X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=getdown%2Fsrc%2Fgetdown%2Fcore%2Fsrc%2Fmain%2Fjava%2Fcom%2Fthreerings%2Fgetdown%2Fdata%2FApplication.java;h=435ebbd79af662ce55cc90ae336208b48c898b1f;hb=HEAD;hp=b11a380f072d870c6447e166b723253083f9803f;hpb=6402aef8acf127e8c5fee47ccaeb0b33aab07663;p=jalview.git

diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
index b11a380..435ebbd 100644
--- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
+++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
@@ -9,6 +9,8 @@ import java.io.*;
 import java.lang.reflect.Method;
 import java.net.MalformedURLException;
 import java.net.Proxy;
+import java.net.SocketAddress;
+import java.net.InetSocketAddress;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
@@ -29,7 +31,7 @@ import java.util.zip.GZIPInputStream;
 
 import jalview.bin.HiDPISetting;
 import jalview.bin.MemorySetting;
-//import com.install4j.api.launcher.Variables;
+import jalview.util.LaunchUtils;
 
 import com.threerings.getdown.util.*;
 // avoid ambiguity with java.util.Base64 which we can't use as it's 1.8+
@@ -1058,13 +1060,33 @@ public class Application
         }
 
         // pass along our proxy settings
-        String proxyHost;
-        if ((proxyHost = System.getProperty("http.proxyHost")) != null) {
+        String proxyHost = System.getProperty("http.proxyHost");
+	String proxyPort = StringUtil.isBlank(System.getProperty("http.proxyPort")) ? "80" : System.getProperty("http.proxyPort");
+        if (StringUtil.isBlank(proxyHost) && ! proxy.equals(Proxy.NO_PROXY)) {
+	    try {
+		SocketAddress a = proxy.address();
+		if (a != null && a instanceof InetSocketAddress) {
+		    InetSocketAddress ia = (InetSocketAddress)a;
+		    proxyHost = ia.getHostString();
+		    proxyPort = String.valueOf(ia.getPort());
+		}
+	    } catch (Exception e) {
+		log.error("Problem obtaining proxy settings from Proxy object");
+		e.printStackTrace();
+	    }
+	}
+        if (proxyHost != null) {
+	    log.info("Using proxy settings "+proxyHost+":"+proxyPort);
             args.add("-Dhttp.proxyHost=" + proxyHost);
-            args.add("-Dhttp.proxyPort=" + System.getProperty("http.proxyPort"));
+            args.add("-Dhttp.proxyPort=" + proxyPort);
             args.add("-Dhttps.proxyHost=" + proxyHost);
-            args.add("-Dhttps.proxyPort=" + System.getProperty("http.proxyPort"));
-        }
+            args.add("-Dhttps.proxyPort=" + proxyPort);
+	} else {
+	    log.info("Not setting proxy");
+	}
+
+        // add the getdowninstanceappbase property.  getdownappdir is added by getdown.txt
+        args.add("-Dgetdowninstanceappbase=" + getAppbase().toString());
 
         // add the marker indicating the app is running in getdown
         args.add("-D" + Properties.GETDOWN + "=true");
@@ -1115,7 +1137,6 @@ public class Application
                 String query = jalviewUri.getQuery();
                 
                 _appargs.clear();
-                _appargs.add("-open");
                 if (host != null && host.length() > 0) {
                   URL newUrl = new URL(
                           (https?"https":"http")
@@ -1162,6 +1183,17 @@ public class Application
             continue;
           }
         }
+
+        // use saved preferences if no cmdline args
+        LaunchUtils.loadChannelProps(getAppDir());
+        if (LaunchUtils.getBooleanUserPreference(MemorySetting.CUSTOMISED_SETTINGS)) {
+          if (jvmmempc == null) {
+            jvmmempc = LaunchUtils.getUserPreference(MemorySetting.MEMORY_JVMMEMPC);
+          }
+          if (jvmmemmax == null) {
+            jvmmemmax = LaunchUtils.getUserPreference(MemorySetting.MEMORY_JVMMEMMAX);
+          }
+        }
         
         // add the memory setting from jvmmempc and jvmmemmax
         long maxMemLong = -1;
@@ -1218,10 +1250,8 @@ public class Application
           if (j > -1) {
             ext = filename.substring(j+1);
           }
-          if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase())) {
+          if (ext != null && LOCATOR_FILE_EXTENSION.equals(ext.toLowerCase(Locale.ROOT))) {
             // this file extension should have been dealt with in Getdown class
-          } else {
-            _appargs.add(0, "-open");
           }
         }
 
@@ -1234,7 +1264,9 @@ public class Application
         String[] sargs = args.toArray(new String[args.size()]);
         log.info("Running " + StringUtil.join(sargs, "\n  "));
 
-        return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+        // don't set the working dir, leave it the same as the working dir of the invocation
+        //return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+        return Runtime.getRuntime().exec(sargs, envp);
     }
 
     /**
@@ -1419,6 +1451,8 @@ public class Application
             clearValidationMarkers();
             // if the new copy validates, reinitialize ourselves; otherwise report baffling hoseage
             if (_digest.validateResource(crsrc, null)) {
+                // unset _initialisedConfig so new file is initialised
+                _initialisedConfig = null;
                 init(true);
             } else {
                 log.warning(CONFIG_FILE + " failed to validate even after redownloading. " +
@@ -1963,7 +1997,7 @@ public class Application
         String locatorFilename = filenames.length >= 1 ? filenames[0] : null;
         if (
                 !StringUtil.isBlank(locatorFilename)
-                && locatorFilename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)
+                && locatorFilename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)
                 ) {
           setLocatorFile(locatorFilename);
           // remove the locator filename from the filenames array
@@ -1977,7 +2011,7 @@ public class Application
           // skip any other locator files in a multiple file list
           if (filename.startsWith("jalview://") || filename.startsWith("jalviews://")) {
             setJalviewUri(filename);
-          } else if (! filename.toLowerCase().endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
+          } else if (! filename.toLowerCase(Locale.ROOT).endsWith("."+Application.LOCATOR_FILE_EXTENSION)) {
             addStartupFile(filename);
           }
         }