- NEW: Modified the loading code to take ABH data and split the H bac…

…k into A/B. Refs #2.
cropgeeks · Apr 8, 2021 · 32c76a3 · 32c76a3
1 parent bbf426f
commit 32c76a3
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Showing 5 changed files with 29 additions and 2 deletions.
diff --git a/src/jhi/flapjack/analysis/OptimizeStateTable.java b/src/jhi/flapjack/analysis/OptimizeStateTable.java
@@ -37,6 +37,23 @@ public void collapseHomzEncodedAsHet()
 		optimize(true);
 	}
 
+	public void detectABH()
+	{
+		if (stateTable.containsABHData() == false)
+			return;
+
+		for (int i = 1; i < stateTable.size(); i++)
+		{
+			AlleleState s = stateTable.getAlleleState(i);
+
+			if (s.isHomozygous() && s.homzAllele().equals("H"))
+			{
+				s = new AlleleState("A/B", "/");
+				stateTable.getStates().set(i, s);
+			}
+		}
+	}
+
 	public void optimize(boolean compareHomzOnly)
 	{
 		// This lookup table will hold remapped references to the AlleleState

diff --git a/src/jhi/flapjack/io/DataImporter.java b/src/jhi/flapjack/io/DataImporter.java
@@ -107,6 +107,8 @@ public void runJob(int jobIndex) throws Exception
 
 			// Collapse (eg) A/A into A
 			pio.collapseHomzEncodedAsHet();
+			// Change ABH data into A and B and A/B
+			pio.detectABH();
 			// Collapse heterozyous states
 			if (Prefs.ioHeteroCollapse)
 				pio.optimizeStateTable();

diff --git a/src/jhi/flapjack/io/PostImportOperations.java b/src/jhi/flapjack/io/PostImportOperations.java
@@ -35,6 +35,12 @@ public void optimizeStateTable()
 		c.optimize(false);
 	}
 
+	public void detectABH()
+	{
+		OptimizeStateTable c = new OptimizeStateTable(dataSet);
+		c.detectABH();
+	}
+
 	public void setName(File importFile, BrapiClient client)
 	{
 		if (importFile != null)
@@ -91,8 +97,8 @@ else if (dataSet.getBinnedData().containsBins() || st.containsBins())
 			viewSet.setColorScheme(ColorScheme.BINNED_10);
 
 		// ABH
-		else if (dataSet.getStateTable().containsABHData())
-			viewSet.setColorScheme(ColorScheme.ABH_DATA);
+//		else if (dataSet.getStateTable().containsABHData())
+//			viewSet.setColorScheme(ColorScheme.ABH_DATA);
 		// Two colour
 		else if (hCount > 0 && hCount < 10)
 			viewSet.setColorScheme(ColorScheme.SIMPLE_TWO_COLOR);

diff --git a/src/jhi/flapjack/io/cmd/CreateProject.java b/src/jhi/flapjack/io/cmd/CreateProject.java
@@ -131,6 +131,7 @@ private void createProject()
 
 		PostImportOperations pio = new PostImportOperations(dataSet);
 		pio.collapseHomzEncodedAsHet();
+		pio.detectABH();
 		if (importSettings.isCollapseHeteozygotes())
 			pio.optimizeStateTable();
 		pio.createDefaultView(importSettings.isForceNucScheme());

diff --git a/src/jhi/flapjack/io/cmd/CreateProjectBatch.java b/src/jhi/flapjack/io/cmd/CreateProjectBatch.java
@@ -157,6 +157,7 @@ private void createProject(DataSet dataSet, File mapFile, File genoFile, String
 
 		PostImportOperations pio = new PostImportOperations(dataSet);
 		pio.collapseHomzEncodedAsHet();
+		pio.detectABH();
 		if (importSettings.isCollapseHeteozygotes())
 			pio.optimizeStateTable();
 		pio.createDefaultView(importSettings.isForceNucScheme());