buildjembossform.java

emboss的linux版本的源代码

            String rangeSuffix = rangeText.substring(blank+1,rangeText.length());
            rangeText = rangePrefix.concat(rangeSuffix);
          }
          options = options.concat(" -" + val + " " + 
                         rangeText + " ");
        } 
      }
      else if ( att.startsWith("infile") || att.startsWith("datafile") ||
                att.startsWith("matrix") )
      {
        if(!(textf[h].getText()).equals("") && textf[h].isVisible()
                                            && textf[h].isEnabled())
        {
          if(withSoap)
            options = filesForSoap(textf[h].getText(),options,val,filesToMove);
          else
            options = options.concat(" -" + val + " " +  textf[h].getText());
        }

      }
      else if ( att.startsWith("filelist") )
      {
        if(withSoap)
        {
          String fns = filelist[h].getListFile();
          String ls = System.getProperty("line.separator");
          options = filesForSoap("internalList::internalList"+ls+
                                 fns,options,val,filesToMove);
        }
        else
        {
          String fl[] = filelist[h].getArrayListFile();
          String flist = fl[0];
          for(int i=1;i<fl.length;i++)
            flist = flist.concat(","+fl[i]);
          options = options.concat(" -" + val + " " + flist);
        }
      }
      else if ( att.startsWith("seqset") || att.startsWith("seqall") ||
                att.startsWith("sequence") )
      {
        int seq = h+1;
        if(inSeq[h].isFileName())                     // file or database
        {
          fn = new String(inSeq[h].getFileChosen());
          
          fn = fn.trim();
          if((fn.indexOf(":")>-1) && (fn.indexOf(":\\") < 0))  //remove spaces
          {                                                    //from db entries
            int n;
            while((n = fn.indexOf(" ")) > -1)
              fn = new String(fn.substring(0,n) + fn.substring(n+1));
          }

          if(withSoap)
            options = filesForSoap(fn,options,val,filesToMove);
          else
            options = options.concat(" -" + val + " " +  fn);

          if(fn.endsWith(":") || fn.endsWith(":*"))
          {
             String ls = PlafMacros.getLineSeparator();
             int n = JOptionPane.showConfirmDialog(f,
                       "Do you really want to extract"+ls+
                       "the whole of " + fn + " database?",
                       "Confirm the sequence entry",
                       JOptionPane.YES_NO_OPTION);
             if(n == JOptionPane.NO_OPTION)
             {
               options = "NOT OK";
               break;
             }
          }

        }
        else if(inSeq[h].isListFile())                     // list file
        {
          String fns = inSeq[h].getListFile();
          String ls = System.getProperty("line.separator");
          if(withSoap)
          {
            options = filesForSoap("internalList::internalList"+ls+
                                   fns,options,val,filesToMove);
          }
          else
          { 
            String fna = System.getProperty("user.dir")+
                         System.getProperty("file.separator")+"seq.list";

            boolean ok = inSeq[h].writeListFile(fna);
            options = options.concat(" -" + val + " list::" +  fna);
          }
        } 
        else                                               // cut 'n paste
        {
          String cp = inSeq[h].getCutNPasteText();
          fn = new String(applName + (new Integer(h)).toString());

          if(withSoap)
          {
            MakeFileSafe sf = new MakeFileSafe(fn);
            sfn = sf.getSafeFileName();
            filesToMove.put(sfn,cp.getBytes());
            options = options.concat(" -" + val + " " + sfn);

          }
          else
          {
            String tmp = null;
            try
            {
              File tf;
              try
              {
                if(mysettings.isCygwin())
                  tmp = mysettings.getCygwinRoot()+System.getProperty("file.separator")+"tmp";
                else
                  tmp = System.getProperty("java.io.tmpdir");

                tf = File.createTempFile(fn, ".jembosstmp", new File(tmp));
              }
              catch(IOException ioe)
              {
                tf = File.createTempFile(fn, ".jembosstmp",
                                            new File(cwd));
              }

