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 java.io.Serializable;
   7
   8 import javax.persistence.Entity;
   9 import javax.persistence.FetchType;
  10 import javax.persistence.Lob;
  11 import javax.persistence.OneToOne;
  12 import javax.xml.bind.annotation.XmlAccessType;
  13 import javax.xml.bind.annotation.XmlAccessorType;
  14 import javax.xml.bind.annotation.XmlElement;
  15 import javax.xml.bind.annotation.XmlIDREF;
  16 import javax.xml.bind.annotation.XmlRootElement;
  17 import javax.xml.bind.annotation.XmlSchemaType;
  18 import javax.xml.bind.annotation.XmlType;
  19
  20 import org.hibernate.annotations.Cascade;
  21 import org.hibernate.annotations.CascadeType;
  22 import org.hibernate.annotations.Type;
  23 import org.hibernate.envers.Audited;
  24
  25 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  26
  27 /**
  28  * @author a.mueller
  29  */
  30 @XmlAccessorType(XmlAccessType.FIELD)
  31 @XmlType(name = "SingleReadAlignment", propOrder = {
  32         "consensusAlignment",
  33         "singleRead",
  34         "shifts",
  35         "editedSequence",
  36         "reverseComplement",
  37         "firstSeqPosition",
  38         "leftCutPosition",
  39         "rightCutPosition"
  40 })
  41 @XmlRootElement(name = "SingleReadAlignment")
  42 @Entity
  43 @Audited
  44 public class SingleReadAlignment extends VersionableEntity implements Serializable {
  45         private static final long serialVersionUID = 6141518347067279304L;
  46
  47         /** @see #getDnaMarker() */
  48         @XmlElement(name = "ConsensusAlignment")
  49     @XmlIDREF
  50     @XmlSchemaType(name = "IDREF")
  51     @OneToOne(fetch = FetchType.LAZY)
  52         //for now we do not cascade but expect the user to save the sequence manually
  53         private Sequence consensusAlignment;
  54
  55         /** @see #getDnaMarker() */
  56         @XmlElement(name = "SingleRead")
  57     @XmlIDREF
  58     @XmlSchemaType(name = "IDREF")
  59     @OneToOne(fetch = FetchType.LAZY)
  60         @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
  61         private SingleRead singleRead;
  62
  63         //TODO XML mapping / user type
  64         @Type(type="shiftUserType")
  65     private Shift[] shifts = new Shift[0];
  66
  67         private Integer firstSeqPosition;
  68
  69         private Integer leftCutPosition;
  70
  71         private Integer rightCutPosition;
  72
  73         @XmlElement(name = "EditedSequence")
  74     @Lob
  75     private String editedSequence;
  76
  77         @XmlElement(name = "ReverseComplement")
  78     private boolean reverseComplement;
  79
  80
  81         public static class Shift implements Cloneable, Serializable {
  82                 public int position;
  83                 public int shift;
  84
  85                 public Shift(){};
  86                 public Shift(int position, int steps) {
  87                         this.position = position;
  88                         this.shift = steps;
  89                 }
  90
  91                 @Override
  92                 public String toString(){
  93                         return String.valueOf(position) + "," + String.valueOf(shift);
  94                 }
  95                 @Override
  96                 protected Object clone() throws CloneNotSupportedException {
  97                         return super.clone();
  98                 }
  99         }
 100
 101 //****************** FACTORY *******************/
 102
 103         public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead){
 104                 return new SingleReadAlignment(consensusSequence, singleRead, null, null);
 105         }
 106
 107         public static SingleReadAlignment NewInstance(Sequence consensusSequence, SingleRead singleRead,
 108                         Shift[] shifts, String editedSequence){
 109                 return new SingleReadAlignment(consensusSequence, singleRead, shifts, editedSequence);
 110         }
 111
 112 // ***************** CONSTRUCTOR *************************/
 113
 114         protected SingleReadAlignment(){};
 115
 116         private SingleReadAlignment(Sequence consensusAlignment, SingleRead singleRead,
 117                         Shift[] shifts, String editedSequence){
 118                 setConsensusAlignment(consensusAlignment);
 119                 setSingleRead(singleRead);
 120                 this.shifts = shifts;
 121                 this.editedSequence = editedSequence;
 122         }
 123
 124
 125 // ****************** GETTER / SETTER ***********************/
 126
 127         //consensus sequence
 128         public Sequence getConsensusSequence() {
 129                 return consensusAlignment;
 130         }
 131         public void setConsensusAlignment(Sequence consensusAlignment) {
 132                 if (this.consensusAlignment != null && this.consensusAlignment.getSingleReadAlignments().contains(this)){
