sectionpanel.java

emboss的linux版本的源代码

          lab[nf].add(bxlab);
          pan.add(textf[h]);
          pan.add(lab[nf]);
        }
        else if(att.startsWith("seqset")) 
        {
          inSeq[h] = new SetInFileCard(sectionPane,h,db,
                              "Multiple Sequence Filename",
                              appName,inSeqAttr,true,mysettings);
          pan.add(inSeq[h]);
        }
        else if(att.startsWith("sequence") || att.startsWith("seqall"))
        {
          String tit = parseAcd.getInfoParamValue(nf);
          if(tit.equals(""))
            tit = "Sequence Filename";

          inSeq[h] = new SetInFileCard(sectionPane,h,db,tit,
                                appName,inSeqAttr,true,mysettings);
          pan.add(inSeq[h]);
        }
        else if(att.startsWith("filelist"))
        {
          filelist[h] = new ListFilePanel(15,mysettings);
          pan.add(filelist[h]);
          pan.add(Box.createVerticalStrut(100));
        }
        else if(att.startsWith("range"))
        {
          pan.add(rangeField[h]);
          pan.add(lab[nf]);
        }
        else if(att.startsWith("bool"))
        {
//        checkBox[h] = new JCheckBox();
          if(parseAcd.isDefaultParamValueStr(nf))
            if(parseAcd.getDefaultParamValueStr(nf).equalsIgnoreCase("Y") ||
               parseAcd.getDefaultParamValueStr(nf).equalsIgnoreCase("Yes") )
              checkBox[h].setSelected(true);

          pan.add(checkBox[h]);
          pan.add(lab[nf]);
        }
        else if(att.startsWith("report"))
        {
          // possible report formats
          rf = new ReportFormat(parseAcd,nf);

          pan.add(rf.getComboPopup());
          pan.add(new LabelTextBox(" Report format ("+
                             rf.getDefaultFormat()+")",
                             ReportFormat.getToolTip()));

          section.add(rf.getReportCheckBox());
        }
        else if(att.startsWith("align"))
        {
          af = new AlignFormat(parseAcd,nf);
          pan.add(af.getComboPopup());
          pan.add(new LabelTextBox(" Align format ("+
                           af.getDefaultFormat()+")",
                           af.getToolTip()));
        }
        else if(att.startsWith("list") || att.startsWith("select"))
        {
          String list[];
          if(att.startsWith("list"))
            list = parseAcd.getList(nf);
          else
            list = parseAcd.getSelect(nf);

          double max = 1.;
          if(parseAcd.isMaxParamValue(nf))
            max = Double.parseDouble(parseAcd.getMaxParam(nf));

          if(max > 1.0)
          {
            multiOption[h] = new JList(list);
            multiOption[h].setSelectionMode
               (ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
    
            Vector def = parseAcd.getListOrSelectDefault();

            int selectedIndeces[] = new int[def.size()];
            for(int i=0;i<def.size();i++)
              selectedIndeces[i] = ((Integer)def.get(i)).intValue();

            multiOption[h].setSelectedIndices(selectedIndeces);

            JScrollPane scrollPane = new JScrollPane(multiOption[h]);
            Dimension d = new Dimension(150,100);
            scrollPane.setMinimumSize(d);
            scrollPane.setMaximumSize(d);
            scrollPane.setPreferredSize(d);
            pan.add(scrollPane);
          }
          else
          {
            fieldOption[h] = new JembossComboPopup(list);

            Vector def = parseAcd.getListOrSelectDefault();

            for(int i=0;i<def.size();i++)
              fieldOption[h].setSelectedIndex( ((Integer)def.get(i)).intValue() );

            Dimension d = fieldOption[h].getPreferredSize();
            d = new Dimension(150,(int)d.getHeight());
            
            fieldOption[h].setMaximumSize(d);
            fieldOption[h].setPreferredSize(d);
            pan.add(fieldOption[h]);
          }
          pan.add(lab[nf]);
        }

        pan.add(Box.createHorizontalGlue());
        section.add(Box.createVerticalStrut(10));
      }

