From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 22 Aug 2016 14:39:43 +0000 (+0100)
Subject: JAL-2175 code tidying
X-Git-Tag: Release_2_10_0~96
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aa709f20d35020ddec8e63d18c272a09d0823234;p=jalview.git

JAL-2175 code tidying
---

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 4ec077f..6d94616 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -305,20 +305,6 @@ public class FormatAdapter extends AppletFormatAdapter
     return this.formatSequences(format, alignment, suffix);
   }
 
-  public AlignmentI readFile(String inFile, String type, String format)
-          throws java.io.IOException
-  {
-    AlignmentI al = super.readFile(inFile, type, format);
-    return al;
-  }
-
-  public AlignmentI readFromFile(FileParse source, String format)
-          throws java.io.IOException
-  {
-    AlignmentI al = super.readFromFile(source, format);
-    return al;
-  }
-
   /**
    * validate format is valid for IO in Application. This is basically the
    * AppletFormatAdapter.isValidFormat call with additional checks for
diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index dbe1258..2a111ee 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.Jalview2XML;
 import jalview.io.AnnotationFile;
+import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -49,6 +50,7 @@ import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
 public class RNAStructExportImport
@@ -88,9 +90,9 @@ public class RNAStructExportImport
       Assert.fail("no web service");
     }
 
-    jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+    FileLoader fl = new FileLoader(false);
 
-    af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+    af = fl.LoadFileWaitTillLoaded(testseqs, FormatAdapter.FILE);
 
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
 
@@ -143,7 +145,6 @@ public class RNAStructExportImport
       } catch (InterruptedException x)
       {
       }
-      ;
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
@@ -177,7 +178,6 @@ public class RNAStructExportImport
       } catch (InterruptedException x)
       {
       }
-      ;
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
@@ -196,11 +196,11 @@ public class RNAStructExportImport
 
       String anfileout = new AnnotationFile()
               .printAnnotationsForAlignment(al);
-      assertTrue(
+      assertNotNull(
               "Test "
                       + testname
                       + "\nAlignment annotation file was not regenerated. Null string",
-              anfileout != null);
+              anfileout);
       assertTrue(
               "Test "
                       + testname
@@ -235,8 +235,8 @@ public class RNAStructExportImport
   @Test(groups = { "Functional" })
   public void testRnaalifoldSettingsRecovery()
   {
-    List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
-    for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) rnaalifoldws
+    List<Argument> opts = new ArrayList<Argument>();
+    for (Argument rg : (List<Argument>) rnaalifoldws
             .getRunnerConfig().getArguments())
     {
       if (rg.getDescription().contains("emperature"))