diff --git a/src/main/java/org/broad/igv/sam/AlignmentRenderer.java b/src/main/java/org/broad/igv/sam/AlignmentRenderer.java index 199fec1ef..12ed96470 100644 --- a/src/main/java/org/broad/igv/sam/AlignmentRenderer.java +++ b/src/main/java/org/broad/igv/sam/AlignmentRenderer.java @@ -758,7 +758,7 @@ private void drawAlignment( else if (block.getCigarOperator() == 'X') g = context.getGraphics2D("MISMATCH"); } - if(renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.TEXTURED && alignment.isDuplicate()) { + if(renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.TEXTURE && alignment.isDuplicate()) { final Graphics2D tg = (Graphics2D) g.create(); final TexturePaint tp = getDuplicateTexture(tg.getColor()); diff --git a/src/main/java/org/broad/igv/sam/AlignmentTileLoader.java b/src/main/java/org/broad/igv/sam/AlignmentTileLoader.java index 284f129d3..2ea3f2a28 100644 --- a/src/main/java/org/broad/igv/sam/AlignmentTileLoader.java +++ b/src/main/java/org/broad/igv/sam/AlignmentTileLoader.java @@ -26,7 +26,6 @@ package org.broad.igv.sam; import htsjdk.samtools.SAMFileHeader; -import htsjdk.samtools.SAMTag; import htsjdk.samtools.util.CloseableIterator; import org.broad.igv.event.IGVEvent; import org.broad.igv.logging.*; @@ -43,7 +42,6 @@ import org.broad.igv.util.ObjectCache; import org.broad.igv.util.RuntimeUtils; -import javax.swing.*; import java.io.IOException; import java.lang.ref.WeakReference; import java.text.DecimalFormat; @@ -135,7 +133,7 @@ AlignmentTile loadTile(String chr, boolean filterSupplementaryAlignments = prefMgr.getAsBoolean(SAM_FILTER_SUPPLEMENTARY_ALIGNMENTS); ReadGroupFilter filter = ReadGroupFilter.getFilter(); boolean filterDuplicates = renderOptions != null - ? renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.FILTERED + ? renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.FILTER : prefMgr.getAsBoolean(SAM_FILTER_DUPLICATES); int qualityThreshold = prefMgr.getAsInt(SAM_QUALITY_THRESHOLD); diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrack.java b/src/main/java/org/broad/igv/sam/AlignmentTrack.java index 983abf17c..feaccdef4 100644 --- a/src/main/java/org/broad/igv/sam/AlignmentTrack.java +++ b/src/main/java/org/broad/igv/sam/AlignmentTrack.java @@ -136,9 +136,9 @@ public boolean isSMRTKinetics() { } public enum DuplicatesOption { - FILTERED("filtered", true), - VISIBLE("visible", false), - TEXTURED("textured", false); + FILTER("filter duplicates", true), + SHOW("show duplicates", false), + TEXTURE("texture duplicates", false); public final String label; public final boolean filtered; @@ -1493,8 +1493,8 @@ public DuplicatesOption getDuplicatesOption() { return duplicatesOption; } else { duplicatesOption = prefs.getAsBoolean(SAM_FILTER_DUPLICATES) - ? DuplicatesOption.FILTERED - : DuplicatesOption.VISIBLE; + ? DuplicatesOption.FILTER + : DuplicatesOption.SHOW; } return duplicatesOption; }