jembossparams.java

emboss的linux版本的源代码

  }

/**
*
* Initialize the server redundancy data. This is a separate
* method because the server info might not be initialized in
* the constructor, but may be imported later from the command line.
*
*/
  protected void setupServerRedundancy() 
  {
    if (!serverPublicList.equals("")) 
    {
      if(debug) 
	System.out.println("JembossParams: Redundant public servers\n  "
			   +serverPublicList);
  
      publicServerFailOver = true;
      StringTokenizer tok = new StringTokenizer(serverPublicList,"|");
      while (tok.hasMoreTokens()) 
      {
	String toks = tok.nextToken();
	publicServers.add(toks);
	if(debug) 
	  System.out.println(" Entry " + toks);
	
	serverStatusHash.put(toks, new Integer(SERVER_OK));
      }
    }

    if(!serverPrivateList.equals("")) 
    {
      if(debug) 
	System.out.println("JembossParams: Redundant private servers\n  "
			   +serverPrivateList);
      
      privateServerFailOver = true;
      StringTokenizer tok = new StringTokenizer(serverPrivateList,"|");
      while (tok.hasMoreTokens()) 
      {
	String toks = tok.nextToken();
	privateServers.add(toks);
	if(debug) 
	  System.out.println(" Entry " + toks);
	
	serverStatusHash.put(toks,new Integer(SERVER_OK));
      }
    }
  }


/**
*
* If using a proxy server
*
*/
  public boolean getUseProxy() 
  {
    return useProxy;
  }


/**
*
* If using an https proxy server
*
*/
  public boolean getUseHTTPSProxy()
  {
    return useHTTPSProxy;
  }


/**
*
* If using a proxy server for a given URL
* @param s 	the URL we wish to connect to
*
*/
  public boolean getUseProxy(String s) 
  {
    if(proxyOverride) 
      return useProxy;
    else 
    {
      if(!useJavaProxy) 
	return useProxy;
      else 
      {
	boolean jp = true;
	if (useJavaNoProxy) 
        {
	  int ip = javaNoProxyEntries.size();
	  for(int j = 0 ; j<ip ; ++j) 
	    if(s.indexOf((String)javaNoProxyEntries.get(j).toString()) != -1) 
	      jp = false;
	}
	return jp;
      }
    }
  }

/**
*
* The name of the proxy server
* @return 	name of the proxy host
*
*/
  public String getProxyHost() 
  {
    if (proxyOverride) 
      return proxyHost;
    else 
    {
      if(!useJavaProxy) 
	return proxyHost;
      else 
	return javaProxyHost;
    }
  }

/**
*
* The port the proxy server listens on
* @return 	proxy port number
*
*/
  public int getProxyPortNum() 
  {
    if(proxyOverride) 
      return proxyPortNum;
    else
    { 
      if(!useJavaProxy) 
	return proxyPortNum;
      else
	return javaProxyPortNum;
    }
  }

/**
*
* Determine if the a proxy server is being used for web browsing
* @return 	true if using a proxy server for the browser
*
*/
  public boolean isBrowserProxy()
  {
    return useBrowserProxy;
  }

/**
*
* Get the name of the proxy server for the browser
* @return 	the name of the proxy host
*
*/
  public String getBrowserProxyHost()
  {
    return browserProxyHost;
  }


/**
*
* The port number of the proxy server for the browser
* @return 	proxy port number 
*
*/
  public int getBrowserProxyPort()
  {
    return browserProxyPort;
  }


  public boolean isUseTFM() { return useTFM; }
  

/**
*
* If using authenticate with the proxy 
* @return	true if unix authentication used
*
*/
  public boolean getUseProxyAuth() 
  {
    return useProxyAuth;
  }

/**
*
* Username needed to use for the proxy server
*
*/
  public String getProxyAuthUser() 
  {
    return proxyAuthUser;
  }

/**
*
* Password needed to use for the proxy server
*
*/
  public String getProxyAuthPasswd() 
  {
    return proxyAuthPasswd;
  }

