sequencelist.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;

import java.awt.*;
import java.io.*;
import java.util.*;
import javax.swing.*;
import javax.swing.event.*;
import javax.swing.table.*;
import javax.swing.border.*;
import java.awt.event.*;
import java.net.MalformedURLException;
import java.net.URL;
import java.awt.datatransfer.*;
import java.awt.dnd.*;

import org.emboss.jemboss.parser.*;
import org.emboss.jemboss.soap.*;
import org.emboss.jemboss.JembossParams;
import org.emboss.jemboss.gui.filetree.*;
import org.emboss.jemboss.programs.RunEmbossApplication2;

/**
*
* SequenceList extends JFrame to display a set of sequences
* that the user is working on in a session. The sequence list
* can be stored and read back in by the application. This allows
* the user to usefully maintain a list of sequence that are
* being worked on and easily drag and drop them into sequence
* fields of applications.
*
*/
public class SequenceList extends JFrame
{

  /** drag and drop table containing the list of sequences */
  private DragJTable table;
  /** model for the sequence table */
  private SequenceListTableModel seqModel;
  /** select to save the sequence list between sessions */
  private JCheckBoxMenuItem storeSeqList;

  final Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
  final Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);

  /**
  *
  * @param withSoap	true if in client-server mode
  * @param mysettings	jemboss properties
  *
  */
  public SequenceList(final boolean withSoap,final JembossParams mysettings)
  {
    super("Sequence List");
    setSize(400,155);
    seqModel = new SequenceListTableModel();
    table = new DragJTable(seqModel);
    table.setModel(seqModel);
    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);

    //column width
    for(int i=0;i<SequenceListTableModel.modelColumns.length;i++)
    {
      TableColumn column = table.getColumn(
            SequenceListTableModel.modelColumns[i].title);
      column.setPreferredWidth(
             SequenceListTableModel.modelColumns[i].width);
    }

    JScrollPane scrollpane = new JScrollPane(table);
    scrollpane.setSize(300,100);
    getContentPane().add(scrollpane, BorderLayout.CENTER);

//setup menu bar 
    JMenuBar menuPanel = new JMenuBar();
    new BoxLayout(menuPanel,BoxLayout.X_AXIS);
    setJMenuBar(menuPanel);

    JMenu fileMenu = new JMenu("File");
    fileMenu.setMnemonic(KeyEvent.VK_F);
    menuPanel.add(fileMenu);
    JMenu toolMenu = new JMenu("Tools");
    toolMenu.setMnemonic(KeyEvent.VK_T);
    menuPanel.add(toolMenu);

    JMenuItem openMenuItem = new JMenuItem("Open");
    openMenuItem.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        int nrow = table.getSelectedRow();
        String fileName = (String)table.getValueAt(nrow,
                table.convertColumnIndexToView(SequenceListTableModel.COL_NAME));

        SequenceData row = (SequenceData)seqModel.modelVector.elementAt(nrow);

        if(!(row.s_remote.booleanValue()))
          DragTree.showFilePane(fileName,mysettings);        //local file
        else
          RemoteDragTree.showFilePane(fileName,mysettings);  //remote file
      }
    });
    fileMenu.add(openMenuItem);

    JMenuItem ajaxSeq = new JMenuItem("Calculate Sequence Attributes");
    ajaxSeq.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {

        int row = table.getSelectedRow();
        String fn = table.getFileName(row);

        if(!fn.equals("") && fn!=null)
        {
          setCursor(cbusy);
          if(table.isListFile(row).booleanValue())
            fn = "list::"+fn;
        
          String fc = AjaxUtil.getFileOrDatabaseForAjax(fn,
                      BuildProgramMenu.getDatabaseList(),
                      null,withSoap);
        
          boolean ok = false;
          int ajaxLength=0;
          float ajaxWeight;
          boolean ajaxProtein;

          if(!withSoap && fc!=null)    //Ajax without SOAP
          {
            if(mysettings.isCygwin())
            {
              ajaxLength = cygwinSeqAttr(fc,mysettings);
              if(ajaxLength > -1)
                ok = true;
            }
            else
            {
              Ajax aj = new Ajax();
              ok = aj.seqType(fc);
              if(ok)
              {
                ajaxLength  = aj.length;
                ajaxWeight  = aj.weight;
                ajaxProtein = aj.protein;
              }
            }

          }
          else if(fc!=null)    //Ajax with SOAP
          {
            try
            {  
              CallAjax ca = new CallAjax(fc,"sequence",mysettings);
              if(ca.getStatus().equals("0"))
              {
                ajaxLength  = ca.getLength();
                ajaxWeight  = ca.getWeight();
                ajaxProtein = ca.isProtein();
                ok = true;
              }
            }
            catch (JembossSoapException eae)
            {
              System.out.println("Call to Ajax library failed");
              setCursor(cdone);
            }
          }

          if(!ok && fc!=null)                          //Ajax failed
          {
            if( mysettings.getServicePasswdByte()!=null ||
                mysettings.getUseAuth() == false )
            {
              JOptionPane.showMessageDialog(null,
                     "Sequence not found!", "Error Message",
                     JOptionPane.ERROR_MESSAGE);
            }
            else 
            {
              AuthPopup ap = new AuthPopup(mysettings,null);
              ap.setBottomPanel();
              ap.setSize(380,170);
              ap.pack();
              ap.setVisible(true);
            }
          }
          else
          {
            seqModel.setValueAt(new Integer(1),row,
                      SequenceListTableModel.COL_BEG);
            seqModel.setValueAt(new Integer(ajaxLength),row,
                      SequenceListTableModel.COL_END);
            table.repaint();
          }
          setCursor(cdone);
        }
      }
    });
    toolMenu.add(ajaxSeq);


