X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=d076b7aaf3670ddc6e46a059f89c0597a8771137;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=ba5b8a0a283a47effd2f6b737adcd107286e7dc1;hpb=e5e719a4db6db7d165261151d4638547923fa5d2;p=jalview.git
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index ba5b8a0..d076b7a 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,227 +1,817 @@
- /*
- * 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");
- formats.addElement("STH");
- formats.addElement("PDB");
- }
-
-
- 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;
-
- /**
- * 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
- {
- 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);
- }
-
-
- return afile.getSeqsAsArray();
- }
- 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");
- 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();
- }
- else if (format.equalsIgnoreCase("STH"))
- {
- afile = new StockholmFile();
- }
-
-
- 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 jalview.api.AlignViewportI;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.util.MessageManager;
+
+import java.io.File;
+import java.io.InputStream;
+import java.util.List;
+
+/**
+ * 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", PhylipFile.FILE_DESC, "HTML" }; // ,
+ // "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", PhylipFile.FILE_DESC };
+
+ /**
+ * 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",
+ "sto,stk", PhylipFile.FILE_EXT, "jvp" };
+
+ /**
+ * 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", "STH",
+ PhylipFile.FILE_DESC, "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", PhylipFile.FILE_EXT,
+ "html" }; // ".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", PhylipFile.FILE_DESC, "HTML" };// ,
+
+ // "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";
+
+ /**
+ * add jalview-derived non-secondary structure annotation from PDB structure
+ */
+ boolean annotFromStructure = false;
+
+ /**
+ * add secondary structure from PDB data with built-in algorithms
+ */
+ boolean localSecondaryStruct = false;
+
+ /**
+ * process PDB data with web services
+ */
+ boolean serviceSecondaryStruct = false;
+
+ 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 (String element : format_list)
+ {
+ if (element.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(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, 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(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile(inFile, type);
+ }
+ // else if (format.equals(HtmlFile.FILE_DESC))
+ // {
+ // afile = new HtmlFile(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(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, 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);
+ }
+ else if (format.equals(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile(source);
+ }
+ // else if (format.equals(HtmlFile.FILE_DESC))
+ // {
+ // afile = new HtmlFile(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(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile();
+ }
+ // else if (format.equalsIgnoreCase(HtmlFile.FILE_DESC))
+ // {
+ // afile = new HtmlFile();
+ // }
+ 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;
+ }
+}