JAL-2388 Renamed viewport position props to viewport ranges

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 4ffb86d..c5a80e3 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -64,7 +64,7 @@ public class AppletFormatAdapter
    */
   boolean serviceSecondaryStruct = false;
 
-  private AlignmentFileI alignFile = null;
+  private AlignmentFileReaderI alignFile = null;
 
   String inFile;
 
@@ -75,63 +75,18 @@ public class AppletFormatAdapter
 
   private AlignExportSettingI exportSettings;
 
-  /**
-   * 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", "PHYLIP", "JSON",
-  // IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
-
-  /**
-   * 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",
-  // "sto,stk", "xml,rnaml", "phy", "json", ".gff2,gff3", "jar,jvp",
-  // "html", "cif" };
-
-  //
-  // /**
-  // * 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",
-  // "PHYLIP", "JSON", IdentifyFile.FeaturesFile,
-  // "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
-
-  /**
-   * 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",
-  // "PHYLIP", "JSON" };
-
-  /**
-   * 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",
-  // "sto,stk", "phy", "json", "jvp" };
+  public static String INVALID_CHARACTERS = "Contains invalid characters";
 
   /**
-   * List of writable formats by the application. Order must correspond with the
-   * WRITABLE_EXTENSIONS list of formats.
+   * Returns an error message with a list of supported readable file formats
+   * 
+   * @return
    */
-  // public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
-  // "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP",
-  // "JSON", "Jalview" };
-
-  public static String INVALID_CHARACTERS = "Contains invalid characters";
-
-  // TODO: make these messages dynamic
-  public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
-          + prettyPrint(FileFormat.getReadableFormats());
-
+  public static String getSupportedFormats()
+  {
+    return "Formats currently supported are\n"
+          + prettyPrint(FileFormats.getInstance().getReadableFormats());
+  }
   public AppletFormatAdapter()
   {
   }
@@ -194,25 +149,22 @@ public class AppletFormatAdapter
     this.inFile = file;
     try
     {
-      if (FileFormat.PDB.equals(fileFormat)
-              || FileFormat.MMCif.equals(fileFormat))
+      if (fileFormat.isStructureFile())
       {
-        boolean isParseWithJMOL = StructureImportSettings
-                .getDefaultPDBFileParser().equalsIgnoreCase(
+        String structureParser = StructureImportSettings
+                .getDefaultPDBFileParser();
+        boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
                         StructureImportSettings.StructureParser.JMOL_PARSER
                                 .toString());
+        StructureImportSettings.addSettings(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct);
         if (isParseWithJMOL)
         {
-          StructureImportSettings.addSettings(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, inFile,
-                  sourceType);
+          alignFile = new JmolParser(inFile, sourceType);
         }
         else
         {
-          StructureImportSettings.addSettings(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct);
+          // todo is MCview parsing obsolete yet? JAL-2120
           StructureImportSettings.setShowSeqFeatures(true);
           alignFile = new MCview.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
@@ -223,24 +175,10 @@ public class AppletFormatAdapter
       }
       else
       {
-        alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+        // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+        alignFile = fileFormat.getReader(new FileParse(inFile,
+                sourceType));
       }
-      // new FastaFile(inFile, sourceType);
-      // new MSFfile(inFile, sourceType);
-      // new PileUpfile(inFile, sourceType);
-      // new ClustalFile(inFile, sourceType);
-      // new BLCFile(inFile, sourceType);
-      // new PIRFile(inFile, sourceType);
-      // new PfamFile(inFile, sourceType);
-      // alignFile = new JPredFile(inFile, sourceType);
-      // ((JPredFile) alignFile).removeNonSequences();
-      // new StockholmFile(inFile, sourceType);
-      // new SimpleBlastFile(inFile, sourceType);
-      // new PhylipFile(inFile, sourceType);
-      // new JSONFile(inFile, sourceType);
-      // new HtmlFile(inFile, sourceType);
-      // new RnamlFile(inFile, sourceType);
-      // alignFile = new FeaturesFile(true, inFile, sourceType);
       return buildAlignmentFromFile();
     } catch (Exception e)
     {
@@ -279,7 +217,7 @@ public class AppletFormatAdapter
         throw new IOException(e.getMessage());
       }
     }
-    throw new FileFormatException(SUPPORTED_FORMATS);
+    throw new FileFormatException(getSupportedFormats());
   }
 
   /**
@@ -307,8 +245,7 @@ public class AppletFormatAdapter
         {
           StructureImportSettings.addSettings(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct);
-          alignFile = new JmolParser(annotFromStructure,
-                  localSecondaryStruct, serviceSecondaryStruct, source);
+          alignFile = new JmolParser(source);
         }
         else
         {
@@ -320,7 +257,7 @@ public class AppletFormatAdapter
       }
       else
       {
-        alignFile = format.getAlignmentFile(source);
+        alignFile = format.getReader(source);
       }
 
       return buildAlignmentFromFile();
@@ -359,7 +296,7 @@ public class AppletFormatAdapter
       }
 
       // If we get to this stage, the format was not supported
-      throw new FileFormatException(SUPPORTED_FORMATS);
+      throw new FileFormatException(getSupportedFormats());
     }
   }
 
@@ -433,7 +370,7 @@ public class AppletFormatAdapter
   {
     try
     {
-      AlignmentFileI afile = format.getAlignmentFile(alignment);
+      AlignmentFileWriterI afile = format.getWriter(alignment);
 
       afile.setNewlineString(newline);
       afile.setExportSettings(exportSettings);
@@ -461,7 +398,8 @@ public class AppletFormatAdapter
       return afileresp;
     } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '" + format
+      System.err.println("Failed to write alignment as a '"
+              + format.getName()
               + "' file\n");
       e.printStackTrace();
     }
@@ -710,7 +648,7 @@ public class AppletFormatAdapter
     return null;
   }
 
-  public AlignmentFileI getAlignFile()
+  public AlignmentFileReaderI getAlignFile()
   {
     return alignFile;
   }