fix fasta format bug #437

LinguaPhylo · Jan 19, 2024 · 20713be · 20713be
1 parent 1adcf57
commit 20713be
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/FastaAlignment.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/FastaAlignment.java
@@ -30,7 +30,7 @@ public List<String> getTextForFile() {
         for (int i=0; i < ntaxa(); i++) {
             try {
                 String taxonName = getTaxaNames()[i];
-                lines.add(taxonName);
+                lines.add(">" + taxonName);
                 String sequence = getSequence(i);
                 lines.add(sequence);
             } catch (Exception ex) {

diff --git a/lphy/src/main/java/lphy/core/logger/ValueFileLoggerListener.java b/lphy/src/main/java/lphy/core/logger/ValueFileLoggerListener.java
@@ -142,6 +142,8 @@ else if (index < 1) // index starts from 0
                     LoggerUtils.log.severe("Cannot write " + canonicalId + " to file : " +
                             outputFile.getAbsolutePath() +  " !");
                 }
+                System.out.println("Create file : " + fileName +
+                        " in the directory " + OutputSystem.getOrCreateOutputDirectory());
 
             } else { // default, ValueFormatter not accessible to lphy extension developer