JAL-1499 first pass update of parsing and tests, more to come

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 02de02e..d2d607b 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignmentView;
 import jalview.util.MessageManager;
 
 import java.io.File;
+import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
 
@@ -82,52 +83,56 @@ public class AppletFormatAdapter
   /**
    * List of valid format strings used in the isValidFormat method
    */
-  public static final String[] READABLE_FORMATS = new String[]
-  { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
-      "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
-      "HTML" };
+  public static final String[] READABLE_FORMATS = new String[] { "BLC",
+      "CLUSTAL", "FASTA", "MEGA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+      "PDB",
+      "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+      IdentifyFile.GFF3File, "HTML" };
 
   /**
    * List of readable format file extensions by application in order
    * corresponding to READABLE_FNAMES
    */
-  public static final String[] READABLE_EXTENSIONS = new String[]
-  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+  public static final String[] READABLE_EXTENSIONS = new String[] {
+      "fa, fasta, mfa, fastq", "aln", "pfam", "meg", "msf", "pir", "blc",
+      "amsa",
       "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
-      ".gff2,gff3",
-      "jar,jvp", HtmlFile.FILE_EXT };
+      ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT };
 
   /**
    * List of readable formats by application in order corresponding to
    * READABLE_EXTENSIONS
    */
-  public static final String[] READABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
-      "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
-      HtmlFile.FILE_DESC };
+  public static final String[] READABLE_FNAMES = new String[] { "Fasta",
+      "Clustal", "PFAM", "MEGA", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
+      "RNAML",
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
+      "Jalview", HtmlFile.FILE_DESC };
 
   /**
    * List of valid format strings for use by callers of the formatSequences
    * method
    */
-  public static final String[] WRITEABLE_FORMATS = new String[]
-          { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
-    "STH", PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
+  public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
+      "CLUSTAL", "FASTA", "MEGA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
+      "STH",
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
 
   /**
    * List of extensions corresponding to file format types in WRITABLE_FNAMES
    * that are writable by the application.
    */
-  public static final String[] WRITABLE_EXTENSIONS = new String[]
-  { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+  public static final String[] WRITABLE_EXTENSIONS = new String[] {
+      "fa, fasta, mfa, fastq", "aln", "pfam", "meg", "msf", "pir", "blc",
+      "amsa",
       "sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
 
   /**
    * List of writable formats by the application. Order must correspond with the
    * WRITABLE_EXTENSIONS list of formats.
    */
-  public static final String[] WRITABLE_FNAMES = new String[]
-  { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
+  public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
+      "Clustal", "PFAM", "MEGA", "MSF", "PIR", "BLC", "AMSA", "STH",
       PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
@@ -169,7 +174,6 @@ public class AppletFormatAdapter
     return list.toString();
   }
 
-
   public void setNewlineString(String nl)
   {
     newline = nl;
@@ -307,6 +311,10 @@ public class AppletFormatAdapter
       {
         alignFile = new RnamlFile(inFile, type);
       }
+      else if (format.equals("MEGA"))
+      {
+        alignFile = new MegaFile(inFile, type);
+      }
       else if (format.equals(IdentifyFile.GFF3File))
       {
         alignFile = new Gff3File(inFile, type);
@@ -343,7 +351,10 @@ public class AppletFormatAdapter
           ex.printStackTrace();
         }
       }
-
+      if (format.equalsIgnoreCase("HTML"))
+      {
+        throw new IOException(e.getMessage());
+      }
       // If we get to this stage, the format was not supported
       throw new java.io.IOException(SUPPORTED_FORMATS);
     }
@@ -416,6 +427,10 @@ public class AppletFormatAdapter
       {
         alignFile = new RnamlFile(source);
       }
+      else if (format.equals("MEGA"))
+      {
+        alignFile = new MegaFile(source);
+      }
       else if (format.equals("SimpleBLAST"))
       {
         alignFile = new SimpleBlastFile(source);
@@ -476,7 +491,6 @@ public class AppletFormatAdapter
     }
   }
 
-
   /**
    * boilerplate method to handle data from an AlignFile and construct a new
    * alignment or import to an existing alignment
@@ -500,6 +514,7 @@ public class AppletFormatAdapter
 
   /**
    * create an alignment flatfile from a Jalview alignment view
+   * 
    * @param format
    * @param jvsuffix
    * @param av
@@ -588,18 +603,23 @@ public class AppletFormatAdapter
       {
         afile = new PhylipFile();
       }
-       else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
-       {
+      else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+      {
         afile = new JSONFile();
-       }
+      }
       else if (format.equalsIgnoreCase("RNAML"))
       {
         afile = new RnamlFile();
       }
-
+      else if (format.equalsIgnoreCase("MEGA"))
+      {
+        afile = new MegaFile();
+      }
       else
       {
-        throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
+        throw new Exception(
+                MessageManager
+                        .getString("error.implementation_error_unknown_file_format_string"));
       }
 
       afile.setNewlineString(newline);
@@ -680,7 +700,7 @@ public class AppletFormatAdapter
             } catch (Exception e)
             {
               System.err
-              .println("Couln't format the alignment for output as a FASTA file.");
+                      .println("Couln't format the alignment for output as a FASTA file.");
               e.printStackTrace(System.err);
             }
           }
@@ -690,8 +710,8 @@ public class AppletFormatAdapter
           }
           System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
           System.out
-          .println("Difference between free memory now and before is "
-                  + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
+                  .println("Difference between free memory now and before is "
+                          + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
         } catch (Exception e)
         {
           System.err.println("Exception when dealing with " + i
@@ -757,7 +777,7 @@ public class AppletFormatAdapter
     } catch (Exception ex)
     {
       System.err
-      .println("Exception checking resources: " + file + " " + ex);
+              .println("Exception checking resources: " + file + " " + ex);
     }
 
     if (file.indexOf("://") > -1)
@@ -859,7 +879,7 @@ public class AppletFormatAdapter
           if (debug)
           {
             System.out
-            .println("File deemed not accessible via " + protocol);
+                    .println("File deemed not accessible via " + protocol);
           }
           fp.close();
           return null;