X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=00fcb9c39c598d12dc6d285b5b9720bb080ba129;hb=dc5a5883cfe90255079e41538e56bc433bd1e4a5;hp=a91a1b085024e8a37b6c97bfb43c28592d5cd727;hpb=0ba2cdf46e967155efab9b457598f2112e2e2033;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index a91a1b0..00fcb9c 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,222 +1,319 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  *
- * This program is free software; you can redistribute it and/or
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
  *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE.  See the GNU General Public License for more details.
  *
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import java.io.File;
+import java.util.Locale;
 
-import jalview.datamodel.*;
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
+import jalview.util.Platform;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
 
 /**
- * A low level class for alignment and feature IO
- * with alignment formatting methods used by both applet 
- * and application for generating flat alignment files.
- * It also holds the lists of magic format names
- * that the applet and application will allow the user to read or write files with.
+ * A low level class for alignment and feature IO with alignment formatting
+ * methods used by both applet and application for generating flat alignment
+ * files. It also holds the lists of magic format names that the applet and
+ * application will allow the user to read or write files with.
  *
  * @author $author$
  * @version $Revision$
  */
 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"
-  };
+  private AlignmentViewPanel viewpanel;
+
   /**
-   * List of valid format strings for use by callers of the formatSequences method
+   * add jalview-derived non-secondary structure annotation from PDB structure
    */
-  public static final String[] WRITEABLE_FORMATS = new String[]
-      {
-      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" , "AMSA"
-  };
+  boolean annotFromStructure = false;
+
   /**
-   * List of extensions corresponding to file format types 
-   * in WRITABLE_FNAMES that are writable by the
-   * application.
+   * add secondary structure from PDB data with built-in algorithms
    */
-  public static final String[] WRITABLE_EXTENSIONS = new String[]
-        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" };
+  boolean localSecondaryStruct = false;
+
   /**
-   * List of writable formats by the application. Order must
-   * correspond with the WRITABLE_EXTENSIONS list of formats.
+   * process PDB data with web services
    */
-  public static final String[] WRITABLE_FNAMES = new String[]
-        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+  boolean serviceSecondaryStruct = false;
+
+  private AlignmentFileReaderI alignFile = null;
+
+  String inFile;
 
   /**
-   * List of readable format file extensions by application in order
-   * corresponding to READABLE_FNAMES 
+   * character used to write newlines
    */
-  public static final String[] READABLE_EXTENSIONS =         new String[]
-        {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "amsa","jar"
-    };
+  protected String newline = System.getProperty("line.separator");
+
+  private AlignExportSettingsI exportSettings;
+
+  private File selectedFile;
+
+  public static String INVALID_CHARACTERS = "Contains invalid characters";
+
   /**
-   * List of readable formats by application in order
-   * corresponding to READABLE_EXTENSIONS
+   * Returns an error message with a list of supported readable file formats
+   * 
+   * @return
    */
-  public static final String[] READABLE_FNAMES =         new String[]
-        {
-        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA","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);
+  public static String getSupportedFormats()
+  {
+    return "Formats currently supported are\n"
+            + prettyPrint(FileFormats.getInstance().getReadableFormats());
+  }
+
+  public AppletFormatAdapter()
+  {
+  }
+
+  public AppletFormatAdapter(AlignmentViewPanel viewpanel)
+  {
+    this.viewpanel = viewpanel;
+  }
+
+  public AppletFormatAdapter(AlignmentViewPanel alignPanel,
+          AlignExportSettingsI settings)
+  {
+    viewpanel = alignPanel;
+    exportSettings = settings;
+  }
+
   /**
+   * Formats a grammatically correct(ish) list consisting of the given objects
    * 
-   * @param els
-   * @return grammatically correct(ish) list consisting of els elements.
+   * @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(",");
+      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();
   }
-  public static String FILE = "File";
-  public static String URL = "URL";
-  public static String PASTE = "Paste";
-  public static String CLASSLOADER = "ClassLoader";
 
-  AlignFile afile = null;
-  String inFile;
-  /**
-   * 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)
+  public void setNewlineString(String nl)
   {
-    boolean valid = false;
-    for (int i = 0; i < READABLE_FORMATS.length; i++)
-    {
-      if (READABLE_FORMATS[i].equalsIgnoreCase(format))
-      {
-        return true;
-      }
-    }
+    newline = nl;
+  }
 
-    return valid;
+  public String getNewlineString()
+  {
+    return newline;
   }
 
