Jpan_PhyTreeMenu.java

package moduls.frm.Panels;

import java.awt.Color;
import java.awt.Font;
import java.awt.GridBagConstraints;
import java.awt.GridBagLayout;
import java.awt.Insets;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.util.LinkedList;

import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JTextField;

import newickTreeParsing.Tree;
import newickTreeParsing.TreeParser;

import moduls.frm.FrmPrincipalDesk;

public class Jpan_PhyTreeMenu extends JPanel implements ActionListener {

	//fields
	private FrmPrincipalDesk f;
	
	//GUI components
	private Font fontStandard = new Font("Dialog", Font.BOLD, 10);
	private JLabel LoadPhyTreeBanner;
	private String strLoadPhyTreeBanner = " LOAD A PHYLOGENETIC TREE";
	private JButton btnPhyTree;
	private String strPhyTree = "Load";
	private JTextField CurrentTree, TreeType;
	private String strCurrentTree = " Current Tree: ";
	private String strTreeType = " Tree Type:";
	private JLabel CurrentlyEnabledBanner;
	private String strCurrentlyEnabledBanner = " AVAILABLE PHYLOGENETIC TREES";
	private JComboBox<String> menuLoadedPhyTrees;
	private JButton btnRemoveSelectedPhyTree;
	private String strRemoveSelectedPhyTree = "Remove Selected";
	
	private JLabel DisplayOptionsBanner;
	private String strDisplayOptions = " PHYLOGENETIC TREE DISPLAY OPTIONS";
	private ButtonGroup PhyloDisplayOptions, PhyloTreeType;
	private JRadioButton radCladogram, radPhylogram;
	private JRadioButton radSpecies, radGene;
	private String strSpecies = "Species Tree";
	private String strGene = "Gene Tree";
	private JCheckBox chkDashed, chkWeights;
	private String strCladogram = "Cladogram";
	private String strPhylogram = "Phylogram";
	private String strchkDashed = "Draw dashed line to label";
	private String strchkWeights = "Display support values";
			
	//Data components
	private File FilePath = null;
	private LinkedList<File> LoadedPhyTrees = new LinkedList<File>();
	private LinkedList<Tree> ParsedPhyTrees = new LinkedList<Tree>();
	private Tree CurrentParsedTree;
	
	//constructor
	public Jpan_PhyTreeMenu(FrmPrincipalDesk fr){
		this.f = fr;
		this.FilePath = fr.getFileChooserSource();
		
		//build components
		this.getPanel();
	}
	
	//build components
	public void getPanel(){
		//initialize panel
		this.setLayout(new GridBagLayout());
		this.setBorder(BorderFactory.createTitledBorder("Phylogenetic Tree Settings")); // title
		final GridBagConstraints c = new GridBagConstraints();
		int gridy = 0;
		
		//initial GridBagLayout parameters
		c.anchor = GridBagConstraints.FIRST_LINE_START;
		c.weightx = 1;
		//c.weighty = 1;
		c.insets = new Insets(1,1,1,1);

		//Load Phylogenetic Tree banner
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.gridwidth = 4;
		LoadPhyTreeBanner = new JLabel(strLoadPhyTreeBanner);
		LoadPhyTreeBanner.setBackground(Color.GRAY);
		LoadPhyTreeBanner.setOpaque(true);
		LoadPhyTreeBanner.setFont(fontStandard);
		add(LoadPhyTreeBanner,c);
		gridy++;
		
		//Load Phylogenetic Tree button
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.NONE;
		c.gridwidth = 4;
		btnPhyTree = new JButton(strPhyTree);
		btnPhyTree.setFont(fontStandard);
		btnPhyTree.addActionListener(this);
		add(btnPhyTree,c);
		gridy++;

		//Currently Loaded banner
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.gridwidth = 4;
		CurrentlyEnabledBanner = new JLabel(strCurrentlyEnabledBanner);
		CurrentlyEnabledBanner.setBackground(Color.GRAY);
		CurrentlyEnabledBanner.setOpaque(true);
		CurrentlyEnabledBanner.setFont(fontStandard);
		add(CurrentlyEnabledBanner,c);
		gridy++;

		//Currently Loaded tree tag
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.NONE;
		c.gridwidth = 1;
		CurrentTree = new JTextField(strCurrentTree);
		CurrentTree.setFont(fontStandard);
		CurrentTree.setEditable(false);
		add(CurrentTree,c);
		gridy++;
		
