From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 23 Sep 2021 16:26:33 +0000 (+0100)
Subject: JAL-3821 less ambiguous base class name for EMBL and GenBank flat file parsers
X-Git-Tag: Release_2_11_2_0~32^2^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2ed4d627d3eb73a49299aad68bf719881ec4538d;p=jalview.git

JAL-3821 less ambiguous base class name for EMBL and GenBank flat file parsers
---

diff --git a/src/jalview/io/FlatFile.java b/src/jalview/io/EMBLLikeFlatFile.java
similarity index 99%
rename from src/jalview/io/FlatFile.java
rename to src/jalview/io/EMBLLikeFlatFile.java
index 9e5c652..64943b2 100644
--- a/src/jalview/io/FlatFile.java
+++ b/src/jalview/io/EMBLLikeFlatFile.java
@@ -45,7 +45,7 @@ import jalview.util.MappingUtils;
  * each line is formatted differently in GenBank and EMBL. See
  * http://www.insdc.org/files/feature_table.html#7.1.
  */
-public abstract class FlatFile extends AlignFile
+public abstract class EMBLLikeFlatFile extends AlignFile
 {
   protected static final String LOCATION = "location";
 
@@ -194,7 +194,7 @@ public abstract class FlatFile extends AlignFile
    * @param sourceId
    * @throws IOException
    */
-  public FlatFile(FileParse fp, String sourceId) throws IOException
+  public EMBLLikeFlatFile(FileParse fp, String sourceId) throws IOException
   {
     super(false, fp); // don't parse immediately
     this.sourceDb = sourceId;
diff --git a/src/jalview/io/EmblFlatFile.java b/src/jalview/io/EmblFlatFile.java
index 19496ef..7808d1a 100644
--- a/src/jalview/io/EmblFlatFile.java
+++ b/src/jalview/io/EmblFlatFile.java
@@ -25,7 +25,7 @@ import jalview.util.DBRefUtils;
  * @see ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt
  * @see ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html
  */
-public class EmblFlatFile extends FlatFile
+public class EmblFlatFile extends EMBLLikeFlatFile
 {
   /**
    * Constructor given a data source and the id of the source database
diff --git a/src/jalview/io/GenBankFile.java b/src/jalview/io/GenBankFile.java
index ba7b4b4..f1ca0e3 100644
--- a/src/jalview/io/GenBankFile.java
+++ b/src/jalview/io/GenBankFile.java
@@ -16,7 +16,7 @@ import java.io.IOException;
  * @author gmcarstairs
  * @see https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
  */
-public class GenBankFile extends FlatFile
+public class GenBankFile extends EMBLLikeFlatFile
 {
   private static final String DEFINITION = "DEFINITION";
 
diff --git a/test/jalview/io/GenBankFileTest.java b/test/jalview/io/GenBankFileTest.java
index 89f0d0e..97e4754 100644
--- a/test/jalview/io/GenBankFileTest.java
+++ b/test/jalview/io/GenBankFileTest.java
@@ -42,7 +42,7 @@ public class GenBankFileTest
     File dataFile = new File("test/jalview/io/J03321.gb");
     FileParse fp = new FileParse(dataFile.getAbsolutePath(),
             DataSourceType.FILE);
-    FlatFile parser = new GenBankFile(fp, "GenBankTest");
+    EMBLLikeFlatFile parser = new GenBankFile(fp, "GenBankTest");
     List<SequenceI> seqs = parser.getSeqs();
 
     assertEquals(seqs.size(), 1);