   /**
    * Constructs the correct filetype parser for a characterised datasource
    *
-   * @param inFile data/data location
-   * @param type type of datasource
-   * @param format File format of data provided by datasource
+   * @param inFile
+   *          data/data location
+   * @param sourceType
+   *          type of datasource
+   * @param fileFormat
    *
-   * @return DOCUMENT ME!
+   * @return
    */
-  public Alignment readFile(String inFile, String type, String format)
-      throws java.io.IOException
+  public AlignmentI readFile(String file, DataSourceType sourceType,
+          FileFormatI fileFormat) throws IOException
   {
-    this.inFile = inFile;
+    return readFile(null, file, sourceType, fileFormat);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat)
+          throws IOException
+  {
+
+    this.selectedFile = selectedFile;
+    if (selectedFile != null)
+    {
+      this.inFile = selectedFile.getPath();
+    }
+    this.inFile = file;
     try
     {
-      if (format.equals("FASTA"))
-      {
-        afile = new FastaFile(inFile, type);
-      }
-      else if (format.equals("MSF"))
+      if (fileFormat.isStructureFile())
       {
-        afile = new MSFfile(inFile, type);
-      }
-      else if (format.equals("PileUp"))
-      {
-        afile = new PileUpfile(inFile, type);
+        String structureParser = StructureImportSettings
+                .getDefaultPDBFileParser();
+        boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
+                StructureImportSettings.StructureParser.JMOL_PARSER
+                        .toString());
+        StructureImportSettings.addSettings(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct);
+        if (isParseWithJMOL)
+        {
+          // needs a File option
+          alignFile = new JmolParser(
+                  selectedFile == null ? inFile : selectedFile, sourceType);
+        }
+        else
+        {
+          // todo is mc_view parsing obsolete yet? JAL-2120
+          StructureImportSettings.setShowSeqFeatures(true);
+          alignFile = new mc_view.PDBfile(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct, inFile,
+                  sourceType);
+        }
+        ((StructureFile) alignFile).setDbRefType(
+                FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
       }
-      else if (format.equals("CLUSTAL"))
+      else if (selectedFile != null)
       {
-        afile = new ClustalFile(inFile, type);
+        alignFile = fileFormat
+                .getReader(new FileParse(selectedFile, sourceType));
       }
-      else if (format.equals("BLC"))
+      else
       {
-        afile = new BLCFile(inFile, type);
+        // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+        alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
       }
-      else if (format.equals("PIR"))
+      return buildAlignmentFromFile();
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+      System.err.println("Failed to read alignment using the '" + fileFormat
+              + "' reader.\n" + e);
+
+      if (e.getMessage() != null
+              && e.getMessage().startsWith(INVALID_CHARACTERS))
       {
-        afile = new PIRFile(inFile, type);
+        throw new IOException(e.getMessage());
       }
-      else if (format.equals("PFAM"))
+
+      // Finally test if the user has pasted just the sequence, no id
+      if (sourceType == DataSourceType.PASTE)
       {
-        afile = new PfamFile(inFile, type);
+        try
+        {
+          // Possible sequence is just residues with no label
+          alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+                  DataSourceType.PASTE);
+          return buildAlignmentFromFile();
+
+        } catch (Exception ex)
+        {
+          if (ex.toString().startsWith(INVALID_CHARACTERS))
+          {
+            throw new IOException(e.getMessage());
+          }
+
+          ex.printStackTrace();
+        }
       }
-      else if (format.equals("JnetFile"))
+      if (FileFormat.Html.equals(fileFormat))
       {
-        afile = new JPredFile(inFile, type);
-        ( (JPredFile) afile).removeNonSequences();
+        throw new IOException(e.getMessage());
       }
-      else if (format.equals("PDB"))
+    }
+    throw new FileFormatException(getSupportedFormats());
+  }
+
+  /**
+   * Constructs the correct filetype parser for an already open datasource
+   *
+   * @param source
+   *          an existing datasource
+   * @param format
+   *          File format of data that will be provided by datasource
+   *
+   * @return
+   */
+  public AlignmentI readFromFile(FileParse source, FileFormatI format)
+          throws IOException
+  {
+    this.inFile = source.getInFile();
+    DataSourceType type = source.dataSourceType;
+    try
+    {
+      if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
       {
-        afile = new MCview.PDBfile(inFile, type);
+        // TODO obtain config value from preference settings
+        boolean isParseWithJMOL = false;
+        if (isParseWithJMOL)
+        {
+          StructureImportSettings.addSettings(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct);
+          alignFile = new JmolParser(source);
+        }
+        else
+        {
+          StructureImportSettings.setShowSeqFeatures(true);
+          alignFile = new mc_view.PDBfile(annotFromStructure,
+                  localSecondaryStruct, serviceSecondaryStruct, source);
+        }
+        ((StructureFile) alignFile).setDbRefType(Type.PDB);
       }
-      else if (format.equals("STH"))
+      else
       {
-        afile = new StockholmFile(inFile, type);
+        alignFile = format.getReader(source);
       }
 
