X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=00d6d2f57bd596d95c8fc6038cfd9b03efc4090b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=b37c60ebdd4a3f84434cef9a9eab86d2e45a3715;hpb=c1bfcc47304d63daebe01519f466e753c567afe4;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b37c60e..00d6d2f 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,122 +1,219 @@
 /*
- * 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 2.9)
+ * Copyright (C) 2015 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 jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.util.MessageManager;
 
-import jalview.datamodel.*;
+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 
+  private AlignmentViewPanel viewpanel;
+
+  public static String FILE = "File";
+
+  public static String URL = "URL";
+
+  public static String PASTE = "Paste";
+
+  public static String CLASSLOADER = "ClassLoader";
+
+  /**
+   * add jalview-derived non-secondary structure annotation from PDB structure
    */
-  public static final String[] READABLE_FORMATS = new String[]
-      {
-      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB", "JnetFile"
-  };
+  boolean annotFromStructure = false;
+
   /**
-   * List of valid format strings for use by callers of the formatSequences method
+   * add secondary structure from PDB data with built-in algorithms
    */
-  public static final String[] WRITEABLE_FORMATS = new String[]
-      {
-      "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" , "AMSA"
-  };
+  boolean localSecondaryStruct = false;
+
   /**
-   * List of extensions corresponding to file format types 
-   * in WRITABLE_FNAMES that are writable by the
-   * application.
+   * process PDB data with web services
    */
-  public static final String[] WRITABLE_EXTENSIONS = new String[]
-        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" };
+  boolean serviceSecondaryStruct = false;
+
+  private AlignFile alignFile = null;
+
+  String inFile;
+
   /**
-   * List of writable formats by the application. Order must
-   * correspond with the WRITABLE_EXTENSIONS list of formats.
+   * character used to write newlines
    */
-  public static final String[] WRITABLE_FNAMES = new String[]
-        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+  protected String newline = System.getProperty("line.separator");
+
+  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", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+      IdentifyFile.GFF3File, "HTML" };
 
