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