    %.1f%n", r.getFrom(), r.getTo(),
  87                                                 score);
  88                         }
  89                 }
  90
  91                 return out;
  92         }
  93
  94         @Override
  95         public boolean equals(Object obj) {
  96                 if (obj == null) {
  97                         return false;
  98                 }
  99                 if (!(obj instanceof RNAStruct)) {
 100                         return false;
 101                 }
 102                 RNAStruct other = (RNAStruct) obj;
 103                 if (structs == null) {
 104                         if (other.structs != null) {
 105                                 return false;
 106                         }
 107                 } else if (!structs.equals(other.structs))
 108                         return false;
 109                 if (data == null) {
 110                         if (other.data != null)
 111                                 return false;
 112                 } else if (!data.equals(other.data))
 113                         return false;
 114
 115                 return true;
 116         }
 117 }
 118
 119