   /**
    * List of readable format file extensions by application in order
-   * corresponding to READABLE_FNAMES 
+   * corresponding to READABLE_FNAMES
    */
-  public static final String[] READABLE_EXTENSIONS =         new String[]
-        {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "amsa","jar"
-    };
+  public static final String[] READABLE_EXTENSIONS = new String[] {
+      "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+      "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
+      ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT };
+
   /**
-   * List of readable formats by application in order
-   * corresponding to READABLE_EXTENSIONS
+   * 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","Jalview"
-    };
-        
+  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 };
+
+  /**
+   * 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 };
+
+  /**
+   * 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", 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",
+      PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "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 SUPPORTED_FORMATS = "Formats currently supported are\n"
+          + prettyPrint(READABLE_FORMATS);
+
+  public AppletFormatAdapter()
+  {
+  }
+
+  public AppletFormatAdapter(AlignmentViewPanel viewpanel)
+  {
+    this.viewpanel = viewpanel;
+  }
+
+  public AppletFormatAdapter(AlignmentViewPanel alignPanel,
+          AlignExportSettingI settings)
+  {
+    viewpanel = alignPanel;
+    exportSettings = settings;
+  }
+
   /**
-   * 
+   *
    * @param els
    * @return grammatically correct(ish) list consisting of els elements.
    */
-  public static String prettyPrint(String[] els) {
+  public static String prettyPrint(String[] els)
+  {
     StringBuffer list = new StringBuffer();
-    for (int i=0,iSize=els.length-1; i<iSize;i++)
+    for (int i = 0, iSize = els.length - 1; i < iSize; i++)
     {
       list.append(els[i]);
-      list.append(",");
+      list.append(", ");
     }
-    list.append(" and "+els[els.length-1]+".");
+    list.append(" and " + els[els.length - 1] + ".");
     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;
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
   /**
    * check that this format is valid for reading
-   * @param format a format string to be compared with READABLE_FORMATS
+   *
+   * @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;
-    for (int i = 0; i < READABLE_FORMATS.length; i++)
+    String[] format_list = (forwriting) ? WRITEABLE_FORMATS
+            : READABLE_FORMATS;
+    for (String element : format_list)
     {
-      if (READABLE_FORMATS[i].equalsIgnoreCase(format))
+      if (element.equalsIgnoreCase(format))
       {
         return true;
       }
@@ -128,75 +225,100 @@ public class AppletFormatAdapter
   /**
    * 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 type
+   *          type of datasource
+   * @param format
+   *          File format of data provided by datasource
    *
    * @return DOCUMENT ME!
    */
-  public Alignment readFile(String inFile, String type, String format)
-      throws java.io.IOException
+  public AlignmentI readFile(String inFile, String type, String format)
+          throws java.io.IOException
   {
-    // TODO: generalise mapping between format string and io. class instances using Constructor.invoke reflection
+    // TODO: generalise mapping between format string and io. class instances
+    // using Constructor.invoke reflection
     this.inFile = inFile;
     try
     {
       if (format.equals("FASTA"))
       {
-        afile = new FastaFile(inFile, type);
+        alignFile = new FastaFile(inFile, type);
       }
       else if (format.equals("MSF"))
       {
-        afile = new MSFfile(inFile, type);
+        alignFile = new MSFfile(inFile, type);
       }
       else if (format.equals("PileUp"))
       {
-        afile = new PileUpfile(inFile, type);
+        alignFile = new PileUpfile(inFile, type);
       }
       else if (format.equals("CLUSTAL"))
       {
-        afile = new ClustalFile(inFile, type);
+        alignFile = new ClustalFile(inFile, type);
       }
       else if (format.equals("BLC"))
       {
-        afile = new BLCFile(inFile, type);
+        alignFile = new BLCFile(inFile, type);
       }
       else if (format.equals("PIR"))
       {
-        afile = new PIRFile(inFile, type);
+        alignFile = new PIRFile(inFile, type);
       }
       else if (format.equals("PFAM"))
       {
-        afile = new PfamFile(inFile, type);
+        alignFile = new PfamFile(inFile, type);
       }
       else if (format.equals("JnetFile"))
       {
-        afile = new JPredFile(inFile, type);
-        ( (JPredFile) afile).removeNonSequences();
+        alignFile = new JPredFile(inFile, type);
+        ((JPredFile) alignFile).removeNonSequences();
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(inFile, type);
+        alignFile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, inFile, type);
+        // Uncomment to test Jmol data based PDB processing: JAL-1213
+        // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
       }
       else if (format.equals("STH"))
       {
-        afile = new StockholmFile(inFile, type);
+        alignFile = new StockholmFile(inFile, type);
       }
-
-      Alignment al = new Alignment(afile.getSeqsAsArray());
-
-      afile.addAnnotations(al);
-
-      return al;
-    }
-    catch (Exception e)
+      else if (format.equals("SimpleBLAST"))
+      {
+        alignFile = new SimpleBlastFile(inFile, type);
+      }
+      else if (format.equals(PhylipFile.FILE_DESC))
+      {
+        alignFile = new PhylipFile(inFile, type);
+      }
+      else if (format.equals(JSONFile.FILE_DESC))
+      {
+        alignFile = new JSONFile(inFile, type);
+      }
+      else if (format.equals(HtmlFile.FILE_DESC))
+      {
+        alignFile = new HtmlFile(inFile, type);
+      }
+      else if (format.equals("RNAML"))
+      {
+        alignFile = new RnamlFile(inFile, type);
+      }
+      else if (format.equals(IdentifyFile.GFF3File))
+      {
+        alignFile = new Gff3File(inFile, type);
+      }
+      return buildAlignmentFrom(alignFile);
+    } 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());
       }
@@ -207,13 +329,10 @@ public class AppletFormatAdapter
         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, "Paste");
+          return buildAlignmentFrom(alignFile);
 
