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 = new Shift[0];
  61
  62
  63         private Integer firstSeqPosition;
  64
  65         private Integer leftCutPosition;
  66
  67         private Integer rightCutPosition;
  68
  69         @XmlElement(name = "EditedSequence")
  70     @Lob
  71     private String editedSequence;
  72
  73         @XmlElement(name = "ReverseComplement")
  74     private boolean reverseComplement;
  75
  76
  77         public static class Shift implements Cloneable{
  78                 public int position;
  79                 public int shift;
  80
  81                 public Shift(){};
  82                 public Shift(int position, int steps) {
  83                         this.position = position;
  84                         this.shift = steps;
  85                 }
  86
  87                 @Override
  88                 public String toString(){
  89                         return String.valueOf(position) + "," + String.valueOf(shift);
  90                 }
  91                 @Override
  92                 protected Object clone() throws CloneNotSupportedException {
  93                         return super.clone();
  94                 }
  95         }
  96
  97 //****************** FACTORY *******************/
  98
  99         public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead){
 100                 return new SingleReadAlignment(consensusSequence, singleRead, null, null);
 101         }
 102
 103         public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead,
 104                         Shift[] shifts, String editedSequence){
 105                 return new SingleReadAlignment(consensusSequence, singleRead, shifts, editedSequence);
 106         }
 107
 108 // ***************** CONSTRUCTOR *************************/
 109
 110         protected SingleReadAlignment(){};
 111
 112         private SingleReadAlignment(Sequence consensusAlignment, SingleRead singleRead,
 113                         Shift[] shifts, String editedSequence){
 114                 setConsensusAlignment(consensusAlignment);
 115                 setSingleRead(singleRead);
 116                 this.shifts = shifts;
 117                 this.editedSequence = editedSequence;
 118         }
 119
 120
 121 // ****************** GETTER / SETTER ***********************/
 122
 123         //consensus sequence
 124         public Sequence getConsensusSequence() {
 125                 return consensusAlignment;
 126         }
 127         public void setConsensusAlignment(Sequence consensusAlignment) {
 128                 if (this.consensusAlignment != null && this.consensusAlignment.getSingleReadAlignments().contains(this)){
 129                         this.consensusAlignment.removeSingleReadAlignment(this);
 130                 }
 131                 this.consensusAlignment = consensusAlignment;
 132                 if (consensusAlignment != null && ! consensusAlignment.getSingleReadAlignments().contains(this)){
 133                         consensusAlignment.addSingleReadAlignment(this);
 134                 }
 135         }
 136
 137         public SingleRead getSingleRead() {
 138                 return singleRead;
 139         }
 140         public void setSingleRead(SingleRead singleRead) {
 141 //              if (this.singleRead != null xxx){
 142 //                      this.singleRead.removeSingleReadAlignment(this);
 143 //              }
 144                 this.singleRead = singleRead;
 145 //              if (singleRead != null && singleRead.getSingleReadAlignments().contains(this)){
 146 //                      singleRead.addSingleReadAlignment(this);
 147 //              }
 148         }
 149
 150         //shifts
 151         public Shift[] getShifts() {
 152                 return shifts == null ? new Shift[0] : shifts;
 153         }
 154         public void setShifts(Shift[] shifts) {
 155                 this.shifts = shifts;
 156                 if (shifts == null){
 157                         shifts = new Shift[0];
 158                 }
 159         }
 160
 161         //edited sequence
 162         public String getEditedSequence() {
 163                 return editedSequence;
 164         }
 165
 166         public void setEditedSequence(String editedSequence) {
 167                 this.editedSequence = editedSequence;
 168         }
 169
 170
 171         public boolean isReverseComplement() {
 172                 return reverseComplement;
 173         }
 174
 175         public void setReverseComplement(boolean reverseComplement) {
 176                 this.reverseComplement = reverseComplement;
 177         }
 178
 179 // ******************* CLONE *********************/
 180
 181
 182
 183         @Override
 184         public Object clone() throws CloneNotSupportedException {
 185                 SingleReadAlignment result = (SingleReadAlignment)super.clone();
 186
 187                 //deep copy shifts
 188                 Shift[] oldShifts = this.getShifts();
 189                 int shiftLength = oldShifts.length;
 190                 Shift[] newShift = new Shift[shiftLength];
 191                 for (int i = 0; i< shiftLength; i++){
 192                         Shift oldShift = oldShifts[i];
 193                         newShift[0] = (Shift)oldShift.clone();
 194                 }
 195
 196                 //all other objects can be reused
 197                 return result;
 198         }
 199
 200     /**
 201      * Returns the position in the {@link Sequence sequence}
 202      * this {@link SingleReadAlignment single read align} is attached to
 203      * where the output of the visible part of the pherogram starts.
 204      * @return a valid index in the sequence carrying this data area
 205      * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/dataarea/implementations/pherogram/PherogramArea.html#getFirstSeqPos
 206      *
 207      */
 208     public Integer getFirstSeqPosition() {
 209         return firstSeqPosition;
 210     }
 211
 212     /**
 213      * @see #getFirstSeqPosition()
 214      */
 215     public void setFirstSeqPosition(Integer firstSeqPosition) {
 216         this.firstSeqPosition = firstSeqPosition;
 217     }
 218
 219     /**
 220      * Returns the first base call index of the pherogram which has not been cut off.
 221      * @return a base call index > 0
 222      * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/pherogram/PherogramComponent.html#getLeftCutPosition
 223      */
 224     public Integer getLeftCutPosition() {
 225         return leftCutPosition;
 226     }
 227
 228     /**
 229      * @param see {@link #getLeftCutPosition()}
 230      */
 231     public void setLeftCutPosition(Integer leftCutPosition) {
 232         this.leftCutPosition = leftCutPosition;
 233     }
 234
 235     /**
 236      * Returns the first base call index of the pherogram that has been cut off (so that the length of the visible
 237      * area of the pherogram can be calculated as getRightCutPosition()
 238      * @return a base call inde
 239      * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/pherogram/PherogramComponent.html#getRightCutPosition
 240      */
 241     public Integer getRightCutPosition() {
 242         return rightCutPosition;
 243     }
 244
 245     /**
 246      * @param see {@link #getRightCutPosition()}
 247      */
 248     public void setRightCutPosition(Integer rightCutPosition) {
 249         this.rightCutPosition = rightCutPosition;
 250     }
 251
 252 }