diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java index feedc67e8b0ab82e61ed70d6affdc31f58fe18e3..5f44cd1a6b5256087269930e491363c6ecc4207f 100644 --- a/uk/ac/sanger/artemis/components/variant/VCFview.java +++ b/uk/ac/sanger/artemis/components/variant/VCFview.java @@ -171,6 +171,7 @@ public class VCFview extends JPanel private boolean concatSequences = false; protected static Pattern tabPattern = Pattern.compile("\t"); + private Color lighterGrey = new Color(220,220,220); public static String VCFFILE_SUFFIX = ".*\\.[bv]{1}cf(\\.gz)*$"; private static String FILE_SUFFIX = "\\.[bv]{1}cf(\\.gz)*$"; @@ -947,7 +948,7 @@ public class VCFview extends JPanel } - private void drawRegion(Graphics g, + private void drawRegion(Graphics2D g, String chr, int sbeg, int send, @@ -1138,7 +1139,7 @@ public class VCFview extends JPanel } - private void drawVariantCall(Graphics g, VCFRecord record, int start, int index, + private void drawVariantCall(Graphics2D g, VCFRecord record, int start, int index, float pixPerBase, FeatureVector features, boolean vcf_v4) { int basePosition = record.getPos() + getSequenceOffset(record.getChrom()); @@ -1158,7 +1159,7 @@ public class VCFview extends JPanel else if(record.getAlt().isDeletion(vcf_v4)) g.setColor(Color.gray); else if(record.getAlt().isInsertion(vcf_v4)) - g.setColor(Color.yellow); + g.setColor(Color.magenta); else if(record.getAlt().length() == 1 && record.getRef().length() == 1) { g.setColor(getColourForSNP(record, features, basePosition)); @@ -1225,7 +1226,7 @@ public class VCFview extends JPanel else if(variant.equals("T")) return Color.black; else - return Color.magenta; // non-variant + return lighterGrey; // non-variant } /**