From 3426c60a0b8395025536021e2742162cd20ebe2b Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Fri, 27 Nov 2020 17:24:08 +0000 Subject: [PATCH] JAL-3660 Fix for specified output format when using command line arg to convert a file --- src/jalview/bin/Jalview.java | 37 +++++++++++++++++++++++++++++-------- 1 file changed, 29 insertions(+), 8 deletions(-) diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index e130277..08cbcb2 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -60,6 +60,7 @@ import jalview.io.DataSourceType; 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; @@ -793,17 +794,37 @@ public class Jalview af.createEPS(outputFile); continue; } - - af.saveAlignment(file, format); - if (af.isSaveAlignmentSuccessful()) + FileFormatI outFormat = null; + try + { + outFormat = FileFormats.getInstance().forName(outputFormat); + } catch (Exception formatP) { - System.out.println("Written alignment in " + format - + " format to " + file); + 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 + { + af.saveAlignment(file, outFormat); + if (af.isSaveAlignmentSuccessful()) + { + System.out.println("Written alignment in " + + outFormat.getName() + " format to " + file); + } + else + { + System.out.println("Error writing file " + file + " in " + + outFormat.getName() + " format!!"); + } + } } } -- 1.7.10.2