diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java index c789b88a2b6fd5b49886deeedbd2b6ec9907a8fe..0a69f718add3b0acc61c65572245071d91b9a580 100644 --- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java +++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java @@ -21,7 +21,8 @@ package uk.ac.sanger.artemis.plot; import uk.ac.sanger.artemis.Entry; -import uk.ac.sanger.artemis.sequence.*; +import uk.ac.sanger.artemis.sequence.Bases; +import uk.ac.sanger.artemis.sequence.Strand; import uk.ac.sanger.artemis.util.Document; import uk.ac.sanger.artemis.util.FileDocument; import uk.ac.sanger.artemis.util.LinePushBackReader; @@ -77,7 +78,6 @@ public class UserDataAlgorithm extends BaseAlgorithm /** The maximum value in the data array. */ private float data_max = Float.MIN_VALUE; - /** The minimum value in the data array. */ private float data_min = Float.MAX_VALUE; @@ -96,11 +96,8 @@ public class UserDataAlgorithm extends BaseAlgorithm public int FORMAT = BASE_PER_LINE_FORMAT; private LineAttributes lines[]; - - public Wiggle wiggle[]; - - public TabixIdxGraph idxReader; - + private Wiggle wiggle[]; + private TabixIdxGraph idxReader; private static org.apache.log4j.Logger logger4j = org.apache.log4j.Logger.getLogger(UserDataAlgorithm.class); @@ -196,11 +193,8 @@ public class UserDataAlgorithm extends BaseAlgorithm private static boolean isIndexed(Document doc) { if(doc instanceof FileDocument) - { - final File idx = new File( - ((FileDocument)doc).getFile().getAbsolutePath() + ".tbi"); - return idx.exists(); - } + return (new File( + ((FileDocument)doc).getFile().getAbsolutePath() + ".tbi")).exists(); return false; }