From 79a22e3a0f7747d42199b0d873a6fe1b0be45c23 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 13 Nov 2012 10:38:06 +0000
Subject: [PATCH] change visibility of wiggle and idxReader
---
.../sanger/artemis/plot/UserDataAlgorithm.java | 18 ++++++------------
1 file changed, 6 insertions(+), 12 deletions(-)
diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
index c789b88a2..0a69f718a 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;
}
--
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