-      Alignment al = new Alignment(afile.getSeqsAsArray());
+      return buildAlignmentFromFile();
 
-      afile.addAnnotations(al);
-
-      return al;
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format +
-                         "' reader.\n" + e);
+      System.err.println("Failed to read alignment using the '" + format
+              + "' reader.\n" + e);
 
-      if (e.getMessage() != null &&
-          e.getMessage().startsWith(INVALID_CHARACTERS))
+      if (e.getMessage() != null
+              && e.getMessage().startsWith(INVALID_CHARACTERS))
       {
-        throw new java.io.IOException(e.getMessage());
+        throw new FileFormatException(e.getMessage());
       }
 
       // Finally test if the user has pasted just the sequence, no id
-      if (type.equalsIgnoreCase("Paste"))
+      if (type == DataSourceType.PASTE)
       {
         try
         {
           // Possible sequence is just residues with no label
-          afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
-          Alignment al = new Alignment(afile.getSeqsAsArray());
-          afile.addAnnotations(al);
-          return al;
+          alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+                  DataSourceType.PASTE);
+          return buildAlignmentFromFile();
 
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
           if (ex.toString().startsWith(INVALID_CHARACTERS))
           {
-            throw new java.io.IOException(e.getMessage());
+            throw new IOException(e.getMessage());
           }
 
           ex.printStackTrace();
@@ -224,101 +321,386 @@ public class AppletFormatAdapter
       }
 
       // If we get to this stage, the format was not supported
-      throw new java.io.IOException(SUPPORTED_FORMATS);
+      throw new FileFormatException(getSupportedFormats());
     }
   }
 
   /**
-   * Construct an output class for an alignment in a particular filetype
+   * boilerplate method to handle data from an AlignFile and construct a new
+   * alignment or import to an existing alignment
+   * 
+   * @return AlignmentI instance ready to pass to a UI constructor
+   */
+  private AlignmentI buildAlignmentFromFile()
+  {
+    // Standard boilerplate for creating alignment from parser
+    // alignFile.configureForView(viewpanel);
+
+    AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
+
+    alignFile.addAnnotations(al);
+
+    alignFile.addGroups(al);
+
+    return al;
+  }
+
+  /**
+   * create an alignment flatfile from a Jalview alignment view
+   * 
+   * @param format
+   * @param jvsuffix
+   * @param av
+   * @param selectedOnly
+   * @return flatfile in a string
+   */
+  public String formatSequences(FileFormatI format, boolean jvsuffix,
+          AlignmentViewPanel ap, boolean selectedOnly)
+  {
+
+    AlignmentView selvew = ap.getAlignViewport()
+            .getAlignmentView(selectedOnly, false);
+    AlignmentI aselview = selvew
+            .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
+    List<AlignmentAnnotation> ala = (ap.getAlignViewport()
+            .getVisibleAlignmentAnnotation(selectedOnly));
+    if (ala != null)
+    {
+      for (AlignmentAnnotation aa : ala)
+      {
+        aselview.addAnnotation(aa);
+      }
+    }
+    viewpanel = ap;
+    return formatSequences(format, aselview, jvsuffix);
+  }
+
+  /**
+   * Construct an output class for an alignment in a particular filetype TODO:
+   * allow caller to detect errors and warnings encountered when generating
+   * output
    *
-   * @param format string name of alignment format 
-   * @param alignment the alignment to be written out
-   * @param jvsuffix passed to AlnFile class controls whether /START-END is added to sequence names
+   * @param format
+   *          string name of alignment format
+   * @param alignment
+   *          the alignment to be written out
+   * @param jvsuffix
+   *          passed to AlnFile class controls whether /START-END is added to
+   *          sequence names
    *
    * @return alignment flat file contents
    */
-  public String formatSequences(String format,
-                                AlignmentI alignment,
-                                boolean jvsuffix)
+  public String formatSequences(FileFormatI format, AlignmentI alignment,
+          boolean jvsuffix)
   {
     try
     {
-      AlignFile afile = null;
+      AlignmentFileWriterI afile = format.getWriter(alignment);
 
