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JAL-1499 patch from Mungo Carstairs
[jalview.git]
/
src
/
jalview
/
io
/
AppletFormatAdapter.java
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
old mode 100755
(executable)
new mode 100644
(file)
index
d7da302
..
288d476
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-20,11
+20,12
@@
*/
package jalview.io;
*/
package jalview.io;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+
import java.io.File;
import java.io.InputStream;
import java.io.File;
import java.io.InputStream;
-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
/**
* A low level class for alignment and feature IO with alignment formatting
* methods used by both applet and application for generating flat alignment
@@
-40,22
+41,23
@@
public class AppletFormatAdapter
* List of valid format strings used in the isValidFormat method
*/
public static final String[] READABLE_FORMATS = new String[]
* 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", "RNAML" }; // , "SimpleBLAST" };
-
+ { "BLC", "CLUSTAL", "FASTA", "MEGA", "MSF", "PileUp", "PIR", "PFAM",
+ "PDB", "JnetFile", "RNAML" };
/**
* List of valid format strings for use by callers of the formatSequences
* method
*/
public static final String[] WRITEABLE_FORMATS = new String[]
/**
* 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", "MEGA", "MSF", "PileUp", "PIR", "PFAM",
+ "STH",
+ "AMSA" };
/**
* 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[]
/**
* 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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "meg", "msf", "pir", "blc", "amsa",
"jvp", "sto,stk", "jar" };
/**
"jvp", "sto,stk", "jar" };
/**
@@
-63,15
+65,16
@@
public class AppletFormatAdapter
* WRITABLE_EXTENSIONS list of formats.
*/
public static final String[] WRITABLE_FNAMES = new String[]
* WRITABLE_EXTENSIONS list of formats.
*/
public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "STH", "Jalview" };
+ { "Fasta", "Clustal", "PFAM", "MEGA", "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[]
/**
* List of readable format file extensions by application in order
* corresponding to READABLE_FNAMES
*/
public static final String[] READABLE_EXTENSIONS = new String[]
- { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ { "fa, fasta, mfa, fastq", "aln", "pfam", "meg", "msf", "pir", "blc", "amsa",
"jar,jvp", "sto,stk", "xml,rnaml" }; // ".blast"
/**
"jar,jvp", "sto,stk", "xml,rnaml" }; // ".blast"
/**
@@
-79,8
+82,8
@@
public class AppletFormatAdapter
* READABLE_EXTENSIONS
*/
public static final String[] READABLE_FNAMES = new String[]
* READABLE_EXTENSIONS
*/
public static final String[] READABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
- "Stockholm", "RNAML" };// ,
+ { "Fasta", "Clustal", "PFAM", "MEGA", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "Stockholm", "RNAML" };
// "SimpleBLAST"
// };
// "SimpleBLAST"
// };
@@
-245,6
+248,10
@@
public class AppletFormatAdapter
{
afile = new RnamlFile(inFile, type);
}
{
afile = new RnamlFile(inFile, type);
}
+ else if (format.equals("MEGA"))
+ {
+ afile = new MegaFile(inFile, type);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
Alignment al = new Alignment(afile.getSeqsAsArray());
@@
-360,6
+367,10
@@
public class AppletFormatAdapter
{
afile = new SimpleBlastFile(source);
}
{
afile = new SimpleBlastFile(source);
}
+ else if (format.equals("MEGA"))
+ {
+ afile = new MegaFile(source);
+ }
Alignment al = new Alignment(afile.getSeqsAsArray());
Alignment al = new Alignment(afile.getSeqsAsArray());
@@
-467,7
+478,10
@@
public class AppletFormatAdapter
{
afile = new RnamlFile();
}
{
afile = new RnamlFile();
}
-
+ else if (format.equalsIgnoreCase("MEGA"))
+ {
+ afile = new MegaFile();
+ }
else
{
throw new Exception(
else
{
throw new Exception(