add methods to read from current position of existing fileParse object.

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d9b0b55..b37c60e 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -137,6 +137,7 @@ public class AppletFormatAdapter
   public Alignment 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
     this.inFile = inFile;
     try
     {
@@ -227,7 +228,111 @@ public class AppletFormatAdapter
       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
+   *
+   * @return DOCUMENT ME!
+   */
+  public Alignment 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'
+    this.inFile = source.getInFile();
+    String type = source.type;
+    try
+    {
+      if (format.equals("FASTA"))
+      {
+        afile = new FastaFile(source);
+      }
+      else if (format.equals("MSF"))
+      {
+        afile = new MSFfile(source);
+      }
+      else if (format.equals("PileUp"))
+      {
+        afile = new PileUpfile(source);
+      }
+      else if (format.equals("CLUSTAL"))
+      {
+        afile = new ClustalFile(source);
+      }
+      else if (format.equals("BLC"))
+      {
+        afile = new BLCFile(source);
+      }
+      else if (format.equals("PIR"))
+      {
+        afile = new PIRFile(source);
+      }
+      else if (format.equals("PFAM"))
+      {
+        afile = new PfamFile(source);
+      }
+      else if (format.equals("JnetFile"))
+      {
+        afile = new JPredFile(source);
+        ( (JPredFile) afile).removeNonSequences();
+      }
+      else if (format.equals("PDB"))
+      {
+        afile = new MCview.PDBfile(source);
+      }
+      else if (format.equals("STH"))
+      {
+        afile = new StockholmFile(source);
+      }
 
+      Alignment al = new Alignment(afile.getSeqsAsArray());
+
+      afile.addAnnotations(al);
+
+      return al;
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+      System.err.println("Failed to read alignment using the '" + format +
+                         "' reader.\n" + e);
+
+      if (e.getMessage() != null &&
+          e.getMessage().startsWith(INVALID_CHARACTERS))
+      {
+        throw new java.io.IOException(e.getMessage());
+      }
+
+      // Finally test if the user has pasted just the sequence, no id
+      if (type.equalsIgnoreCase("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;
+
+        }
+        catch (Exception ex)
+        {
+          if (ex.toString().startsWith(INVALID_CHARACTERS))
+          {
+            throw new java.io.IOException(e.getMessage());
+          }
+
+          ex.printStackTrace();
+        }
+      }
+
+      // If we get to this stage, the format was not supported
+      throw new java.io.IOException(SUPPORTED_FORMATS);
+    }
+  }
+  
   /**
    * Construct an output class for an alignment in a particular filetype
    *