/**
*
* A description of the proxy settings
* @return 	a description of the proxy settings
*
*/
  public String proxyDescription() 
  {
    String pdesc = "";
    if (proxyOverride) 
    {
      if(useProxy)
      {
	String spnum = new Integer(proxyPortNum).toString();
	pdesc = "Current Settings: " + "Proxy Host: " + proxyHost + 
                                           " Proxy Port: " + spnum;
      } 
      else 
	pdesc = "No proxies, connecting direct.";
    } 
    else 
    {
      if (useJavaProxy) 
      {
	pdesc = "Settings Imported from Java: " + "Proxy Host: " + javaProxyHost
	                                      + " Proxy Port: " + javaProxyPort;
	if(useJavaNoProxy) 
	  pdesc = pdesc + "\nNo Proxy On: " + javaNoProxy;
      } 
      else
      {
	if(useProxy) 
        {
	  String spnum = new Integer(proxyPortNum).toString();
	  pdesc = "Current Settings: " + "Proxy Host: " + proxyHost + 
                                             " Proxy Port: " + spnum;
	} 
        else 
	  pdesc = "No proxies, connecting direct.";
      }
    }
    return pdesc;
  }

/**
*
* Whether the main service requires authentication
* @return 	true if the server is using unix authentication
*
*/
  public boolean getUseAuth() 
  {
    return useAuth;
  }

/**
*
* Returns the URL of the public soap server
* @return 	the public services URL
*
*/
  public String getPublicSoapURL() 
  {
    return publicSoapURL;
  }

/**
*
*  @return   	true if using a Jemboss server
*
*/
  public static boolean isJembossServer()
  {
    return jembossServer;
  }

/**
*
*  @return      true if using cygwin
*
*/
  public static boolean isCygwin()
  {
    if(cygwin == null || cygwin.equals(""))
      return false;
    else
      return true;
  }


/**
*
*  Get the cygwin root 
*  @return      cygwin root
*
*/
  public static String getCygwinRoot()
  {
    return cygwin;
  }



/**
*
* Get the location of plplot
* @return 	the location of plplot 
*
*/
  public String getPlplot()
  {
    return plplot;
  }

/**
*
* Get the user home directory
* @return	the user home directory
*
*/
  public String getUserHome()
  {
    return userHome;
  }

/**
*
* Set the user home directory property
* @param s	the user home directory
*
*/
  public void setUserHome(String s)
  {
    userHome = s;
  }


/**
*
* Get the standalone results directory
* @return       the results directory
*
*/
  public String getResultsHome()
  {
    String fs = System.getProperty("file.separator");

    if(!resultsHome.endsWith(fs))
      resultsHome = resultsHome + fs;
    return resultsHome;
  }

/**
*
* Set the standalone results directoryproperty
* @param s      the results directory
*
*/
  public void setResultsHome(String s)
  {
    resultsHome = s;
  }


/**
*
* @return 	the documentation URL 
*
*/
  public String getembURL()
  {
    return embURL;
  }

/**
*
* @return	the location of the emboss data
*
*/
  public String getEmbossData()
  {
    return embossData;
  }
  
/**
*
* @return	the location of the emboss binaries
*
*/
  public String getEmbossBin()
  {
    return embossBin;
  }

/**
*
* Get the path for emboss
* @return	the path for emboss
*
*/
  public String getEmbossPath()
  {
    return embossPath;
  }

/**
*
* Get the environment for emboss
* @return	the environment for emboss
*
*/
  public String getEmbossEnvironment()
  {
    embossEnvironment = embossEnvironment.trim();
    embossEnvironment = embossEnvironment.replace(':',' ');
    embossEnvironment = embossEnvironment.replace(',',' ');
    return embossEnvironment;
  }

/**
*
* Get the emboss environment as a String array
* @return 	the emboss environment as a String array
*
*/
  public String[] getEmbossEnvironmentArray(String[] envp)
  {
    embossEnvironment = embossEnvironment.trim();
    embossEnvironment = embossEnvironment.replace(',',' ');

    if(embossEnvironment.equals(""))
      return envp;

    StringTokenizer st = new StringTokenizer(embossEnvironment," ");