JAL-1807 - Bob's last(?) before leaving Dundee -- adds fast file loading

[jalviewjs.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index c908b15..ad3224a 100644 (file)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -34,7 +34,6 @@ import java.util.List;
 
 import javajs.J2SIgnoreImport;
 
-import jalview.jsdev.Constants;
 import jalview.jsdev.GenericFileAdapter;
 
 /**
@@ -90,7 +89,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FORMATS = new String[]
   { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile", "RNAML", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, IdentifyFile.GFF3File,
+      "PDB", "JnetFile", "RNAML", GenericFileAdapter.Phylip_FILE_DESC, GenericFileAdapter.JSON_FILE_DESC, IdentifyFile.GFF3File,
       "HTML" };
 
   /**
@@ -99,9 +98,9 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "sto,stk", "xml,rnaml", Constants.Phylip_FILE_EXT, Constants.JSON_FILE_EXT,
+      "sto,stk", "xml,rnaml", GenericFileAdapter.Phylip_FILE_EXT, GenericFileAdapter.JSON_FILE_EXT,
       ".gff2,gff3",
-      "jar,jvp", Constants.Html_FILE_EXT };
+      "jar,jvp", GenericFileAdapter.Html_FILE_EXT };
 
   /**
    * List of readable formats by application in order corresponding to
@@ -109,8 +108,8 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
-      "RNAML", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, IdentifyFile.GFF3File, "Jalview",
-      Constants.Html_FILE_DESC };
+      "RNAML", GenericFileAdapter.Phylip_FILE_DESC, GenericFileAdapter.JSON_FILE_DESC, IdentifyFile.GFF3File, "Jalview",
+      GenericFileAdapter.Html_FILE_DESC };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
@@ -118,7 +117,7 @@ public class AppletFormatAdapter
    */
   public static final String[] WRITEABLE_FORMATS = new String[]
           { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
-    "STH", Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC };
+    "STH", GenericFileAdapter.Phylip_FILE_DESC, GenericFileAdapter.JSON_FILE_DESC };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
@@ -126,7 +125,7 @@ public class AppletFormatAdapter
    */
   public static final String[] WRITABLE_EXTENSIONS = new String[]
   { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
-      "sto,stk", Constants.Phylip_FILE_EXT, Constants.JSON_FILE_EXT, "jvp" };
+      "sto,stk", GenericFileAdapter.Phylip_FILE_EXT, GenericFileAdapter.JSON_FILE_EXT, "jvp" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
@@ -134,7 +133,7 @@ public class AppletFormatAdapter
    */
   public static final String[] WRITABLE_FNAMES = new String[]
   { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
-      Constants.Phylip_FILE_DESC, Constants.JSON_FILE_DESC, "Jalview" };
+      GenericFileAdapter.Phylip_FILE_DESC, GenericFileAdapter.JSON_FILE_DESC, "Jalview" };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
@@ -297,11 +296,11 @@ public class AppletFormatAdapter
       {
         alignFile = GenericFileAdapter.getFile("PhylipFile", inFile, type);
       }
-      else if (format.equals(Constants.JSON_FILE_DESC))
+      else if (format.equals(GenericFileAdapter.JSON_FILE_DESC))
       {
         alignFile = GenericFileAdapter.getFile("JSONFile", inFile, type);
       }
-      else if (format.equals(Constants.Html_FILE_DESC))
+      else if (format.equals(GenericFileAdapter.Html_FILE_DESC))
       {
         alignFile = GenericFileAdapter.getFile("HtmlFile", inFile, type);
       }
@@ -422,7 +421,7 @@ public class AppletFormatAdapter
       {
         alignFile = GenericFileAdapter.getFile("SimpleBlastFile", source);
       }
-      else if (format.equals(Constants.Phylip_FILE_DESC))
+      else if (format.equals(GenericFileAdapter.Phylip_FILE_DESC))
       {
         alignFile = GenericFileAdapter.getFile("PhylipFile", source);
       }
@@ -430,11 +429,11 @@ public class AppletFormatAdapter
       {
         alignFile = GenericFileAdapter.getFile("Gff3File", inFile, type);
       }
-      else if (format.equals(Constants.JSON_FILE_DESC))
+      else if (format.equals(GenericFileAdapter.JSON_FILE_DESC))
       {
         alignFile = GenericFileAdapter.getFile("JSONFile", source);
       }
-      else if (format.equals(Constants.Html_FILE_DESC))
+      else if (format.equals(GenericFileAdapter.Html_FILE_DESC))
       {
         alignFile = GenericFileAdapter.getFile("HtmlFile", source);
       }
@@ -586,11 +585,11 @@ public class AppletFormatAdapter
       {
         afile = GenericFileAdapter.getFile("AMSAFile", alignment);
       }
-      else if (format.equalsIgnoreCase(Constants.Phylip_FILE_DESC))
+      else if (format.equalsIgnoreCase(GenericFileAdapter.Phylip_FILE_DESC))
       {
         afile = GenericFileAdapter.getFile("PhylipFile");
       }
-       else if (format.equalsIgnoreCase(Constants.JSON_FILE_DESC))
+       else if (format.equalsIgnoreCase(GenericFileAdapter.JSON_FILE_DESC))
        {
         afile = GenericFileAdapter.getFile("JSONFile");
        }