From 047030f6f574b9a3208fab789388f77b658f6877 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 3 Sep 2007 13:40:25 +0000
Subject: [PATCH] add FeatureLoc comparator
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6341 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/util/DatabaseDocument.java | 36 +++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 7c6f81776..13da9002f 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -61,6 +61,8 @@ import java.sql.*;
import java.text.SimpleDateFormat;
import java.io.*;
import java.net.ConnectException;
+import java.util.Collections;
+import java.util.Comparator;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.HashMap;
@@ -1854,6 +1856,7 @@ public class DatabaseDocument extends Document
}
}
+ Collections.sort(cdsFeatureLocs, new LocationComarator());
return cdsFeatureLocs;
}
@@ -2641,4 +2644,37 @@ public class DatabaseDocument extends Document
{
return singleSchema;
}
+
+ /**
+ * Ensure exon featurelocs are in the correct order
+ */
+ class LocationComarator implements Comparator
+ {
+
+ public int compare(Object o1, Object o2)
+ {
+ int loc1 = ((FeatureLoc)o1).getFmin().intValue();
+ int loc2 = ((FeatureLoc)o2).getFmin().intValue();
+
+ if(loc2 == loc1)
+ return 0;
+ int strand = ((FeatureLoc)o1).getStrand().intValue();
+
+ if(strand < 0)
+ {
+ if(loc2 > loc1)
+ return 1;
+ else
+ return -1;
+ }
+ else
+ {
+ if(loc2 > loc1)
+ return -1;
+ else
+ return 1;
+ }
+ }
+
+ }
}
--
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