/***************************************************************************
 * Author:  Jianwei (Jerry) Li
 * Name:  GenepixVsTav (Version 1.0)
 * Date:  Created: 04/02/2003 and modified:  04/04/2002
 * Descp: A Java panel that is the interface for converting a ScanArray file format
 *        to Tav and Mev format.
 ***************************************************************************/
package org.tigr.microarray.converter;

import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.util.*;
import javax.swing.*;
import javax.swing.border.*;
import javax.swing.event.*;
import javax.swing.Timer;
import org.tigr.util.awt.GBA;
import org.tigr.util.*;
import org.tigr.util.io.IOUtil;

public class ScanArrayPanel extends ConvertPanel {
  private JComboBox intensityModeCombx;
  private JPanel intensityPanel;
  private JCheckBox keepAllCB, gSwapChanCB;
  private JList gInputFileList;
  private JLabel intensityLB;

    // variable declare
  private String gfName;  // GenePix file name
  private String tfName;  // tav file name
  private String info;
  private int quantWay;
  private boolean keepAll, gSwapChan;

  private final String NUM_FILE = "  Number of Files:  ";
  private final String INTEN_MODE[] = {"Total", "Mean", "Mode", "Median"};
  private final int TOTAL = 0;
  private final int MEAN = 1;
  private final int MODE = 2;
  private final int MEDIAN = 3;

  public ScanArrayPanel(ExpressConverter convt) {
    super(convt);
    keepAll = false;
    gSwapChan = false;
    quantWay = TOTAL;
    info = new String("");
    createGUI();
  }

  /****************************************************************************
   * <b>Description: </b>
   *    alters the interface to meet the requirement for output file type.
   * <p><b>Parameter: </b>
   * <br> index -- the selected index of the combobox.
   ***************************************************************************/
  public void adjustGUI(int index){
    int numFiles;
    String tmpName = new String("");

    outputType = index;

    if(outputType == TAV_OUT){
      gOutputFileLB.setText(TAV_FILE);
      keepAllCB.setEnabled(true);
      this.activeIntensityWay(false);
    } else {
      gOutputFileLB.setText(MEV_FILE);
      keepAllCB.setEnabled(false);
      this.activeIntensityWay(true);
    }
    numFiles = outputFileNames.size();

    for(int i=0; i<numFiles; i++){
      tmpName = (String)outputFileNames.elementAt(i);
      tmpName = IOUtil.dropExtension(tmpName);
      tmpName += "." + FILE_TYPE[outputType];
      outputFileNames.setElementAt(tmpName, i);
    }
    validate();
  }

  /***************************************************************************
   * <b>Description: </b>
   *    changes the number of input and output files based on testing on the
   *    system to see if an exsiting file is to be overwritten.
   * <p><b>Paramters: </b>
   * <br> inFiles -- the input files.
   * <br> outFiles -- the output files.
   ***************************************************************************/
  public void changeFileList(Vector inFiles, Vector outFiles){
    selectedFiles = inFiles;
    outputFileNames = outFiles;
    gInputFileList.setListData(inFiles);
    gOutputFileList.setListData(outFiles);
    gFileNumLB.setText(NUM_FILE + selectedFiles.size());
  }

  /****************************************************************************
   * <b>Description: </b>
   *    modifies the output file names.
   * <p><b>Parameter: </b>
   * <br>  path -- the new directory.
   ***************************************************************************/
  public void editDirectory(String path){
    int selected = -1;
    int num;
    String tempName, tempPath;

    tempPath = path;
    selected = gOutputFileList.getSelectedIndex();

    num = outputFileNames.size();
    for(int i=0; i<num; i++){
      tempName = (String)outputFileNames.elementAt(i);
      tempName = IOUtil.extractFileNameFromPath(tempName);
      tempName = tempPath + "\\" + tempName;
      outputFileNames.setElementAt(tempName, i);
    }
    gOutputFileList.setListData(outputFileNames);
    if(selected >=0){
      gOutputFileList.setSelectedIndex(selected);
    } else {
      gOutputFileList.setSelectedIndex(0);
    }
  }

