FileFormatI further tweaks, clean compile

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index abb6848..1b66e9c 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -217,10 +217,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormat.getWritableFormats())
     {
-      MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(ff);
 
       item.addActionListener(this);
       outputmenu.add(item);

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 2ee86f1..e1b01a8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -3241,11 +3241,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     inputText.addActionListener(this);
     Menu outputTextboxMenu = new Menu(
             MessageManager.getString("label.out_to_textbox"));
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormat.getWritableFormats())
     {
-
-      MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(ff);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 38223c7..e585e28 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1263,9 +1263,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void outputText_actionPerformed(ActionEvent e)
   {
 
-    FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
-    AlignmentExportData exportData = getAlignmentForExport(
-fileFormat,
+    FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+    AlignmentExportData exportData = getAlignmentForExport(fileFormat,
             viewport, null);
     if (exportData.getSettings().isCancelled())
     {

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 52a0d41..4d9dc4d 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -258,10 +258,9 @@ public class PopupMenu extends JPopupMenu
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
 
-    for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormat.getWritableFormats())
     {
-      JMenuItem item = new JMenuItem(
-              jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+      JMenuItem item = new JMenuItem(ff);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 798249f..34eace4 100644 (file)
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -24,6 +24,8 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
+import java.io.IOException;
+
 public class AMSAFile extends jalview.io.FastaFile
 {
 
@@ -37,11 +39,23 @@ public class AMSAFile extends jalview.io.FastaFile
     this.al = al;
   }
 
+  public AMSAFile(String inFile, DataSourceType sourceType)
+          throws IOException
+  {
+    super(inFile, sourceType);
+  }
+
+  public AMSAFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
   /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     super.print(sqs, jvsuffix);

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 04d68e8..e0a607b 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -78,58 +78,59 @@ 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", "PHYLIP", "JSON",
-      IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
+  // 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" };
+  // 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" };
+  // 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 final String[] WRITABLE_EXTENSIONS = new String[] {
+  // "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+  // "sto,stk", "phy", "json", "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",
-      "PHYLIP", "JSON", "Jalview" };
+  // 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(READABLE_FORMATS);
+          + prettyPrint(FileFormat.getReadableFormats());
 
   public AppletFormatAdapter()
   {
@@ -148,19 +149,21 @@ public class AppletFormatAdapter
   }
 
   /**
-   *
-   * @param els
-   * @return grammatically correct(ish) list consisting of els elements.
+   * Formats a grammatically correct(ish) list consisting of the given objects
+   * 
+   * @param things
+   * @return
    */
-  public static String prettyPrint(String[] els)
+  public static String prettyPrint(List<? extends Object> things)
   {
     StringBuffer list = new StringBuffer();
-    for (int i = 0, iSize = els.length - 1; i < iSize; i++)
+    for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
     {
-      list.append(els[i]);
+      list.append(things.get(i).toString());
       list.append(", ");
     }
-    list.append(" and " + els[els.length - 1] + ".");
+    // could i18n 'and' here
+    list.append(" and " + things.get(things.size() - 1).toString() + ".");
     return list.toString();
   }
 
@@ -224,29 +227,28 @@ public class AppletFormatAdapter
       {
         alignFile = fileFormat.getAlignmentFile(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);
+      // 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)
     {
       e.printStackTrace();
       System.err.println("Failed to read alignment using the '"
-              + fileFormat
-              + "' reader.\n" + e);
+              + fileFormat + "' reader.\n" + e);
 
       if (e.getMessage() != null
               && e.getMessage().startsWith(INVALID_CHARACTERS))
@@ -666,8 +668,7 @@ public class AppletFormatAdapter
     {
       try
       {
-        FileFormatI idformat = new IdentifyFile().identify(file,
-                protocol);
+        FileFormatI idformat = new IdentifyFile().identify(file, protocol);
         if (idformat == null)
         {
           if (debug)

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 20c44bc..07a3b25 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -712,7 +712,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       dataset = new Alignment(new SequenceI[] {});
     }
 
-    boolean parseResult = parse(dataset, null, false, true);
+    Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
+    boolean parseResult = parse(dataset, featureColours, false, true);
     if (!parseResult)
     {
       // pass error up somehow

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index a7113f6..770f762 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -5,12 +5,14 @@ import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
 
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 public enum FileFormat implements FileFormatI
 {
-  Fasta("FASTA", "fa, fasta, mfa, fastq", true, true)
+  Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
   {
     @Override
     public AlignmentFileI getAlignmentFile(String inFile,
@@ -54,7 +56,7 @@ public enum FileFormat implements FileFormatI
       return new PfamFile();
     }
   },
-  Stockholm("STH", "sto,stk", true, true)
+  Stockholm("Stockholm", "sto,stk", true, true)
   {
     @Override
     public AlignmentFileI getAlignmentFile(String inFile,
@@ -118,6 +120,28 @@ public enum FileFormat implements FileFormatI
       return new BLCFile();
     }
   },
+  AMSA("AMSA", "amsa", true, true)
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new AMSAFile(inFile, sourceType);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new AMSAFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new BLCFile();
+    }
+  },
   Html("HTML", "html", true, false)
   {
     @Override
@@ -193,7 +217,7 @@ public enum FileFormat implements FileFormatI
     }
 
