igvteam · jrobinso · Jan 5, 2026 · Jan 5, 2026 · Jan 5, 2026
diff --git a/src/main/java/org/igv/batch/CommandExecutor.java b/src/main/java/org/igv/batch/CommandExecutor.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.batch;
 

diff --git a/src/main/java/org/igv/blast/BlastMapping.java b/src/main/java/org/igv/blast/BlastMapping.java
@@ -1,6 +1,5 @@
 package org.igv.blast;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.BasicFeature;
 import org.igv.feature.Strand;

diff --git a/src/main/java/org/igv/data/AbstractDataSource.java b/src/main/java/org/igv/data/AbstractDataSource.java
@@ -1,6 +1,5 @@
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;

diff --git a/src/main/java/org/igv/data/BasicScore.java b/src/main/java/org/igv/data/BasicScore.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.feature.LocusScore;

diff --git a/src/main/java/org/igv/data/Bin.java b/src/main/java/org/igv/data/Bin.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.data;
 

diff --git a/src/main/java/org/igv/data/CharArrayList.java b/src/main/java/org/igv/data/CharArrayList.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.data;
 

diff --git a/src/main/java/org/igv/data/ChromosomeSummary.java b/src/main/java/org/igv/data/ChromosomeSummary.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 /**

diff --git a/src/main/java/org/igv/data/CompositeScore.java b/src/main/java/org/igv/data/CompositeScore.java
@@ -1,6 +1,5 @@
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.LocusScore;
 import org.igv.track.WindowFunction;

diff --git a/src/main/java/org/igv/data/DataSource.java b/src/main/java/org/igv/data/DataSource.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.data;
 

diff --git a/src/main/java/org/igv/data/DataStatistics.java b/src/main/java/org/igv/data/DataStatistics.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.track.WindowFunction;

diff --git a/src/main/java/org/igv/data/DataTile.java b/src/main/java/org/igv/data/DataTile.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 /**

diff --git a/src/main/java/org/igv/data/Dataset.java b/src/main/java/org/igv/data/Dataset.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.track.TrackProperties;

diff --git a/src/main/java/org/igv/data/DatasetDataSource.java b/src/main/java/org/igv/data/DatasetDataSource.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;

diff --git a/src/main/java/org/igv/data/GenomeSummaryData.java b/src/main/java/org/igv/data/GenomeSummaryData.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.logging.*;

diff --git a/src/main/java/org/igv/data/IGVDataset.java b/src/main/java/org/igv/data/IGVDataset.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.feature.genome.Genome;

diff --git a/src/main/java/org/igv/data/IGVDatasetParser.java b/src/main/java/org/igv/data/IGVDatasetParser.java
@@ -1,6 +1,5 @@
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import htsjdk.samtools.seekablestream.SeekableStream;
 import org.igv.logging.*;

diff --git a/src/main/java/org/igv/data/SummaryTile.java b/src/main/java/org/igv/data/SummaryTile.java
@@ -1,6 +1,5 @@
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.LocusScore;
 

diff --git a/src/main/java/org/igv/data/WiggleDataset.java b/src/main/java/org/igv/data/WiggleDataset.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.genome.Genome;
 import org.igv.track.TrackProperties;

diff --git a/src/main/java/org/igv/data/ZipUtils.java b/src/main/java/org/igv/data/ZipUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.util.FileUtils;

diff --git a/src/main/java/org/igv/data/expression/ExpressionFileParser.java b/src/main/java/org/igv/data/expression/ExpressionFileParser.java
@@ -10,7 +10,6 @@
  */
 package org.igv.data.expression;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;

diff --git a/src/main/java/org/igv/feature/AbstractFeature.java b/src/main/java/org/igv/feature/AbstractFeature.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.ui.IGV;

diff --git a/src/main/java/org/igv/feature/AbstractFeatureParser.java b/src/main/java/org/igv/feature/AbstractFeatureParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import org.igv.logging.*;

diff --git a/src/main/java/org/igv/feature/CytoBandFileParser.java b/src/main/java/org/igv/feature/CytoBandFileParser.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import htsjdk.tribble.readers.AsciiLineReader;

diff --git a/src/main/java/org/igv/feature/EmblFeatureTableParser.java b/src/main/java/org/igv/feature/EmblFeatureTableParser.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.feature.genome.Genome;

diff --git a/src/main/java/org/igv/feature/FeatureDB.java b/src/main/java/org/igv/feature/FeatureDB.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import com.jidesoft.utils.SortedList;
 import htsjdk.tribble.Feature;

diff --git a/src/main/java/org/igv/feature/FeatureParser.java b/src/main/java/org/igv/feature/FeatureParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.feature;
 

diff --git a/src/main/java/org/igv/feature/GisticFileParser.java b/src/main/java/org/igv/feature/GisticFileParser.java
@@ -8,7 +8,6 @@
  */
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.exceptions.ParserException;

diff --git a/src/main/java/org/igv/feature/GisticScore.java b/src/main/java/org/igv/feature/GisticScore.java
@@ -9,7 +9,6 @@
 
