src/jalview/ws/jws2/RNAalifoldClient.java

   1 package jalview.ws.jws2;
   2
   3 import jalview.api.AlignCalcWorkerI;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.Annotation;
   6 import jalview.gui.AlignFrame;
   7 import jalview.ws.jws2.jabaws2.Jws2Instance;
   8 import jalview.ws.params.WsParamSetI;
   9
  10 import java.util.ArrayList;
  11 import java.util.Iterator;
  12 import java.util.List;
  13 import java.util.Map;
  14 import java.util.TreeMap;
  15 import java.util.TreeSet;
  16
  17 import compbio.data.msa.jaxws.Align;
  18 import compbio.data.sequence.Range;
  19 import compbio.data.sequence.Score;
  20 import compbio.data.sequence.RNAStructScoreManager;
  21 import compbio.data.sequence.ScoreManager;
  22 import compbio.metadata.Argument;
  23
  24 public class RNAalifoldClient extends JabawsAlignCalcWorker implements
  25                 AlignCalcWorkerI
  26 {
  27
  28         String methodName;
  29
  30         AlignFrame af;
  31
  32         public RNAalifoldClient(Jws2Instance sh, AlignFrame alignFrame,
  33                         WsParamSetI preset, List<Argument> paramset)
  34         {
  35                 super(sh, alignFrame, preset, paramset);
  36
  37
  38                 af = alignFrame;
  39
  40                 methodName = sh.serviceType;
  41
  42         }
  43
  44          @Override
  45           public String getServiceActionText()
  46           {
  47             return "Submitting RNA alignment for Secondary Structure prediction using"
  48                         + "RNAalifold Service";
  49           }
  50
  51         @Override
  52         public void updateResultAnnotation(boolean immediate)
  53         {
  54
  55                 if (immediate || !calcMan.isWorking(this) && scoremanager != null)
  56                 {
  57
  58
  59
  60                         List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
  61 //                      ourAnnots = new ArrayList<AlignmentAnnotation>();
  62
  63                         // So I don't have to do any more casting
  64                         List<String> structs = ((RNAStructScoreManager) scoremanager).getStructs();
  65                         List<TreeSet<Score>> data = ((RNAStructScoreManager) scoremanager).getData();
  66
  67                         // Deal with the consensus structure and (?)BasePair Probabilities
  68                         Annotation[] anns = new Annotation[structs.get(1).length()];
  69
  70                         // check if the first Score object is populated with base pair probabilities
  71                         Score fscore = data.get(0).first();
  72                         boolean BPScores = (fscore.getScores().size() > 0
  73                                         && fscore.getRanges() != null);
  74
  75                         TreeMap<Range, Float> basePairs = null;
  76                         if (BPScores) {
  77                                 // The base pair probabilities are stored in a set in scoremanager... we want a map
  78                                 basePairs = new TreeMap<Range, Float>();
  79                                 for (Score score : data.get(0)) {
  80                                         // The Score objects contain a set of size one containing the range and
  81                                         //  an ArrayList<float> of size one containing the probabilty
  82                                         basePairs.put(score.getRanges().first(), new Float(score.getScores().get(0)));
  83                                 }
  84                         }
  85
  86                         // ignoring the Consensus alignemnt for now, get the Structure and make an AlignmentAnnotation
  87                         String struct = structs.get(1);
  88                         for (int i = 0; i < struct.length(); i++) {
  89
  90                                 if (BPScores) {
  91                                         // Return all the contacts associated with position i
  92                                         List<Range> contacts = isContact(basePairs, i+1);
  93
  94                                         if (contacts.size() == 0) {
  95                                                 anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), 0f);
  96                                         }
  97                                         else if (contacts.size() == 1) {
  98                                                 // There is only one contact associated with this base
  99                                                 float prob = basePairs.get(contacts.get(i));
 100                                                 anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), prob);
 101                                         }
 102                                         else if (contacts.size() > 1) {
 103                                                 // For now we will simply deal with alternate contact information by mentioning its
 104                                                 //  existance in the description
 105                                                 float prob = basePairs.get(contacts.get(i));
 106                                                 anns[i] = new Annotation(struct.substring(i, i+1), "This base has alternate contact(s)",
 107                                                                 struct.charAt(i), prob);
 108                                         }
 109                                 }
 110                                 else {
 111                                         // Same as the first if from the previous block
 112                                         anns[i] = new Annotation(struct.substring(i, i+1), "", struct.charAt(i), 0f);
 113                                 }
 114                         }
 115
 116                         AlignmentAnnotation annot = new AlignmentAnnotation("Consensus Structure", "Free Energy", anns);
 117                         annot.setScore(data.get(1).first().getScores().get(0));
 118
 119                         if (ourAnnot.size() > 0) {
 120                                 updateOurAnnots(ourAnnot);
 121                         }
 122
 123                 }
 124         }
 125
 126         // Check whether, at position i there is a base contact and return all the
 127         //  contacts at this position. Should be in order of descending probability.
 128         private List<Range> isContact(TreeMap<Range, Float> basePairs, int i) {
 129
 130                 List<Range> contacts = new ArrayList<Range>();
 131
 132                 for (Range contact : basePairs.keySet()) {
 133                         // finds the contacts associtated with position i ordered by the natural
 134                         //  ordering of the Scores TreeSet in ScoreManager which is, descending probability
 135                         if (contact.from == i || contact.to == i) contacts.add(contact);
 136                 }
 137
 138                 return contacts;
 139         }
 140 }