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 public final class JpredAlignment extends Alignment{\r
  47 \r
  48         private JpredAlignment() {\r
  49                 // This has to has a default constructor for JaxB\r
  50         }\r
  51 \r
  52         /**\r
  53          * @param sequences\r
  54          * @param program\r
  55          * @param gapchar\r
  56          */\r
  57         public JpredAlignment(List<FastaSequence> sequences, Program program, char gapchar) {\r
  58                 this.sequences = sequences;\r
  59                 this.metadata = new AlignmentMetadata(Program.Jpred, gapchar);\r
  60         }\r
  61 \r
  62         /**\r
  63          * \r
  64          * @param sequences\r
  65          * @param metadata\r
  66          */\r
  67         public JpredAlignment(List<FastaSequence> sequences, AlignmentMetadata metadata) {\r
  68                 this.sequences = sequences;\r
  69                 this.metadata = metadata;\r
  70         }\r
  71 \r
  72         private List<FastaSequence> getRealSeqs() {\r
  73                 List<FastaSequence> realsequences = new ArrayList<FastaSequence>();\r
  74                 for (FastaSequence s : this.sequences) {\r
  75                         if (s.getId().equals("jnetpred") || \r
  76                                 s.getId().equals("JNETCONF") ||\r
  77                                 s.getId().equals("JNETSOL25") ||\r
  78                                 s.getId().equals("JNETSOL5") ||\r
  79                                 s.getId().equals("JNETSOL0") ||\r
  80                                 s.getId().equals("JNETHMM") ||\r
  81                                 s.getId().equals("JNETHMM") ||\r
  82                                 s.getId().equals("JNETSOL0") ||\r
  83                                 s.getId().equals("JNETHMM")) {\r
  84                                 // do nothing;\r
  85                         } else {\r
  86                                 realsequences.add(s);\r
  87                         }\r
  88                 }\r
  89                 return realsequences;\r
  90         }\r
  91 \r
  92 \r
  93         public List<FastaSequence> getJpredSequences() {\r
  94                 List<FastaSequence> realsequences = new ArrayList<FastaSequence>();\r
  95                 for (FastaSequence s : this.sequences) {\r
  96                         if (s.getId().equals("jnetpred") || \r
  97                                 s.getId().equals("JNETCONF") ||\r
  98                                 s.getId().equals("JNETSOL25") ||\r
  99                                 s.getId().equals("JNETSOL5") ||\r
 100                                 s.getId().equals("JNETSOL0") ||\r
 101                                 s.getId().equals("JNETHMM") ||\r
 102                                 s.getId().equals("JNETHMM") ||\r
 103                                 s.getId().equals("JNETSOL0") ||\r
 104                                 s.getId().equals("JNETSOL0") ||\r
 105                                 s.getId().equals("QUERY")) {\r
 106                                 realsequences.add(s);\r
 107                         }\r
 108                 }\r
 109                 return realsequences;\r
 110         }\r
 111         /**\r
 112          * \r
 113          * @return Jpred prediction \r
 114          */\r
 115         public String getJpredPrediction() {\r
 116                 for (FastaSequence s : this.sequences) {\r
 117                         if (s.getId().equals("jnetpred")) {\r
 118                           return s.getSequence();\r
 119                         }\r
 120                 }\r
 121                 return new String("");\r
 122         }\r
 123 \r
 124         /**\r
 125          * \r
 126          * @return Jpred JNETSOL25 line\r
 127          */\r
 128         public String getJpredSOL25() {\r
 129                 for (FastaSequence s : this.sequences) {\r
 130                         if (s.getId().equals("JNETSOL25")) {\r
 131                           return s.getSequence();\r
 132                         }\r
 133                 }\r
 134                 return new String("");\r
 135         }\r
 136 \r
 137         /**\r
 138          * \r
 139          * @return Jpred JNETSOL5 line\r
 140          */\r
 141         public String getJpredSOL5() {\r
 142                 for (FastaSequence s : this.sequences) {\r
 143                         if (s.getId().equals("JNETSOL5")) {\r
 144                           return s.getSequence();\r
 145                         }\r
 146                 }\r
 147                 return new String("");\r
 148         }\r
 149         /**\r
 150          * \r
 151          * @return Jpred JNETSOL0 line\r
 152          */\r
 153         public String getJpredSOL0() {\r
 154                 for (FastaSequence s : this.sequences) {\r
 155                         if (s.getId().equals("JNETSOL0")) {\r
 156                           return s.getSequence();\r
 157                         }\r
 158                 }\r
 159                 return new String("");\r
 160         }\r
 161         /**\r
 162          * \r
 163          * @return Jpred JNETCONF line\r
 164          */\r
 165         public String getJpredJNETCONF() {\r
 166                 for (FastaSequence s : this.sequences) {\r
 167                         if (s.getId().equals("JNETCONF")) {\r
 168                           return s.getSequence();\r
 169                         }\r
 170                 }\r
 171                 return new String("");\r
 172         }\r
 173 \r
 174         /**\r
 175          * \r
 176          * @return list of FastaSequence records\r
 177          */\r
 178         @Override\r
 179         public List<FastaSequence> getSequences() {\r
 180                 return this.getRealSeqs();\r
 181         }\r
 182 \r
 183         /**\r
 184          * \r
 185          * @return a number of sequence in the alignment\r
 186          */\r
 187         @Override\r
 188         public int getSize() {\r
 189                 return this.getRealSeqs().size();\r
 190         }\r
 191 \r
 192         /**\r
 193          * Please note that this implementation does not take the order of sequences\r
 194          * into account!\r
 195          */\r
 196         @Override\r
 197         public boolean equals(Object obj) {\r
 198                 if (obj == null) {\r
 199                         return false;\r
 200                 }\r
 201                 if (!(obj instanceof JpredAlignment)) {\r
 202                         return false;\r
 203                 }\r
 204                 JpredAlignment al = (JpredAlignment) obj;\r
 205                 if (this.getSize() != al.getSize()) {\r
 206                         return false;\r
 207                 }\r
 208                 if (!this.getMetadata().equals(al.getMetadata())) {\r
 209                         return false;\r
 210                 }\r
 211                 int outerCounter = 0;\r
 212                 int matchCounter = 0;\r
 213                 for (FastaSequence fs : getSequences()) {\r
 214                         outerCounter++;\r
 215                         for (FastaSequence fs1 : al.getSequences()) {\r
 216                                 if (fs.equals(fs1)) {\r
 217                                         matchCounter++;\r
 218                                         continue;\r
 219                                 }\r
 220                         }\r
 221                         // Match for at lease one element was not found!\r
 222                         if (outerCounter != matchCounter) {\r
 223                                 return false;\r
 224                         }\r
 225                 }\r
 226                 return true;\r
 227         }\r
 228 \r
 229 }\r