From 3e24e422280ee0a231739034319afd0818f5625e Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 20 Sep 2013 13:31:43 +0100
Subject: [PATCH] indexed user plot
---
.../ac/sanger/artemis/plot/UserPlotTest.java | 35 +++++++++++++++++--
1 file changed, 33 insertions(+), 2 deletions(-)
diff --git a/test/uk/ac/sanger/artemis/plot/UserPlotTest.java b/test/uk/ac/sanger/artemis/plot/UserPlotTest.java
index 6b02c985c..461b4817b 100644
--- a/test/uk/ac/sanger/artemis/plot/UserPlotTest.java
+++ b/test/uk/ac/sanger/artemis/plot/UserPlotTest.java
@@ -57,7 +57,7 @@ public class UserPlotTest
int start = 278;
alg.getValues(start, start+10, values);
assertEquals("Number of plots",values.length,6);
- assertTrue("Value of plot 1 at base position 278",values[0]==804.99f);
+ assertTrue("Value of plot 1 at base position "+start,values[0]==804.99f);
}
catch(IOException e)
{
@@ -87,7 +87,38 @@ public class UserPlotTest
int start = 278;
alg.getValues(start, start+10, values);
assertEquals("Number of plots",values.length,6);
- assertTrue("Value of plot 1 at base position 278",values[0]==804.99f);
+ assertTrue("Value of plot 1 at base position "+start,values[0]==804.99f);
+ }
+ catch(IOException e)
+ {
+ Assert.fail(e.getMessage());
+ }
+ }
+
+ @Test
+ /**
+ * Indexed (tabix) user plot.
+ */
+ public void indexed()
+ {
+ URL gffURL = UserPlotTest.class.getResource("/data/plot/index_tab_sorted.plot.gz");
+ EntryGroup entryGrp = Utils.getEntryGroup("/data/MAL1.embl.gz");
+ final Strand fwdStrand = entryGrp.getBases ().getForwardStrand ();
+ final FileDocument doc = new FileDocument (new File(gffURL.getFile()));
+ try
+ {
+ final UserDataAlgorithm alg = new UserDataAlgorithm (fwdStrand, doc, false);
+
+ alg.readIndexValues(true, entryGrp.getSequenceEntry(), 1, 120);
+ float [] values = new float [alg.getValueCount()];
+
+ int start = 20;
+ alg.getValues(start, start+1, values);
+ assertEquals("Number of plots",values.length,6);
+ assertTrue("Value of plot 5 at base position "+start+"="+values[5],values[5]==(234.f/2.f));
+
+ alg.getValues(start, start+4, values);
+ assertTrue("Value of plot 5 at base position "+start+"="+values[5],values[5]==(234.f/5.f));
}
catch(IOException e)
{
--
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