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Merge branch 'JAL-1403' into develop
[jalview.git]
/
src
/
jalview
/
io
/
AppletFormatAdapter.java
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
d42157b
..
eac7cf2
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 2.6)
- * 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
@@
-52,22
+52,24
@@
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",
+ "sto,stk" };
/**
* 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[]
/**
* 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" };
/**
* List of readable format file extensions by application in order
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
/**
* 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" }; // ,
+ { "fa,faa,fasta,fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ "sto,stk","xml,rnaml" }; // ,
// ".blast"
// };
// ".blast"
// };
@@
-78,7
+80,7
@@
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"
// };
@@
-117,18
+119,22
@@
public class AppletFormatAdapter
AlignFile afile = null;
String inFile;
AlignFile afile = null;
String inFile;
+
/**
/**
- * character used to write newlines
+ * character used to write newlines
*/
protected String newline = System.getProperty("line.separator");
*/
protected String newline = System.getProperty("line.separator");
+
public void setNewlineString(String nl)
{
newline = nl;
}
public void setNewlineString(String nl)
{
newline = nl;
}
+
public String getNewlineString()
{
return newline;
}
public String getNewlineString()
{
return newline;
}
+
/**
* check that this format is valid for reading
*
/**
* check that this format is valid for reading
*
@@
-223,7
+229,9
@@
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);
+ // Uncomment to test Jmol data based PDB processing: JAL-1213
+ // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
}
else if (format.equals("STH"))
{
}
else if (format.equals("STH"))
{
@@
-233,7
+241,11
@@
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);
@@
-288,7
+300,7
@@
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
@@
-340,6
+352,10
@@
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);
@@
-441,12
+457,17
@@
public class AppletFormatAdapter
}
else if (format.equalsIgnoreCase("STH"))
{
}
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("AMSA"))
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase("RNAML"))
+ {
+ afile = new RnamlFile();
+ }
+
else
{
throw new Exception(
else
{
throw new Exception(
@@
-477,8
+498,9
@@
public class AppletFormatAdapter
public static String checkProtocol(String file)
{
String protocol = FILE;
public static String checkProtocol(String file)
{
String protocol = FILE;
-
- if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+ String ft = file.toLowerCase().trim();
+ if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+ || ft.indexOf("file:") == 0)
{
protocol = URL;
}
{
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");
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
} catch (Exception e)
{
System.err.println("Exception when dealing with " + i