  /****************************************************************************
   * <b>Description: </b>
   *    modifies the output file names.
   ***************************************************************************/
  public void editFileName(){
    int selected = -1;
    String tempName;

    selected = gOutputFileList.getSelectedIndex();
    if(selected >= 0){
      tempName = (String)(gOutputFileList.getModel()).getElementAt(selected);
      LongTextChanger changer = new LongTextChanger(parent, true, tempName);
      changer.setTitle(parent.TITLE);
      changer.show();

      if(changer.isTextChanged()){
        tempName = changer.getText();

        StringTokenizer token = new StringTokenizer(tempName, ":");

        if(token.countTokens() <= 1){
          tempName = "c:\\" + tempName;
        }

        tempName = IOUtil.dropExtension(tempName);
        if(tempName.lastIndexOf('.') == tempName.length()-1){
          tempName += FILE_TYPE[outputType];
        } else {
          tempName += "." + FILE_TYPE[outputType];
        }
        outputFileNames.setElementAt(tempName, selected);
        gOutputFileList.setListData(outputFileNames);
        gOutputFileList.setSelectedIndex(selected);
      }
    }
  }


  public Vector getOutputFileNames() { return outputFileNames; }
  public int getQuantiationWay() { return quantWay; }
  public Vector getSelectedFiles() { return selectedFiles; }
  public boolean isOutputReady() { return outputReady; }
  public boolean keepAllInformation() { return keepAll; }
  public boolean swapOriginalChannel() { return gSwapChan; }

  /***************************************************************************
   * <b>Description: </b>
   *    removes a set of files from the selected list.
   ***************************************************************************/
  public void removeFileFromList(){
    int addrs[], i, indx;

    addrs = gOutputFileList.getSelectedIndices();
    if(addrs.length > 0){
      for(i=0; i<addrs.length; i++){
        selectedFiles.remove(addrs[i]);
        outputFileNames.remove(addrs[i]);
      }
      gInputFileList.setListData(selectedFiles);
      gOutputFileList.setListData(outputFileNames);
      if(outputFileNames.size() > 0){
        gOutputFileList.setSelectedIndex(0);
      }
      gFileNumLB.setText(NUM_FILE + selectedFiles.size());
    }
  }

  /****************************************************************************
   * <b>Description: </b>
   *   set the interface to its original status.
   **************************************************************************/
   public void reset(){
    selectedFiles.removeAllElements();
    outputFileNames.removeAllElements();
    gFileNumLB.setText(NUM_FILE);

    gInputFileList.setListData(selectedFiles);
    gOutputFileList.setListData(outputFileNames);

    wantSort = true;
    keepAll = false;
    outputReady = false;
    gSwapChan = false;

    sortCB.setSelected(wantSort);
    keepAllCB.setSelected(keepAll);
    gSwapChanCB.setSelected(gSwapChan);
    parent.activateButton(outputReady, outputReady);
  }

  /***************************************************************************
   * <b>Description: </b>
   *    places the selected file names to both genepix and output file lists.
   **************************************************************************/
  public void setSelectedFiles(String[] newFiles){
    int num, i;
    String temp = new String("");

    num = newFiles.length;

    for(i=0; i<num; i++){
      if(!selectedFiles.contains(newFiles[i])){
        selectedFiles.add(newFiles[i]);
        outputFileNames.add(IOUtil.dropExtension(newFiles[i]) + "." + FILE_TYPE[outputType]);
      }
    }
    gInputFileList.setListData(selectedFiles);
    gOutputFileList.setListData(outputFileNames);
    gOutputFileList.setSelectedIndex(0);
    gFileNumLB.setText(NUM_FILE + selectedFiles.size());
  }

  /*****************************************************************************
   * <b>Description: </b>
   *  finds a selected file as a File object

