JAL-3477 Javadoc, addition of -jvmmempc and -jvmmemmax args detection and some small...

diff --git a/src/jalview/bin/Launcher.java b/src/jalview/bin/Launcher.java
index 041a7b1..1541615 100644 (file)
--- a/src/jalview/bin/Launcher.java
+++ b/src/jalview/bin/Launcher.java
@@ -4,19 +4,43 @@ import java.io.File;
 import java.io.IOException;
 import java.lang.management.ManagementFactory;
 import java.util.ArrayList;
-
+import java.util.List;
+
+/**
+ * A Launcher class for Jalview. This class is used to launch Jalview from the
+ * shadowJar when Getdown is not used or available. It attempts to take all the
+ * command line arguments to pass on to the jalview.bin.Jalview class, but to
+ * insert a -Xmx memory setting to a sensible default, using the -jvmmempc and
+ * -jvmmemmax application arguments if specified. If not specified then system
+ * properties will be looked for by jalview.bin.MemorySetting. If the user has
+ * provided the JVM with a -Xmx setting directly and not set -jvmmempc or
+ * -jvmmemmax then this setting will be used and system properties ignored. If
+ * -Xmx is set as well as -jvmmempc or -jvmmemmax as argument(s) then the -Xmx
+ * argument will NOT be passed on to the main application launch.
+ * 
+ * @author bsoares
+ *
+ */
 public class Launcher
 {
   private final static String startClass = "jalview.bin.Jalview";
 
   private final static String dockIconPath = "JalviewLogo_Huge.png";
 
+  /**
+   * main method for jalview.bin.Launcher. This restarts the same JRE's JVM with
+   * the same arguments but with memory adjusted based on extracted -jvmmempc and
+   * -jvmmemmax application arguments. If on a Mac then extra dock:icon and
+   * dock:name arguments are also set.
+   * 
+   * @param args
+   */
   public static void main(String[] args)
   {
     final String javaBin = System.getProperty("java.home") + File.separator
             + "bin" + File.separator + "java";
 
-    ArrayList<String> command = new ArrayList<>();
+    List<String> command = new ArrayList<>();
     command.add(javaBin);
 
     String memSetting = null;
@@ -30,23 +54,48 @@ public class Launcher
     }
     command.add("-cp");
     command.add(ManagementFactory.getRuntimeMXBean().getClassPath());
+
+    String jvmmempc = null;
+    String jvmmemmax = null;
     ArrayList<String> arguments = new ArrayList<>();
     for (String arg : args)
     {
-      arguments.add(arg);
+      // jvmmempc and jvmmemmax args used to set memory and are not passed on to
+      // startClass
+      if (arg.startsWith(
+              "-" + MemorySetting.MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "="))
+      {
+        jvmmempc = arg.substring(
+                MemorySetting.MAX_HEAPSIZE_PERCENT_PROPERTY_NAME.length()
+                        + 2);
+      }
+      else if (arg.startsWith(
+              "-" + MemorySetting.MAX_HEAPSIZE_PROPERTY_NAME + "="))
+      {
+        jvmmemmax = arg.substring(
+                MemorySetting.MAX_HEAPSIZE_PROPERTY_NAME.length() + 2);
+      }
+      else
+      {
+        arguments.add(arg);
+      }
     }
 
     // add memory setting if not specified
     boolean memSet = false;
     boolean dockIcon = false;
     boolean dockName = false;
-    ARG: for (int i = 0; i < command.size(); i++)
+    for (int i = 0; i < command.size(); i++)
     {
       String arg = command.get(i);
       if (arg.startsWith("-Xmx"))
       {
-        memSetting = arg;
-        memSet = true;
+        // only use -Xmx if jvmmemmax and jvmmempc have not been set
+        if (jvmmempc == null && jvmmemmax == null)
+        {
+          memSetting = arg;
+          memSet = true;
+        }
       }
       else if (arg.startsWith("-Xdock:icon"))
       {
@@ -60,11 +109,12 @@ public class Launcher
 
     if (!memSet)
     {
-      long maxMemLong = MemorySetting.getMemorySetting();
+      long maxMemLong = MemorySetting.getMemorySetting(jvmmemmax, jvmmempc);
       
       if (maxMemLong > 0)
       {
         memSetting = "-Xmx" + Long.toString(maxMemLong);
+        memSet = true;
         command.add(memSetting);
       }
     }
@@ -90,10 +140,9 @@ public class Launcher
 
     // System.out.println("COMMAND: " + String.join(" ", builder.command()));
     System.out.println("Running " + startClass + " with "
-            + (memSetting == null ? "no memSetting" : memSetting));
+            + (memSetting == null ? "no memory setting" : memSetting));
 
-    if (System.getProperty("launcherstop") != null
-            && System.getProperty("launcherstop").equals("true"))
+    if (Boolean.parseBoolean(System.getProperty("launcherstop")))
     {
       System.exit(0);
     }
@@ -118,7 +167,7 @@ public class Launcher
         }
         final ProcessBuilder builderNoMem = new ProcessBuilder(
                 commandNoMem);
-        System.out.println("NO MEM COMMAND: "
+        System.out.println("Command without memory setting: "
                 + String.join(" ", builderNoMem.command()));
         try
         {

diff --git a/src/jalview/bin/MemorySetting.java b/src/jalview/bin/MemorySetting.java
index f7c40cf..7849ba2 100644 (file)
--- a/src/jalview/bin/MemorySetting.java
+++ b/src/jalview/bin/MemorySetting.java
@@ -257,9 +257,8 @@ public class MemorySetting
     // jvmmempc was set OR neither jvmmempc nor jvmmemmax were set), let's cap
     // maxMemLong to 8GB
     if (memoryPercentError && mempc == -1
-    // && (jvmmempcarg != null || (jvmmempcarg == null && jvmmemmaxarg == null))
-    // the above is easier to understand but simplified to
-            && !(jvmmempcarg == null && jvmmemmaxarg != null)
+            && !(jvmmempcarg == null && jvmmemmaxarg != null) // the same as (jvmmempcarg != null || (jvmmempcarg == null && jvmmemmaxarg
+                                                              // == null))
             && memmax > NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE)
     {
       System.out.println(