    JMenuItem addSeq = new JMenuItem("Add Sequence");
    addSeq.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        int row = table.getSelectedRow();
        seqModel.insertRow(row+1);
        table.tableChanged(new TableModelEvent(seqModel, row+1, row+1, 
                TableModelEvent.ALL_COLUMNS, TableModelEvent.INSERT));
      }
    });
    toolMenu.add(addSeq);

    JMenuItem deleteSeq = new JMenuItem("Delete Sequence");
    deleteSeq.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        int row = table.getSelectedRow();
        if(seqModel.deleteRow(row))
          table.tableChanged(new TableModelEvent(seqModel, row, row,
                TableModelEvent.ALL_COLUMNS, TableModelEvent.DELETE));
        
      }
    });
    toolMenu.add(deleteSeq);
 

    JMenuItem reset = new JMenuItem("Remove All Sequences");
    reset.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        seqModel.setDefaultData();
        table.repaint();
      }
    });
    toolMenu.add(reset);

    toolMenu.addSeparator();

    storeSeqList = new JCheckBoxMenuItem("Save Sequence List");
    File fseq = new File(System.getProperty("user.home")
                           + System.getProperty("file.separator")
                           + ".jembossSeqList");
    if(fseq.canRead())
      storeSeqList.setSelected(true);
    else
      storeSeqList.setSelected(false);
    toolMenu.add(storeSeqList);

    fileMenu.addSeparator();

    JMenuItem closeFrame = new JMenuItem("Close");
    closeFrame.setAccelerator(KeyStroke.getKeyStroke(
                    KeyEvent.VK_E, ActionEvent.CTRL_MASK));

    closeFrame.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        setVisible(false);
      }
    });
    fileMenu.add(closeFrame);

    // help menu
   JMenu helpMenu = new JMenu("Help");
   helpMenu.setMnemonic(KeyEvent.VK_H);
   JMenuItem fmh = new JMenuItem("About Sequence List");
   fmh.addActionListener(new ActionListener()
   {
     public void actionPerformed(ActionEvent e)
     {
        ClassLoader cl = this.getClass().getClassLoader();
        try
        {
          URL inURL = cl.getResource("resources/seqList.html");
          new Browser(inURL,"resources/seqList.html");
        }
        catch (MalformedURLException mex)
        {
          System.out.println("Didn't find resources/seqList.html");
        }
        catch (IOException iex)
        {
          System.out.println("Didn't find resources/seqList.html");
        }
      }
    });
    helpMenu.add(fmh);
    menuPanel.add(helpMenu);
  }

  /**
  *
  * Look for first set to default in the table.
  * @return 	index to row
  *
  */
  private int getDefaultRow()
  {
    int nrow = seqModel.getRowCount();
    for(int i =0;i<nrow;i++)
    {
      Boolean isDef = (Boolean)seqModel.getValueAt(i,
                        SequenceListTableModel.COL_DEF);
      if(isDef.booleanValue())
        return i;
    }
    return -1;
  }

  /**
  *
  * Cygwin uses infoseq to get sequence length and type
  * and uses infoalign to get the sequence weight.
  *
  */
  private int cygwinSeqAttr(String fc, JembossParams mysettings)
  {
    String[] envp = new String[2];  /* environment vars */
    String ps = new String(System.getProperty("path.separator"));
    String embossPath = mysettings.getEmbossPath();
    embossPath = new String("PATH" + ps +
                      embossPath + ps + mysettings.getEmbossBin() + ps);
    envp[0] = "PATH=" + embossPath;
    envp[1] = "EMBOSS_DATA=" + mysettings.getEmbossData();

    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 -1;

    StringTokenizer stok = new StringTokenizer(stdout,"\n ");
    stok.nextToken();
    return Integer.parseInt(stok.nextToken().trim());
  }

  /**
  *
  * Get the default Sequence name
  * @return 	default sequence name or null if no default 
  *
  */
  public String getDefaultSequenceName()
  {
    int ndef = getDefaultRow();
    if(ndef<0)
      return null;

    String seqName = (String)seqModel.getValueAt(ndef,
             SequenceListTableModel.COL_NAME);

    if(table.isListFile(ndef).booleanValue())
      seqName = "@".concat(seqName);

    return seqName;
  }

  /**
  *
  * Return the number of rows in the table
  * @return 	number of rows in the table
  *
  */
  public int getRowCount()
  {
    return seqModel.getRowCount();
  }

  /**
  *
  * The <code>SequenceData</code> for a given row
  * number.
  * @param row 	number
  * @return 	<code>SequenceData</code> for the row
  *
  */
  public SequenceData getSequenceData(int nrow)
  {
    return seqModel.getSequenceData(nrow);
  }

  /**
  *
  * Determines if a sequence list has been stored
  * ("~/.jembossSeqList")
  * @return 	true if a sequence list has been stored
  *
  */
  public boolean isStoreSequenceList()
  {
    return storeSeqList.isSelected();
  }

}


/**
*
* Extend JTable to implement a drag and drop table for
* storing sequence lists (SequenceList)
*
*/
class DragJTable extends JTable implements DragGestureListener,
             DragSourceListener, DropTargetListener
{

  /** model for the sequence table */
  private SequenceListTableModel seqModel;

  /**
  *
  * @param seqModel	model for the sequence table
  *
  */
  public DragJTable(SequenceListTableModel seqModel)
  {
    super();
    this.seqModel = seqModel;
    DragSource dragSource = DragSource.getDefaultDragSource();
    dragSource.createDefaultDragGestureRecognizer(
           this,                              // component where drag originates
           DnDConstants.ACTION_COPY_OR_MOVE,  // actions
           this);
    setDropTarget(new DropTarget(this,this));
  }