datamodel/compbio/data/sequence/JpredAlignment.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  * Copyright (c) 2013 Alexander Sherstnev\r
   3  *  \r
   4  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\r
   5  * \r
   6  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   7  *  Apache License version 2 as published by the Apache Software Foundation\r
   8  * \r
   9  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
  10  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  11  *  License for more details.\r
  12  * \r
  13  *  A copy of the license is in apache_license.txt. It is also available here:\r
  14  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  15  * \r
  16  * Any republication or derived work distributed in source code form\r
  17  * must include this copyright and license notice.\r
  18  */\r
  19 \r
  20 package compbio.data.sequence;\r
  21 \r
  22 import java.util.List;\r
  23 import java.util.ArrayList;\r
  24 \r
  25 import javax.xml.bind.annotation.XmlAccessType;\r
  26 import javax.xml.bind.annotation.XmlAccessorType;\r
  27 \r
  28 import compbio.util.annotation.Immutable;\r
  29 import compbio.data.sequence.Alignment;\r
  30 /**\r
  31  * Multiple sequence alignment and Jpred prediction.\r
  32  * \r
  33  * Does not give any guarantees on the content of individual FastaSequece\r
  34  * records. It does not guarantee neither the uniqueness of the names of\r
  35  * sequences nor it guarantees the uniqueness of the sequences.\r
  36  * \r
  37  * @see FastaSequence\r
  38  * @see AlignmentMetadata\r
  39  * \r
  40  * @author pvtroshin\r
  41  * \r
  42  * @version 1.0 September 2009\r
  43  * \r
  44  */\r
  45 @XmlAccessorType(XmlAccessType.FIELD)\r
  46 @Immutable\r
  47 public final class JpredAlignment extends Alignment{\r
  48 \r
  49         private AlignmentMetadata metadata;\r
  50         private List<FastaSequence> sequences;\r
  51         \r
  52         FastaSequence jnetpred;\r
  53         FastaSequence JNETCONF;\r
  54         FastaSequence JNETSOL25;\r
  55         FastaSequence JNETSOL5;\r
  56         FastaSequence JNETSOL0;\r
  57         FastaSequence JNETHMM;\r
  58         FastaSequence JNETPSSM;\r
  59         FastaSequence JNETJURY;\r
  60 \r
  61         private JpredAlignment() {\r
  62                 // This has to has a default constructor for JaxB\r
  63         }\r
  64 \r
  65         /**\r
  66          * @param sequences\r
  67          * @param program\r
  68          * @param gapchar\r
  69          */\r
  70         public JpredAlignment(List<FastaSequence> sequences, Program program,\r
  71                         char gapchar) {\r
  72                 DecomposeInitalJpredSeq(sequences);\r
  73                 this.metadata = new AlignmentMetadata(Program.CLUSTAL, gapchar);\r
  74         }\r
  75 \r
  76         /**\r
  77          * \r
  78          * @param sequences\r
  79          * @param metadata\r
  80          */\r
  81         public JpredAlignment(List<FastaSequence> sequences, AlignmentMetadata metadata) {\r
  82                 DecomposeInitalJpredSeq(sequences);\r
  83                 this.metadata = metadata;\r
  84         }\r
  85 \r
  86         /**\r
  87          * \r
  88          * @param sequences\r
  89          */\r
  90         private void DecomposeInitalJpredSeq(List<FastaSequence> sequences) {\r
  91                 List<FastaSequence> realsequences = new ArrayList<FastaSequence>();\r
  92                 for (FastaSequence s : sequences) {\r
  93                         if (s.getId().equals("jnetpred")) {\r
  94                                 this.jnetpred = s;\r
  95                         } else if (s.getId().equals("JNETCONF")) {\r
  96                                 this.JNETCONF = s;\r
  97                         } else if (s.getId().equals("JNETSOL25")) {\r
  98                                 this.JNETSOL25 = s;\r
  99                         } else if (s.getId().equals("JNETSOL5")) {\r
 100                                 this.JNETSOL5 = s;\r
 101                         } else if (s.getId().equals("JNETSOL0")) {\r
 102                                 this.JNETSOL0 = s;\r
 103                         } else if (s.getId().equals("JNETHMM")) {\r
 104                                 this.JNETSOL0 = s;\r
 105                         } else if (s.getId().equals("JNETHMM")) {\r
 106                                 this.JNETHMM = s;\r
 107                         } else if (s.getId().equals("JNETSOL0")) {\r
 108                                 this.JNETPSSM = s;\r
 109                         } else if (s.getId().equals("JNETHMM")) {\r