              PrintWriter out = new PrintWriter(new FileWriter(tf));
              out.println(cp);
              out.close();
              fn = tf.getCanonicalPath();
            }
            catch (IOException ioe) 
            {
              JOptionPane.showMessageDialog(null,
                       "Cannot write to\n"+
                       tmp+"\n"+
                       "or\n"+
                       cwd,
                       "Problem creating a temporary file!", JOptionPane.ERROR_MESSAGE);
            }
            options = options.concat(" -" + val + " " + fn );
          }
        }

        options = options.concat(inSeqAttr[h].getInputSeqAttr(seq));

      } 
    }

    return options;
  }


  private String filesForSoap(String fn, String options, String val,
                             Hashtable filesToMove)
  {

    String sfn;

    if (fn.startsWith("@")||fn.startsWith("list::")||
        fn.startsWith("internalList::"))        // list file
    {
      String lfn = "";
      if (fn.startsWith("@"))
        lfn = fn.substring(1);
      else if(fn.startsWith("list::"))
        lfn = fn.substring(6);

      File inFile = new File(lfn);  
      if( (inFile.exists() && inFile.canRead() && 
           inFile.isFile())||
           fn.startsWith("internalList::") )    // local list file 
      {
        ListFile.parse(fn, filesToMove);
        if(fn.startsWith("internalList::"))
          options = options.concat(" -" + val + " list::internalList");
        else
        {
          MakeFileSafe sf = new MakeFileSafe(lfn);
          String sfs = sf.getSafeFileName();
          options = options.concat(" -" + val + " list::" +  sfs);
        }
      }
      else                                      // presume remote
      {
//      System.out.println("Can't find list file "+lfn);
        options = options.concat(" -" + val + " list::" +  lfn);
      }
      
      sfn=lfn;
    }
    else                                        // not list file
    {                                  
      MakeFileSafe sf = new MakeFileSafe(fn);
      sfn = sf.getSafeFileName();

      File inFile = new File(fn);
      if(inFile.exists() && inFile.canRead() 
                         && inFile.isFile())    // read & add to transfer list
      {
        filesToMove.put(sfn,getLocalFile(inFile));
        options = options.concat(" -" + val + " " +  sfn);
      }
      else     //presume remote
      {
//      System.out.println("Can't find plain file "+fn);
        options = options.concat(" -" + val + " " +  fn);
      }
    }

    return options;
  }


  private byte[] getLocalFile(File name)
  {
    byte[] b = null;
    try
    {
      long s = name.length();
      b = new byte[(int)s];
      FileInputStream fi = new FileInputStream(name);
      fi.read(b);
      fi.close();
    }
    catch (IOException ioe)
    {
      System.out.println("Cannot read file: " + name);
    }
    return b;
  }


/**
*
* Get the command line for the Standalone version.
* @param Hashtable of the files to be transferrred
* @return String command line to use
*
*/
/*  private String getCommand()
  {

    String command = embossBin.concat(applName);
    int numofFields = parseAcd.getNumofFields();

    String options = checkParameters(parseAcd, numofFields, new Hashtable());
         
    if(options.equals("NOT OK"))
      command = "NOT OK";
    else
      command = command.concat(options + " -stdout -auto");

    return command;
  }*/


/**
*
* Get the command line for the SOAP version.
* @param Hashtable of the files to be transferrred
* @return String command line to use
*
*/
  private String getCommand(Hashtable filesToMove)
  {

    String command = applName;
    int numofFields = parseAcd.getNumofFields();

