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

Refactor to read/write files of graph and map data

Browse Source
This commit is contained in:
efischer
2022-02-19 21:46:01 -06:00
parent 568a6be3c7
commit 13fb7168bf
9 changed files with 281 additions and 204 deletions
Download Patch File Download Diff File Expand all files Collapse all files

42
src/main/java/Simulator.java
View File

@@ -55,13 +55,13 @@ public class Simulator {
// }
//Make the maps needed for matching CDR3s
public static MapData makeMaps(List<Integer[]> distinctCells,
Plate samplePlate, Integer lowThreshold, boolean verbose) {
//Make the graph needed for matching CDR3s
public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, Integer lowThreshold,
Integer highThreshold, boolean verbose) {
Instant start = Instant.now();
int numWells = samplePlate.getSize();
int[] alphaIndex = {cdr3AlphaIndex};
int[] betaIndex = {cdr3BetaIndex};
int numWells = samplePlate.getSize();
if(verbose){System.out.println("Making cell maps");}
//HashMap keyed to Alphas, values Betas
@@ -109,24 +109,6 @@ public class Simulator {
//keys are betas, values are sequential integer vertices from previous map
Map<Integer, Integer> plateBtoVMap = invertVertexMap(plateVtoBMap);
if(verbose){System.out.println("Vertex maps made");}
Instant stop = Instant.now();
Duration time = Duration.between(start, stop);
return new MapData(distCellsMapAlphaKey, allAlphas, allBetas, plateVtoAMap, plateVtoBMap, plateAtoVMap,
plateBtoVMap, time);
}
//Make the graph needed for matching CDR3s
public static GraphWithMapData makeGraph(Plate samplePlate, MapData maps, Integer lowThreshold,
Integer highThreshold, boolean verbose) {
int[] alphaIndex = {cdr3AlphaIndex};
int[] betaIndex = {cdr3BetaIndex};
Instant start = Instant.now();
Map<Integer, Integer> plateVtoAMap = maps.getPlateVtoAMap();
Map<Integer, Integer> plateVtoBMap = maps.getPlateVtoBMap();
Map<Integer, Integer> plateAtoVMap = maps.getPlateAtoVMap();
Map<Integer, Integer> plateBtoVMap = maps.getPlateBtoVMap();
Map<Integer, Integer> allAlphas = maps.getAllAlphas();
Map<Integer, Integer> allBetas = maps.getAllBetas();
if(verbose){System.out.println("Creating adjacency matrix");}
//Count how many wells each alpha appears in
@@ -160,16 +142,18 @@ public class Simulator {
if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
Instant stop = Instant.now();
Duration time = Duration.between(start, stop);
time = time.plus(maps.getTime());
return new GraphWithMapData(graph, maps, alphaWellCounts, betaWellCounts, time);
return new GraphWithMapData(graph, numWells, lowThreshold, highThreshold, distCellsMapAlphaKey, allAlphas,
allBetas, plateVtoAMap, plateVtoBMap, plateAtoVMap, plateBtoVMap, alphaWellCounts, betaWellCounts,
time);
}
//match CDR3s
public static MatchingResult matchCDR3s(Plate samplePlate, GraphWithMapData data, Integer lowThreshold,
Integer highThreshold, Integer maxOccupancyDifference,
public static MatchingResult matchCDR3s(GraphWithMapData data, Integer maxOccupancyDifference,
Integer minOverlapPercent, boolean verbose) {
Instant start = Instant.now();
int numWells = samplePlate.getSize();
int numWells = data.getNumWells();
Integer highThreshold = data.getHighThreshold();
Integer lowThreshold = data.getLowThreshold();
Map<Integer, Integer> distCellsMapAlphaKey = data.getDistCellsMapAlphaKey();
Map<Integer, Integer> plateVtoAMap = data.getPlateVtoAMap();
Map<Integer, Integer> plateVtoBMap = data.getPlateVtoBMap();
@@ -280,7 +264,7 @@ public class Simulator {
System.out.println(s);
}
}
return new MatchingResult(samplePlate.getSourceFileName(), comments, header, allResults, matchMap, time);
return new MatchingResult(data.getSourceFilename(), comments, header, allResults, matchMap, time);
}
public static MatchingResult matchCDR3s(List<Integer[]> distinctCells,
@@ -371,7 +355,7 @@ public class Simulator {
if(verbose){System.out.println("Graph created");}
//write graph to file
GraphFileWriter writer = new GraphFileWriter("graph", graph);
GraphMLFileWriter writer = new GraphMLFileWriter("graph", graph);
writer.writeGraphToFile();
if(verbose){System.out.println("Eliminating edges with weights outside threshold values");}