From 593dd6c60f535df9b01987efe543f473a1c924ff Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Fri, 30 Sep 2022 02:58:15 -0500
Subject: [PATCH] Add sample cell filename, cell sample size, and sample plate
 size to metadata

---
 src/main/java/CellFileReader.java    |  4 +++-
 src/main/java/CellSample.java        |  6 ++++++
 src/main/java/GraphMLFileWriter.java |  2 +-
 src/main/java/GraphWithMapData.java  | 20 +++++++++++++++-----
 src/main/java/Simulator.java         | 13 ++++++++++---
 5 files changed, 35 insertions(+), 10 deletions(-)

diff --git a/src/main/java/CellFileReader.java b/src/main/java/CellFileReader.java
index 41a1b1f..17e85cd 100644
--- a/src/main/java/CellFileReader.java
+++ b/src/main/java/CellFileReader.java
@@ -58,7 +58,9 @@ public class CellFileReader {
     }
 
     public CellSample getCellSample() {
-        return new CellSample(distinctCells, cdr1Freq);
+        CellSample sample = new CellSample(distinctCells, cdr1Freq);
+        sample.setFilename(filename);
+        return sample;
     }
 
     public String getFilename() { return filename;}
diff --git a/src/main/java/CellSample.java b/src/main/java/CellSample.java
index b32e912..681d3ef 100644
--- a/src/main/java/CellSample.java
+++ b/src/main/java/CellSample.java
@@ -7,6 +7,7 @@ public class CellSample {
 
     private List<String[]> cells;
     private Integer cdr1Freq;
+    private String filename;
 
     public CellSample(Integer numDistinctCells, Integer cdr1Freq){
         this.cdr1Freq = cdr1Freq;
@@ -38,6 +39,7 @@ public class CellSample {
             distinctCells.add(tmp);
         }
         this.cells = distinctCells;
+        this.filename = filename;
     }
 
     public CellSample(List<String[]> cells, Integer cdr1Freq){
@@ -57,4 +59,8 @@ public class CellSample {
         return cells.size();
     }
 
+    public String getFilename() { return filename; }
+
+    public void setFilename(String filename) { this.filename = filename; }
+
 }
diff --git a/src/main/java/GraphMLFileWriter.java b/src/main/java/GraphMLFileWriter.java
index 18e16b0..e709620 100644
--- a/src/main/java/GraphMLFileWriter.java
+++ b/src/main/java/GraphMLFileWriter.java
@@ -43,7 +43,7 @@ public class GraphMLFileWriter {
     private Map<String, Attribute> createGraphAttributes(){
         Map<String, Attribute> attributes = new HashMap<>();
         //Sample plate filename
-        attributes.put("sample plate filename", DefaultAttribute.createAttribute(data.getSourceFilename()));
+        attributes.put("sample plate filename", DefaultAttribute.createAttribute(data.getPlateFilename()));
         // Number of wells
         attributes.put("well count", DefaultAttribute.createAttribute(data.getNumWells().toString()));
         //Well populations
diff --git a/src/main/java/GraphWithMapData.java b/src/main/java/GraphWithMapData.java
index d9720b1..5321324 100644
--- a/src/main/java/GraphWithMapData.java
+++ b/src/main/java/GraphWithMapData.java
@@ -9,7 +9,9 @@ import java.util.Map;
 //Custom vertex class means a lot of the map data can now be encoded in the graph itself
 public class GraphWithMapData implements java.io.Serializable {
 
-    private String sourceFilename;
+    private String cellFilename;
+    private int cellSampleSize;
+    private String plateFilename;
     private final SimpleWeightedGraph graph;
     private final int numWells;
     private final Integer[] wellPopulations;
@@ -112,12 +114,20 @@ public class GraphWithMapData implements java.io.Serializable {
         return time;
     }
 
-    public void setSourceFilename(String filename) {
-        this.sourceFilename = filename;
+    public void setCellFilename(String filename) { this.cellFilename = filename; }
+
+    public String getCellFilename() { return this.cellFilename; }
+
+    public Integer getCellSampleSize() { return this.cellSampleSize; }
+
+    public void setCellSampleSize(int size) { this.cellSampleSize = size;}
+
+    public void setPlateFilename(String filename) {
+        this.plateFilename = filename;
     }
 
-    public String getSourceFilename() {
-        return sourceFilename;
+    public String getPlateFilename() {
+        return plateFilename;
     }
 
     public Double getReadErrorRate() {
diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 2fd5c64..8a0702e 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -137,8 +137,12 @@ public class Simulator implements GraphModificationFunctions {
         //create GraphWithMapData object
         GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey,
                 alphaCount, betaCount, samplePlate.getError(), readDepth, readErrorRate, errorCollisionRate, realSequenceCollisionRate, time);
-        //Set source file name in graph to name of sample plate
-        output.setSourceFilename(samplePlate.getFilename());
+        //Set cell sample file name in graph to name of cell sample
+        output.setCellFilename(cellSample.getFilename());
+        //Set cell sample size in graph
+        output.setCellSampleSize(cellSample.getCellCount());
+        //Set sample plate file name in graph to name of sample plate
+        output.setPlateFilename(samplePlate.getFilename());
         //return GraphWithMapData object
         return output;
     }
@@ -304,7 +308,10 @@ public class Simulator implements GraphModificationFunctions {
 
 
         Map<String, String> metadata = new LinkedHashMap<>();
-        metadata.put("sample plate filename", data.getSourceFilename());
+        metadata.put("cell sample filename", data.getCellFilename());
+        metadata.put("cell sample size", data.getCellSampleSize().toString());
+        metadata.put("sample plate filename", data.getPlateFilename());
+        metadata.put("sample plate well count", data.getNumWells().toString());
         metadata.put("sequence dropout rate", data.getDropoutRate().toString());
         metadata.put("graph filename", dataFilename);
         metadata.put("MWM algorithm type", algoType);