From 81da38a64f3e2856a0a3239f9939d0fdb2fdb9f8 Mon Sep 17 00:00:00 2001
From: Daniel <daniel.huson@uni-tuebingen.de>
Date: Sun, 21 Feb 2021 18:56:08 +0100
Subject: [PATCH] bug fix

---
 src/megan/core/Document.java    | 24 ++++++++++++------------
 src/megan/core/MeganFile.java   |  8 +++++---
 src/megan/daa/io/DAAParser.java |  5 ++---
 3 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/src/megan/core/Document.java b/src/megan/core/Document.java
index b2c3ec0a..8570a2b9 100644
--- a/src/megan/core/Document.java
+++ b/src/megan/core/Document.java
@@ -974,19 +974,19 @@ public int getPairedReadSuffixLength() {
     public BlastMode getBlastMode() {
         BlastMode blastMode = dataTable.getBlastMode();
         if (blastMode == BlastMode.Unknown) {
-            if (meganFile.isDAAFile()) {
-                dataTable.setBlastMode(0, DAAParser.getBlastMode(meganFile.getFileName()));
-            } else if (meganFile.isRMA3File()) {
-                try (final RMA3File rma3File = new RMA3File(meganFile.getFileName(), "r")) {
-                    dataTable.setBlastMode(0, rma3File.getBlastMode());
-                } catch (IOException ignored) {
-                }
-            } else if (meganFile.isRMA6File()) {
-                try (final RMA6File rma6File = new RMA6File(meganFile.getFileName(), "r")) {
-                    dataTable.setBlastMode(0, rma6File.getHeaderSectionRMA6().getBlastMode());
-                } catch (IOException ignored) {
+                if (meganFile.isDAAFile()) {
+                        dataTable.setBlastMode(0, DAAParser.getBlastMode(meganFile.getFileName()));
+                } else if (meganFile.isRMA3File()) {
+                    try (final RMA3File rma3File = new RMA3File(meganFile.getFileName(), "r")) {
+                        dataTable.setBlastMode(0, rma3File.getBlastMode());
+                    } catch (IOException ignored) {
+                    }
+                } else if (meganFile.isRMA6File()) {
+                    try (final RMA6File rma6File = new RMA6File(meganFile.getFileName(), "r")) {
+                        dataTable.setBlastMode(0, rma6File.getHeaderSectionRMA6().getBlastMode());
+                    } catch (IOException ignored) {
+                    }
                 }
-            }
         }
 
         if (blastMode == BlastMode.Unknown && !meganFile.isMeganSummaryFile() && meganFile.hasDataConnector() && !meganFile.isMeganServerFile()) {
diff --git a/src/megan/core/MeganFile.java b/src/megan/core/MeganFile.java
index 9f3c64bd..c7316a43 100644
--- a/src/megan/core/MeganFile.java
+++ b/src/megan/core/MeganFile.java
@@ -66,8 +66,8 @@ public void setFileFromExistingFile(String fileName, boolean readOnly) {
         this.fileName = fileName;
         this.readOnly = readOnly;
 
-        if (fileName.contains("::"))
-            meganServerFile = true;
+        meganServerFile = fileName.contains("::");
+
         if (fileName.toLowerCase().endsWith(".rma1")) {
             fileType = Type.RMA1_FILE;
         } else if (fileName.toLowerCase().endsWith(".rma2")) {
@@ -173,8 +173,10 @@ public String getFileName() {
     }
 
     public void setFileName(String fileName) {
-        if (fileName == null || !fileName.equals(this.fileName))
+        if (fileName == null || !fileName.equals(this.fileName)) {
             connector = null;
+            meganServerFile=false;
+        }
         this.fileName = fileName;
     }
 
diff --git a/src/megan/daa/io/DAAParser.java b/src/megan/daa/io/DAAParser.java
index 0d227542..2d30c865 100644
--- a/src/megan/daa/io/DAAParser.java
+++ b/src/megan/daa/io/DAAParser.java
@@ -137,10 +137,9 @@ public static jloda.util.BlastMode getBlastMode(String fileName) {
         try {
             DAAParser daaParser = new DAAParser(fileName);
             return daaParser.getBlastMode();
-        } catch (IOException e) {
-            Basic.caught(e);
-            return jloda.util.BlastMode.Unknown;
+        } catch (IOException ignored) {
         }
+        return jloda.util.BlastMode.Unknown;
     }
 
     /**