efischer/BiGpairSEQ
1
0
Fork 0
Code Issues Pull Requests Projects Releases 13 Wiki Activity

Refactor sequences to be strings instead of integers, to make simulating read errors easier

Browse Source
This commit is contained in:
eugenefischer
2022-09-26 13:37:48 -05:00
parent f84dfb2b4b
commit 02c8e6aacb
10 changed files with 101 additions and 115 deletions
Download Patch File Download Diff File Expand all files Collapse all files

11
src/main/java/Vertex.java
View File

@@ -5,7 +5,7 @@ import java.io.Serializable;
public class Vertex implements Serializable, Comparable<Vertex> {
private SequenceType type;
private Integer vertexLabel;
private Integer sequence;
private String sequence;
private Integer occupancy;
private Integer readCount;
private Double potential;
@@ -18,14 +18,14 @@ public class Vertex implements Serializable, Comparable<Vertex> {
this.vertexLabel = Integer.parseInt((vertexLabel));
}
public Vertex(SequenceType type, Integer sequence, Integer occupancy, Integer vertexLabel) {
public Vertex(SequenceType type, String sequence, Integer occupancy, Integer vertexLabel) {
this.type = type;
this.vertexLabel = vertexLabel;
this.sequence = sequence;
this.occupancy = occupancy;
}
public Vertex(SequenceType type, Integer sequence, Integer occupancy, Integer vertexLabel, Integer readCount) {
public Vertex(SequenceType type, String sequence, Integer occupancy, Integer vertexLabel, Integer readCount) {
this.type = type;
this.vertexLabel = vertexLabel;
this.sequence = sequence;
@@ -50,13 +50,12 @@ public class Vertex implements Serializable, Comparable<Vertex> {
this.vertexLabel = Integer.parseInt(label);
}
public Integer getSequence() {
public String getSequence() {
return sequence;
}
public void setSequence(String sequence) {
this.sequence = Integer.parseInt(sequence);
this.sequence = sequence;
}
public Integer getOccupancy() {