JAL-3660 Fix for specified output format when using command line arg to convert a...

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 78d8dde..08cbcb2 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -60,6 +60,7 @@ 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;
@@ -465,6 +466,7 @@ public class Jalview
 
     if (!headless)
     {
+
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -792,17 +794,37 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-
-          af.saveAlignment(file, format);
-          if (af.isSaveAlignmentSuccessful())
+          FileFormatI outFormat = null;
+          try
+          {
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP)
           {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
+            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
+            {
+              af.saveAlignment(file, outFormat);
+              if (af.isSaveAlignmentSuccessful())
+              {
+                System.out.println("Written alignment in "
+                        + outFormat.getName() + " format to " + file);
+              }
+              else
+              {
+                System.out.println("Error writing file " + file + " in "
+                        + outFormat.getName() + " format!!");
+              }
+            }
           }
 
         }
@@ -1030,6 +1052,8 @@ public class Jalview
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+                    + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+                    + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
                     + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
   }