 110                                 this.JNETJURY = s;\r
 111                         } else {\r
 112                                 realsequences.add(s);\r
 113                         }\r
 114                 }\r
 115                 this.sequences = realsequences;\r
 116         }\r
 117 \r
 118         /**\r
 119          * \r
 120          * @return Jpred prediction \r
 121          */\r
 122         public String getJpredPrediction() {\r
 123                 return this.jnetpred.getSequence();\r
 124         }\r
 125 \r
 126         /**\r
 127          * \r
 128          * @return Jpred JNETSOL25 line\r
 129          */\r
 130         public String getJpredSOL25() {\r
 131                 return this.JNETSOL25.getSequence();\r
 132         }\r
 133 \r
 134         /**\r
 135          * \r
 136          * @return Jpred JNETSOL5 line\r
 137          */\r
 138         public String getJpredSOL5() {\r
 139                 return this.JNETSOL5.getSequence();\r
 140         }\r
 141         /**\r
 142          * \r
 143          * @return Jpred JNETSOL0 line\r
 144          */\r
 145         public String getJpredSOL0() {\r
 146                 return this.JNETSOL0.getSequence();\r
 147         }\r
 148         /**\r
 149          * \r
 150          * @return Jpred JNETCONF line\r
 151          */\r
 152         public String getJpredJNETCONF() {\r
 153                 return this.JNETCONF.getSequence();\r
 154         }\r
 155         /**\r
 156          * \r
 157          * @return list of FastaSequence records\r
 158          */\r
 159         public List<FastaSequence> getSequences() {\r
 160                 return sequences;\r
 161         }\r
 162 \r
 163         /**\r
 164          * \r
 165          * @return a number of sequence in the alignment\r
 166          */\r
 167         public int getSize() {\r
 168                 return this.sequences.size();\r
 169         }\r
 170 \r
 171         /**\r
 172          * \r
 173          * @return AlignmentMetadata object\r
 174          */\r
 175         public AlignmentMetadata getMetadata() {\r
 176                 return metadata;\r
 177         }\r
 178 \r
 179         @Override\r
 180         public String toString() {\r
 181                 String sseq = "";\r
 182                 for (FastaSequence fs : getSequences()) {\r
 183                         sseq += fs.toString() + "\n";\r
 184                 }\r
 185                 return sseq;\r
 186         }\r
 187 \r
 188         @Override\r
 189         public int hashCode() {\r
 190                 final int prime = 31;\r
 191                 int result = 1;\r
 192                 result = prime * result\r
 193                                 + ((metadata == null) ? 0 : metadata.hashCode());\r
 194                 result = prime * result\r
 195                                 + ((sequences == null) ? 0 : sequences.hashCode());\r
 196                 return result;\r
 197         }\r
 198 \r
 199         /**\r
 200          * Please note that this implementation does not take the order of sequences\r
 201          * into account!\r
 202          */\r
 203         @Override\r
 204         public boolean equals(Object obj) {\r
 205                 if (obj == null) {\r
 206                         return false;\r
 207                 }\r
 208                 if (!(obj instanceof Alignment)) {\r
 209                         return false;\r
 210                 }\r
 211                 Alignment al = (Alignment) obj;\r
 212                 if (this.getSize() != al.getSize()) {\r
 213                         return false;\r
 214                 }\r
 215                 if (!this.getMetadata().equals(al.getMetadata())) {\r
 216                         return false;\r
 217                 }\r
 218                 int outerCounter = 0;\r
 219                 int matchCounter = 0;\r
 220                 for (FastaSequence fs : getSequences()) {\r
 221                         outerCounter++;\r
 222                         for (FastaSequence fs1 : al.getSequences()) {\r
 223                                 if (fs.equals(fs1)) {\r
 224                                         matchCounter++;\r
 225                                         continue;\r
 226                                 }\r
 227                         }\r
 228                         // Match for at lease one element was not found!\r
 229                         if (outerCounter != matchCounter) {\r
 230                                 return false;\r
 231                         }\r
 232                 }\r
 233 \r
 234                 return true;\r
 235         }\r
 236 \r
 237 }\r