-      if (format.equalsIgnoreCase("FASTA"))
-      {
-        afile = new FastaFile();
-      }
-      else if (format.equalsIgnoreCase("MSF"))
+      afile.setNewlineString(newline);
+      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 = new MSFfile();
+        seqs = alignment.getSequencesArray();
       }
-      else if (format.equalsIgnoreCase("PileUp"))
+      else
       {
-        afile = new PileUpfile();
+        seqs = viewpanel.getAlignment().getSequencesArray();
       }
-      else if (format.equalsIgnoreCase("CLUSTAL"))
+
+      String afileresp = afile.print(seqs, jvsuffix);
+      if (afile.hasWarningMessage())
       {
-        afile = new ClustalFile();
+        System.err.println("Warning raised when writing as " + format
+                + " : " + afile.getWarningMessage());
       }
-      else if (format.equalsIgnoreCase("BLC"))
+      return afileresp;
+    } catch (Exception e)
+    {
+      System.err.println("Failed to write alignment as a '"
+              + format.getName() + "' file\n");
+      e.printStackTrace();
+    }
+
+    return null;
+  }
+
+  /**
+   * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
+   * data
+   * 
+   * BH 2018 allows File or String, and can return RELATIVE_URL
+   *
+   * @param dataObject
+   *          File or String
+   * @return the protocol for the input data
+   */
+  public static DataSourceType checkProtocol(Object dataObject)
+  {
+    if (dataObject instanceof File)
+    {
+      return DataSourceType.FILE;
+    }
+
+    String data = dataObject.toString();
+    DataSourceType protocol = DataSourceType.PASTE;
+    String ft = data.toLowerCase(Locale.ROOT).trim();
+    if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+            || ft.indexOf("file:") == 0)
+    {
+      protocol = DataSourceType.URL;
+    }
+    else if (Platform.isJS())
+    {
+      protocol = DataSourceType.RELATIVE_URL;
+    }
+    else if (new File(data).exists())
+    {
+      protocol = DataSourceType.FILE;
+    }
+    return protocol;
+  }
+
+  /**
+   * @param args
+   * @j2sIgnore
+   */
+  public static void main(String[] args)
+  {
+    int i = 0;
+    while (i < args.length)
+    {
+      File f = new File(args[i]);
+      if (f.exists())
       {
-        afile = new BLCFile();
+        try
+        {
+          System.out.println("Reading file: " + f);
+          AppletFormatAdapter afa = new AppletFormatAdapter();
+          Runtime r = Runtime.getRuntime();
+          System.gc();
+          long memf = -r.totalMemory() + r.freeMemory();
+          long t1 = -System.currentTimeMillis();
+          AlignmentI al = afa.readFile(args[i], DataSourceType.FILE,
+                  new IdentifyFile().identify(args[i],
+                          DataSourceType.FILE));
+          t1 += System.currentTimeMillis();
+          System.gc();
+          memf += r.totalMemory() - r.freeMemory();
+          if (al != null)
+          {
+            System.out.println("Alignment contains " + al.getHeight()
+                    + " sequences and " + al.getWidth() + " columns.");
+            try
+            {
+              System.out.println(new AppletFormatAdapter()
+                      .formatSequences(FileFormat.Fasta, al, true));
+            } catch (Exception e)
+            {
+              System.err.println(
+                      "Couln't format the alignment for output as a FASTA file.");
+              e.printStackTrace(System.err);
+            }
+          }
+          else
+          {
+            System.out.println("Couldn't read alignment");
+          }
+          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");
+        } catch (Exception e)
+        {
+          System.err.println("Exception when dealing with " + i
+                  + "'th argument: " + args[i] + "\n" + e);
+        }
       }
-      else if (format.equalsIgnoreCase("PIR"))
+      else
       {
-        afile = new PIRFile();
+        System.err.println("Ignoring argument '" + args[i] + "' (" + i
+                + "'th)- not a readable file.");
       }
-      else if (format.equalsIgnoreCase("PFAM"))
+      i++;
+    }
+  }
+
+  /**
+   * try to discover how to access the given file as a valid datasource that
+   * will be identified as the given type.
+   *
+   * @param file
+   * @param format
+   * @return protocol that yields the data parsable as the given type
+   */
+  public static DataSourceType resolveProtocol(String file,
+          FileFormatI format)
+  {
+    return resolveProtocol(file, format, false);
+  }
+
+  public static DataSourceType resolveProtocol(String file,
+          FileFormatI format, boolean debug)
+  {
+    // TODO: test thoroughly!
+    DataSourceType protocol = null;
+    if (debug)
+    {
+      System.out.println("resolving datasource started with:\n>>file\n"
+              + file + ">>endfile");
+    }
+
+    // This might throw a security exception in certain browsers
+    // Netscape Communicator for instance.
+    try
+    {
+      boolean rtn = false;
+      InputStream is = System.getSecurityManager().getClass()
+              .getResourceAsStream("/" + file);
+      if (is != null)
       {
-        afile = new PfamFile();
+        rtn = true;
+        is.close();
       }
-      else if (format.equalsIgnoreCase("STH"))
+      if (debug)
       {
-        afile = new StockholmFile();
+        System.err.println("Resource '" + file + "' was "
+                + (rtn ? "" : "not") + " located by classloader.");
       }
-      else if (format.equalsIgnoreCase("AMSA"))
+      if (rtn)
       {
-        afile = new AMSAFile(alignment);
-      } else {
-        throw new Exception("Implementation error: Unknown file format string");
+        protocol = DataSourceType.CLASSLOADER;
       }
 
