datamodel/compbio/data/sequence/RNAStructScoreManager.java

   1 package compbio.data.sequence;\r
   2 \r
   3 \r
   4 import java.io.IOException;\r
   5 import java.io.Writer;\r
   6 import java.util.ArrayList;\r
   7 import java.util.Iterator;\r
   8 import java.util.List;\r
   9 import java.util.Map;\r
  10 import java.util.Set;\r
  11 import java.util.TreeMap;\r
  12 import java.util.TreeSet;\r
  13 \r
  14 import javax.xml.bind.annotation.XmlAccessType;\r
  15 import javax.xml.bind.annotation.XmlAccessorType;\r
  16 import javax.xml.bind.annotation.XmlTransient;\r
  17 \r
  18 import compbio.data.sequence.ScoreManager.ScoreHolder;\r
  19 import compbio.util.SysPrefs;\r
  20 \r
  21 @XmlAccessorType(XmlAccessType.FIELD)\r
  22 public class RNAStructScoreManager extends ScoreManager {\r
  23 \r
  24         \r
  25         private RNAStructScoreManager() {\r
  26                 //Default JAXB constructor\r
  27         }\r
  28         \r
  29 \r
  30         public RNAStructScoreManager(List<String> structs, List<TreeSet<Score>> data) {\r
  31                 assert(structs.size() == data.size());\r
  32                 \r
  33                 List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
  34                 \r
  35                 for (int i = 0; i < structs.size(); i++) {\r
  36                         seqScores.add(new ScoreHolder(structs.get(i), data.get(i)));\r
  37                 }\r
  38                 this.seqScores = seqScores;\r
  39         }\r
  40         \r
  41         // I put this in purely because it mirrors a method in ScoreManager, not because I need it :/\r
  42         public static RNAStructScoreManager newInstance(List<String> structs, List<TreeSet<Score>> data) {\r
  43                 return new RNAStructScoreManager(structs, data);\r
  44         }\r
  45         \r
  46         public List<String> getStructs() {\r
  47                 List<String> structs = new ArrayList<String>();\r
  48                 for (ScoreHolder sch : this.seqScores) {\r
  49                         structs.add(sch.id);\r
  50                 }\r
  51                 return structs;\r
  52         }\r
  53         \r
  54         public List<TreeSet<Score>> getData() {\r
  55                 List<TreeSet<Score>> data = new ArrayList<TreeSet<Score>>();\r
  56                 for (ScoreHolder sch : this.seqScores) {\r
  57                         data.add(sch.scores);\r
  58                 }\r
  59                 return data;\r
  60         }\r
  61 \r
  62         // Send this data Structure back to something approximating the stdoutFile\r
  63         // with extra information from alifold.out\r
  64         @Override\r
  65         public String toString() {\r
  66                 String out = "";\r
  67                 // The first objects hold the Consensus Alignment and the alifold.out info\r
  68                 out += this.getStructs().get(0) + SysPrefs.newlinechar;\r
  69 \r
  70                 // Now the rest of the structures with energies/frequencies\r
  71                 for (int i = 1; i < this.getStructs().size(); i++) {\r
  72                         out = out + this.getStructs().get(i).toString();\r
  73 \r
  74                         if (this.getData().get(i).first().getScores().size() > 0) {\r
  75                                 List<Float> scores = this.getData().get(i).first().getScores();\r
  76                                 if (scores.size() >= 3) {\r
  77                                         out = out + " (" + scores.get(0).toString() + " = " \r
  78                                                         + scores.get(1).toString() + " + " + scores.get(2).toString()\r
  79                                                         + ")" + SysPrefs.newlinechar;\r
  80                                 }\r
  81                                 else if (this.getData().get(i).first().getMethod().equals("alifoldMEA")) {\r
  82                                         out = out + " { " + scores.get(0).toString() + " MEA=" \r
  83                                                         + scores.get(1).toString() + "}" + SysPrefs.newlinechar;\r
  84                                 }\r
  85                                 else if (scores.size() >= 2) {\r
  86                                         out = out + " [" + scores.get(0).toString() + ", " \r
  87                                                         + scores.get(1).toString() + "]" + SysPrefs.newlinechar;\r
  88 \r
  89                                 }\r
  90                         } else out += SysPrefs.newlinechar; \r
  91                 }\r
  92                 if (this.getData().get(0).first().getScores().size() > 0) {\r
  93                         Iterator<Score> iScores = this.getData().get(0).iterator();\r
  94                         out += "Base Pairings followed by probability" + SysPrefs.newlinechar;\r
  95                         for (int i = 0; i < this.getData().get(0).size(); i++) {\r
  96                                 Score s = iScores.next();\r
  97                                 Range r = s.getRanges().first();\r
  98                                 Float score = s.getScores().get(0);\r
  99                                 out += String.format("%4d  %4d    %.1f%n", r.getFrom(), r.getTo(),\r
 100                                                 score);\r
 101                         }\r
 102                 }\r
 103 \r
 104 \r
 105                 return out;\r
 106         }\r
 107 \r
 108         @Override \r
 109         public boolean equals(Object obj) {\r
 110                 if (obj == null) {\r
 111                         return false;\r
 112                 }\r
 113                 if (!(obj instanceof RNAStructScoreManager)) {\r
 114                         return false;\r
 115                 }\r
 116                 RNAStructScoreManager other = (RNAStructScoreManager) obj;\r
 117                 if (this.getStructs() == null) {\r
 118                         if (other.getStructs() != null) {\r
 119                                 return false;\r
 120                         }\r
 121                 } else if (!this.getStructs().equals(other.getStructs()))\r
 122                         return false;\r
 123                 if (this.getData() == null) {\r
 124                         if (other.getData() != null)\r
 125                                 return false;\r
 126                 } else if (!this.getData().equals(other.getData()))\r
 127                         return false;\r
 128 \r
 129                 return true;\r
 130         }\r
 131 }\r