 133                         this.consensusAlignment.removeSingleReadAlignment(this);
 134                 }
 135                 this.consensusAlignment = consensusAlignment;
 136                 if (consensusAlignment != null && ! consensusAlignment.getSingleReadAlignments().contains(this)){
 137                         consensusAlignment.addSingleReadAlignment(this);
 138                 }
 139         }
 140
 141         public SingleRead getSingleRead() {
 142                 return singleRead;
 143         }
 144         public void setSingleRead(SingleRead singleRead) {
 145 //              if (this.singleRead != null xxx){
 146 //                      this.singleRead.removeSingleReadAlignment(this);
 147 //              }
 148                 this.singleRead = singleRead;
 149 //              if (singleRead != null && singleRead.getSingleReadAlignments().contains(this)){
 150 //                      singleRead.addSingleReadAlignment(this);
 151 //              }
 152         }
 153
 154         //shifts
 155         public Shift[] getShifts() {
 156                 return shifts == null ? new Shift[0] : shifts;
 157         }
 158         public void setShifts(Shift[] shifts) {
 159                 this.shifts = shifts;
 160                 if (shifts == null){
 161                         shifts = new Shift[0];
 162                 }
 163         }
 164
 165         //edited sequence
 166         public String getEditedSequence() {
 167                 return editedSequence;
 168         }
 169
 170         public void setEditedSequence(String editedSequence) {
 171                 this.editedSequence = editedSequence;
 172         }
 173
 174
 175         public boolean isReverseComplement() {
 176                 return reverseComplement;
 177         }
 178
 179         public void setReverseComplement(boolean reverseComplement) {
 180                 this.reverseComplement = reverseComplement;
 181         }
 182
 183 // ******************* CLONE *********************/
 184
 185         @Override
 186         public SingleReadAlignment clone() throws CloneNotSupportedException {
 187
 188             SingleReadAlignment result = (SingleReadAlignment)super.clone();
 189
 190                 //deep copy shifts
 191                 Shift[] oldShifts = this.getShifts();
 192                 int shiftLength = oldShifts.length;
 193                 Shift[] newShift = new Shift[shiftLength];
 194                 for (int i = 0; i< shiftLength; i++){
 195                         Shift oldShift = oldShifts[i];
 196                         newShift[0] = (Shift)oldShift.clone();
 197                 }
 198
 199                 //all other objects can be reused
 200                 return result;
 201         }
 202
 203     /**
 204      * Returns the position in the {@link Sequence sequence}
 205      * this {@link SingleReadAlignment single read align} is attached to
 206      * where the output of the visible part of the pherogram starts.
 207      * @return a valid index in the sequence carrying this data area
 208      * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/dataarea/implementations/pherogram/PherogramArea.html#getFirstSeqPos
 209      *
 210      */
 211     public Integer getFirstSeqPosition() {
 212         return firstSeqPosition;
 213     }
 214
 215     /**
 216      * @see #getFirstSeqPosition()
 217      */
 218     public void setFirstSeqPosition(Integer firstSeqPosition) {
 219         this.firstSeqPosition = firstSeqPosition;
 220     }
 221
 222     /**
 223      * Returns the first base call index of the pherogram which has not been cut off.
 224      * @return a base call index > 0
 225      * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/pherogram/PherogramComponent.html#getLeftCutPosition
 226      */
 227     public Integer getLeftCutPosition() {
 228         return leftCutPosition;
 229     }
 230
 231     /**
 232      * @param see {@link #getLeftCutPosition()}
 233      */
 234     public void setLeftCutPosition(Integer leftCutPosition) {
 235         this.leftCutPosition = leftCutPosition;
 236     }
 237
 238     /**
 239      * Returns the first base call index of the pherogram that has been cut off (so that the length of the visible
 240      * area of the pherogram can be calculated as getRightCutPosition()
 241      * @return a base call inde
 242      * @see http://bioinfweb.info/LibrAlign/Documentation/api/latest/info/bioinfweb/libralign/pherogram/PherogramComponent.html#getRightCutPosition
 243      */
 244     public Integer getRightCutPosition() {
 245         return rightCutPosition;
 246     }
 247
 248     /**
 249      * @param see {@link #getRightCutPosition()}
 250      */
 251     public void setRightCutPosition(Integer rightCutPosition) {
 252         this.rightCutPosition = rightCutPosition;
 253     }
 254
 255 }