buildjembossform.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.Box;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JEditorPane;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JProgressBar;
import javax.swing.JScrollPane;
import javax.swing.JTabbedPane;
import javax.swing.JTextField;
import javax.swing.JTextPane;
import javax.swing.WindowConstants;
import javax.swing.event.ChangeListener;
import javax.swing.event.ChangeEvent;
import org.apache.regexp.*;

import java.util.Hashtable;
import java.util.Vector;
import java.util.Arrays;
import java.util.Comparator;

import java.awt.event.*;
import java.io.*;
import org.emboss.jemboss.parser.ParseAcd;
import org.emboss.jemboss.programs.*;
import org.emboss.jemboss.*;
import org.emboss.jemboss.gui.*;
import org.emboss.jemboss.soap.*;
import org.emboss.jemboss.gui.sequenceChooser.*;
import org.emboss.jemboss.graphics.Graph2DPlot;
import org.emboss.jemboss.server.JembossServer;

/**
*
* Responsible for displaying the graphical representation
* of the ACD EMBOSS files.
*
* Generates & runs command lines and display results.
*
* @author T. J. Carver
*
*/
public class BuildJembossForm implements ActionListener 
{

  private ReportFormat rf;
  private AlignFormat af;
  private TextFieldSink textf[];
  private TextFieldInt textInt[];
  private TextFieldFloat textFloat[];
  private JTextField rangeField[];
  private JCheckBox  checkBox[];
  private InputSequenceAttributes inSeqAttr[];
  private ListFilePanel filelist[];
  private MultiTextField multiTextField[];
  /** png/jemboss graphics selection */
  private JComboBox graphics;

  protected static OutputSequenceAttributes outSeqAttr;

  private Box advSectionBox;
  private Box addSectionBox;
  protected static JPanel advSection;
  protected static JPanel addSection;
  protected static JPanel reqdSection;
  protected static JPanel outSection;
  protected static JPanel inpSection;

  private JembossComboPopup fieldOption[];
  private JList multiOption[];
  private SetInFileCard inSeq[];
  private JButton balign;
  private String applName;
  private String db[];
  private String[] envp;

  private String cwd;
  private ParseAcd parseAcd;

  private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
  private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
// result files
  private String seqoutResult;
  private String outfileResult;
  private String helptext = "";
  private boolean withSoap;
  private JFrame f;
  private ScrollPanel p2;
  private String embossBin;

  private int numofFields;
  private JembossParams mysettings;
  
  public BuildJembossForm(String appDescription, String db[],
        final String applName, String[] envp, String cwd, 
        String acdText, final boolean withSoap, ScrollPanel p2, 
        final JembossParams mysettings, final JFrame f)
  {

    this.f = f;
    this.p2 = p2;
    this.db = db;
    this.cwd = cwd;
    this.mysettings = mysettings;
    this.withSoap = withSoap;

    embossBin  = mysettings.getEmbossBin();
    this.envp = envp;
    this.applName = applName;

    JPanel pC = new JPanel();
//  pC.setBackground(Color.white);

    p2.add(pC, applName);
    pC.setLayout(new BorderLayout());

    Box fieldPane = Box.createVerticalBox();

    parseAcd = new ParseAcd(acdText,false);
    numofFields = parseAcd.getNumofFields();

    attach(pC, fieldPane, appDescription);

//  JScrollPane scroll = new JScrollPane(fieldPane);
//  pC.add(scroll, BorderLayout.CENTER);
    pC.add(fieldPane,BorderLayout.CENTER);

// get help for current application
    if(!withSoap) 
    {
      String command = embossBin.concat("tfm " + applName + " -html -nomore");
      RunEmbossApplication2 rea = new RunEmbossApplication2(command,envp,null);
      rea.waitFor();
      helptext = rea.getProcessStdout(); 
    }