   },
-  Pileup("PileUp", "?", false, false)
+  Pileup("PileUp", "pileup", false, true)
   {
     @Override
     public AlignmentFileI getAlignmentFile(String inFile,
@@ -235,7 +259,7 @@ public enum FileFormat implements FileFormatI
     }
 
   },
-  Clustal("CLUSTAL", "aln", true, true)
+  Clustal("Clustal", "aln", true, true)
   {
     @Override
     public AlignmentFileI getAlignmentFile(String inFile,
@@ -465,6 +489,44 @@ public enum FileFormat implements FileFormatI
 
   private String name;
 
+  /**
+   * Answers a list of writeable file formats (as string, corresponding to the
+   * toString() and forName() methods)
+   * 
+   * @return
+   */
+  public static List<String> getWritableFormats()
+  {
+    List<String> l = new ArrayList<String>();
+    for (FileFormatI ff : values())
+    {
+      if (ff.isWritable())
+      {
+        l.add(ff.toString());
+      }
+    }
+    return l;
+  }
+
+  /**
+   * Answers a list of readable file formats (as string, corresponding to the
+   * toString() and forName() methods)
+   * 
+   * @return
+   */
+  public static List<String> getReadableFormats()
+  {
+    List<String> l = new ArrayList<String>();
+    for (FileFormatI ff : values())
+    {
+      if (ff.isReadable())
+      {
+        l.add(ff.toString());
+      }
+    }
+    return l;
+  }
+
   @Override
   public boolean isComplexAlignFile()
   {
@@ -527,4 +589,10 @@ public enum FileFormat implements FileFormatI
   {
     return extensions;
   }
+
+  @Override
+  public String toString()
+  {
+    return name;
+  }
 }

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 88f9ae5..e17fe04 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -317,7 +317,7 @@ public class FileLoader implements Runnable
             if (source != null)
             {
               // read from the provided source
-              al = new FormatAdapter().readFromFile(source, format);
+            al = new FormatAdapter().readFromFile(source, format);
             }
             else
             {

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 1408cd1..724170e 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -242,14 +242,6 @@ public class FormatAdapter extends AppletFormatAdapter
             getCacheSuffixDefault(format), colSel, null);
   }
 
-  public String formatSequences(FileFormatI format, AlignmentI alignment,
-          String[] omitHidden, int[] exportRange, ColumnSelection colSel,
-          SequenceGroup sgp)
-  {
-    return formatSequences(format, alignment, omitHidden, exportRange,
-            getCacheSuffixDefault(format), colSel, sgp);
-  }
-
   /**
    * hack function to replace seuqences with visible sequence strings before
    * generating a string of the alignment in the given format.
@@ -337,4 +329,12 @@ public class FormatAdapter extends AppletFormatAdapter
             selectedOnly);
   }
 
+  public AlignmentI readFromFile(AlignmentFileI source, FileFormatI format)
+          throws IOException
+  {
+    FileParse fp = new FileParse(source.getInFile(),
+            source.getDataSourceType());
+    return readFromFile(fp, format);
+  }
+
 }

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 89fc3cd..bc91e09 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -74,6 +74,13 @@ public class IdentifyFile
     // preserves original behaviour prior to version 2.3
   }
 
+  public FileFormatI identify(AlignmentFileI file, boolean closeSource)
+          throws IOException
+  {
+    FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
+    return identify(fp, closeSource);
+  }
+
   /**
    * Identify contents of source, closing it or resetting source to start
    * afterwards.
@@ -343,6 +350,7 @@ public class IdentifyFile
               .println("File Identification failed! - Empty file was read.");
       throw new FileFormatException("EMPTY DATA FILE");
     }
+    System.out.println("File format identified as " + reply.toString());
     return reply;
   }
 

diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index a4362dc..7e1aaa1 100755 (executable)
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -241,6 +241,7 @@ public class JalviewFileChooser extends JFileChooser
     }
 
     String format = getFileFilter().getDescription();
+    format = format.substring(0, format.indexOf("(") - 1);
     return FileFormat.valueOf(format);
   }
 

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index d7def6b..73d1b3c 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,7 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.io.FileFormat;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 
@@ -244,10 +245,9 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+      for (String ff : FileFormat.getWritableFormats())
       {
-        JMenuItem item = new JMenuItem(
-                jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+        JMenuItem item = new JMenuItem(ff);
 
         item.addActionListener(new ActionListener()
         {

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index c78bced..08a242d 100644 (file)
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -38,7 +38,6 @@ import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
@@ -199,13 +198,27 @@ public class Alignment extends InputType
             writeAsFile, null));
 
     lst.add(new Option("format", "Alignment upload format", true,
-            FileFormat.Fasta.toString(),
- format.toString(), Arrays
-                    .asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS),
+            FileFormat.Fasta.toString(), format.toString(), getWritableFormats(),
             null));
     lst.add(createMolTypeOption("type", "Sequence type", false, type, null));
 
     return lst;
   }
 
+  /**
+   * @return
+   */
+  protected List<String> getWritableFormats()
+  {
+    List<String> formats = new ArrayList<String>();
+    for (FileFormatI ff : FileFormat.values())
+    {
+      if (ff.isWritable())
+      {
+        formats.add(ff.toString());
+      }
+    }
+    return formats;
+  }
+
 }