/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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 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
*/
public static final String[] READABLE_FORMATS = new String[]
{ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile" , "RNAML"}; // , "SimpleBLAST" };
+ "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" };
+ { "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,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+ { "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" };
+ { "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,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk","xml,rnaml" }; // ,
-
- // ".blast"
- // };
+ { "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
*/
public static final String[] READABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm","RNAML" };// ,
+ "Stockholm", "RNAML" };// ,
// "SimpleBLAST"
// };
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(inFile, type);
+ 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 RnamlFile(inFile, type);
}
-
+
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
*
* @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
}
}
+
+ /**
+ * 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
}
else if (format.equalsIgnoreCase("STH"))
{
- afile = new StockholmFile();
+ afile = new StockholmFile(alignment);
}
else if (format.equalsIgnoreCase("AMSA"))
{
{
afile = new RnamlFile();
}
-
+
else
{
- throw new Exception(
- "Implementation error: Unknown file format string");
+ throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
}
afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
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
git://source.jalview.org / jalview.git / blobdiff