// Help button
    ClassLoader cl = this.getClass().getClassLoader();
    JButton bhelp = new JButton(new ImageIcon(
           cl.getResource("images/Information_button.gif")));
    bhelp.addActionListener(this);
    bhelp.setMargin(new Insets(0,1,0,1));
    bhelp.setToolTipText("Help");

    bhelp.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        String text = "";
        String url = null;
        if(!withSoap)
          text = helptext;
        else 
        {
          String urlEmbassyPrefix = parseAcd.getUrlPrefix();
          url = mysettings.getembURL();
          if(urlEmbassyPrefix != null)
            url = url + "apps/release/4.0/embassy/" +applName+ "/" ;
          else
            url = url + "apps/release/4.0/emboss/apps/";

          url = url+applName+".html";
        }

        JEditorPane htmlPane = null;
        if(url == null)
        {
          try
          {
            new Browser(url,applName,true,text,mysettings);
          }
          catch(IOException ioe1){}
        }
        else if(mysettings.isUseTFM())
        {
          GetHelp thishelp = new GetHelp(applName,mysettings);
          text = thishelp.getHelpText();
          try
          {
            new Browser(url,applName,true,text,mysettings);
          }
          catch(IOException ioe3){}
        }
        else
        { 
          try
          { 
            new Browser(url,applName,mysettings);  
          }
          catch(IOException ioe2)
          {
            GetHelp thishelp = new GetHelp(applName,mysettings);
            text = thishelp.getHelpText();
            
            try
            {
              new Browser(url,applName,true,text,mysettings);
            }
            catch(IOException ioe3){}
          }

        }
      }
    });


    balign = new JButton("Show Alignment");
    balign.addActionListener(this);

// Go button
    
    ImageIcon rfii = new ImageIcon(cl.getResource("images/Go_button.gif"));
    JButton bgo = new JButton(rfii);
    bgo.setActionCommand("GO");
    bgo.setMargin(new Insets(0,0,0,0));
    bgo.addActionListener(this);

    Box tools;
    tools = Box.createHorizontalBox();
    tools.add(Box.createRigidArea(new Dimension(2,0)));
    tools.add(bgo);
    tools.add(Box.createRigidArea(new Dimension(4,0)));
    tools.add(bhelp);
      
// Advanced options
    if(advSectionBox != null ||
       addSectionBox != null)
    {
      JButton badvanced = new JButton("Advanced Options");
      badvanced.addActionListener(this);
      tools.add(Box.createRigidArea(new Dimension(4,0)));
      tools.add(badvanced);
    }

    tools.add(Box.createRigidArea(new Dimension(4,0)));
    tools.add(balign);
    balign.setVisible(false);

    tools.add(Box.createHorizontalGlue());
    fieldPane.add(Box.createRigidArea(new Dimension(0,10)));
    fieldPane.add(tools);

    fieldPane.add(Box.createVerticalStrut(10));
    bgo.setMinimumSize(new Dimension(200, 40));
    bgo.setMaximumSize(new Dimension(200, 40));

// additional section
    if(addSectionBox != null)
    {
      fieldPane.add(addSectionBox);
      addSectionBox.setVisible(false);
    }

// advanced section
    if(advSectionBox != null)
    {
      fieldPane.add(advSectionBox);
      advSectionBox.setVisible(false);
    }

    fieldPane.add(Box.createVerticalGlue());
  }


  public void attach(JPanel p3, Box fieldPane, 
                     String appDescription)
  {

    String appN = "";

// get total number of Swing components
    int ntextf = parseAcd.getNumTextf();
    int nint   = parseAcd.getNumNint();
    int nfloat = parseAcd.getNumNfloat();
    int nbool  = parseAcd.getNumBool();
    int nseqs  = parseAcd.getNumSeq();
    int nlist  = parseAcd.getNumList();
    int mlist  = parseAcd.getNumMList();
    int nrange = parseAcd.getNumRange();
    int nflist = parseAcd.getNumFileList();
    int nmultiText = parseAcd.getNumMultiTextField();

    textf     = new TextFieldSink[ntextf];
    textInt   = new TextFieldInt[nint];
    textFloat = new TextFieldFloat[nfloat];
    checkBox  = new JCheckBox[nbool];
    inSeqAttr = new InputSequenceAttributes[nseqs];
    filelist  = new ListFilePanel[nflist];
    fieldOption = new JembossComboPopup[nlist];
    multiOption = new JList[mlist];
    rangeField  = new JTextField[nrange];

    inSeq  = new SetInFileCard[nseqs];
    
    multiTextField = new MultiTextField[nmultiText];
    
