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proxy commit for Anne Menard <menard.annec@gmail.com> throw generic exceptions (just...
[jalview.git]
/
src
/
jalview
/
io
/
AppletFormatAdapter.java
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
42e881c
..
637db81
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-1,13
+1,13
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* 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.
*
* 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
* 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
@@
-38,7
+38,7
@@
public class AppletFormatAdapter
*/
public static final String[] READABLE_FORMATS = new String[]
{ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
*/
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
/**
* List of valid format strings for use by callers of the formatSequences
@@
-52,7
+52,7
@@
public class AppletFormatAdapter
* that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
* 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,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
/**
* List of writable formats by the application. Order must correspond with the
/**
* List of writable formats by the application. Order must correspond with the
@@
-66,8
+66,8
@@
public class AppletFormatAdapter
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto" }; // ,
+ { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ "sto,stk","xml,rnaml" }; // ,
// ".blast"
// };
// ".blast"
// };
@@
-78,7
+78,7
@@
public class AppletFormatAdapter
*/
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",
- "Stockholm" };// ,
+ "Stockholm","RNAML" };// ,
// "SimpleBLAST"
// };
// "SimpleBLAST"
// };
@@
-119,6
+119,21
@@
public class AppletFormatAdapter
String inFile;
/**
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
* check that this format is valid for reading
*
* @param format
@@
-212,7
+227,7
@@
public class AppletFormatAdapter
}
else if (format.equals("PDB"))
{
}
else if (format.equals("PDB"))
{
- afile = new MCview.PDBfile(inFile, type);
+ afile = new MCview.PDBfile(inFile, type);
}
else if (format.equals("STH"))
{
}
else if (format.equals("STH"))
{
@@
-222,7
+237,11
@@
public class AppletFormatAdapter
{
afile = new SimpleBlastFile(inFile, type);
}
{
afile = new SimpleBlastFile(inFile, type);
}
-
+ else if (format.equals("RNAML"))
+ {
+ afile = new RnamlFile(inFile, type);
+ }
+
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
Alignment al = new Alignment(afile.getSeqsAsArray());
afile.addAnnotations(al);
@@
-277,7
+296,7
@@
public class AppletFormatAdapter
*
* @return DOCUMENT ME!
*/
*
* @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
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
@@
-329,6
+348,10
@@
public class AppletFormatAdapter
{
afile = new StockholmFile(source);
}
{
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("SimpleBLAST"))
{
afile = new SimpleBlastFile(source);
@@
-436,12
+459,17
@@
public class AppletFormatAdapter
{
afile = new AMSAFile(alignment);
}
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase("RNAML"))
+ {
+ afile = new RnamlFile();
+ }
+
else
{
throw new Exception(
"Implementation error: Unknown file format string");
}
else
{
throw new Exception(
"Implementation error: Unknown file format string");
}
-
+ afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
afile.setSeqs(alignment.getSequencesArray());
afile.addJVSuffix(jvsuffix);
afile.setSeqs(alignment.getSequencesArray());
@@
-463,6
+491,18
@@
public class AppletFormatAdapter
return null;
}
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;
public static void main(String[] args)
{
int i = 0;
@@
-597,11
+637,14
@@
public class AppletFormatAdapter
if (!fp.isValid())
{
fp = null;
if (!fp.isValid())
{
fp = null;
- } else {
- if (debug)
+ }
+ else
{
{
- System.out.println("Successful.");
- }}
+ if (debug)
+ {
+ System.out.println("Successful.");
+ }
+ }
} catch (Exception e)
{
if (debug)
} catch (Exception e)
{
if (debug)
@@
-690,4
+733,4
@@
public class AppletFormatAdapter
}
return null;
}
}
return null;
}
-}
\ No newline at end of file
+}