/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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 2
+ * as published by the Free Software Foundation, either version 3
* 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.File;
+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 jalview.datamodel.*;
+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 $Revision$
*/
* 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" };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+ "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC }; // , "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" };
+ { "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, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "jvp", "sto,stk", "jar", PhylipFile.FILE_EXT };
/**
* 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" };
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "STH", "Jalview", PhylipFile.FILE_DESC };
/**
* 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" };
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "jar,jvp", "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT }; // ".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" };
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "Stockholm", "RNAML", PhylipFile.FILE_DESC };// ,
+
+ // "SimpleBLAST"
+ // };
public static String INVALID_CHARACTERS = "Contains invalid characters";
+ prettyPrint(READABLE_FORMATS);
/**
- *
+ *
* @param els
* @return grammatically correct(ish) list consisting of els elements.
*/
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
+ * a format string to be compared with READABLE_FORMATS
* @return true if format is readable
*/
public static final boolean isValidFormat(String format)
/**
* validate format is valid for IO
- *
+ *
* @param format
- * a format string to be compared with either READABLE_FORMATS
- * or WRITEABLE_FORMATS
+ * 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
+ * when true, format is checked for containment in WRITEABLE_FORMATS
* @return true if format is valid
*/
public static final boolean isValidFormat(String format,
boolean valid = false;
String[] format_list = (forwriting) ? WRITEABLE_FORMATS
: READABLE_FORMATS;
- for (int i = 0; i < format_list.length; i++)
+ for (String element : format_list)
{
- if (format_list[i].equalsIgnoreCase(format))
+ if (element.equalsIgnoreCase(format))
{
return true;
}
/**
* Constructs the correct filetype parser for a characterised datasource
- *
+ *
* @param inFile
- * data/data location
+ * data/data location
* @param type
- * type of datasource
+ * type of datasource
* @param format
- * File format of data provided by datasource
- *
+ * File format of data provided by datasource
+ *
* @return DOCUMENT ME!
*/
public Alignment readFile(String inFile, String type, String format)
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(inFile, type);
+ 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("RNAML"))
+ {
+ afile = new RnamlFile(inFile, type);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
/**
* Constructs the correct filetype parser for an already open datasource
- *
+ *
* @param source
- * an existing datasource
+ * an existing datasource
* @param format
- * File format of data that will be provided by datasource
- *
+ * File format of data that will be provided by datasource
+ *
* @return DOCUMENT ME!
*/
- public Alignment readFromFile(FileParse source, String format)
+ public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(source);
+ 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);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
}
}
+
/**
- * Construct an output class for an alignment in a particular filetype
- * TODO: allow caller to detect errors and warnings encountered when generating output
+ * 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<AlignmentAnnotation> 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
+ * string name of alignment format
* @param alignment
- * the alignment to be written out
+ * the alignment to be written out
* @param jvsuffix
- * passed to AlnFile class controls whether /START-END is added
- * to sequence names
- *
+ * 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,
}
else if (format.equalsIgnoreCase("STH"))
{
- afile = new StockholmFile();
+ afile = new StockholmFile(alignment);
}
else if (format.equalsIgnoreCase("AMSA"))
{
afile = new AMSAFile(alignment);
}
- else
+ else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile();
+ }
+ else if (format.equalsIgnoreCase("RNAML"))
{
- throw new Exception(
- "Implementation error: Unknown file format string");
+ 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());
+ System.err.println("Warning raised when writing as " + format
+ + " : " + afile.getWarningMessage());
}
return afileresp;
} catch (Exception e)
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;
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));
+ Alignment al = afa.readFile(args[i], FILE,
+ new IdentifyFile().Identify(args[i], FILE));
t1 += System.currentTimeMillis();
System.gc();
memf += r.totalMemory() - r.freeMemory();
{
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("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");
-
+ .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
}
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;
}
}
git://source.jalview.org / jalview.git / blobdiff