buildjembossform.java

emboss的linux版本的源代码

  public void actionPerformed(ActionEvent ae)
  {

    String line;

    if( ae.getActionCommand().startsWith("Advanced Option"))
    {
      if(advSectionBox != null)
        advSectionBox.setVisible(!advSectionBox.isVisible());
      if(addSectionBox != null)
        addSectionBox.setVisible(!addSectionBox.isVisible());

      p2.setVisible(false);
      p2.setVisible(true);
    }
    else if ( ae.getActionCommand().startsWith("GO"))
    {
      f.setCursor(cbusy);
      if(!withSoap)
      {
        Hashtable filesToMove = new Hashtable();
        String embossCommand = getCommand(filesToMove);

//      String embossCommand = getCommand();

        if(!embossCommand.equals("NOT OK"))
        {
          if(mysettings.getCurrentMode().equals("batch"))
          {
            BatchSoapProcess bsp = new BatchSoapProcess(embossCommand,filesToMove,mysettings);
            bsp.setWithSoap(false);
            bsp.start();
          }
          else
          {
            JembossServer js = new JembossServer(mysettings.getResultsHome());
            Vector result = js.run_prog(embossCommand, mysettings.getCurrentMode(), 
                                        filesToMove);
            new ShowResultSet(convert(result,false),filesToMove,mysettings);
          }
        }
      }
      else
      {
        Hashtable filesToMove = new Hashtable();
        String embossCommand = getCommand(filesToMove);

        if(!embossCommand.equals("NOT OK"))
        {
          if (mysettings.getUseAuth() == true)
            if (mysettings.getServiceUserName() == null)
              System.out.println("OOPS! Authentication required!");

          try
          {
            if(mysettings.getCurrentMode().equals("batch"))
            {
              BatchSoapProcess bsp = new BatchSoapProcess(embossCommand,filesToMove,mysettings);
              bsp.start();
            }
            else
            {
              JembossRun thisrun = new JembossRun(embossCommand,"",
                                           filesToMove,mysettings);
              new ShowResultSet(thisrun.hash(),filesToMove,mysettings);
            }
          }
          catch (JembossSoapException eae)
          {
            AuthPopup ap = new AuthPopup(mysettings,f);
            ap.setBottomPanel();
            ap.setSize(380,170);
            ap.pack();
            ap.setVisible(true);
            f.setCursor(cdone);
          }
        }
      }
      f.setCursor(cdone);
    }
    else if( ae.getActionCommand().startsWith("Show Alignment"))
    {
       org.emboss.jemboss.editor.AlignJFrame ajFrame =
               new org.emboss.jemboss.editor.AlignJFrame(new File(seqoutResult));
       ajFrame.setVisible(true);
    }
  }

  public static Hashtable convert(Vector vans, boolean keepStatus)
  {
    Hashtable proganswer = new Hashtable();
    // assumes it's even sized
    int n = vans.size();
    for(int j=0;j<n;j+=2)
    {
      String s = (String)vans.get(j);
      if(s.equals("msg"))
      {
        String msg = (String)vans.get(j+1);
        if(msg.startsWith("Error"))
          JOptionPane.showMessageDialog(null, msg, "alert",
                                JOptionPane.ERROR_MESSAGE);
      }
      else if(keepStatus || !s.equals("status"))
        proganswer.put(s,vans.get(j+1));
    }
    return proganswer;
  }

  /**
  *
  * Show standalone results in a tabbed pane.
  *
  */
  private void showStandaloneResults(String stdout)
  {
    final JFrame res = new JFrame(applName + " Results  : " + seqoutResult);
    res.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
    final JTabbedPane fresults = new JTabbedPane();
    res.getContentPane().add(fresults,BorderLayout.CENTER);
    Hashtable hashRes = new Hashtable();

    Dimension d = res.getToolkit().getScreenSize();
    res.setSize((int)d.getWidth()/2,(int)d.getHeight()/2);

    JPanel presults;
    ScrollPanel pscroll;
    JScrollPane rscroll;

    if(!stdout.equals("") &&
       !(stdout.startsWith("Created") && (stdout.endsWith(".png") || stdout.endsWith(".dat")) ))
    {
      presults = new JPanel(new BorderLayout());
      pscroll = new ScrollPanel(new BorderLayout());
      rscroll = new JScrollPane(pscroll);
      rscroll.getViewport().setBackground(Color.white);
      presults.add(rscroll, BorderLayout.CENTER);
      JTextPane atext = new JTextPane();
      atext.setText(stdout);
      atext.setFont(new Font("monospaced", Font.PLAIN, 12));
      pscroll.add(atext, BorderLayout.CENTER);
      atext.setCaretPosition(0);
      fresults.add(applName+" output",presults);
      hashRes.put(applName+" output",stdout);
    }

    boolean seenGraphs = false;
    for(int j=0;j<numofFields;j++)
    {
      presults = new JPanel(new BorderLayout());
      pscroll = new ScrollPanel(new BorderLayout());
      rscroll = new JScrollPane(pscroll);
      rscroll.getViewport().setBackground(Color.white);
      presults.add(rscroll, BorderLayout.CENTER);

      if(parseAcd.isOutputSequence(j) || parseAcd.isOutputFile(j))
      {
        try
        {
          String name = null;
          if(parseAcd.isOutputSequence(j))
            name = seqoutResult;
          else
            name = outfileResult;

