X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=9f148bec36d7f904c0213f77c1a4b392dc67387d;hb=8a33c09bdd60c4b0f1c85136d1f8596240151c67;hp=c7b057578fbccdb3974aec814a330f0fe3ab9ba3;hpb=f49e86c9f8e7c0301f2b8824d0c033a3df291e6a;p=jalview.git
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index c7b0575..9f148be 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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;
@@ -23,108 +22,125 @@ 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.
- *
+ * 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
+ /**
+ * 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" }; // , "SimpleBLAST" };
+
/**
- * List of valid format strings for use by callers of the formatSequences method
+ * 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" };
+
/**
- * List of extensions corresponding to file format types
- * in WRITABLE_FNAMES that are writable by the
- * application.
+ * 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, 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.
+ * 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" };
/**
* List of readable format file extensions by application in order
- * corresponding to READABLE_FNAMES
+ * corresponding to READABLE_FNAMES
*/
- public static final String[] READABLE_EXTENSIONS = new String[]
- {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "amsa","jar"
- };
+ public static final String[] READABLE_EXTENSIONS = new String[]
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" }; // ,
+ // ".blast"
+ // };
+
/**
- * List of readable formats by application in order
- * corresponding to READABLE_EXTENSIONS
+ * 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"
- };
-
+ public static final String[] READABLE_FNAMES = new String[]
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };// ,
+ // "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);
+ 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) {
+ public static String prettyPrint(String[] els)
+ {
StringBuffer list = new StringBuffer();
- for (int i=0,iSize=els.length-1; i