parseacd.java

emboss的linux版本的源代码

  */
  private void setGuiHandleNumber(String dataType, ApplicationFields appF)
  {

    if ( dataType.startsWith("datafile") || dataType.startsWith("featout") ||
         dataType.startsWith("string")   || dataType.startsWith("seqout")  ||
         dataType.startsWith("outfile")  || dataType.startsWith("matrix")  ||
         dataType.startsWith("infile")   || dataType.startsWith("regexp")  ||
         dataType.startsWith("codon")    || dataType.startsWith("dirlist") )
    {
      appF.setGuiHandleNumber(ntextf);
      ntextf++;
    }
    else if(dataType.startsWith("pattern"))
    {
      appF.setGuiHandleNumber(nmultiTextField);
      nmultiTextField++;
    }
    else if (dataType.startsWith("int"))
    {
      appF.setGuiHandleNumber(nint);
      nint++;
    }
    else if (dataType.startsWith("float"))
    {
      appF.setGuiHandleNumber(nfloat);
      nfloat++;
    }
    else if (dataType.startsWith("bool"))
    {
      appF.setGuiHandleNumber(nbool);
      nbool++;
    }
    else if (dataType.startsWith("seqset") ||
             dataType.startsWith("seqall") ||
             dataType.startsWith("sequence") )
    {
      appF.setGuiHandleNumber(nseqs);
      nseqs++;
    }
    else if (dataType.startsWith("filelist") )
    {
      appF.setGuiHandleNumber(nflist);
      nflist++;
    }
    else if (dataType.startsWith("list") || dataType.startsWith("select"))
    {
      double max = 1.;
      if(isMaxParamValue(numofFields))
        max = Double.parseDouble(getMaxParam(numofFields));

      if(max > 1.0)       // multiple list selection
      {
        appF.setGuiHandleNumber(mlist);
        mlist++;
      }
      else                // single selection
      {
        appF.setGuiHandleNumber(nlist);
        nlist++;
      }
    }
    else if (dataType.startsWith("range"))
    {
      appF.setGuiHandleNumber(nrange);
      nrange++;
    }

  }


  /**
  *
  * Gets the double value of a parameter.
  * @return 	double value of the parameter. 
  *
  */
  public double getParamValueDbl(int field, int param) 
  {
    ApplicationFields aF = (ApplicationFields)vappF.get(field);
    return aF.getParamValueDbl(param);
  }


  /**
  *
  * Determine if there is a default parameter in a field of the ACD.
  * @param  field 	field number
  * @return 		true if the default parameter value is a String
  *
  */
  public boolean isDefaultParamValueStr(int field) 
  {
    int num = getNumofParams(field);
    int i;

    for(i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("def")) 
        return isParamValueStr(field,i);
    }
    return false;
  }


  /**
  *
  * Return a double default parameter
  * @param  field 	field number
  * @return 		default parameter value as a double.
  *
  */
  public double getDefaultParamValueDbl(int field) 
  {
    int num = getNumofParams(field);
    
    ApplicationFields aF = (ApplicationFields)vappF.get(field);
    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("def")) 
        return aF.getParamValueDbl(i);
    }
    return 0.0;
  }


//  Methods for dealing with dependent variables. 

  /**
  *
  * Always start by calling isDependents(), which calculates
  * the number of dependents and construct the Dependent array.
  *
  * @param attr 	String name of the attribute
  * @param field 	field number
  * @param numofFields	total number of fields  
  * @return  		true if there are dependent parameters.
  *
  */
  public boolean isDependents(String attr, int field, int numofFields)
  {

    numOfDependents = 0;

    for(int i=field+1;i<numofFields;i++) 
    {
      int num = getNumofParams(i);
      for(int j=0;j<num;j++) 
      {
        if(isParamValueStr(i,j))   
        {
          String val = getParamValueStr(i,j);
          if(val.startsWith("$") || val.startsWith("@")) 
            numOfDependents++;
        }
      }
    }

    dep = new Dependent[numOfDependents];
    
    numOfDependents = 0;
    for(int i=field+1;i<numofFields;i++) 
    {
      int num = getNumofParams(i);

      for(int j=0;j<num;j++) 
      {
        if(isParamValueStr(i,j)) 
        {
          String val = getParamValueStr(i,j);
          if(val.startsWith("$") || val.startsWith("@")) 
          {
            String type = getParameterAttribute(i,j);
            dep[numOfDependents] = new Dependent(i,j,val,type);
            numOfDependents++;            
          }
        } 
      }
    }

    if(numOfDependents>0)
      return true;
    else
      return false;
  }


  /**
  *
  * Gets the dependents associated with the ACD.
  * @return 	the Dependent array for those fields
  *         	with dependents
  *
  */
  public Dependent[] getDependents() 
  {
    return dep;
  }


  /**
  *
  * Gets the number of dependent parameters in the ACD.
  * @return 	number of Dependent making up the array
  *
  */
  public int getNumOfDependents() 
  {
    return numOfDependents;
  }


  /**
  *
  * Locates the min parameter in a field and returns it as a String.
  * @param field	field number
  * @return  		minimum value defined in a field.
  *
  */
  public String getMinParam(int field) 
  {
    int num = getNumofParams(field);
    String min = "";

