sectionpanel.java

emboss的linux版本的源代码

                aj = new Ajax();
                if(att.startsWith("seqset"))
                  ok = aj.seqsetType(fc);
                else
                  ok = aj.seqType(fc);
              }

              if(ok)
              {
                if(!mysettings.isCygwin())
                {
                  ajaxLength  = aj.length;
                  ajaxWeight  = aj.weight;
                  ajaxProtein = aj.protein;
                }
 
                if( (updateBeginEnd(inSeqAttr[h].getBegSeq(),
                                    inSeqAttr[h].getEndSeq())) &&
                    (!att.startsWith("seqset")) &&
                    (!att.startsWith("seqall"))  )
                {
                  inSeqAttr[h].setBegSeq(1);
                  inSeqAttr[h].setEndSeq(ajaxLength);
                }
                resolveDependents(nod,dep,sifc.getFileChosen(),varName);
              }
              else
                JOptionPane.showMessageDialog(sectionPane,
                          "Sequence not found.\n" +
                          "Check the sequence entered.",
                          "Error Message", JOptionPane.ERROR_MESSAGE);

            }
            else if(fc!=null)    //Ajax with SOAP
            {

              try
              {
                CallAjax ca = new CallAjax(fc,att,mysettings);  
                if(ca.getStatus().equals("0") && ca.getLength() > 0)
                {
                  ajaxLength  = ca.getLength();
                  ajaxWeight  = ca.getWeight();
                  ajaxProtein = ca.isProtein();
                  int seqLen  = ca.getLength();
                  if( (updateBeginEnd(inSeqAttr[h].getBegSeq(),
                                    inSeqAttr[h].getEndSeq())) &&
                    (!att.startsWith("seqset")) &&
                    (!att.startsWith("seqall"))  )
                  {
                    inSeqAttr[h].setBegSeq(1);     
                    inSeqAttr[h].setEndSeq(seqLen);
                  }
                  resolveDependents(nod,dep,sifc.getFileChosen(),varName);
                }
                else
                {
                  JOptionPane.showMessageDialog(sectionPane,
                          "Sequence not found." +
                          "\nCheck the sequence entered.",
                          "Error Message", JOptionPane.ERROR_MESSAGE);
                }
//              System.out.println("PROPERTIES::: "+ca.getStatus()+"  "+ajaxLength+" "+ajaxWeight);
              }
              catch (JembossSoapException eae)
              {
                System.out.println("Call to Ajax library failed");
              }
            }
            f.setCursor(cdone);
//          resolveDependents(nod,dep,sifc.getFileChosen(),varName);
          }
        });
      }
      else if(att.startsWith("list") || att.startsWith("select"))
      {
        double max = 1.;
        if(parseAcd.isMaxParamValue(nff))
          max = Double.parseDouble(parseAcd.getMaxParam(nff));

        if(max <= 1.0)
        {
          fieldOption[h].addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e)
            {
              String sel = "";
              int index = fieldOption[h].getSelectedIndex();
              if(att.startsWith("select"))
                sel = new String((new Integer(index+1)).toString());
              else if(att.startsWith("list"))
                sel = new String(parseAcd.getListLabel(nff,index));
              resolveDependents(nod,dep,sel,varName);
            }
          });
        }
      }
      else if(att.startsWith("bool"))
      {
        checkBox[h].addActionListener(new ActionListener()
        {
          public void actionPerformed(ActionEvent e)
          {
            String sel = "";
            if(checkBox[h].isSelected())
              sel = new String("true");
            else
              sel = new String("false");
            resolveDependents(nod,dep,sel,varName);
          }
        });
        // resolve dependents as for is loaded in
        String sel = "";
        if(checkBox[h].isSelected())
          sel = new String("true");
        else
          sel = new String("false");
        resolveDependents(nod,dep,sel,varName);
      }
    }

  }


  /**
  *
  * Cygwin uses infoseq to get sequence length and type
  * and uses infoalign to get the sequence weight.  
  *
  */
  private boolean cygwinSeqAttr(String fc, String[] envp, String att)
  {
    String command = mysettings.getEmbossBin().concat(
     "infoseq -only -type -length -nohead -auto "+fc);
    RunEmbossApplication2 rea = new RunEmbossApplication2(command,envp,null);
    rea.waitFor();

