X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=d7da302962d95a3fdf0af2d5b5a2b2d73a113aab;hb=3c436f044004e6c8cc04782701e8f65c097297ac;hp=fc1d870498b692a6af6b21f8ae20ba1680454489;hpb=9de5a036e2a12a895cece39abda685841b219ad3;p=jalview.git
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index fc1d870..d7da302 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 .
+ * 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;
@@ -38,7 +41,7 @@ public class AppletFormatAdapter
*/
public static final String[] READABLE_FORMATS = new String[]
{ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile" }; // , "SimpleBLAST" };
+ "PDB", "JnetFile", "RNAML" }; // , "SimpleBLAST" };
/**
* List of valid format strings for use by callers of the formatSequences
@@ -52,25 +55,24 @@ public class AppletFormatAdapter
* 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" };
/**
* 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, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" }; // ,
-
- // ".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
@@ -78,7 +80,7 @@ public class AppletFormatAdapter
*/
public static final String[] READABLE_FNAMES = new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm" };// ,
+ "Stockholm", "RNAML" };// ,
// "SimpleBLAST"
// };
@@ -117,18 +119,22 @@ public class AppletFormatAdapter
AlignFile afile = null;
String inFile;
+
/**
- * character used to write newlines
+ * 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
*
@@ -224,6 +230,8 @@ public class AppletFormatAdapter
else if (format.equals("PDB"))
{
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"))
{
@@ -233,6 +241,10 @@ public class AppletFormatAdapter
{
afile = new SimpleBlastFile(inFile, type);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(inFile, type);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
@@ -288,7 +300,7 @@ public class AppletFormatAdapter
*
* @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
@@ -340,6 +352,10 @@ public class AppletFormatAdapter
{
afile = new StockholmFile(source);
}
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(source);
+ }
else if (format.equals("SimpleBLAST"))
{
afile = new SimpleBlastFile(source);
@@ -441,12 +457,17 @@ public class AppletFormatAdapter
}
else if (format.equalsIgnoreCase("STH"))
{
- afile = new StockholmFile();
+ afile = new StockholmFile(alignment);
}
else if (format.equalsIgnoreCase("AMSA"))
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase("RNAML"))
+ {
+ afile = new RnamlFile();
+ }
+
else
{
throw new Exception(
@@ -478,7 +499,8 @@ public class AppletFormatAdapter
{
String protocol = FILE;
String ft = file.toLowerCase().trim();
- if (ft.indexOf("http:") ==0 || ft.indexOf("https:") ==0 || ft.indexOf("file:") == 0)
+ if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+ || ft.indexOf("file:") == 0)
{
protocol = URL;
}
@@ -529,7 +551,6 @@ public class AppletFormatAdapter
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