sectionpanel.java

emboss的linux版本的源代码

/********************************************************************
*
*  This library is free software; you can redistribute it and/or
*  modify it under the terms of the GNU Library General Public
*  License as published by the Free Software Foundation; either
*  version 2 of the License, or (at your option) any later version.
*
*  This library is distributed in the hope that it will be useful,
*  but WITHOUT ANY WARRANTY; without even the implied warranty of
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
*  Library General Public License for more details.
*
*  You should have received a copy of the GNU Library General Public
*  License along with this library; if not, write to the
*  Free Software Foundation, Inc., 59 Temple Place - Suite 330,
*  Boston, MA  02111-1307, USA.
*
*  @author: Copyright (C) Tim Carver
*
********************************************************************/

package org.emboss.jemboss.gui.form;

import java.awt.*;
import javax.swing.*;
import javax.swing.border.TitledBorder;
import javax.swing.border.Border;
import java.util.Vector;
import java.util.Enumeration;
import java.util.StringTokenizer;
import java.awt.event.*;
import java.io.*;

import org.emboss.jemboss.programs.RunEmbossApplication2;
import org.emboss.jemboss.gui.AdvancedOptions;
import org.emboss.jemboss.gui.BuildProgramMenu;
import org.emboss.jemboss.parser.*;
import org.emboss.jemboss.programs.ListFile;
import org.emboss.jemboss.gui.sequenceChooser.*;
import org.emboss.jemboss.soap.CallAjax;
import org.emboss.jemboss.soap.JembossSoapException;
import org.emboss.jemboss.JembossParams;

/**
*
* Responsible for displaying the Jemboss application form
* generated from the ACD file. This also handles events related to
* dependent parameters.
*
*/
public class SectionPanel
{

  private MultiTextField multiTextField[];
  /** text field sink    */
  private TextFieldSink textf[];
  /** integer field sink */
  private TextFieldInt textInt[];
  /** float field sink   */
  private TextFieldFloat textFloat[];
  /** range field        */
  private JTextField rangeField[];
  /** boolean fields     */
  private JCheckBox  checkBox[];
  /** input sequence attributes */
  private InputSequenceAttributes inSeqAttr[];
  /** list file panel    */
  private ListFilePanel filelist[];
  /** checkbox popup field for list and select */
  private JembossComboPopup fieldOption[];
  /** multiple option field for list and select */
  private JList multiOption[];
  /** input sequence field */
  private SetInFileCard inSeq[];
  /** field label container */
  private Box lab[];
  /** available databases */
  private String db[];

//private JComboBox graphics;

  /** ACD parser for the application selected */
  private ParseAcd parseAcd;
  /** number of fields in the ACD */
  private int numofFields;
  /** field number to start from */
  private int nf;
  /** sequence length */
  public static int ajaxLength;
  /** sequence weight */
  public static float ajaxWeight;
  /** sequence type   */
  public static boolean ajaxProtein;
  /** true if in client-server mode */
  private boolean withSoap;
  /** application name   */
  private String appName = "";
  /** Jemboss form panel */
  private JPanel p3;
  /** container for this ACD section */
  private JPanel sectionPane;
  /** container for this ACD section */
  private Box sectionBox;
  /** jemboss properties */
  private JembossParams mysettings;

// input, required, advanced & output sections
  /** true if the input section    */
  private boolean isInp = false;
  /** true if the required section */
  private boolean isReq = false;
  /** true if the advanced section */
  private boolean isAdv = false;
  /** true if the additional section */
  private boolean isAdd = false;
  /** true if the output section   */
  private boolean isOut = false;

  /** true if shading disabled fields, otherwise they 
      are removed from the form */
  private boolean isShadedGUI;

  /** label colour */
  public static Color labelColor = new Color(0, 0, 0);
  /** label font   */
  public static Font labfont = new Font("SansSerif", Font.BOLD, 12);  
  /** small label font */
  public static Font labfont2 = new Font("SansSerif", Font.BOLD, 11);

  /** maximum width of the form */
  private final int maxSectionWidth = 498;
  /** Jemboss frame    */
  private JFrame f;
  /** report format    */
  private ReportFormat rf=null;
  /** alignment format */
  private AlignFormat af=null;

  /**
  *
  * @param f 		Jemboss frame
  * @param p3		JPanel ACD form panel
  * @param fieldPane	containing all the fields 
  * @param parseAcd	representing the ACD file to display as a form
  * @param nff		field number
  * @param textf		text fields in the form
  * @param textInt	integer fields in the form
  * @param textFloat	float fields in the form
  * @param rangeField	ranges in the form
  * @param checkBox	for the boolean switches
  * @param inSeqAttr	the input sequence(s) attributes
  * @param fieldOption	for the list/selection data types
  * @param multiOption	for multiple selection lists
  * @param inSeq 		the input sequence(s)
  * @param filelist	list file panel
  * @param db		String array containing the databases
  * @param des		String containing the one line description for the application
  * @param lab		Box for all the component labels
  * @param numofFields	total number of fields
  * @param mysettings	jemboss properties
  * @param withSoap 	true if using a soap server
  *
  */
  protected SectionPanel(JFrame f, JPanel p3, Box fieldPane, 
            ParseAcd parseAcd, int nff, final MultiTextField multiTextField[],
            final TextFieldSink textf[], 
            TextFieldInt textInt[], TextFieldFloat textFloat[],
            JTextField rangeField[], JCheckBox  checkBox[],
            InputSequenceAttributes inSeqAttr[],
            JembossComboPopup fieldOption[], JList multiOption[], 
            SetInFileCard inSeq[], ListFilePanel filelist[], JComboBox graphics,
            String db[], String des, Box lab[], int numofFields,
            JembossParams mysettings, boolean withSoap, String[] envp)
  {

