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

Change plate reader/writer to use columns as wells

Browse Source
This commit is contained in:
efischer
2022-02-20 19:12:11 -06:00
parent 9adb7dffb8
commit d1bb49b482
2 changed files with 48 additions and 16 deletions
Download Patch File Download Diff File Expand all files Collapse all files

BIN
out/artifacts/BiGpairSEQ_Sim_jar/BiGpairSEQ_Sim.jar
View File

Binary file not shown.

64
src/main/java/PlateFileReader.java
View File

@@ -31,23 +31,55 @@ public class PlateFileReader {
BufferedReader reader = Files.newBufferedReader(Path.of(filename)); BufferedReader reader = Files.newBufferedReader(Path.of(filename));
CSVParser parser = new CSVParser(reader, plateFileFormat); CSVParser parser = new CSVParser(reader, plateFileFormat);
){ ){
for(CSVRecord record: parser.getRecords()) { //old code for wells as rows
List<Integer[]> well = new ArrayList<>(); // for(CSVRecord record: parser.getRecords()) {
for(String s: record) { // List<Integer[]> well = new ArrayList<>();
if(!"".equals(s)) { // for(String s: record) {
String[] intString = s.replaceAll("\\[", "") // if(!"".equals(s)) {
.replaceAll("]", "") // String[] intString = s.replaceAll("\\[", "")
.replaceAll(" ", "") // .replaceAll("]", "")
.split(","); // .replaceAll(" ", "")
//System.out.println(intString); // .split(",");
Integer[] arr = new Integer[intString.length]; // //System.out.println(intString);
for (int i = 0; i < intString.length; i++) { // Integer[] arr = new Integer[intString.length];
arr[i] = Integer.valueOf(intString[i]); // for (int i = 0; i < intString.length; i++) {
} // arr[i] = Integer.valueOf(intString[i]);
well.add(arr); // }
} // well.add(arr);
// }
// }
// wells.add(well);
for(CSVRecord record: parser) {
if (record.hasComment()) {
continue;
}
if (wells.size() == 0) {
int num = record.size();
for (int i = 0; i < num; i++) {
wells.add(new ArrayList<>());
}
continue;
} else {
int i = 0;
for (String s : record) {
if (!"".equals(s)) { //if value isn't the empty string
//get rid of brackts, split at commas into a string array
String[] intsAsStrings = s.replaceAll("\\[", "")
.replaceAll("]", "")
.replaceAll(" ", "")
.split(",");
//Make Integer array with the same values
Integer[] arr = new Integer[intsAsStrings.length];
for (int j = 0; j < intsAsStrings.length; j++) {
arr[j] = Integer.valueOf(intsAsStrings[j]);
}
//Add Integer array to the correct well
wells.get(i).add(arr);
i++;
}
}
} }
wells.add(well);
} }
} catch(IOException ex){ } catch(IOException ex){
System.out.println("plate file " + filename + " not found."); System.out.println("plate file " + filename + " not found.");