eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CDMAlignmentObjectPlaceholder.java

   1 package eu.etaxonomy.taxeditor.editor.molecular;
   2
   3
   4 import info.bioinfweb.libralign.pherogram.model.ShiftChange;
   5
   6 import java.util.ArrayList;
   7 import java.util.List;
   8 import java.util.Map;
   9 import java.util.TreeMap;
  10
  11 import org.biojava3.core.sequence.compound.NucleotideCompound;
  12 import org.biojava3.core.sequence.template.Sequence;
  13
  14
  15
  16 /**
  17  * This class is used as a replacement for a class representing the CMD objects storing an contig alignment during early
  18  * development phase.
  19  *
  20  * @author Ben Stöver
  21  * @date 06.08.2014
  22  */
  23 public class CDMAlignmentObjectPlaceholder {
  24         /**
  25          * Represents information in the contig alignment describing a single read sequence and the relation to its associated
  26          * pherogram.
  27          *
  28          * @author Ben Stöver
  29      * @date 06.08.2014
  30          */
  31         public static class Read {
  32                 private long pherogramObjectID = Long.MIN_VALUE;  // The ID used in the CMD to identify the object storing the pherogram URL. (Dont' know if this is long, just as an example-)
  33                 private final Sequence<NucleotideCompound> editableSequence = null;  // Could also be of type String, if helpful for CDM architecture.
  34                 private final List<ShiftChange> shiftChangeList = new ArrayList<ShiftChange>();
  35                 private String readName = "";
  36                 private boolean reverseComplemeted = false;
  37
  38
  39                 public Read(long pherogramObjectID) {
  40                         super();
  41                         this.pherogramObjectID = pherogramObjectID;
  42                 }
  43
  44
  45                 public long getPherogramObjectID() {
  46                         return pherogramObjectID;
  47                 }
  48
  49
  50                 public void setPherogramObjectID(long pherogramObjectID) {
  51                         this.pherogramObjectID = pherogramObjectID;
  52                 }
  53
  54
  55                 public List<ShiftChange> getShiftChangeList() {
  56                         return shiftChangeList;
  57                 }
  58
  59
  60                 public Sequence<NucleotideCompound> getEditableSequence() {
  61                         return editableSequence;
  62                 }
  63
  64
  65                 public String getReadName() {
  66                         return readName;
  67                 }
  68
  69
  70                 public void setReadName(String readName) {
  71                         this.readName = readName;
  72                 }
  73
  74
  75                 public boolean isReverseComplemeted() {
  76                         return reverseComplemeted;
  77                 }
  78
  79
  80                 public void setReverseComplemeted(boolean reverseComplemeted) {
  81                         this.reverseComplemeted = reverseComplemeted;
  82                 }
  83         }
  84
  85
  86         private final Map<String, Sequence<NucleotideCompound>> consensusSequences = new TreeMap<String, Sequence<NucleotideCompound>>();    // Could also be of type Map<String, String>, if helpful for CDM architecture.
  87         private final Map<Long, Read> readSequences = new TreeMap<Long, Read>();
  88
  89
  90         public Map<String, Sequence<NucleotideCompound>> getConsensusSequences() {
  91                 return consensusSequences;
  92         }
  93
  94
  95         public Map<Long, Read> getReadSequences() {
  96                 return readSequences;
  97         }
  98 }