    Border etched = BorderFactory.createEtchedBorder();
    isShadedGUI = AdvancedOptions.prefShadeGUI.isSelected();

    this.p3 = p3;
    this.textf = textf;
    this.textInt = textInt;
    this.textFloat = textFloat;
    this.rangeField = rangeField;
    this.checkBox = checkBox;
    this.inSeqAttr = inSeqAttr;
    this.fieldOption = fieldOption;
    this.multiOption = multiOption;
    this.inSeq = inSeq;
    this.numofFields = numofFields;
    this.db = db;
    this.lab = lab;
    this.parseAcd = parseAcd;
    this.mysettings = mysettings;
    this.withSoap = withSoap; 
    this.f = f;
//  this.graphics = graphics;

//using JNI?
    nf = nff;

    String att = parseAcd.getParameterAttribute(nf,0).toLowerCase();

//set the ACD title
    if(att.startsWith("appl"))
    {
      setAppTitle(des,p3);
      nf++;
      att = parseAcd.getParameterAttribute(nf,0).toLowerCase();
    }
  
    Box section = new Box(BoxLayout.Y_AXIS);
    fieldPane.add(Box.createRigidArea(new Dimension(0,10)));

    JLabel bxlab = new JLabel();
    bxlab.setFont(labfont);

    sectionPane = new JPanel(new GridLayout(1,1));
    sectionPane.setBorder(BorderFactory.createEtchedBorder());
    String nameSect = parseAcd.getParamValueStr(nf, 0);

    if(att.equals("section"))
    {
      TitledBorder title;
      title = BorderFactory.createTitledBorder(etched, 
                parseAcd.getInfoParamValue(nf).toLowerCase(),
                TitledBorder.LEFT,TitledBorder.TOP,
                new Font("SansSerif", Font.BOLD, 13),
                Color.blue);
      sectionPane.setBorder(title);

      String secType = parseAcd.getInfoParamValue(nf).toLowerCase();
      if(secType.startsWith("advanced "))
        isAdv = true;
      else if(secType.startsWith("additional "))
        isAdd = true;
      else if(secType.startsWith("input "))
        isInp = true;
      else if(secType.startsWith("output "))
        isOut = true;
      else if(secType.startsWith("required "))
        isOut = true;
      else
        System.out.println("Unknown section type " + secType);

      nf++;
      att = parseAcd.getParameterAttribute(nf,0).toLowerCase();
    }
    String varName = parseAcd.getParamValueStr(nf, 0);

    int numberOfParameters = 0;

// loop over all the fields in the section or the all fields in the ACD
    while( !( att.equals("endsection")  && varName.equals(nameSect)) &&
            nf < numofFields )
    {
     
      if(!(att.equals("var") || att.equals("variable"))) 
      {
        numberOfParameters++;
        final int h = parseAcd.getGuiHandleNumber(nf);
        Box pan = new Box(BoxLayout.X_AXIS);
        section.add(pan);

        String l = getMinMaxDefault(null,null,null,nf);

      	lab[nf] = new LabelTextBox(parseAcd.getInfoParamValue(nf),
                                  parseAcd.getHelpParamValue(nf));

        if(l != null && !att.startsWith("bool"))
        {
          bxlab = new JLabel(" " + l);
          bxlab.setFont(labfont2);
          bxlab.setForeground(Color.blue);
          lab[nf].add(bxlab);
        }

        if(att.startsWith("appl"))
        {
          setAppTitle(des,p3);
        }
        else if(att.endsWith("graph"))
        {
          Dimension d  = graphics.getPreferredSize();
          d = new Dimension(150,(int)d.getHeight());
          graphics.setMaximumSize(d);
          graphics.setPreferredSize(d);

