'STRAP:multiple sequence alignments '

charite.christo
Class Web

java.lang.Object
  extended by charite.christo.Web
All Implemented Interfaces:
ChRunnable

public class Web
extends java.lang.Object
implements ChRunnable

HELP

Internet and Web-proxy

In some institutions all Internet connections are going through a Web proxy (see WIKI:Proxy_server). If the proxy is not set correctly, STRAP is unable to download files from the Web. The proxy cannot be set in the running application. The way how the proxy is set depends on whether the application is started via WIKI:Webstart (See WIKI:JNLP) or started directly.

Webstart

In Windows or Linux there is a program called Java control panel which allows to set the proxy (Button "Network settings"): STRING:charite.christo.ChUtils#fileJcontrol() located in STRING:ChUtils#dirJavaws(). Under Macintosh, however, the system wide proxy setting is also used in Java.

Direct start without Webstart

The proxy is specified with command line arguments. Example:
java -Dhttp.proxyHost=realproxy.charite.de -Dhttp.proxyPort=888   ...
If there are addresses that should bypass the proxy use vertical bar separated list of hosts as in the following example:
 ....  -Dhttp.nonProxyHosts="localhost|host.mydomain.com" ...

Testing the Proxy settings

Use the item BUTTON:charite.christo.ChUtils#buttn(BUT_TEST_PROXY)! In the menu "Preferences" is. Further reading http://java.sun.com/javase/6/docs/technotes/guides/net/proxies.html


Field Summary
static java.util.Map<java.lang.String,java.lang.String> MAP_VIA_PORT_MSG
           
static long SHOW_EXCEPTION
           
 
Fields inherited from interface charite.christo.ChRunnable
APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT
 
Method Summary
static void autoProbeProxy()
           
static void checkForNewVersion(java.lang.String title)
           
static BA getServerResponse(long options, java.lang.String url, java.lang.Object[][] variables)
           
static java.io.InputStream getServerResponseAsStream(long options, java.lang.String url, BA httpData)
           
static java.io.InputStream getServerResponseAsStream(long options, java.lang.String url, java.lang.Object[][] data)
           
static void insertBaseTag(java.net.URL url, java.io.File fDest, BA html)
           
static boolean localhost_sendData(java.lang.String url, BA log)
           
static java.net.Socket newSocket(java.lang.String host)
           
static javax.swing.JComponent pnlProxyInfo()
           
static int proxyPort(java.lang.Object text, int from0, int to0)
           
 java.lang.Object run(java.lang.String id, java.lang.Object arg)
           
static void runAfterProbeProxy(long options, java.lang.Runnable r, int maxWaitMS)
           
static boolean sendDataToPort(long options, int port, java.lang.CharSequence data, java.lang.String wordUnderMouse)
           
static void showProxyInfo()
           
static void startJnlp(java.net.URL url, ChTextReplacement rplc)
           
static ChTextView tfAutoprobeProxy()
           
static java.lang.Thread thread_autoProbeProxy()
           
static java.lang.Thread thread_sendDataToPort(long options, int port, java.lang.CharSequence data, java.lang.String wordUnderMouse)
           
static java.lang.Thread thread_startJnlp(java.net.URL url, ChTextReplacement rplc)
           
static boolean uploadPermission(long frameOpts, BA httpData, java.lang.String url)
           
static java.net.URL[] urls(java.lang.Object urlBase, java.lang.String files)
           
static java.net.URL[] urls(java.lang.Object urlBase, java.lang.String[] tokens)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

SHOW_EXCEPTION

public static final long SHOW_EXCEPTION
See Also:
Constant Field Values

MAP_VIA_PORT_MSG

public static final java.util.Map<java.lang.String,java.lang.String> MAP_VIA_PORT_MSG
Method Detail

getServerResponse

public static BA getServerResponse(long options,
                                   java.lang.String url,
                                   java.lang.Object[][] variables)

getServerResponseAsStream

public static java.io.InputStream getServerResponseAsStream(long options,
                                                            java.lang.String url,
                                                            java.lang.Object[][] data)

uploadPermission

public static boolean uploadPermission(long frameOpts,
                                       BA httpData,
                                       java.lang.String url)

getServerResponseAsStream

public static java.io.InputStream getServerResponseAsStream(long options,
                                                            java.lang.String url,
                                                            BA httpData)

thread_sendDataToPort

public static java.lang.Thread thread_sendDataToPort(long options,
                                                     int port,
                                                     java.lang.CharSequence data,
                                                     java.lang.String wordUnderMouse)

sendDataToPort

public static boolean sendDataToPort(long options,
                                     int port,
                                     java.lang.CharSequence data,
                                     java.lang.String wordUnderMouse)

localhost_sendData

public static boolean localhost_sendData(java.lang.String url,
                                         BA log)

urls

public static java.net.URL[] urls(java.lang.Object urlBase,
                                  java.lang.String files)

urls

public static java.net.URL[] urls(java.lang.Object urlBase,
                                  java.lang.String[] tokens)

insertBaseTag

public static void insertBaseTag(java.net.URL url,
                                 java.io.File fDest,
                                 BA html)

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)
Specified by:
run in interface ChRunnable

checkForNewVersion

public static void checkForNewVersion(java.lang.String title)

proxyPort

public static int proxyPort(java.lang.Object text,
                            int from0,
                            int to0)

thread_startJnlp

public static java.lang.Thread thread_startJnlp(java.net.URL url,
                                                ChTextReplacement rplc)

tfAutoprobeProxy

public static final ChTextView tfAutoprobeProxy()

thread_autoProbeProxy

public static final java.lang.Thread thread_autoProbeProxy()

runAfterProbeProxy

public static void runAfterProbeProxy(long options,
                                      java.lang.Runnable r,
                                      int maxWaitMS)

autoProbeProxy

public static final void autoProbeProxy()

showProxyInfo

public static void showProxyInfo()

pnlProxyInfo

public static javax.swing.JComponent pnlProxyInfo()

startJnlp

public static void startJnlp(java.net.URL url,
                             ChTextReplacement rplc)
                      throws java.io.IOException
Throws:
java.io.IOException

newSocket

public static java.net.Socket newSocket(java.lang.String host)
                                 throws java.io.IOException
Throws:
java.io.IOException

'STRAP:multiple sequence alignments '

'The most important classes are StrapAlign, Protein and StrapEvent.'