    String options = checkParameters(parseAcd, numofFields, filesToMove);

    if(options.equals("NOT OK"))
      command = "NOT OK";
    else
      command = command.concat(options + " -auto");

    return command;
  }


/**
*
* Ensures garbaged collected when there are
* no more pointers to this.
* 
*/
  public void finalize() throws Throwable
  {
    super.finalize();
  }


  public class BatchSoapProcess extends Thread
  {
    private String embossCommand;
    private Hashtable filesToMove;
    private JembossParams mysettings;
    private boolean withSoap = true;

    public BatchSoapProcess(String embossCommand, Hashtable filesToMove,
                            JembossParams mysettings)
    {
      this.embossCommand = embossCommand;
      this.filesToMove   = filesToMove;
      this.mysettings    = mysettings;
    }

    public void setWithSoap(boolean withSoap)
    {
      this.withSoap = withSoap;
    }

    public void run()
    {
      try
      {
        JFrame fsend = new JFrame("Batch");
        final int max = 20;
        final JProgressBar progressBar = new JProgressBar(0,max);
        progressBar.setStringPainted(true);
        progressBar.setString("Sending batch process now!");
        progressBar.setBackground(Color.white);

        SwingWorker batchWorker = new SwingWorker()
        {
          public Object construct()
          {
            try
            {
              for(int i=0; i<max; i++)
              {
                sleep(500);
                progressBar.setValue(i);
              }
            }
            catch(InterruptedException intr){}
            return null;
          }
        };

        fsend.getContentPane().add(progressBar);
        fsend.pack();
        Dimension d = f.getToolkit().getScreenSize();
        fsend.setLocation( (int)(d.getWidth()-fsend.getWidth())/2,
                           (int)(d.getHeight()-fsend.getHeight())/2 );
        fsend.setVisible(true);
        batchWorker.start();

        final JembossProcess er;
        if(withSoap)
        {
          JembossRun thisrun = new JembossRun(embossCommand,"",
                                       filesToMove,mysettings);
          er = new JembossProcess((String)thisrun.get("jobid"));
        }
        else
        {
          JembossServer js = new JembossServer(mysettings.getResultsHome());
          Vector result = js.run_prog(embossCommand,mysettings.getCurrentMode(),
                                        filesToMove);
          Hashtable resultHash = convert(result, false);
          er = new JembossProcess((String)resultHash.get("jobid"));
        }

        Jemboss.resultsManager.addResult(er);
        Jemboss.resultsManager.updateStatus();
        if(!Jemboss.resultsManager.isAutoUpdate())
        {
          Jemboss.resultsManager.setAutoUpdate(true);
          String freq = (String)AdvancedOptions.jobMgr.getSelectedItem();
          int ind = freq.indexOf(" ");
          new BatchUpdateTimer(Integer.parseInt(freq.substring(0,ind)));
        }

        fsend.setVisible(false);
        fsend.dispose();
      }
      catch (JembossSoapException eae)
      {
        AuthPopup ap = new AuthPopup(mysettings,f);
        ap.setBottomPanel();
        ap.setSize(380,170);
        ap.pack();
        ap.setVisible(true);
        f.setCursor(cdone);
      }

    }
  }


  public class NameComparator implements Comparator
  {
    public int compare(Object o1, Object o2) 
    {
      int obj1 = findInt((String)o1);
      int obj2 = findInt((String)o2);     
      if(obj1 < obj2)
        return -1;
      else if(obj1 > obj2)
        return 1;
      return 0;
    }
    
    public boolean equals(Object obj)
    {
      return ((Object)this).equals(obj);
    } 

    /**
    *
    * Find the number in a string expression
    * @param exp  string expression
    * @return     number in a string expression or -1 
    *             if none found
    *
    */
    private int findInt(String exp)
    {

      RECompiler rec = new RECompiler();
      try
      {
        REProgram  rep = rec.compile("^(.*?)([:digit:]+)");
        RE regexp = new RE(rep);
        if(regexp.match(exp))
        {
          int ia = (new Integer(regexp.getParen(2))).intValue();
          return ia;
        }
      }
      catch (RESyntaxException rese)
      {
        System.out.println("RESyntaxException ");
      }
      return -1;
    }

  }

}