pass any warning messages to StdErr - also todo to allow caller to check for any...

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d2dc8f3..8e05b44 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -365,7 +365,8 @@ public class AppletFormatAdapter
 
   /**
    * Construct an output class for an alignment in a particular filetype
-   * 
+   * TODO: allow caller to detect errors and warnings encountered when generating output
+   *
    * @param format
    *                string name of alignment format
    * @param alignment
@@ -429,7 +430,12 @@ public class AppletFormatAdapter
 
       afile.setSeqs(alignment.getSequencesArray());
 
-      return afile.print();
+      String afileresp = afile.print();
+      if (afile.hasWarningMessage())
+      {
+        System.err.println("Warning raised when writing as "+format+" : "+afile.getWarningMessage());
+      }
+      return afileresp;
     } catch (Exception e)
     {
       System.err.println("Failed to write alignment as a '" + format

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 25e2fea..2735fb3 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -63,6 +63,8 @@ public class FormatAdapter extends AppletFormatAdapter
 
   /**
    * Format a vector of sequences as a flat alignment file.
+   * TODO: allow caller to detect errors and warnings encountered when generating output
+   *
    * 
    * @param format
    *                Format string as givien in the AppletFormatAdaptor list
@@ -130,8 +132,12 @@ public class FormatAdapter extends AppletFormatAdapter
        */
 
       afile.setSeqs(seqs);
-
-      return afile.print();
+      String afileresp = afile.print();
+      if (afile.hasWarningMessage())
+      {
+        System.err.println("Warning raised when writing as "+format+" : "+afile.getWarningMessage());
+      }
+      return afileresp;
     } catch (Exception e)
     {
       System.err.println("Failed to write alignment as a '" + format