*/
package jalview.io;
+import java.io.File;
+
import jalview.datamodel.*;
/**
- * DOCUMENT ME!
+ * 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
{
- /** DOCUMENT ME!! */
+ /**
+ * 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"
};
-
+ /**
+ * 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"
};
-
+ /**
+ * 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, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" };
-
+ /**
+ * 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", "Jalview" };
+ /**
+ * List of readable format file extensions by application in order
+ * corresponding to READABLE_FNAMES
+ */
public static final String[] READABLE_EXTENSIONS = new String[]
{
"fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
"amsa","jar"
};
+ /**
+ * 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 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;
}
return valid;
}
-
+
/**
* Constructs the correct filetype parser for a characterised datasource
*
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
{
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
*
- * @param format DOCUMENT ME!
- * @param seqs DOCUMENT ME!
- * @param jvsuffix passed to AlnFile class
+ * @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
*/
return null;
}
+ public static void main(String[] args)
+ {
+ int i=0;
+ while (i<args.length)
+ {
+ File f = new File(args[i]);
+ if (f.exists())
+ {
+ 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();
+ Alignment al = afa.readFile(args[i], FILE, new IdentifyFile().Identify(args[i], 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.");
+ } 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 {
+ System.err.println("Ignoring argument '"+args[i]+"' ("+i+"'th)- not a readable file.");
+ }
+ i++;
+ }
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff