/*
* 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
+ * 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
+ *
+ * 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 <http://www.gnu.org/licenses/>.
* 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;
-import jalview.api.AlignViewportI;
-import jalview.datamodel.*;
-import jalview.util.MessageManager;
-
/**
* 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", "RNAML" }; // , "SimpleBLAST" };
+ { "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", "STH" };
+ { "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",
- "jvp", "sto,stk", "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",
- "STH", "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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "jar,jvp", "sto,stk", "xml,rnaml" }; // ".blast"
+ { "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",
- "Stockholm", "RNAML" };// ,
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "Stockholm", "RNAML", PhylipFile.FILE_DESC };// ,
// "SimpleBLAST"
// };
+ prettyPrint(READABLE_FORMATS);
/**
- *
+ *
* @param els
* @return grammatically correct(ish) list consisting of els elements.
*/
/**
* 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
/**
* validate format is valid for IO
- *
+ *
* @param format
* a format string to be compared with either READABLE_FORMATS or
* WRITEABLE_FORMATS
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
* @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)
{
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);
/**
* 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)
{
afile = new SimpleBlastFile(source);
}
-
+ else if (format.equals(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile(source);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
/**
- * create an alignment flatfile from a Jalview alignment view
+ * create an alignment flatfile from a Jalview alignment view
* @param format
* @param jvsuffix
* @param av
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
* @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,
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile();
+ }
else if (format.equalsIgnoreCase("RNAML"))
{
afile = new RnamlFile();
} catch (Exception e)
{
System.err
- .println("Couln't format the alignment for output as a FASTA file.");
+ .println("Couln't format the alignment for output as a FASTA file.");
e.printStackTrace(System.err);
}
}
}
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
/**
* 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
} catch (Exception ex)
{
System.err
- .println("Exception checking resources: " + file + " " + ex);
+ .println("Exception checking resources: " + file + " " + ex);
}
if (file.indexOf("://") > -1)
if (debug)
{
System.out
- .println("File deemed not accessible via " + protocol);
+ .println("File deemed not accessible via " + protocol);
}
fp.close();
return null;
git://source.jalview.org / jalview.git / blobdiff