X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=67e2433774858ebc61f2e3ff4586e7192bd01585;hb=bcc114c5106c3cee78db99955fee2392edece7df;hp=ee03e7755a0df6445f864a12052c1249247099b3;hpb=5b14c48157e617dd00342429090bb0be5193d9a5;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index ee03e77..67e2433 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -23,8 +23,6 @@ package jalview.bin;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertTrue;
 
-import jalview.gui.JvOptionPane;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
@@ -43,6 +41,7 @@ import org.testng.annotations.Test;
 import io.github.classgraph.ClassGraph;
 import io.github.classgraph.ModuleRef;
 import io.github.classgraph.ScanResult;
+import jalview.gui.JvOptionPane;
 
 public class CommandLineOperations
 {
@@ -54,12 +53,12 @@ public class CommandLineOperations
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  private static final int TEST_TIMEOUT = 12500; // Note longer timeout needed
-                                                // on
-                                                // full test run than on
-                                                // individual tests
+  private static final int TEST_TIMEOUT = 13000; // Note longer timeout needed
+                                                 // on
+                                                 // full test run than on
+                                                 // individual tests
 
-  private static final int SETUP_TIMEOUT = 9000;
+  private static final int SETUP_TIMEOUT = 9500;
 
   private static final int MINFILESIZE_SMALL = 2096;
 
@@ -167,8 +166,8 @@ public class CommandLineOperations
     // not expanded by the shell
     String classpath = getClassPath();
     String _cmd = java_exe + " "
-            + (withAwt ? "-Djava.awt.headless=true" : "")
-            + " -classpath " + classpath
+            + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
+            + classpath
             + (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
                     : "")
             + " jalview.bin.Jalview ";
@@ -228,7 +227,7 @@ public class CommandLineOperations
   {
     String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/bin/testProps.jvprops -colour zappo "
             + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
-            + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
+            + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree --debug";
     Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
     String ln = null;
     while ((ln = worker.getOutputReader().readLine()) != null)
@@ -248,16 +247,16 @@ public class CommandLineOperations
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
     final Worker worker = getJalviewDesktopRunner(false, cmds,
             SETUP_TIMEOUT);
-    
-    
+
     // number of lines expected on STDERR when Jalview starts up normally
     // may need to adjust this if Jalview is excessively noisy ?
-    final int STDERR_SETUPLINES=30;
-    
+    final int STDERR_SETUPLINES = 50;
+
     // thread monitors stderr - bails after SETUP_TIMEOUT or when
     // STDERR_SETUPLINES have been read
     Thread runner = new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         String ln = null;
@@ -380,26 +379,26 @@ public class CommandLineOperations
         " -eps", workingDir + "test_uniref50_out.eps", true,
         MINFILESIZE_BIG, TEST_TIMEOUT },
         { "nodisplay -open examples/uniref50.fa", " -eps",
-            workingDir + "test_uniref50_out.eps", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "nogui -open examples/uniref50.fa", " -eps",
-            workingDir + "test_uniref50_out.eps", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -eps",
             workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -svg",
-            workingDir + "test_uniref50_out.svg", false,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -png",
             workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
             TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -html",
-            workingDir + "test_uniref50_out.html", true,
-            MINFILESIZE_BIG, TEST_TIMEOUT },
+            workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
         { "headless -open examples/uniref50.fa", " -fasta",
             workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
             TEST_TIMEOUT },