    String stdout = rea.getProcessStdout();
    if(stdout.trim().equals(""))
      return false;

    StringTokenizer stok = new StringTokenizer(stdout,"\n ");

    if(stok.nextToken().trim().equalsIgnoreCase("P"))
      ajaxProtein = true;
    else
      ajaxProtein = false;

    ajaxLength = Integer.parseInt(stok.nextToken().trim());

    if(att.startsWith("seqset"))
    {
      command = mysettings.getEmbossBin().concat(
                 "infoalign -only -weight  -nohead -out stdout -auto "+fc);
      rea = new RunEmbossApplication2(command,envp,null);
      rea.waitFor();
      stok = new StringTokenizer(rea.getProcessStdout(),"\n");
      ajaxWeight = 0.f;
      while(stok.hasMoreTokens())
        ajaxWeight+= Float.parseFloat(stok.nextToken());
    }
//  System.out.println(command+"\n"+rea.getProcessStdout());
    return true;
  }

  /**
  *
  * Check sbeg and send values before updating in the
  * panel to avoid overriding user selection
  * @param s	start
  * @param e	end
  * @return 	true to automatically update
  *
  */
  private boolean updateBeginEnd(String s, String e)
  {
    if( ((s!=null) && (!s.equals(""))) ||
        ((e!=null) && (!e.equals(""))) )
    {
      int n = JOptionPane.showConfirmDialog(f,
            "Overwrite the input sequence \n" + 
            "start :" + s + "\n" + "end :" + e + 
            "\n" + "values already set?",
            "Confirm",
            JOptionPane.YES_NO_OPTION);

      if(n == JOptionPane.NO_OPTION)
        return false;
    }

    return true;
  }


  /**
  *
  * Given an ACD variable and the value it takes, resolve any dependent 
  * attribute values.
  * @param nod 		number of dependent values
  * @param dep[] 	dependents
  * @param textVal 	value of variable
  * @param varName 	variable name
  *
  */
  private void resolveDependents(int nod, Dependent dep[], String textVal, 
                                 String varName)
  {
    for(int i=0;i<nod;i++)
    {
      String exp = dep[i].getDependentExp();
      int field = dep[i].getDependentField();
      int param = dep[i].getDependentParam();

      try
      {
        AcdVarResolve avr = new AcdVarResolve(exp,textVal,varName,parseAcd,
                            numofFields,textf,textInt,textFloat,fieldOption,
                            checkBox);

//      System.out.println(exp + "EXP ==> " + avr.getResult() + " " + textVal);
        exp = avr.getResult();
      }
      catch(NullPointerException npe)
      {
        continue;
      }

      AcdFunResolve afr = new AcdFunResolve(exp);
      String result = afr.getResult();
      String att = parseAcd.getParameterAttribute(
                    dep[i].getDependentField(),0).toLowerCase();
      String type = dep[i].getDependentType();
//    System.out.println(varName + " RES => " + result +" "+ type +" att "+ att
//            +" : "+ parseAcd.getParamValueStr(dep[i].getDependentField(),0));
      int h = parseAcd.getGuiHandleNumber(field);


      // ACD changes:
      // required is now standard
      // optional is now additional
      if( (att.equals("list")     || att.equals("select")) && 
          (type.startsWith("stand") || type.startsWith("add")) ) 
//        (type.startsWith("req") || type.startsWith("opt")) ) 
      {
        double max = 1.;
        if(parseAcd.isMaxParamValue(field))
          max = Double.parseDouble(parseAcd.getMaxParam(field));

        if(max <= 1.0)
        {
          if(result.equals("false"))
            setShadingAndVisibility(fieldOption[h], false, field);
          else
            setShadingAndVisibility(fieldOption[h], true , field);
        }
        else
        {
          if(result.equals("false"))
            setShadingAndVisibility(multiOption[h], false, field);
          else
            setShadingAndVisibility(multiOption[h], true, field);
        }