		// currently loaded motifs drop-down menu
		c.ipady = 0;
		c.gridx = 0;
		c.gridy = gridy;
		c.gridwidth = 4;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		menuLoadedPhyTrees = new JComboBox<String>(getLoadedPhyTrees());
		menuLoadedPhyTrees.addActionListener(this);
		menuLoadedPhyTrees.setEnabled(true);
		menuLoadedPhyTrees.setFont(fontStandard);
		add(menuLoadedPhyTrees, c);
		gridy++;
		
		//Remove phylogenetic tree button
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.NONE;
		c.gridwidth = 4;
		btnRemoveSelectedPhyTree = new JButton(strRemoveSelectedPhyTree);
		btnRemoveSelectedPhyTree.setFont(fontStandard);
		btnRemoveSelectedPhyTree.addActionListener(this);
		add(btnRemoveSelectedPhyTree,c);
		gridy++;
		
		//Currently Loaded tree tag
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.NONE;
		c.gridwidth = 1;
		TreeType = new JTextField(strTreeType);
		TreeType.setFont(fontStandard);
		TreeType.setEditable(false);
		//add(TreeType,c);
		gridy++;
		
		//define button group
		PhyloTreeType = new ButtonGroup();
		radSpecies = new JRadioButton(strSpecies);
		radGene = new JRadioButton(strGene);
		PhyloTreeType.add(radSpecies);
		PhyloTreeType.add(radGene);
		
		//Tree option 1: Species Tree
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.gridwidth = 1;
		radSpecies.setSelected(true);
		radSpecies.addActionListener(this);
		//add(radSpecies, c);
		
		//Tree option 2: Gene Tree
		c.gridx = 1;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.insets = new Insets(1,1,10,1);
		c.gridwidth = 1;
		radGene.setSelected(false);
		radGene.addActionListener(this);
		//add(radGene, c);
		gridy++;
		
		//Display Options banner
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.gridwidth = 4;
		c.insets = new Insets(0,0,0,0);
		DisplayOptionsBanner = new JLabel(strDisplayOptions);
		DisplayOptionsBanner.setBackground(Color.GRAY);
		DisplayOptionsBanner.setOpaque(true);
		DisplayOptionsBanner.setFont(fontStandard);
		add(DisplayOptionsBanner,c);
		gridy++;
		
		//define button group
		PhyloDisplayOptions = new ButtonGroup();
		radCladogram = new JRadioButton(strCladogram);
		radPhylogram = new JRadioButton(strPhylogram);
		PhyloDisplayOptions.add(radCladogram);
		PhyloDisplayOptions.add(radPhylogram);
		
		//Display option 1: cladogram
		c.gridx = 0;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.gridwidth = 1;
		radCladogram.setSelected(false);
		radCladogram.addActionListener(this);
		add(radCladogram, c);
		
		//Display option 2: phylogram
		c.gridx = 1;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.gridwidth = 3;
		radPhylogram.setSelected(true);
		radPhylogram.addActionListener(this);
		add(radPhylogram, c);
		gridy++;
		
		//option: draw dashed line to label
		c.gridx = 1;
		c.gridy = gridy;
		c.gridheight = 1;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.gridwidth = 3;
		chkDashed = new JCheckBox(strchkDashed);
		chkDashed.addActionListener(this);
		chkDashed.setSelected(true);
		chkDashed.setEnabled(true);
		this.add(chkDashed, c);
		gridy++;
		
		c.gridx = 0;
		c.gridy = gridy;
		c.fill = GridBagConstraints.HORIZONTAL;
		c.gridwidth = 4;
		chkWeights = new JCheckBox(strchkWeights);
		chkWeights.setSelected(true);
		chkWeights.addActionListener(this);
		this.add(chkWeights, c);
		gridy++;
		
	}
	
	//convert motifs from linked list to integer array
	public String[] getLoadedPhyTrees(){
		String PhyTrees[];
		if (LoadedPhyTrees.size() > 0){
			PhyTrees = new String[LoadedPhyTrees.size()];
			for (int i = 0; i < LoadedPhyTrees.size(); i++){
				PhyTrees[i] = LoadedPhyTrees.get(i).getName();
			}
		} else {
			PhyTrees =  new String[1];
			PhyTrees[0] = "<none>";
		}
		
		return PhyTrees;
	}
	
	//parse a tree
	public Tree ParseNewickTree(File NewickTreeFile){

	  //Initialize output
	  Tree t;
		