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.track.WindowFunction;
 

diff --git a/src/main/java/org/igv/feature/Locus.java b/src/main/java/org/igv/feature/Locus.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import java.text.NumberFormat;

diff --git a/src/main/java/org/igv/feature/LocusScore.java b/src/main/java/org/igv/feature/LocusScore.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import org.igv.track.WindowFunction;

diff --git a/src/main/java/org/igv/feature/Mutation.java b/src/main/java/org/igv/feature/Mutation.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.genome.GenomeManager;
 import org.igv.logging.*;

diff --git a/src/main/java/org/igv/feature/Strand.java b/src/main/java/org/igv/feature/Strand.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.feature;
 

diff --git a/src/main/java/org/igv/feature/aa/AminoAcid.java b/src/main/java/org/igv/feature/aa/AminoAcid.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 /**

diff --git a/src/main/java/org/igv/feature/aa/AminoAcidManager.java b/src/main/java/org/igv/feature/aa/AminoAcidManager.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 import org.igv.logging.*;

diff --git a/src/main/java/org/igv/feature/aa/AminoAcidSequence.java b/src/main/java/org/igv/feature/aa/AminoAcidSequence.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 import org.igv.feature.Strand;

diff --git a/src/main/java/org/igv/feature/aa/CodonTableManager.java b/src/main/java/org/igv/feature/aa/CodonTableManager.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 import org.igv.logging.*;

diff --git a/src/main/java/org/igv/feature/basepair/BasePairRenderer.java b/src/main/java/org/igv/feature/basepair/BasePairRenderer.java
@@ -1,6 +1,5 @@
 package org.igv.feature.basepair;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.feature.basepair.BasePairTrack.*;

diff --git a/src/main/java/org/igv/feature/dranger/DRangerFeature.java b/src/main/java/org/igv/feature/dranger/DRangerFeature.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.dranger;
 
 import org.igv.feature.AbstractFeature;

diff --git a/src/main/java/org/igv/feature/dranger/DRangerParser.java b/src/main/java/org/igv/feature/dranger/DRangerParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.dranger;
 
 import org.igv.logging.*;

diff --git a/src/main/java/org/igv/feature/dranger/DRangerRenderer.java b/src/main/java/org/igv/feature/dranger/DRangerRenderer.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.dranger;
 
 import org.igv.feature.IGVFeature;

diff --git a/src/main/java/org/igv/feature/genome/GenomeImporter.java b/src/main/java/org/igv/feature/genome/GenomeImporter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.genome;
 
 import org.igv.logging.*;

diff --git a/src/main/java/org/igv/feature/genome/SequenceWrapper.java b/src/main/java/org/igv/feature/genome/SequenceWrapper.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.genome;
 
 import org.igv.feature.Chromosome;

diff --git a/src/main/java/org/igv/maf/MAFReader.java b/src/main/java/org/igv/maf/MAFReader.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.maf;
 

diff --git a/src/main/java/org/igv/maf/MAFTile.java b/src/main/java/org/igv/maf/MAFTile.java
@@ -1,6 +1,5 @@
 package org.igv.maf;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;

diff --git a/src/main/java/org/igv/maf/MAFTileCodec.java b/src/main/java/org/igv/maf/MAFTileCodec.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.maf;
 
 import org.igv.maf.MAFTile.MASequence;

diff --git a/src/main/java/org/igv/maf/MAFUtils.java b/src/main/java/org/igv/maf/MAFUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.maf;
 

diff --git a/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java b/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 /*
  * MAFConfigurationDialog.java

diff --git a/src/main/java/org/igv/prefs/IGVPreferences.java b/src/main/java/org/igv/prefs/IGVPreferences.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.prefs;
 
 

diff --git a/src/main/java/org/igv/renderer/AbstractColorScale.java b/src/main/java/org/igv/renderer/AbstractColorScale.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.renderer;
 

diff --git a/src/main/java/org/igv/renderer/ColorScale.java b/src/main/java/org/igv/renderer/ColorScale.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
 import java.awt.*;
Original file line number	Diff line number	Diff line change
Expand Up		@@ -9,7 +9,6 @@

		package org.igv.feature;

		//~--- non-JDK imports --------------------------------------------------------

		import org.igv.track.WindowFunction;

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