   * <p><b>Parameters: </b>
   *  <br>ext -- file name extension;
   *  <br>fileType -- describe the file type;
   *  <br>path --- the path selected file is located at.
   * <p><b>Return: </b>  the selected file.
   ***************************************************************************/
  private File getFile(String ext, String fileType, String path) {
    int result;
    File temp;
    JFileChooser fileChooser;

    fileChooser = new JFileChooser(path);
    MadamFileFilter wanted = new MadamFileFilter(ext, fileType);
    fileChooser.setFileFilter(wanted);
    fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
    fileChooser.setDialogTitle("Save Output As");
    fileChooser.setMultiSelectionEnabled(false);

    result = fileChooser.showSaveDialog(this);

    if(result == JFileChooser.CANCEL_OPTION) {
      return null;
    }

    temp = fileChooser.getSelectedFile();
    return temp;
  }

  /*****************************************************************************
   * <b>Description: </b>
   *    create a GUI for program
   ****************************************************************************/
  protected void createGUI(){
    this.setLayout(new GridBagLayout());

    gInputFileLB = new JLabel("ScanArray Files:");

    gInputFileList = new JList();
    gInputFileList.setBorder(gLow);
    actionHandler(gInputFileList);
    actionHandler(gOutputFileList);

    gFilesSP = new JScrollPane(gInputFileList);

    intensityLB = new JLabel("Intensity Generated By:");
    intensityPanel = new JPanel(new GridBagLayout());

    gSwapChanCB = new JCheckBox("Swap Channel");
    gSwapChanCB.setToolTipText("If file has channel 1 as Cy5, swap it as Cy3.");
    gSwapChanCB.setSelected(gSwapChan);
    gSwapChanCB.addActionListener(new ActionListener(){
      public void actionPerformed(ActionEvent ce){
        if(gSwapChanCB.isSelected()){
          gSwapChan = true;
        } else {
          gSwapChan = false;
        }
      }
    });

    intensityModeCombx = new JComboBox(INTEN_MODE);
    intensityModeCombx.setBorder(gLow);
    intensityModeCombx.setPreferredSize(new Dimension(80, 23));
    intensityModeCombx.addItemListener(new ItemListener(){
      public void itemStateChanged(ItemEvent ie){
        quantWay = intensityModeCombx.getSelectedIndex();
      }
    });

    keepAllCB = new JCheckBox("Keep All Information in the ScanArray File.");
    keepAllCB.setToolTipText("Attach all anotation info at the end.");
    keepAllCB.setSelected(keepAll);
    keepAllCB.addActionListener(new ActionListener(){
      public void actionPerformed(ActionEvent ce){
        if(keepAllCB.isSelected()){
          keepAll = true;
        } else {
          keepAll = false;
        }
      }
    });

    gba.add(this, gFileSplitPane, 0, 0, 2, 1, 1, 1, GBA.B, GBA.C, 5, 5, 10, 5);
    gba.add(this, sortCB, 0, 1, 1, 1, 1, 0, GBA.H, GBA.C, 10, 15, 3, 5);
    gba.add(this, keepAllCB, 0, 2, 1, 1, 1, 0, GBA.H, GBA.C, 3, 15, 3, 5);
    gba.add(this, gIntenPanel, 1, 1, 1, 2, 1, 0, GBA.H, GBA.W, 10, 0, 3, 5);

    gba.add(intensityPanel, intensityLB, 0, 0, 1, 1, 1, 0, GBA.H, GBA.W, 0, 0, 0, 5);
    gba.add(intensityPanel, intensityModeCombx, 1, 0, 1, 1, 0, 0, GBA.NONE, GBA.E, 0, 5, 0, 10);
    gba.add(intensityPanel, gSwapChanCB, 2, 0, 1, 1, 0, 0, GBA.NONE, GBA.E, 0, 5, 0, 2);

    gba.add(gInputPL, gInputFileLB, 0, 0, 1, 1, 1, 0, GBA.H, GBA.C, 5, 10, 5, 2);
    gba.add(gInputPL, intensityPanel, 1, 0, 1, 1, 0, 0, GBA.NONE, GBA.C, 5, 0, 5, 5);
    gba.add(gInputPL, gFilesSP, 0, 1, 2, 1, 1, 1, GBA.B, GBA.C, 1, 2, 5, 2);
  }
}