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Merge branch 'develop' into develop_m2_8_1_2
[jalview.git]
/
src
/
jalview
/
io
/
AppletFormatAdapter.java
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
637db81
..
eac7cf2
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-52,14
+52,16
@@
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,faa,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
/**
* List of readable format file extensions by application in order
@@
-228,6
+230,8
@@
public class AppletFormatAdapter
else if (format.equals("PDB"))
{
afile = new MCview.PDBfile(inFile, type);
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"))
{
}
else if (format.equals("STH"))
{
@@
-453,7
+457,7
@@
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"))
{
}
else if (format.equalsIgnoreCase("AMSA"))
{
@@
-547,7
+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