fileFormat enum wip changes

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 720bac4..0c99d26 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -26,6 +26,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SequenceI;
 import jalview.structure.StructureImportSettings;
 
 import java.io.File;
@@ -87,7 +88,7 @@ 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", "phy", "json",
-      ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT, "cif" };
+      ".gff2,gff3", "jar,jvp", "html", "cif" };
 
   /**
    * List of readable formats by application in order corresponding to
@@ -172,49 +173,6 @@ public class AppletFormatAdapter
   }
 
   /**
-   * check that this format is valid for reading
-   *
-   * @param format
-   *          a format string to be compared with READABLE_FORMATS
-   * @return true if format is readable
-   */
-  public static final boolean isValidFormat(String format)
-  {
-    return isValidFormat(format, false);
-  }
-
-  /**
-   * validate format is valid for IO
-   *
-   * @param format
-   *          a format string to be compared with either READABLE_FORMATS or
-   *          WRITEABLE_FORMATS
-   * @param forwriting
-   *          when true, format is checked for containment in WRITEABLE_FORMATS
-   * @return true if format is valid
-   */
-  public static final boolean isValidFormat(String format,
-          boolean forwriting)
-  {
-    if (format == null)
-    {
-      return false;
-    }
-    boolean valid = false;
-    String[] format_list = (forwriting) ? WRITEABLE_FORMATS
-            : READABLE_FORMATS;
-    for (String element : format_list)
-    {
-      if (element.equalsIgnoreCase(format))
-      {
-        return true;
-      }
-    }
-
-    return valid;
-  }
-
-  /**
    * Constructs the correct filetype parser for a characterised datasource
    *
    * @param inFile
@@ -440,23 +398,23 @@ public class AppletFormatAdapter
       AlignmentFileI afile = format.getAlignmentFile();
 
       afile.setNewlineString(newline);
-      afile.addJVSuffix(jvsuffix);
       afile.setExportSettings(exportSettings);
       afile.configureForView(viewpanel);
 
       // check whether we were given a specific alignment to export, rather than
       // the one in the viewpanel
+      SequenceI[] seqs = null;
       if (viewpanel == null || viewpanel.getAlignment() == null
               || viewpanel.getAlignment() != alignment)
       {
-        afile.setSeqs(alignment.getSequencesArray());
+        seqs = alignment.getSequencesArray();
       }
       else
       {
-        afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
+        seqs = viewpanel.getAlignment().getSequencesArray();
       }
 
-      String afileresp = afile.print();
+      String afileresp = afile.print(seqs, jvsuffix);
       if (afile.hasWarningMessage())
       {
         System.err.println("Warning raised when writing as " + format