//using jni?
      if(AdvancedOptions.prefjni.isSelected())
        checkDependents(section,envp);

      if((att.startsWith("seqset") || att.startsWith("seqall")||
          att.startsWith("sequence")) && !isInp )
      {
        section.add(new Separator(new Dimension(350,10)));
        section.add(Box.createVerticalStrut(10));
      }

      nf++;
      if(nf<numofFields)
      {
        att = parseAcd.getParameterAttribute(nf,0).toLowerCase();
        varName = parseAcd.getParamValueStr(nf, 0);
      }
    }

    nf++;

    if(numberOfParameters >0)  // ensure there are parameters 
    {                          // in this section
      sectionPane.add(section);
      sectionBox = new Box(BoxLayout.X_AXIS);

      sectionResize(sectionPane);
      sectionBox.add(Box.createRigidArea(new Dimension(2,0)));
      sectionBox.add(sectionPane);
      sectionBox.add(Box.createHorizontalGlue());
    }
    
  }

  /** Get the report format */
  protected ReportFormat getReportFormat() { return rf; }

  /**
  *
  * Determine if report formats are used in the EMBOSS program
  * @return	true if a report format is used
  *
  */
  protected boolean isReportFormat()
  {
    if(rf==null)
      return false;
    return true;
  }

  /** Get the alignment format */
  protected AlignFormat getAlignFormat() { return af; }
  
  /**
  *
  * Determine if alignment formats are used in the EMBOSS program
  * @return     true if a alignment format is used
  *
  */
  protected boolean isAlignFormat()
  {
    if(af==null)
      return false;
    return true;
  }

  /** get the panel for this section */
  protected JPanel getSectionPanel() { return sectionPane; }
  /** get the box or this section    */
  protected Box getSectionBox() { return sectionBox; }
  /** @return     true if the input section  */
  protected boolean isInputSection() { return isInp; }
  /** @return     true if the output section */
  protected boolean isOutputSection() { return isOut; }
  /** @return     true if the required section */
  protected boolean isRequiredSection() { return isReq; }
  /** @return     true if the advanced section */
  protected boolean isAdvancedSection() { return isAdv; }
  /** @return     true if the additional section */
  protected boolean isAdditionalSection() { return isAdd; }

  /** 
  *
  * Get the current field 
  * @return 	current field number
  *
  */
  protected int getFieldNum() { return nf; }

  /**
  *
  * Set the application title panel
  * @param des	short description of the program
  * @param p3	JPanel for the ACD form
  *
  */
  private void setAppTitle(String des, JPanel p3)
  {
    appName = parseAcd.getParamValueStr(nf,0).toUpperCase();
    Box bylabP = new Box(BoxLayout.Y_AXIS);
    Box bxlabP = new Box(BoxLayout.X_AXIS);
  
    JScrollPane mainScroller = (JScrollPane)(p3.getParent().getParent().getParent());

    JPanel jTitle = new JPanel(new BorderLayout());
    jTitle.setBackground(Color.white);

    final ApplicationNamePanel namePanel = new ApplicationNamePanel(
                                              appName,10,18,18);
    bxlabP.add(namePanel);
    bxlabP.add(Box.createHorizontalGlue());
    bylabP.add(bxlabP);

    JLabel labP = new JLabel(des);
    labP.setFont(labfont);
    bxlabP = new Box(BoxLayout.X_AXIS);
    bxlabP.add(Box.createHorizontalStrut(10));
    bxlabP.add(labP);
    bxlabP.add(Box.createHorizontalGlue());
    bylabP.add(bxlabP);

    jTitle.add(bylabP, BorderLayout.WEST);
    mainScroller.setColumnHeaderView(jTitle);
  }


  /**
  *
  * Get the min, max and default values for a field in
  * the ACD as a string representation in the form 
  * (min: max: default:)
  * @param min		minimum value for parameter 
  * @param max		maximum value for parameter
  * @param def		default value for parameter
  * @param nfield	field number in ACD
  * @return		string of (min: max: default:) if specified
  *
  */
  private String getMinMaxDefault(String min,String max,
                                 String def, int nfield)
  {
    String l = new String("");

    if(parseAcd.isMinParamValue(nfield) && min == null)
      min = parseAcd.getMinParam(nfield);
    if(parseAcd.isMaxParamValue(nfield) && max == null)
      max = parseAcd.getMaxParam(nfield);
    if(parseAcd.isDefaultParamValueStr(nfield) && def == null)
      def = parseAcd.getDefaultParamValueStr(nfield);

