refactoring

broadinstitute · Aug 10, 2015 · bafb454 · bafb454
1 parent 3f07135
commit bafb454
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Showing 11 changed files with 204 additions and 182 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/metrics/MultiLevelMetrics.java b/src/main/java/org/broadinstitute/hellbender/metrics/MultiLevelMetrics.java
@@ -1,11 +1,10 @@
 package org.broadinstitute.hellbender.metrics;
 
-import htsjdk.samtools.metrics.MetricBase;
+import org.broadinstitute.hellbender.tools.dataflow.transforms.metrics.SerializableMetric;
 
-import java.io.Serializable;
 import java.util.Comparator;
 
-public abstract class MultiLevelMetrics extends MetricBase implements Serializable{
+public abstract class MultiLevelMetrics extends SerializableMetric{
     private static final long serialVersionUID = 1l;
 
     /** The sample to which these metrics apply.  If null, it means they apply

diff --git a/...ava/org/broadinstitute/hellbender/tools/dataflow/pipelines/InsertSizeMetricsDataflow.java b/...ava/org/broadinstitute/hellbender/tools/dataflow/pipelines/InsertSizeMetricsDataflow.java
@@ -18,8 +18,8 @@
 import org.broadinstitute.hellbender.cmdline.programgroups.DataFlowProgramGroup;
 import org.broadinstitute.hellbender.engine.dataflow.DataflowCommandLineProgram;
 import org.broadinstitute.hellbender.engine.dataflow.datasources.ReadsDataflowSource;
-import org.broadinstitute.hellbender.tools.dataflow.MetricsFileDataflow;
-import org.broadinstitute.hellbender.tools.dataflow.transforms.InsertSizeMetricsDataflowTransform;
+import org.broadinstitute.hellbender.tools.dataflow.transforms.metrics.MetricsFileDataflow;
+import org.broadinstitute.hellbender.tools.dataflow.transforms.metrics.insertsize.InsertSizeMetricsDataflowTransform;
 import org.broadinstitute.hellbender.tools.picard.analysis.InsertSizeMetrics;
 import org.broadinstitute.hellbender.utils.IntervalUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;

diff --git a/...broadinstitute/hellbender/tools/dataflow/transforms/CombineHistogramsIntoMetricsFile.java b/...broadinstitute/hellbender/tools/dataflow/transforms/CombineHistogramsIntoMetricsFile.java
diff --git a/...ataflow/transforms/DataflowHistogram.java → ...transforms/metrics/DataflowHistogram.java b/...ataflow/transforms/DataflowHistogram.java → ...transforms/metrics/DataflowHistogram.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.hellbender.tools.dataflow.transforms;
+package org.broadinstitute.hellbender.tools.dataflow.transforms.metrics;
 
 import com.google.cloud.dataflow.sdk.coders.DefaultCoder;
 import com.google.cloud.dataflow.sdk.coders.SerializableCoder;

diff --git a/...r/tools/dataflow/MetricsFileDataflow.java → ...ansforms/metrics/MetricsFileDataflow.java b/...r/tools/dataflow/MetricsFileDataflow.java → ...ansforms/metrics/MetricsFileDataflow.java
@@ -1,12 +1,11 @@
-package org.broadinstitute.hellbender.tools.dataflow;
+package org.broadinstitute.hellbender.tools.dataflow.transforms.metrics;
 
-import htsjdk.samtools.metrics.MetricBase;
 import htsjdk.samtools.metrics.MetricsFile;
 
 import java.io.Serializable;
 import java.io.StringWriter;
 
-public class MetricsFileDataflow<BEAN extends MetricBase & Serializable, HKEY extends Comparable<HKEY> & Serializable> extends MetricsFile<BEAN, HKEY> implements Serializable {
+public class MetricsFileDataflow<BEAN extends SerializableMetric, HKEY extends Comparable<HKEY> & Serializable> extends MetricsFile<BEAN, HKEY> implements Serializable {
     public static final long serialVersionUID = 1l;
 
     @Override

diff --git a/...a/org/broadinstitute/hellbender/tools/dataflow/transforms/metrics/SerializableMetric.java b/...a/org/broadinstitute/hellbender/tools/dataflow/transforms/metrics/SerializableMetric.java
@@ -0,0 +1,12 @@
+package org.broadinstitute.hellbender.tools.dataflow.transforms.metrics;
+
+import htsjdk.samtools.metrics.MetricBase;
+
+import java.io.Serializable;
+
+/**
+ * Serializable Metric base class
+ */
+public abstract class SerializableMetric extends MetricBase implements Serializable {
+    private static final long serialVersionUID = 1l;
+}