cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/SingleReadAlignment.java

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.cdm.model.molecular;
   5
   6 import javax.persistence.Entity;
   7 import javax.persistence.FetchType;
   8 import javax.persistence.Lob;
   9 import javax.persistence.ManyToOne;
  10 import javax.xml.bind.annotation.XmlAccessType;
  11 import javax.xml.bind.annotation.XmlAccessorType;
  12 import javax.xml.bind.annotation.XmlElement;
  13 import javax.xml.bind.annotation.XmlIDREF;
  14 import javax.xml.bind.annotation.XmlRootElement;
  15 import javax.xml.bind.annotation.XmlSchemaType;
  16 import javax.xml.bind.annotation.XmlType;
  17
  18 import org.hibernate.annotations.Cascade;
  19 import org.hibernate.annotations.CascadeType;
  20 import org.hibernate.annotations.Type;
  21 import org.hibernate.envers.Audited;
  22
  23 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  24
  25 /**
  26  * @author a.mueller
  27  */
  28 @XmlAccessorType(XmlAccessType.FIELD)
  29 @XmlType(name = "SingleReadAlignment", propOrder = {
  30         "consensusAlignment",
  31         "singleRead",
  32         "shifts",
  33         "editedSequence",
  34         "reverseComplement"
  35 })
  36 @XmlRootElement(name = "SingleReadAlignment")
  37 @Entity
  38 @Audited
  39 public class SingleReadAlignment extends VersionableEntity {
  40         private static final long serialVersionUID = 6141518347067279304L;
  41
  42         /** @see #getDnaMarker() */
  43         @XmlElement(name = "ConsensusAlignment")
  44     @XmlIDREF
  45     @XmlSchemaType(name = "IDREF")
  46     @ManyToOne(fetch = FetchType.LAZY)
  47         //for now we do not cascade but expect the user to save the sequence manually
  48         private Sequence consensusAlignment;
  49
  50         /** @see #getDnaMarker() */
  51         @XmlElement(name = "SingleRead")
  52     @XmlIDREF
  53     @XmlSchemaType(name = "IDREF")
  54     @ManyToOne(fetch = FetchType.LAZY)
  55         @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
  56         private SingleRead singleRead;
  57
  58         //TODO XML mapping / user type
  59         @Type(type="shiftUserType")
  60     private Shift[] shifts;
  61
  62         @XmlElement(name = "EditedSequence")
  63     @Lob
  64     private String editedSequence;
  65
  66         @XmlElement(name = "ReverseComplement")
  67     private boolean reverseComplement;
  68
  69
  70         public static class Shift{
  71                 public int position;
  72                 public int shift;
  73
  74                 public Shift(){};
  75                 public Shift(int position, int steps) {
  76                         this.position = position;
  77                         this.shift = steps;
  78                 }
  79
  80                 @Override
  81                 public String toString(){
  82                         return String.valueOf(position) + "," + String.valueOf(shift);
  83                 }
  84         }
  85
  86 //****************** FACTORY *******************/
  87
  88         public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead){
  89                 return new SingleReadAlignment(consensusSequence, singleRead, null, null);
  90         }
  91
  92         public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead,
  93                         Shift[] shifts, String editedSequence){
  94                 return new SingleReadAlignment(consensusSequence, singleRead, shifts, editedSequence);
  95         }
  96
  97 // ***************** CONSTRUCTOR *************************/
  98
  99         protected SingleReadAlignment(){};
 100
 101         private SingleReadAlignment(Sequence consensusAlignment, SingleRead singleRead,
 102                         Shift[] shifts, String editedSequence){
 103                 setConsensusAlignment(consensusAlignment);
 104                 setSingleRead(singleRead);
 105                 this.shifts = shifts;
 106                 this.editedSequence = editedSequence;
 107         }
 108
 109
 110 // ****************** GETTER / SETTER ***********************/
 111
 112         //consensus sequence
 113         public Sequence getConsensusSequence() {
 114                 return consensusAlignment;
 115         }
 116         public void setConsensusAlignment(Sequence consensusAlignment) {
 117                 if (this.consensusAlignment != null && this.consensusAlignment.getSingleReadAlignments().contains(this)){
 118                         this.consensusAlignment.removeSingleReadAlignment(this);
 119                 }
 120                 this.consensusAlignment = consensusAlignment;
 121                 if (consensusAlignment != null && ! consensusAlignment.getSingleReadAlignments().contains(this)){
 122                         consensusAlignment.addSingleReadAlignment(this);
 123                 }
 124         }
 125
 126         public SingleRead getSingleRead() {
 127                 return singleRead;
 128         }
 129         public void setSingleRead(SingleRead singleRead) {
 130 //              if (this.singleRead != null xxx){
 131 //                      this.singleRead.removeSingleReadAlignment(this);
 132 //              }
 133                 this.singleRead = singleRead;
 134 //              if (singleRead != null && singleRead.getSingleReadAlignments().contains(this)){
 135 //                      singleRead.addSingleReadAlignment(this);
 136 //              }
 137         }
 138
 139         //shifts
 140         public Shift[] getShifts() {
 141                 return shifts;
 142         }
 143         public void setShifts(Shift[] shifts) {
 144                 this.shifts = shifts;
 145         }
 146
 147         //edited sequence
 148         public String getEditedSequence() {
 149                 return editedSequence;
 150         }
 151
 152         public void setEditedSequence(String editedSequence) {
 153                 this.editedSequence = editedSequence;
 154         }
 155
 156 // ******************* CLONE *********************/
 157
 158
 159
 160         @Override
 161         public Object clone() throws CloneNotSupportedException {
 162                 //all objects can be reused
 163                 return super.clone();
 164         }
 165 }