-      afile.addJVSuffix(jvsuffix);
-
-      afile.setSeqs(alignment.getSequencesArray());
+    } catch (Exception ex)
+    {
+      System.err
+              .println("Exception checking resources: " + file + " " + ex);
+    }
 
-      return afile.print();
+    if (file.indexOf("://") > -1)
+    {
+      protocol = DataSourceType.URL;
     }
-    catch (Exception e)
+    else
     {
-      System.err.println("Failed to write alignment as a '" + format +
-                         "' file\n");
-      e.printStackTrace();
+      // skipping codebase prepend check.
+      protocol = DataSourceType.FILE;
     }
-
-    return null;
-  }
-  public static void main(String[] args)
-  {
-    int i=0;
-    while (i<args.length)
+    FileParse fp = null;
+    try
     {
-      File f = new File(args[i]);
-      if (f.exists())
+      if (debug)
       {
-        try {
-          AppletFormatAdapter afa = new AppletFormatAdapter();
-          afa.readFile(args[i], FILE, new IdentifyFile().Identify(args[i], FILE));
-        } catch (Exception e)
+        System.out.println(
+                "Trying to get contents of resource as " + protocol + ":");
+      }
+      fp = new FileParse(file, protocol);
+      if (!fp.isValid())
+      {
+        fp = null;
+      }
+      else
+      {
+        if (debug)
         {
-          System.err.println("Exception when dealing with "+i+"'th argument: "+args[i]+"\n"+e);
+          System.out.println("Successful.");
         }
-      } else {
-          System.err.println("Ignoring argument '"+args[i]+"' ("+i+"'th)- not a readable file.");
       }
-      i++;
+    } catch (Exception e)
+    {
+      if (debug)
+      {
+        System.err.println("Exception when accessing content: " + e);
+      }
+      fp = null;
+    }
+    if (fp == null)
+    {
+      if (debug)
+      {
+        System.out.println("Accessing as paste.");
+      }
+      protocol = DataSourceType.PASTE;
+      fp = null;
+      try
+      {
+        fp = new FileParse(file, protocol);
+        if (!fp.isValid())
+        {
+          fp = null;
+        }
+      } catch (Exception e)
+      {
+        System.err.println("Failed to access content as paste!");
+        e.printStackTrace();
+        fp = null;
+      }
     }
-    
+    if (fp == null)
+    {
+      return null;
+    }
+    if (format == null)
+    {
+      return protocol;
+    }
+    else
+    {
+      try
+      {
+        FileFormatI idformat = new IdentifyFile().identify(file, protocol);
+        if (idformat == null)
+        {
+          if (debug)
+          {
+            System.out.println("Format not identified. Inaccessible file.");
+          }
+          return null;
+        }
+        if (debug)
+        {
+          System.out.println("Format identified as " + idformat
+                  + "and expected as " + format);
+        }
+        if (idformat.equals(format))
+        {
+          if (debug)
+          {
+            System.out.println("Protocol identified as " + protocol);
+          }
+          return protocol;
+        }
+        else
+        {
+          if (debug)
+          {
+            System.out
+                    .println("File deemed not accessible via " + protocol);
+          }
+          fp.close();
+          return null;
+        }
+      } catch (Exception e)
+      {
+        if (debug)
+        {
+          System.err.println("File deemed not accessible via " + protocol);
+          e.printStackTrace();
+        }
+      }
+    }
+    return null;
+  }
+
+  public AlignmentFileReaderI getAlignFile()
+  {
+    return alignFile;
   }
 }