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

14
src/main/java/PlateFileReader.java
View File

@@ -13,7 +13,7 @@ import java.util.regex.Pattern;
public class PlateFileReader {
private List<List<Integer[]>> wells = new ArrayList<>();
private List<List<String[]>> wells = new ArrayList<>();
private String filename;
public PlateFileReader(String filename){
@@ -32,17 +32,17 @@ public class PlateFileReader {
CSVParser parser = new CSVParser(reader, plateFileFormat);
){
for(CSVRecord record: parser.getRecords()) {
List<Integer[]> well = new ArrayList<>();
List<String[]> well = new ArrayList<>();
for(String s: record) {
if(!"".equals(s)) {
String[] intString = s.replaceAll("\\[", "")
String[] sequences = s.replaceAll("\\[", "")
.replaceAll("]", "")
.replaceAll(" ", "")
.split(",");
//System.out.println(intString);
Integer[] arr = new Integer[intString.length];
for (int i = 0; i < intString.length; i++) {
arr[i] = Integer.valueOf(intString[i]);
//System.out.println(sequences);
String[] arr = new String[sequences.length];
for (int i = 0; i < sequences.length; i++) {
arr[i] = sequences[i];
}
well.add(arr);
}