          pan.add(graphics);
          pan.add(new JLabel(" Graph Format"));
        }
        else if(att.startsWith("int"))
        {
          if(parseAcd.isDefaultParamValueStr(nf)) 
          {
            if( !(parseAcd.getDefaultParamValueStr(nf).startsWith("@") ||
                  parseAcd.getDefaultParamValueStr(nf).startsWith("$")) )
              textInt[h].setValue(Integer.parseInt(
                           parseAcd.getDefaultParamValueStr(nf)));
          }
          else
          {
            Double val = new Double(parseAcd.getDefaultParamValueDbl(nf));
            textInt[h].setValue(val.intValue());
          }
          pan.add(textInt[h]);
          pan.add(lab[nf]);
        } else if(att.startsWith("float")) {
          if(parseAcd.isDefaultParamValueStr(nf))
          {
            if( !(parseAcd.getDefaultParamValueStr(nf).startsWith("@") ||
                  parseAcd.getDefaultParamValueStr(nf).startsWith("$")) )
              textFloat[h].setValue(Double.parseDouble(
                           parseAcd.getDefaultParamValueStr(nf)));
          }
          else
          {
            Double val = new Double(parseAcd.getDefaultParamValueDbl(nf) );
            textFloat[h].setValue(val.doubleValue());
          }
          pan.add(textFloat[h]);
          pan.add(lab[nf]);
        }
        else if(att.startsWith("matrix"))
        {
          if(parseAcd.isDefaultParamValueStr(nf))
            if( !(parseAcd.getDefaultParamValueStr(nf).startsWith("@") ||
                  parseAcd.getDefaultParamValueStr(nf).startsWith("$")) )
              textf[h].setText( parseAcd.getDefaultParamValueStr(nf));
         
          pan.add(textf[h]);
          pan.add(lab[nf]);
  
          Box pan2 = new Box(BoxLayout.X_AXIS);
          section.add(pan2);
          
          JembossComboPopup selectMatrix = new JembossComboPopup(
                                        BuildProgramMenu.getMatrices());
          selectMatrix.addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e)
            {
              JembossComboPopup cb = (JembossComboPopup)e.getSource();
              String matrix = (String)cb.getSelectedItem();
              textf[h].setText(matrix);
            }
          });

          Dimension d = selectMatrix.getPreferredSize();
          d = new Dimension(150,(int)d.getHeight());

          selectMatrix.setMaximumSize(d);
          selectMatrix.setPreferredSize(d);

          pan2.add(selectMatrix);
          pan2.add(Box.createHorizontalGlue());
          
        }
        else if(att.startsWith("codon"))
        {   
          if(parseAcd.isDefaultParamValueStr(nf))
            if( !(parseAcd.getDefaultParamValueStr(nf).startsWith("@") ||
                  parseAcd.getDefaultParamValueStr(nf).startsWith("$")) )
              textf[h].setText( parseAcd.getDefaultParamValueStr(nf));
          pan.add(textf[h]);
          pan.add(lab[nf]);
   
          Box pan2 = new Box(BoxLayout.X_AXIS);
          section.add(pan2);
          JembossComboPopup selectMatrix = new JembossComboPopup(
                                        BuildProgramMenu.getCodonUsage());
          selectMatrix.addActionListener(new ActionListener()
          {
            public void actionPerformed(ActionEvent e)
            {
              JembossComboPopup cb = (JembossComboPopup)e.getSource();
              String matrix = (String)cb.getSelectedItem();
              textf[h].setText(matrix);
            }
          });

          Dimension d = selectMatrix.getPreferredSize();
          d = new Dimension(150,(int)d.getHeight());

          selectMatrix.setMaximumSize(d);
          selectMatrix.setPreferredSize(d);

          pan2.add(selectMatrix);
          pan2.add(Box.createHorizontalGlue());
        }
        else if(att.startsWith("dirlist") || att.startsWith("string") ||
                att.startsWith("infile")  || att.startsWith("regexp") ||
                att.startsWith("featout") )
        {
          if(parseAcd.isDefaultParamValueStr(nf)) 
            if( !(parseAcd.getDefaultParamValueStr(nf).startsWith("@") ||
                  parseAcd.getDefaultParamValueStr(nf).startsWith("$")) )
              textf[h].setText( parseAcd.getDefaultParamValueStr(nf));

          pan.add(textf[h]);
          pan.add(lab[nf]);
        }
        else if( att.startsWith("pattern") )
        {
          LabelTextBox labs[] = new LabelTextBox[2];
          
          labs[0] = (LabelTextBox)lab[nf];
          labs[1] = new LabelTextBox("Pattern mismatch",
                                     "Number of pattern mismatch");
          
          multiTextField[h] = new MultiTextField(2, labs);
          pan.add(multiTextField[h].getBoxOfTextFields());
        }
        else if(att.startsWith("seqout"))
        {
          new SetOutFileCard(pan,textf[h],labelColor,sectionPane);
        }
        else if(att.startsWith("outfile") || att.startsWith("datafile"))
        {
          if(parseAcd.isDefaultParamValueStr(nf))
            if( !(parseAcd.getDefaultParamValueStr(nf).startsWith("@") ||
                  parseAcd.getDefaultParamValueStr(nf).startsWith("$")) )
              textf[h].setText( parseAcd.getDefaultParamValueStr(nf));

          if(parseAcd.getInfoParamValue(nf).equals(""))
          {
            bxlab = new JLabel(" " + att + " file name");
            bxlab.setForeground(labelColor);
          }