From cee7f3931f46066e9f81a1cac7d29083e49de8d4 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 16 Jun 2020 17:12:54 +0100 Subject: [PATCH] JAL-3660 JAL-3561 output alignment as requested file format as validated by FileFormats - report if format cannot be resolved or FileFormatI does not support export. --- src/jalview/bin/Jalview.java | 35 ++++++++++++++++++++++++++--------- 1 file changed, 26 insertions(+), 9 deletions(-) diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 8c9d391..208a6f1 100755 --- 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.FileFormats; import jalview.io.FileLoader; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; @@ -666,18 +667,34 @@ public class Jalview 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) -- 1.7.10.2