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JAL-3660 JAL-3561 output alignment as requested file format as validated by FileForma...
bug/JAL-3561_translatefileformats
author
Jim Procter
<jprocter@issues.jalview.org>
Tue, 16 Jun 2020 16:12:54 +0000
(17:12 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Tue, 16 Jun 2020 16:12:54 +0000
(17:12 +0100)
src/jalview/bin/Jalview.java
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diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
8c9d391
..
208a6f1
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-30,6
+30,7
@@
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
@@
-666,18
+667,34
@@
public class Jalview
af.createEPS(outputFile);
continue;
}
af.createEPS(outputFile);
continue;
}
-
- if (af.saveAlignment(file, format))
- {
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ FileFormatI outFormat=null;
+ try {
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP) {
+ System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
}
}
- else
+ if (outFormat != null)
{
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ if (!outFormat.isWritable())
+ {
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
+ }
+ else
+ {
+ if (af.saveAlignment(file, outFormat))
+ {
+ System.out.println("Written alignment in " + format
+ + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + format + " format!!");
+ }
+ }
}
}
-
}
while (aparser.getSize() > 0)
}
while (aparser.getSize() > 0)