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("min")) 
      {
        ApplicationFields aF = (ApplicationFields)vappF.get(field);
        if(isParamValueStr(field,i)) 
          min = aF.getParamValueStr(i);
        else 
        {
          Double val = new Double(aF.getParamValueDbl(i));
          if(getParameterAttribute(field,0).startsWith("int"))
            min = (new Integer(val.intValue())).toString();           
          else
            min = val.toString();
        }
        return min;
      }
    }
   
    return min;
  }


  /**
  *
  * Locates the max parameter in a field and returns it as a String.
  * @param field 	field number
  * @return  		maximum value defined in a field.
  *
  */
  public String getMaxParam(int field) 
  {
    int num = getNumofParams(field);
    String max = "";

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("max")) 
      {
        ApplicationFields aF = (ApplicationFields)vappF.get(field);
        if(isParamValueStr(field,i))
          max = aF.getParamValueStr(i);
        else 
        {
          Double val = new Double(aF.getParamValueDbl(i));
          if(getParameterAttribute(field,0).startsWith("int"))
            max = (new Integer(val.intValue())).toString();
          else
            max = val.toString();
        }
        return max;
      }
    }
    return max;
  }


  /**
  *
  * Determine if there is a min parameter in a field of the ACD.
  * @param field 	field number
  * @return  		true if there is a minimum value specified
  *          		in a field.
  *
  */
  public boolean isMinParamValue(int field) 
  {
    int num = getNumofParams(field);

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("min")) 
      {
        ApplicationFields aF = (ApplicationFields)vappF.get(field);
        if(isParamValueStr(field,i) )
          if(aF.getParamValueStr(i).startsWith("$"))
            return false;
        return true;
      }
    }
    return false;
  }


  /**
  *
  * Determine if there is a max parameter in a field of the ACD.
  * @param field 	field number
  * @return  		true if there is a maximum value specified
  *          		in a field.
  *
  */
  public boolean isMaxParamValue(int field) 
  {
    int num = getNumofParams(field);

    for(int i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("max"))    
      {
//      if(isParamValueStr(field,i) )
//        if(appF[field].getParamValueStr(i).startsWith("$"))
//          return false;
        return true;
      }
    }
    return false;
  }


  /**
  *
  * Finds the prompt, info or help parameter in an ACD field, in that
  * order.
  * @param field	field number
  * @return 		information specified by the prompt parameter, if
  *          		present else the information parameter
  *          		or the help parameter.
  *
  */
  public String getInfoParamValue(int field) 
  {
    int num = getNumofParams(field);
    int i;

    ApplicationFields aF = (ApplicationFields)vappF.get(field);

    for(i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("prompt")) 
        return aF.getParamValueStr(i);
    }
    for(i=0;i<num;i++) 
    {
      if (getParameterAttribute(field,i).startsWith("info")) 
        return aF.getParamValueStr(i);
    }
    for(i=0;i<num;i++)
    {
      if (getParameterAttribute(field,i).startsWith("help"))
        return aF.getParamValueStr(i);
    }

    return "";
  }


  /**
  *
  * Finds the help parameter in an ACD field.
  * @param field 	field number
  * @return  		help parameter defined in a field or a blank
  *          		String if not specified.
  *
  */
  public String getHelpParamValue(int field) 
  {
    int num = getNumofParams(field);
    int i;
    String help = "";
    String helpText = "";

    ApplicationFields aF = (ApplicationFields)vappF.get(field);
    for(i=0;i<num;i++) 
      if (getParameterAttribute(field,i).startsWith("help")) 
        return formatHelpText(aF.getParamValueStr(i));

//  for(i=0;i<num;i++) 
//    if (getParameterAttribute(field,i).startsWith("info")) 
//      return formatHelpText(appF[field].getParamValueStr(i));
    
    return "";
  }

  /**
  *
  * Finds if the program is identifies as being able to
  * run in a batch queue
  * @return 	true if the program is suitable for putting
  *         	in a batch queue 
  *
  */
  public boolean isBatchable()
  {

    int num = getNumofParams(0);
    ApplicationFields aF = (ApplicationFields)vappF.get(0);

    for(int i=0;i<num;i++)
    {
      if(getParameterAttribute(0,i).startsWith("batch"))
        if(aF.getParamValueStr(i).equalsIgnoreCase("Y") ||
           aF.getParamValueStr(i).equalsIgnoreCase("Yes") )
             return true;
    }

    return false;
  }


  /**
  *
  * Finds any expected cpu level indicator (low, medium, high)
  * @return 	cpu level indicator
  *
  */
  public String getExpectedCPU()
  {
    String cpu = "";
    int num = getNumofParams(0);
    ApplicationFields aF = (ApplicationFields)vappF.get(0);
    for(int i=0;i<num;i++)
    {
      if(getParameterAttribute(0,i).startsWith("cpu"))
        return aF.getParamValueStr(i);
    }

    return cpu;
  }

  /**
  *
  * Find URL prefix if an embassy application
  * @return     url prefix 
  *
  */
  public String getUrlPrefix()
  {
    int num = getNumofParams(0);
    ApplicationFields aF = (ApplicationFields)vappF.get(0);
    for(int i=0;i<num;i++)
    {
      if(getParameterAttribute(0,i).startsWith("embassy"))
        return aF.getParamValueStr(i);
    }

    return null;
  }



  /**
  *
  * Limits the length of the line for the help text used in
  * the tool tips.
  *
  * @param help	help text
  * @return  	formated help text.
  *
  */
  protected String formatHelpText(String help) 
  {
    String helpText = "";
    int start = 0;
    int stop;

    help = help.replace('\n',' ');