          StringBuffer text = new StringBuffer();
          BufferedReader in = new BufferedReader(new FileReader(name));

          String line = null;
          while((line = in.readLine()) != null)
            text = text.append(line + "\n");

          in.close();

          String txt = text.toString();
          JTextPane seqText = new JTextPane();
          seqText.setText(txt);
          seqText.setFont(new Font("monospaced", Font.PLAIN, 12));
          pscroll.add(seqText, BorderLayout.CENTER);
          seqText.setCaretPosition(0);
          fresults.add(name,presults);
          hashRes.put(name,txt);
        }
        catch (IOException ioe)
        {
          if(mysettings.getDebug())
            System.out.println("Failed to open sequence file " + seqoutResult);
        }
      }
      else if(parseAcd.isOutputGraph(j) && !seenGraphs)
      {
        seenGraphs = true;
        File cwdFile = new File(cwd);
        String pngFiles[] = cwdFile.list(new FilenameFilter()
        {
          public boolean accept(File cwd, String name)
          {
            if(name.endsWith(".png") || name.endsWith(".dat"))
              return name.startsWith(applName);
            else
              return false;
          };
        });

        Arrays.sort(pngFiles, new NameComparator());
        for(int i=0;i<pngFiles.length;i++)
        {
          if(pngFiles[i].endsWith(".dat"))
          {
            Graph2DPlot gp = new Graph2DPlot();
            rscroll = new JScrollPane(gp);
            rscroll.getViewport().setBackground(Color.white);
         
            gp.setFileData(new String((byte [])getLocalFile(new File(pngFiles[i]))),
                           pngFiles[i]);
            fresults.add(pngFiles[i],rscroll);
//          setJMenuBar(gp.getMenuBar(false, this));
          }
          else
          {
            presults = new JPanel(new BorderLayout());
            pscroll  = new ScrollPanel(new BorderLayout());
            rscroll  = new JScrollPane(pscroll);
            rscroll.getViewport().setBackground(Color.white);
            presults.add(rscroll, BorderLayout.CENTER);
            byte pngContents[] = getLocalFile(new File(pngFiles[i]));
            ImageIcon icon = new ImageIcon(pngContents);
            JLabel picture = new JLabel(icon);
            pscroll.add(picture);
            fresults.add(pngFiles[i],presults);
            hashRes.put(pngFiles[i],pngContents);
          }
        }
      }
    }

    final ResultsMenuBar menubar = new ResultsMenuBar(res,fresults,hashRes,mysettings); 
    fresults.addChangeListener(new ChangeListener()
    {
      public void stateChanged(ChangeEvent e)
      {
        setJMenuBar(fresults,res,menubar);
      }
    });

    setJMenuBar(fresults,res,menubar);
    res.setVisible(true);
  }

  /**
  *
  * Set the menu bar based on the title of the
  * tabbed pane
  *
  */
  private void setJMenuBar(JTabbedPane fresults, JFrame res, ResultsMenuBar menuBar)
  {
    int index = fresults.getSelectedIndex();
    String title = fresults.getTitleAt(index);
    
    if(title.endsWith(".dat"))
    {
      Graph2DPlot graph = getGraph2DPlot((JScrollPane)fresults.getSelectedComponent());
      if(graph == null)
        return;

      JMenuBar graphMenuBar = graph.getMenuBar(false, res);
      res.setJMenuBar(graphMenuBar);
    }
    else
      res.setJMenuBar(menuBar);
  }

  /**
  *
  * Locate the Graph2DPlot component in the scrollpane
  *
  */
  private Graph2DPlot getGraph2DPlot(JScrollPane jsp)
  {
    Component comp = jsp.getViewport().getView();
    if(comp instanceof Graph2DPlot)
        return (Graph2DPlot)comp;
  
    return null;
  }


  private String checkParameters(ParseAcd parseAcd, int numofFields, 
                                 Hashtable filesToMove)
  {