    if(min != null && !min.startsWith("$") 
                   && !min.startsWith("@")) 
    {
      l = l.concat("(min:" + min);
      if(parseAcd.isMaxParamValue(nfield) 
                  && !max.startsWith("$") 
                  && !max.startsWith("@"))
        l = l.concat(" max:" + max);

      if(parseAcd.isDefaultParamValueStr(nfield) 
                         && !def.startsWith("$") 
                         && !def.startsWith("@") 
                         && !def.equals(""))
        l = l.concat(" default:" + def + ") ");
      else
        l = l.concat(") ");
    }
    else if(parseAcd.isMaxParamValue(nfield) 
                     && !max.startsWith("$")
                     && !max.startsWith("@"))
    {
      l = l.concat("(max:" + max);
      if(parseAcd.isDefaultParamValueStr(nfield)
                         && !def.startsWith("$")
                         && !def.startsWith("@") 
                         && !def.equals(""))
        l = l.concat(" default:" + def + ") ");
      else
        l = l.concat(") ");
    }
    else if(parseAcd.isDefaultParamValueStr(nfield) 
                            && !def.startsWith("$")
                            && !def.startsWith("@")
                            && !def.equals(""))
    {
      l = l.concat("(default:" + def + ") ");
    }
    else
    {
      if(parseAcd.isMinParamValue(nfield) || 
         parseAcd.isMaxParamValue(nfield) ||
         parseAcd.isDefaultParamValueStr(nfield) )
        l = "";
      else
        l = null;
    }

    return l;
  }


  /**
  *
  * Checks for dependent variables and adds in action listeners
  * @param section	form container for parameters
  *
  */
  private void checkDependents(Box section, final String[] envp)
  {
    final Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
    final Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
    final String att = parseAcd.getParameterAttribute(nf,0).toLowerCase();
    final String varName = parseAcd.getParamValueStr(nf,0);
    final String valS = parseAcd.getParamValueStr(nf,0).toLowerCase();
    final int nff = nf;

    if(parseAcd.isDependents(valS,nf,numofFields)) 
    {
      final int h = parseAcd.getGuiHandleNumber(nf);
      final int nod = parseAcd.getNumOfDependents();
      final Dependent dep[] = parseAcd.getDependents();

      if (att.startsWith("seqset") || att.startsWith("seqall")||
          att.startsWith("sequence") ) 
      {
        Box left = new Box(BoxLayout.X_AXIS);
        JButton upload = new JButton("LOAD SEQUENCE ATTRIBUTES");

        upload.setToolTipText(
                "After entering your sequence above, click here. This\n" +
                "will display the input parameters for " + appName + "\n" +
                "that are dependent on the sequence attributes.");

        upload.setForeground(Color.red);
        Dimension d = upload.getPreferredSize();
        upload.setPreferredSize(new Dimension(maxSectionWidth, 
                                         (int)d.getHeight()));
        left.add(upload);
        left.add(Box.createHorizontalGlue());
        section.add(left);
        section.add(Box.createVerticalStrut(10));

        final SetInFileCard sifc = inSeq[h];
        upload.addActionListener(new ActionListener()
        {
          public void actionPerformed(ActionEvent e)
          {
            f.setCursor(cbusy);
            String fc = null;
            String fname;
            if(sifc.isFileName() || sifc.isListFile())
            {
              if(sifc.isListFile())
                fname = sifc.getSequence(1);
              else
                fname = sifc.getFileChosen();
              fc = AjaxUtil.getFileOrDatabaseForAjax(fname,db,f,withSoap);
            }
            else                                     // Cut-n-Paste
            {
              fc = sifc.getCutNPasteText();

              if(!withSoap)
              {
                String cwd = System.getProperty("user.dir");
                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("attr", ".jembosstmp", new File(tmp));
                  }
                  catch(IOException ioe)
                  {
                    tf = File.createTempFile("attr", ".jembosstmp",
                                                new File(cwd));
                  }

                  PrintWriter out = new PrintWriter(new FileWriter(tf));
                  out.println(fc);
                  out.close();
                  fc = 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);
                }
              }
            }

            if(!withSoap && fc!=null)    //Ajax without SOAP
            {
              boolean ok = true;
              Ajax aj = null;
              if(mysettings.isCygwin())
                ok = cygwinSeqAttr(fc,envp,att);
              else
              {