//  JRadioButton rpaste[] = new JRadioButton [nseqs];
    Box lab[] = new Box[numofFields];

    
    for(int j=0;j<nbool;j++)
      checkBox[j] = new JCheckBox();

    for(int j=0;j<ntextf;j++)
    {
      textf[j] = new TextFieldSink();
      Dimension d = new Dimension(150, 30);
      textf[j].setPreferredSize(d);
      textf[j].setMinimumSize(d);
      textf[j].setMaximumSize(d);
    }

    for(int j=0;j<nint;j++)
    {
      textInt[j] = new TextFieldInt();
      Dimension d = new Dimension(150, 30);
      textInt[j].setPreferredSize(d);
      textInt[j].setMinimumSize(d);
      textInt[j].setMaximumSize(d);
    }

    for(int j=0;j<nfloat;j++)
    {
      textFloat[j] = new TextFieldFloat();
      Dimension d = new Dimension(150, 30);
      textFloat[j].setPreferredSize(d);
      textFloat[j].setMinimumSize(d);
      textFloat[j].setMaximumSize(d);
    }
     
    for(int j=0;j<nrange;j++)
    {
      rangeField[j] = new TextFieldSink();
      Dimension d = new Dimension(150, 30);
      rangeField[j].setPreferredSize(d);
      rangeField[j].setMinimumSize(d);
      rangeField[j].setMaximumSize(d);
    }


    int nsection = parseAcd.getNumSection();
    if(nsection==0)
      nsection = 1;

    int nfield = 0;

    advSectionBox = null;
    addSectionBox = null;
    reqdSection = null;
    outSection = null;
    inpSection = null;

//  if(withSoap)
//  {
      if(parseAcd.isBatchable() && 
         !parseAcd.getExpectedCPU().equalsIgnoreCase("low"))
        Jemboss.resultsManager.updateMode("batch");
      else
        Jemboss.resultsManager.updateMode("interactive");
//  }

    String type[] = {"PNG","Jemboss Graphics"};
    graphics = new JComboBox(type);

    for(int j=0;j<nsection;j++)
    {
      if(nfield < numofFields)
      {
        SectionPanel sp = new SectionPanel(f,p3,fieldPane,parseAcd,
              nfield,multiTextField,textf,textInt,textFloat,rangeField,checkBox,
              inSeqAttr,fieldOption,multiOption,inSeq,filelist,graphics,
              db,appDescription,lab,numofFields,mysettings,withSoap,envp);

        if(sp.isReportFormat())
          rf = sp.getReportFormat();

        if(sp.isAlignFormat())
          af = sp.getAlignFormat();

        if(sp.isAdvancedSection())
        {
          advSectionBox = sp.getSectionBox();
          advSection    = sp.getSectionPanel();
        }
        else if(sp.isAdditionalSection())
        {
          addSectionBox = sp.getSectionBox();
          addSection    = sp.getSectionPanel();
        }
        else if(sp.getSectionBox() != null)
        {
          fieldPane.add(sp.getSectionBox());
          if(sp.isInputSection())
            inpSection = sp.getSectionPanel();     
          else if(sp.isRequiredSection())
            reqdSection = sp.getSectionPanel();
          else if(sp.isOutputSection())
            outSection = sp.getSectionPanel();
        }
        nfield = sp.getFieldNum();
      }
    }
 

  }


/**
*
*  Action events Exit, Help, GO, & Show results
* 
*
*/