enable importing of alignments in files with .txt extension. fixes #78

CompEvol · Dec 3, 2023 · ced29f3 · ced29f3
1 parent b41a9ec
commit ced29f3
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Showing 2 changed files with 16 additions and 1 deletion.
diff --git a/src/beastfx/app/inputeditor/BeautiAlignmentProvider.java b/src/beastfx/app/inputeditor/BeautiAlignmentProvider.java
@@ -134,6 +134,17 @@ public List<BEASTInterface> getAlignments(BeautiDoc doc, File[] files) {
 					availableImporters.add(importer);
 				}
 			}
+			if (availableImporters.size() == 0 && file.getPath().toLowerCase().endsWith(".txt")) {
+				// remove .txt extension and try again
+				String path = file.getPath();
+				path = path.substring(0, path.length() - 4);
+				File file2 = new File(path);
+				for (AlignmentImporter importer : importers) {
+					if (importer.canHandleFile(file2)) {
+						availableImporters.add(importer);
+					}
+				}
+			}
 
 			if (availableImporters.size() > 0) {
 				AlignmentImporter importer = availableImporters.get(0);

diff --git a/src/beastfx/app/inputeditor/FastaImporter.java b/src/beastfx/app/inputeditor/FastaImporter.java
@@ -48,7 +48,11 @@ public List<BEASTInterface> loadFile(File file) {
 				// .ffn = nucleotide coding regions
 				// .frn = non-coding RNA
 				// .ffa = amino acid
-	    		boolean mayBeAminoacid = !(file.getName().toLowerCase().endsWith(".fna") || file.getName().toLowerCase().endsWith(".ffn") || file.getName().toLowerCase().endsWith(".frn"));
+		        String filename = file.getName();
+		        if (filename.toLowerCase().endsWith(".txt")) {
+		        	filename = filename.substring(0, filename.length() - 4);
+		        }
+	    		boolean mayBeAminoacid = !(filename.toLowerCase().endsWith(".fna") || filename.toLowerCase().endsWith(".ffn") || filename.toLowerCase().endsWith(".frn"));
 
 				while (fin.ready()) {
 					String line = fin.readLine();