      }
      else if(att.startsWith("datafile")|| att.startsWith("featout")  ||
              att.startsWith("string")  || att.startsWith("seqout") ||
              att.startsWith("outfile") || att.startsWith("matrix") ||
              att.startsWith("infile")  || att.startsWith("regexp") ||
              att.startsWith("codon")   || att.startsWith("dirlist") )
      {

        if( (type.startsWith("add") || type.startsWith("stand")) 
                                    && result.equals("false"))
          setShadingAndVisibility(textf[h], false, field);
        else if ( (type.startsWith("add") || type.startsWith("stand")) 
                                           && result.equals("true"))
          setShadingAndVisibility(textf[h], true, field);

        if(type.startsWith("def"))
        {
          if(att.startsWith("matrix"))
          {
            Vector mat = BuildProgramMenu.getMatrices();
            Enumeration en = mat.elements();
            while(en.hasMoreElements())
            {
              String m = (String)en.nextElement();
              if(result.equalsIgnoreCase(m))
              {
                textf[h].setText(m);
                break;
              }
            }
          }
          else
            textf[h].setText(result);
        }

      }
      else if(att.startsWith("int"))
      {
        if( (type.startsWith("add") || type.startsWith("stand"))
                                    && result.equals("false"))
          setShadingAndVisibility(textInt[h], false, field);
        else if ( (type.startsWith("add") || type.startsWith("stand"))
                                           && result.equals("true"))
          setShadingAndVisibility(textInt[h], true, field);
        
        if(type.startsWith("def"))
          textInt[h].setValue(Integer.parseInt(result));
      }
      else if(att.startsWith("float"))
      {
        if( (type.startsWith("add") || type.startsWith("stand"))
                                    && result.equals("false"))
          setShadingAndVisibility(textFloat[h], false, field);
        else if ( (type.startsWith("add") || type.startsWith("stand"))
                                           && result.equals("true"))
          setShadingAndVisibility(textFloat[h], true, field);
        
        if(type.startsWith("def"))
          textFloat[h].setValue(Double.parseDouble(result));
      }
      else if(att.startsWith("bool"))
      {
        if(type.startsWith("add") || type.startsWith("stand")) 
        {
          if(result.equals("false"))
            setShadingAndVisibility(checkBox[h], false, field);
          else 
            setShadingAndVisibility(checkBox[h], true, field);
        }
        else if(type.startsWith("def"))
        {
          if(result.equals("false"))
            checkBox[h].setSelected(false);
          else
            checkBox[h].setSelected(true);
        }
      }
                                              //n.b. no default labels on bools
      if(type.startsWith("def") && (!att.startsWith("bool"))) 
      {
        String l = getMinMaxDefault(null,null,result,field);
        if(lab[field] != null)
          ((JLabel)lab[field].getComponent(1)).setText(" " + l);
      }
      else if(type.startsWith("min"))
      {
        String l = getMinMaxDefault(result,null,null,field);
        if(lab[field] != null)
          ((JLabel)lab[field].getComponent(1)).setText(" " + l);
      }
      else if(type.startsWith("max"))
      {
        String l = getMinMaxDefault(null,result,null,field);  
        if(lab[field] != null)
          ((JLabel)lab[field].getComponent(1)).setText(" " + l);
      }

    }

// use to resize sections
//
    if(!isShadedGUI)
    {
      sectionResize(BuildJembossForm.addSection);
      sectionResize(BuildJembossForm.advSection);
      sectionResize(BuildJembossForm.reqdSection);
      sectionResize(BuildJembossForm.outSection);
    }

    p3.setVisible(false);  //this seems to be necessary to force 
    p3.setVisible(true);   //it to re-display sections properly!!

  }

  /**
  *
  * Set the shading or visibility of a component
  * @param c		component 
  * @param useThis	true if enabled/visible
  * @param field	field number in the ACD
  *
  */
  private void setShadingAndVisibility(Component c, 
                        boolean useThis, int field)
  {

    if( c != null)
    {
      if(isShadedGUI)
      {
        c.setEnabled(useThis);
      }
      else
      {
        c.setVisible(useThis);
        if(lab[field] != null)
          lab[field].setVisible(useThis);
      }
    }
  }

  /**
  *
  * Resize the section panel
  * @param p 	section panel
  *
  */
  private void sectionResize(JPanel p)
  {
    if(p != null)
    {
      Dimension min = p.getMinimumSize();
      int w = maxSectionWidth;
      int h = (int)min.getHeight();
      Dimension d = new Dimension (w,h);
      p.setMaximumSize(d);
      p.setPreferredSize(d);
      p.setVisible(false);
      p.setVisible(true);
    }
  }

}