From ae08e9be88ca8cafe0f27ca2d9927db487e35db2 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 30 Mar 2018 15:47:00 +0100
Subject: [PATCH] JAL-2629 tidy code, factory methods for param sets

---
 src/jalview/hmmer/HMMERParamStore.java |   53 ++++++++++++++++++++++----------
 src/jalview/hmmer/HMMERPreset.java     |   10 ------
 2 files changed, 36 insertions(+), 27 deletions(-)

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 17f582e..c668481 100644
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -18,17 +18,38 @@ import java.util.Collection;
 import java.util.List;
 import java.util.Scanner;
 
-public class HMMERParamStore implements ParamDatastoreI
+public final class HMMERParamStore implements ParamDatastoreI
 {
+  private static final String HMMBUILD = "hmmbuild";
+
+  private static final String HMMALIGN = "hmmalign";
+
+  private static final String HMMSEARCH = "hmmsearch";
+
   String name;
 
   List<WsParamSetI> presets = new ArrayList<>();
 
-  public HMMERParamStore(String nam)
+  private HMMERParamStore(String nam)
   {
     this.name = nam;
   }
 
+  public static HMMERParamStore forBuild()
+  {
+    return new HMMERParamStore(HMMBUILD);
+  }
+
+  public static HMMERParamStore forAlign()
+  {
+    return new HMMERParamStore(HMMALIGN);
+  }
+
+  public static HMMERParamStore forSearch()
+  {
+    return new HMMERParamStore(HMMSEARCH);
+  }
+
   @Override
   public List<WsParamSetI> getPresets()
   {
@@ -45,20 +66,20 @@ public class HMMERParamStore implements ParamDatastoreI
   public List<ArgumentI> getServiceParameters()
   {
     List<ArgumentI> args = new ArrayList<>();
-    if ("hmmsearch".equals(name))
+    switch (name)
     {
+    case HMMSEARCH:
       getHMMSearchParams(args);
-    }
-    if ("hmmalign".equals(name))
-    {
+      break;
+    case HMMALIGN:
       getHMMAlignParams(args);
-
-    }
-    if ("hmmbuild".equals(name))
-    {
+      break;
+    case HMMBUILD:
       getHMMBuildParams(args);
-
+      break;
+    default:
     }
+
     return args;
   }
 
@@ -80,7 +101,7 @@ public class HMMERParamStore implements ParamDatastoreI
         while (nameScanner.hasNext())
         {
           String next = nameScanner.next();
-          if (next == "null")
+          if ("null".equals(next))
           {
             Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
             Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
@@ -164,13 +185,13 @@ public class HMMERParamStore implements ParamDatastoreI
   }
 
   @Override
-  public boolean presetExists(String name)
+  public boolean presetExists(String forName)
   {
     return false;
   }
 
   @Override
-  public void deletePreset(String name)
+  public void deletePreset(String forName)
   {
   }
 
@@ -178,8 +199,6 @@ public class HMMERParamStore implements ParamDatastoreI
   public void storePreset(String presetName, String text,
           List<ArgumentI> jobParams)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
@@ -189,7 +208,7 @@ public class HMMERParamStore implements ParamDatastoreI
   }
 
   @Override
-  public WsParamSetI parseServiceParameterFile(String name,
+  public WsParamSetI parseServiceParameterFile(String forName,
           String description, String[] serviceURL, String parameters)
           throws IOException
   {
diff --git a/src/jalview/hmmer/HMMERPreset.java b/src/jalview/hmmer/HMMERPreset.java
index b7cd29a..2712259 100644
--- a/src/jalview/hmmer/HMMERPreset.java
+++ b/src/jalview/hmmer/HMMERPreset.java
@@ -11,57 +11,47 @@ public class HMMERPreset implements WsParamSetI
   @Override
   public String getName()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
   @Override
   public String getDescription()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
   @Override
   public String[] getApplicableUrls()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
   @Override
   public String getSourceFile()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
   @Override
   public void setSourceFile(String newfile)
   {
-    // TODO Auto-generated method stub
-
   }
 
   @Override
   public boolean isModifiable()
   {
-    // TODO Auto-generated method stub
     return false;
   }
 
   @Override
   public List<ArgumentI> getArguments()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
   @Override
   public void setArguments(List<ArgumentI> args)
   {
-    // TODO Auto-generated method stub
-
   }
 
 }
-- 
1.7.10.2