X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=e9e25713efc65af00d03ff8f929b0e98a043924b;hb=93642d621a7f86318a7777b0a70f6113dcd299dc;hp=dca2d0c4759d47a67efc24385bc047586f5adac7;hpb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;p=jalview.git diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java index dca2d0c..e9e2571 100755 --- a/src/jalview/io/AppletFormatAdapter.java +++ b/src/jalview/io/AppletFormatAdapter.java @@ -1,196 +1,521 @@ - /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 - * 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. - * - * 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 - */ - package jalview.io; - - import jalview.datamodel.*; - - import java.util.Vector; - - - /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ - public class AppletFormatAdapter - { - /** DOCUMENT ME!! */ - public static final Vector formats = new Vector(); - - public static String INVALID_CHARACTERS = "Contains invalid characters"; - - public static String SUPPORTED_FORMATS = "Formats currently supported are\n" + - "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM"; - - static - { - formats.addElement("BLC"); - formats.addElement("CLUSTAL"); - formats.addElement("FASTA"); - formats.addElement("MSF"); - formats.addElement("PileUp"); - formats.addElement("PIR"); - formats.addElement("PFAM"); - } - - AlignFile afile = null; - - /** - * DOCUMENT ME! - * - * @param inFile DOCUMENT ME! - * @param type DOCUMENT ME! - * @param format DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceI[] readFile(String inFile, String type, String format) - throws java.io.IOException - { - 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); - } - - return afile.getSeqsAsArray(); - } - catch (Exception e) - { - 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"); - return afile.getSeqsAsArray(); - } - 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); - } - } - - - /** - * DOCUMENT ME! - * - * @param format DOCUMENT ME! - * @param seqs DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String formatSequences(String format, - Vector seqs, - boolean jvsuffix) - { - SequenceI[] s = new SequenceI[seqs.size()]; - - for (int i = 0; i < seqs.size(); i++) - s[i] = (SequenceI) seqs.elementAt(i); - - 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(); - } - - afile.addJVSuffix(jvsuffix); - - afile.setSeqs(s); - - return afile.print(); - } - catch (Exception e) - { - System.err.println("Failed to write alignment as a '" + format + - "' file\n"); - e.printStackTrace(); - } - - return null; - } - } +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.io; + +import java.io.File; + +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" }; // , "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" }; + + /** + * 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", "sto" }; // , + // ".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" };// , + // "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; + + /** + * 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); + } + else if (format.equals("STH")) + { + afile = new StockholmFile(inFile, type); + } + else if (format.equals("SimpleBLAST")) + { + afile = new SimpleBlastFile(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 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); + } + 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); + } + } + + /** + * 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(); + } + else if (format.equalsIgnoreCase("AMSA")) + { + afile = new AMSAFile(alignment); + } + else + { + throw new Exception( + "Implementation error: Unknown file format string"); + } + + 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 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++; + } + + } +}