1 package eu
.etaxonomy
.taxeditor
.editor
.molecular
;
4 import info
.bioinfweb
.libralign
.pherogram
.model
.ShiftChange
;
6 import java
.util
.ArrayList
;
9 import java
.util
.TreeMap
;
11 import org
.biojava3
.core
.sequence
.compound
.NucleotideCompound
;
12 import org
.biojava3
.core
.sequence
.template
.Sequence
;
17 * This class is used as a replacement for a class representing the CMD objects storing an contig alignment during early
23 public class CDMAlignmentObjectPlaceholder
{
25 * Represents information in the contig alignment describing a single read sequence and the relation to its associated
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;
39 public Read(long pherogramObjectID
) {
41 this.pherogramObjectID
= pherogramObjectID
;
45 public long getPherogramObjectID() {
46 return pherogramObjectID
;
50 public void setPherogramObjectID(long pherogramObjectID
) {
51 this.pherogramObjectID
= pherogramObjectID
;
55 public List
<ShiftChange
> getShiftChangeList() {
56 return shiftChangeList
;
60 public Sequence
<NucleotideCompound
> getEditableSequence() {
61 return editableSequence
;
65 public String
getReadName() {
70 public void setReadName(String readName
) {
71 this.readName
= readName
;
75 public boolean isReverseComplemeted() {
76 return reverseComplemeted
;
80 public void setReverseComplemeted(boolean reverseComplemeted
) {
81 this.reverseComplemeted
= reverseComplemeted
;
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
>();
90 public Map
<String
, Sequence
<NucleotideCompound
>> getConsensusSequences() {
91 return consensusSequences
;
95 public Map
<Long
, Read
> getReadSequences() {