/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* 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 3
* of the License, or (at your option) any later version.
*
* 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 Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import java.io.File;
import java.io.InputStream;
import java.util.List;
import jalview.api.AlignViewportI;
import jalview.datamodel.*;
/**
* 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", "RNAML" }; // , "SimpleBLAST" };
/**
* 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" };
/**
* 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",
"jvp", "sto,stk", "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",
"STH", "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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
"jar,jvp", "sto,stk", "xml,rnaml" }; // ".blast"
/**
* 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",
"Stockholm", "RNAML" };// ,
// "SimpleBLAST"
// };
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);
/**
*
* @param els
* @return grammatically correct(ish) list consisting of els elements.
*/
public static String prettyPrint(String[] els)
{
StringBuffer list = new StringBuffer();
for (int i = 0, iSize = els.length - 1; i < iSize; i++)
{
list.append(els[i]);
list.append(",");
}
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;
/**
* character used to write newlines
*/
protected String newline = System.getProperty("line.separator");
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
* @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)
{
boolean valid = false;
String[] format_list = (forwriting) ? WRITEABLE_FORMATS
: READABLE_FORMATS;
for (int i = 0; i < format_list.length; i++)
{
if (format_list[i].equalsIgnoreCase(format))
{
return true;
}
}
return valid;
}
/**
* 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
*
* @return DOCUMENT ME!
*/
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
{
if (format.equals("FASTA"))
{
afile = new FastaFile(inFile, type);
}
else if (format.equals("MSF"))
{
afile = new MSFfile(inFile, type);
}
else if (format.equals("PileUp"))
{
afile = new PileUpfile(inFile, type);
}
else if (format.equals("CLUSTAL"))
{
afile = new ClustalFile(inFile, type);
}
else if (format.equals("BLC"))
{
afile = new BLCFile(inFile, type);
}
else if (format.equals("PIR"))
{
afile = new PIRFile(inFile, type);
}
else if (format.equals("PFAM"))
{
afile = new PfamFile(inFile, type);
}
else if (format.equals("JnetFile"))
{
afile = new JPredFile(inFile, type);
((JPredFile) afile).removeNonSequences();
}
else if (format.equals("PDB"))
{
afile = new MCview.PDBfile(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);
}
else if (format.equals("SimpleBLAST"))
{
afile = new SimpleBlastFile(inFile, type);
}
else if (format.equals("RNAML"))
{
afile = new RnamlFile(inFile, type);
}
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);
}
}
/**
* 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 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'
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);
}
else if (format.equals("RNAML"))
{
afile = new RnamlFile(source);
}
else if (format.equals("SimpleBLAST"))
{
afile = new SimpleBlastFile(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);
}
}
/**
* 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,
AlignViewportI av, boolean selectedOnly)
{
AlignmentView selvew = av.getAlignmentView(selectedOnly, false);
AlignmentI aselview = selvew.getVisibleAlignment(av
.getGapCharacter());
List ala = (av
.getVisibleAlignmentAnnotation(selectedOnly));
if (ala != null)
{
for (AlignmentAnnotation aa : ala)
{
aselview.addAnnotation(aa);
}
}
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
*
* @return alignment flat file contents
*/
public String formatSequences(String format, AlignmentI alignment,
boolean jvsuffix)
{
try
{
AlignFile afile = null;
if (format.equalsIgnoreCase("FASTA"))
{
afile = new FastaFile();
}
else if (format.equalsIgnoreCase("MSF"))
{
afile = new MSFfile();
}
else if (format.equalsIgnoreCase("PileUp"))
{
afile = new PileUpfile();
}
else if (format.equalsIgnoreCase("CLUSTAL"))
{
afile = new ClustalFile();
}
else if (format.equalsIgnoreCase("BLC"))
{
afile = new BLCFile();
}
else if (format.equalsIgnoreCase("PIR"))
{
afile = new PIRFile();
}
else if (format.equalsIgnoreCase("PFAM"))
{
afile = new PfamFile();
}
else if (format.equalsIgnoreCase("STH"))
{
afile = new StockholmFile(alignment);
}
else if (format.equalsIgnoreCase("AMSA"))
{
afile = new AMSAFile(alignment);
}
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.setSeqs(alignment.getSequencesArray());
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");
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)
{
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.");
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);
}
}
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;
}
}