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
           if (ex.toString().startsWith(INVALID_CHARACTERS))
           {
@@ -223,84 +342,113 @@ 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);
     }
   }
+
   /**
    * 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
+   * @param source
+   *          an existing datasource
+   * @param format
+   *          File format of data that will be provided by datasource
    *
    * @return DOCUMENT ME!
    */
-  public Alignment readFromFile(FileParse source, String format)
-      throws java.io.IOException
+  public AlignmentI readFromFile(FileParse source, String format)
+          throws java.io.IOException
   {
-    // TODO: generalise mapping between format string and io. class instances using Constructor.invoke reflection
-    // This is exactly the same as the readFile method except we substitute 'inFile, type' with 'source'
+    // TODO: generalise mapping between format string and io. class instances
+    // using Constructor.invoke reflection
+    // This is exactly the same as the readFile method except we substitute
+    // 'inFile, type' with 'source'
     this.inFile = source.getInFile();
     String type = source.type;
     try
     {
       if (format.equals("FASTA"))
       {
-        afile = new FastaFile(source);
+        alignFile = new FastaFile(source);
       }
       else if (format.equals("MSF"))
       {
-        afile = new MSFfile(source);
+        alignFile = new MSFfile(source);
       }
       else if (format.equals("PileUp"))
       {
-        afile = new PileUpfile(source);
+        alignFile = new PileUpfile(source);
       }
       else if (format.equals("CLUSTAL"))
       {
-        afile = new ClustalFile(source);
+        alignFile = new ClustalFile(source);
       }
       else if (format.equals("BLC"))
       {
-        afile = new BLCFile(source);
+        alignFile = new BLCFile(source);
       }
       else if (format.equals("PIR"))
       {
-        afile = new PIRFile(source);
+        alignFile = new PIRFile(source);
       }
       else if (format.equals("PFAM"))
       {
-        afile = new PfamFile(source);
+        alignFile = new PfamFile(source);
       }
       else if (format.equals("JnetFile"))
       {
-        afile = new JPredFile(source);
-        ( (JPredFile) afile).removeNonSequences();
+        alignFile = new JPredFile(source);
+        ((JPredFile) alignFile).removeNonSequences();
       }
       else if (format.equals("PDB"))
       {
-        afile = new MCview.PDBfile(source);
+        alignFile = new MCview.PDBfile(annotFromStructure,
+                localSecondaryStruct, serviceSecondaryStruct, source);
       }
       else if (format.equals("STH"))
       {
-        afile = new StockholmFile(source);
+        alignFile = new StockholmFile(source);
+      }
+      else if (format.equals("RNAML"))
+      {
+        alignFile = new RnamlFile(source);
+      }
+      else if (format.equals("SimpleBLAST"))
+      {
+        alignFile = new SimpleBlastFile(source);
+      }
+      else if (format.equals(PhylipFile.FILE_DESC))
+      {
+        alignFile = new PhylipFile(source);
+      }
+      else if (format.equals(IdentifyFile.GFF3File))
+      {
+        alignFile = new Gff3File(inFile, type);
+      }
+      else if (format.equals(JSONFile.FILE_DESC))
+      {
+        alignFile = new JSONFile(source);
+      }
+      else if (format.equals(HtmlFile.FILE_DESC))
+      {
+        alignFile = new HtmlFile(source);
       }
 
-      Alignment al = new Alignment(afile.getSeqsAsArray());
-
-      afile.addAnnotations(al);
+      return buildAlignmentFrom(alignFile);
 
-      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());
       }
@@ -311,13 +459,10 @@ public class AppletFormatAdapter
         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, "Paste");
+          return buildAlignmentFrom(alignFile);
 
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
           if (ex.toString().startsWith(INVALID_CHARACTERS))
           {
@@ -332,24 +477,79 @@ public class AppletFormatAdapter
       throw new java.io.IOException(SUPPORTED_FORMATS);
     }
   }
-  
+
   /**
-   * 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
+   * 
+   * @param alignFile2
+   * @return AlignmentI instance ready to pass to a UI constructor
+   */
+  private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
+  {
+    // 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(String 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(String format, AlignmentI alignment,
+          boolean jvsuffix)
   {
     try
     {
       AlignFile afile = null;
-
       if (format.equalsIgnoreCase("FASTA"))
       {
         afile = new FastaFile();
@@ -380,60 +580,315 @@ public class AppletFormatAdapter
       }
       else if (format.equalsIgnoreCase("STH"))
       {
-        afile = new StockholmFile();
+        afile = new StockholmFile(alignment);
       }
       else if (format.equalsIgnoreCase("AMSA"))
       {
         afile = new AMSAFile(alignment);
-      } else {
-        throw new Exception("Implementation error: Unknown file format string");
+      }
+      else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
+      {
+        afile = new PhylipFile();
+      }
+      else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+      {
+        afile = new JSONFile();
+      }
+      else if (format.equalsIgnoreCase("RNAML"))
+      {
+        afile = new RnamlFile();
       }
 
+      else
+      {
+        throw new Exception(
+                MessageManager
+                        .getString("error.implementation_error_unknown_file_format_string"));
+      }
+
+      afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
+      afile.setExportSettings(exportSettings);
+      afile.configureForView(viewpanel);
 
-      afile.setSeqs(alignment.getSequencesArray());
+      // check whether we were given a specific alignment to export, rather than
+      // the one in the viewpanel
+      if (viewpanel == null || viewpanel.getAlignment() == null
+              || viewpanel.getAlignment() != alignment)
+      {
+        afile.setSeqs(alignment.getSequencesArray());
+      }
+      else
+      {
+        afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
+      }
 
-      return afile.print();
-    }
-    catch (Exception e)
+      String afileresp = afile.print();
+      if (afile.hasWarningMessage())
+      {
+        System.err.println("Warning raised when writing as " + format
+                + " : " + afile.getWarningMessage());
+      }
+      return afileresp;
+    } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '" + format +
-                         "' file\n");
+      System.err.println("Failed to write alignment as a '" + format
+              + "' file\n");
       e.printStackTrace();
     }
 
     return null;
   }
+
+  public static String checkProtocol(String file)
+  {
+    String protocol = FILE;
+    String ft = file.toLowerCase().trim();
+    if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+            || ft.indexOf("file:") == 0)
+    {
+      protocol = URL;
+    }
+    return protocol;
+  }
+
   public static void main(String[] args)
   {
-    int i=0;
-    while (i<args.length)
+    int i = 0;
+    while (i < args.length)
     {
       File f = new File(args[i]);
       if (f.exists())
       {
-        try {
+        try
+        {
+          System.out.println("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
           Runtime r = Runtime.getRuntime();
           System.gc();
-          long memf = -r.totalMemory()+r.freeMemory();
+          long memf = -r.totalMemory() + r.freeMemory();
           long t1 = -System.currentTimeMillis();
-          Alignment al = afa.readFile(args[i], FILE, new IdentifyFile().Identify(args[i], FILE));
-          t1 +=System.currentTimeMillis();
+          AlignmentI al = afa.readFile(args[i], FILE,
+                  new IdentifyFile().Identify(args[i], FILE));
+          t1 += System.currentTimeMillis();
           System.gc();
-          memf += r.totalMemory()-r.freeMemory();
-          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");
-          
+          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(
+                      "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);
+          System.err.println("Exception when dealing with " + i
+                  + "'th argument: " + args[i] + "\n" + e);
         }
-      } else {
-          System.err.println("Ignoring argument '"+args[i]+"' ("+i+"'th)- not a readable file.");
+      }
+      else
+      {
+        System.err.println("Ignoring argument '" + args[i] + "' (" + i
+                + "'th)- not a readable file.");
       }
       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 String resolveProtocol(String file, String format)
+  {
+    return resolveProtocol(file, format, false);
+  }
+
+  public static String resolveProtocol(String file, String format,
+          boolean debug)
+  {
+    // TODO: test thoroughly!
+    String 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)
+      {
+        rtn = true;
+        is.close();
+      }
+      if (debug)
+      {
+        System.err.println("Resource '" + file + "' was "
+                + (rtn ? "" : "not") + " located by classloader.");
+      }
+      ;
+      if (rtn)
+      {
+        protocol = AppletFormatAdapter.CLASSLOADER;
+      }
+
+    } catch (Exception ex)
+    {
+      System.err
+              .println("Exception checking resources: " + file + " " + ex);
+    }
+
+    if (file.indexOf("://") > -1)
+    {
+      protocol = AppletFormatAdapter.URL;
+    }
+    else
+    {
+      // skipping codebase prepend check.
+      protocol = AppletFormatAdapter.FILE;
+    }
+    FileParse fp = null;
+    try
+    {
+      if (debug)
+      {
+        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.out.println("Successful.");
+        }
+      }
+    } 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 = AppletFormatAdapter.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 || format.length() == 0)
+    {
+      return protocol;
+    }
+    else
+    {
+      try
+      {
+        String idformat = new jalview.io.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 AlignFile getAlignFile()
+  {
+    return alignFile;
+  }
+
+  public void setAlignFile(AlignFile alignFile)
+  {
+    this.alignFile = alignFile;
   }
 }