srcjar/fr/orsay/lri/varna/models/treealign/RNANodeValue2.java

   1 package fr.orsay.lri.varna.models.treealign;
   2 import java.util.ArrayList;
   3 import java.util.List;
   4
   5
   6
   7 /**
   8  * In this model, nodes are either:
   9  * 1. a couple of paired bases, and in that case they may have children,
  10  *    in this case singleNode is true
  11  * 2. a single base that comes from a broken base pair
  12  *    (broken during planarization), without children,
  13  *    in this case singleNode is true
  14  * 3. a list of consecutive non-paired bases, without children.
  15  *    in this case singleNode is false
  16  * Note that case 2 happens only if original sequences contained
  17  * pseudoknots, otherwise this case can be ignored.
  18  *
  19  * @author Raphael Champeimont
  20  *
  21  */
  22 public class RNANodeValue2 implements GraphvizDrawableNodeValue {
  23         /**
  24          * Says whether we have a single node or a list of nodes.
  25          */
  26         private boolean singleNode = true;
  27
  28         /**
  29          * Defined if singleNode is true.
  30          */
  31         private RNANodeValue node;
  32
  33         /**
  34          * Defined if singleNode is false;
  35          */
  36         private List<RNANodeValue> nodes;
  37
  38         public RNANodeValue2(boolean singleNode) {
  39                 this.singleNode = singleNode;
  40                 if (singleNode) {
  41                         node = new RNANodeValue();
  42                 } else {
  43                         nodes = new ArrayList<RNANodeValue>();
  44                 }
  45         }
  46
  47         /**
  48          * In case of a single node, return it.
  49          * Will throw RNANodeValue2WrongTypeException if singleNode = false.
  50          */
  51         public RNANodeValue getNode() {
  52                 if (singleNode) {
  53                         return node;
  54                 } else {
  55                         throw (new RNANodeValue2WrongTypeException());
  56                 }
  57         }
  58
  59         public void setNode(RNANodeValue node) {
  60                 if (singleNode) {
  61                         this.node = node;
  62                 } else {
  63                         throw (new RNANodeValue2WrongTypeException());
  64                 }
  65         }
  66
  67         /**
  68          * In case of multiple nodes, return them.
  69          * Will throw RNANodeValue2WrongTypeException if singleNode = true.
  70          */
  71         public List<RNANodeValue> getNodes() {
  72                 if (!singleNode) {
  73                         return nodes;
  74                 } else {
  75                         throw (new RNANodeValue2WrongTypeException());
  76                 }
  77         }
  78         /**
  79          * In case of multiple nodes, return the sequence of nucleotides.
  80          */
  81         public char[] computeSequence() {
  82                 if (!singleNode) {
  83                         final int n = nodes.size();
  84                         char[] sequence = new char[n];
  85                         for (int i=0; i<n; i++) {
  86                                 sequence[i] = nodes.get(i).getLeftNucleotide().charAt(0);
  87                         }
  88                         return sequence;
  89                 } else {
  90                         throw (new RNANodeValue2WrongTypeException());
  91                 }
  92         }
  93
  94         public void setNodes(List<RNANodeValue> nodes) {
  95                 if (!singleNode) {
  96                         this.nodes = nodes;
  97                 } else {
  98                         throw (new RNANodeValue2WrongTypeException());
  99                 }
 100         }
 101
 102         public boolean isSingleNode() {
 103                 return singleNode;
 104         }
 105
 106         public String toString() {
 107                 if (singleNode) {
 108                         return node.toString();
 109                 } else {
 110                         String s = "";
 111                         for (RNANodeValue node: nodes) {
 112                                 if (s != "") {
 113                                         s += " ";
 114                                 }
 115                                 s += node.toString();
 116                         }
 117                         return s;
 118                 }
 119         }
 120
 121         public String toGraphvizNodeName() {
 122                 if (singleNode) {
 123                         return node.toGraphvizNodeName();
 124                 } else {
 125                         String s = "";
 126                         for (RNANodeValue node: nodes) {
 127                                 if (s != "") {
 128                                         s += " ";
 129                                 }
 130                                 s += node.toGraphvizNodeName();
 131                         }
 132                         return s;
 133                 }
 134         }
 135
 136 }