    String params = new String("");
    String appN = "";
    String file = "";
    String options = "";
    String fn = "";
    String sfn;
 
    seqoutResult   = "";
    outfileResult  = "";
   
    for(int j=0;j<numofFields;j++)
    {
      String att = parseAcd.getParameterAttribute(j,0).toLowerCase();
      String val = parseAcd.getParamValueStr(j,0).toLowerCase();
      int h = parseAcd.getGuiHandleNumber(j);

      if(att.startsWith("appl"))
        appN = new String(att);
      else if (parseAcd.isOutputGraph(j))
      {
        if(graphics == null)
          System.out.println("graphics is NULL");

        if(((String)graphics.getSelectedItem()).equals("PNG") ) 
          options = options.concat(" -" + val + " png");
        else
          options = options.concat(" -" + val + " data");
      }
      if ( att.startsWith("dirlist") || att.startsWith("featout") ||
           att.startsWith("string")  || att.startsWith("seqout")  ||
           att.startsWith("outfile") || att.startsWith("codon")   ||
           att.startsWith("regexp")  )
      {
        if(!(textf[h].getText()).equals("") && textf[h].isVisible()
                                            && textf[h].isEnabled()) 
        {
          options = options.concat(" -" + val + " " + textf[h].getText());

          if(att.startsWith("seqout"))
            seqoutResult = textf[h].getText();
          else if(att.startsWith("outfile"))
            outfileResult = textf[h].getText();;
        }
        else if(!withSoap && applName.equals("emma") && att.startsWith("seqoutset"))
        {
          options = options.concat(" -" + val + " emma.aln "); 
          seqoutResult = "emma.aln";
        }

        if(att.startsWith("seqout"))
          options = options.concat(outSeqAttr.getOuputSeqAttr());

      }
      else if ( att.startsWith("pattern") )
      {
        JTextField textFields[] = multiTextField[h].getJTextField();
        
        if(textFields[0].getText() != null && !textFields[0].getText().trim().equals(""))
          options = options.concat(" -" + val + " " + textFields[0].getText());
        
        if(textFields[1].getText() != null && !textFields[1].getText().trim().equals(""))
          options = options.concat(" -pmismatch " + textFields[1].getText());
      }
      else if ( att.startsWith("int") )
      {
        if( (textInt[h].getText() != null) && textInt[h].isVisible()
                                           && textInt[h].isEnabled())
          options = options.concat(" -" + val + " " + textInt[h].getValue());
      }
      else if ( att.startsWith("float") )
      {
        if( (textFloat[h].getText() != null) && textFloat[h].isVisible()
                                             && textFloat[h].isEnabled())
          options = options.concat(" -" + val + " " + textFloat[h].getValue());
      }
      else if ( att.startsWith("select") )   
      {
        double max = 1.;
        if(parseAcd.isMaxParamValue(j))
          max = Double.parseDouble(parseAcd.getMaxParam(j));
                                                            //defined by a number
        if(max > 1.0 && multiOption[h].isVisible()
                     && multiOption[h].isEnabled())         //multi selection
        {
          int sel[] = multiOption[h].getSelectedIndices();
          options = options.concat(" -" + val + " ");
          for(int i=0;i<sel.length;i++)
          {
            options = options.concat(Integer.toString(sel[i]+1));
            if(i<sel.length-1)
              options = options.concat(",");
          }
        }
        else if (fieldOption[h].isVisible() && fieldOption[h].isEnabled())
          options = options.concat(" -" + val + " " +        //single selection
                    (fieldOption[h].getSelectedIndex()+1));
      }
      else if ( att.startsWith("list") )    
      {
        double max = 1.;
        if(parseAcd.isMaxParamValue(j))
          max = Double.parseDouble(parseAcd.getMaxParam(j));
                                                             //defined by a label
        if(max > 1.0 && multiOption[h].isVisible()
                     && multiOption[h].isEnabled())          //multi selection
        {
          int sel[] = multiOption[h].getSelectedIndices();
          options = options.concat(" -" + val + " ");
          for(int i=0;i<sel.length;i++)
          {
            options = options.concat(parseAcd.getListLabel(j,sel[i]));
            if(i<sel.length-1)
              options = options.concat(",");
          }
        }
        else if (fieldOption[h].isVisible() 
              && fieldOption[h].isEnabled())
        {
          int index = fieldOption[h].getSelectedIndex();     //single selection
          options = options.concat(" -" + val + " " +
                       parseAcd.getListLabel(j,index));
        }
      }
      else if ( att.startsWith("report") )
      {
        options = options.concat(rf.getReportFormat());
      }
      else if ( att.startsWith("align") )
      {
        options = options.concat(af.getAlignFormat());
      }
      else if ( att.startsWith("bool") && checkBox[h].isVisible()
                                       && checkBox[h].isEnabled())
      {
        if( checkBox[h].isSelected() )
          options = options.concat(" -" + val + " ");
        else
          options = options.concat(" -no" + val + " ");

      }
      else if( att.startsWith("range") && rangeField[h].isVisible()
                                       && rangeField[h].isEnabled() )
      {
        if( !rangeField[h].getText().equals("") )
        {
          String rangeText = rangeField[h].getText();
          int blank;
   
          //remove spaces from the range (not sure if this is 
          //a good idea in all cases)!
          while ((blank = rangeText.indexOf(" ")) > -1)
          {
            String rangePrefix = rangeText.substring(0,blank);