From ea1b74357e517baef19ef6f862bc7775f7a7804e Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 25 Nov 2016 09:01:54 +0000
Subject: [PATCH] JAL-2344 use .equals() to compare FileFormatI objects

---
 src/jalview/gui/AlignFrame.java         |   13 +++++++------
 src/jalview/gui/Desktop.java            |    4 ++--
 src/jalview/io/AppletFormatAdapter.java |   14 ++++++--------
 src/jalview/io/FileLoader.java          |    2 +-
 4 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 453fd3a..8cc1dd5 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1011,7 +1011,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // originating file's format
       // TODO: work out how to recover feature settings for correct view(s) when
       // file is reloaded.
-      if (currentFileFormat == FileFormat.Jalview)
+      if (FileFormat.Jalview.equals(currentFileFormat))
       {
         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
         for (int i = 0; i < frames.length; i++)
@@ -1155,7 +1155,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     boolean success = true;
 
-    if (format == FileFormat.Jalview)
+    if (FileFormat.Jalview.equals(format))
     {
       String shortName = title;
 
@@ -5099,7 +5099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               if (type != null)
               {
-                if (type == FileFormat.PDB)
+                if (FileFormat.PDB.equals(type))
                 {
                   filesmatched.add(new Object[] { file, protocol, mtch });
                   continue;
@@ -5210,7 +5210,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // if the file isn't identified, or not positively identified as some
       // other filetype (PFAM is default unidentified alignment file type) then
       // try to parse as annotation.
-      boolean isAnnotation = (format == null || format == FileFormat.Pfam) ? new AnnotationFile()
+      boolean isAnnotation = (format == null || FileFormat.Pfam
+              .equals(format)) ? new AnnotationFile()
               .annotateAlignmentView(viewport, file, sourceType) : false;
 
       if (!isAnnotation)
@@ -5267,7 +5268,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             format = new IdentifyFile().identify(file, sourceType);
           }
-          if (format == FileFormat.Jnet)
+          if (FileFormat.Jnet.equals(format))
           {
             JPredFile predictions = new JPredFile(
                     file, sourceType);
@@ -5282,7 +5283,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             isAnnotation = true;
           }
           // else if (IdentifyFile.FeaturesFile.equals(format))
-          else if (format == FileFormat.Features)
+          else if (FileFormat.Features.equals(format))
           {
             if (parseFeaturesFile(file, sourceType))
             {
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 624054b..3fa5387 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1031,8 +1031,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               .getSelectedFile().getParent());
 
       FileFormatI format = null;
-      if (chooser.getSelectedFormat() != null
-              && chooser.getSelectedFormat() == FileFormat.Jalview)
+      FileFormatI selectedFormat = chooser.getSelectedFormat();
+      if (FileFormat.Jalview.equals(selectedFormat))
       {
         format = FileFormat.Jalview;
       }
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5f40713..4ffb86d 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -194,10 +194,9 @@ public class AppletFormatAdapter
     this.inFile = file;
     try
     {
-      if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif)
+      if (FileFormat.PDB.equals(fileFormat)
+              || FileFormat.MMCif.equals(fileFormat))
       {
-        // TODO obtain config value from preference settings.
-        // Set value to 'true' to test PDB processing with Jmol: JAL-1213
         boolean isParseWithJMOL = StructureImportSettings
                 .getDefaultPDBFileParser().equalsIgnoreCase(
                         StructureImportSettings.StructureParser.JMOL_PARSER
@@ -219,9 +218,8 @@ public class AppletFormatAdapter
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   sourceType);
         }
-        ((StructureFile) alignFile)
-                .setDbRefType(fileFormat == FileFormat.PDB ? Type.PDB
-                        : Type.MMCIF);
+        ((StructureFile) alignFile).setDbRefType(FileFormat.PDB
+                .equals(fileFormat) ? Type.PDB : Type.MMCIF);
       }
       else
       {
@@ -276,7 +274,7 @@ public class AppletFormatAdapter
           ex.printStackTrace();
         }
       }
-      if (fileFormat == FileFormat.Html)
+      if (FileFormat.Html.equals(fileFormat))
       {
         throw new IOException(e.getMessage());
       }
@@ -301,7 +299,7 @@ public class AppletFormatAdapter
     DataSourceType type = source.dataSourceType;
     try
     {
-      if (format == FileFormat.PDB || format == FileFormat.MMCif)
+      if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
       {
         // TODO obtain config value from preference settings
         boolean isParseWithJMOL = false;
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index e17fe04..830efe2 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -298,7 +298,7 @@ public class FileLoader implements Runnable
       loadtime = -System.currentTimeMillis();
       AlignmentI al = null;
 
-      if (format == FileFormat.Jalview)
+      if (FileFormat.Jalview.equals(format))
       {
         if (source != null)
         {
-- 
1.7.10.2