bug fix for Features/Annotations file parameter parsing in JalviewLite reported and...

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d9b0b55..c7b0575 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -113,10 +113,21 @@ public class AppletFormatAdapter
    */
   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)
+  {
     boolean valid = false;
-    for (int i = 0; i < READABLE_FORMATS.length; i++)
+    String[] format_list = (forwriting) ? WRITEABLE_FORMATS : READABLE_FORMATS;
+    for (int i = 0; i < format_list.length; i++)
     {
-      if (READABLE_FORMATS[i].equalsIgnoreCase(format))
+      if (format_list[i].equalsIgnoreCase(format))
       {
         return true;
       }
@@ -124,7 +135,7 @@ public class AppletFormatAdapter
 
     return valid;
   }
-
+  
   /**
    * Constructs the correct filetype parser for a characterised datasource
    *
@@ -137,6 +148,7 @@ 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 +239,111 @@ 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
    *
@@ -308,6 +424,7 @@ public class AppletFormatAdapter
       if (f.exists())
       {
         try {
+          System.out.println("Reading file: "+f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
           Runtime r = Runtime.getRuntime();
           System.gc();
@@ -317,6 +434,12 @@ public class AppletFormatAdapter
           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.");
+          } 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");