	  //attempt to import file
      try {
          BufferedReader r = new BufferedReader(new FileReader(NewickTreeFile));
          TreeParser tp = new TreeParser(r);
          t = tp.tokenize(NewickTreeFile.length(), NewickTreeFile.getName(), null);
      } catch (FileNotFoundException e) {
          JOptionPane.showMessageDialog(null, "The selected file is not appropriately formatted.");
          t = null;
      }
      
      //return tree file
      return t;
	}
	
	public Tree ParseNexusTree(File NexusTreeFile){
		
		//Initialize output
		Tree t;
		
		  //attempt to import file
	      try {
	          BufferedReader r = new BufferedReader(new FileReader(NexusTreeFile));
	          TreeParser tp = new TreeParser(r);
	          t = tp.tokenize(NexusTreeFile.length(), NexusTreeFile.getName(), null);
	      } catch (FileNotFoundException e) {
	          JOptionPane.showMessageDialog(null, "The selected file is not appropriately formatted.");
	          t = null;
	      }
		
		return t;
	}
	
	
	@Override
	public void actionPerformed(ActionEvent evt) {
		
		if (f.getOS() != null){
			
			
			//load button
			if (evt.getSource().equals(btnPhyTree)){
				ImportPhyTree();
			}
			
			//switch menu to active tree
			if (evt.getSource().equals(menuLoadedPhyTrees)){
				//retrieve name of current tree
				String CurrentName = (String) menuLoadedPhyTrees.getSelectedItem();
				
				//find this tree in the list, and set it to the active one.
				for (Tree t : ParsedPhyTrees){
					if (t.getName().equals(CurrentName)){
						setCurrentParsedTree(t);
						break;
					}
				}
			}
			
			//remove an available phylogenetic tree
			if (evt.getSource().equals(btnRemoveSelectedPhyTree)){
				
				//remove from the list of trees
				for (Tree t : ParsedPhyTrees){
					if (t.getName().equals((String) menuLoadedPhyTrees.getSelectedItem())){
						ParsedPhyTrees.remove(t);
						f.getOS().getParsedPhyTrees().remove(t);
						break;
					}
				}
				
				//remove from the list of files
				for (File f: LoadedPhyTrees){
					if (f.getName().equals((String) menuLoadedPhyTrees.getSelectedItem())){
						LoadedPhyTrees.remove(f);
						break;
					}
				}
				
				
				//remake the menu
				menuLoadedPhyTrees.removeAllItems();
				String[] PhyTrees = getLoadedPhyTrees();
				for (String s : PhyTrees){
					menuLoadedPhyTrees.addItem(s);
				}
			}
			
			//display options
			if (evt.getSource().equals(radPhylogram)){
				this.chkDashed.setEnabled(true);
				
			}
			
			if (evt.getSource().equals(radCladogram)){
				this.chkDashed.setEnabled(false);
			}
			
			//redraw phylogenetic tree
			if (evt.getSource().equals(radPhylogram) || 
					evt.getSource().equals(radCladogram) ||
					evt.getSource().equals(chkDashed) ||
					evt.getSource().equals(chkWeights)){
				
				//update phylogenetic tree, if appropriate.
				if (f.getCurrentFrame() != null){	//frame exists
					
					//phylogenetic tree exists
					if (f.getCurrentFrame().getInternalFrameData().getQD().getAnalysesList().isOptionRenderPhylogeny()){
						
						//repaint!
						f.getCurrentFrame().getInternalFrameData().getPhyloTreePanel().repaint();
						
					}
				}
			}
			
		} else {
			f.NoOS();
		}


	}

	public void ImportPhyTree(){
		
		//create filechooser
		JFileChooser getPhyTree = new JFileChooser();
		getPhyTree.setFileSelectionMode(JFileChooser.FILES_ONLY);
		getPhyTree.setDialogTitle("Select Phylogenetic tree file (Newick format required)");
		
		//open at last open point.
		if (f.getFileChooserSource() != null){
			getPhyTree.setCurrentDirectory(f.getFileChooserSource());
		} else {
			getPhyTree.setCurrentDirectory(new File("."));
		}
		
		getPhyTree.showOpenDialog(getPhyTree);
		
		//retrieve file
		File TreeFile = getPhyTree.getSelectedFile();
		
		//if the file is not null (cancel operation), try to parse
		if (TreeFile != null){
			
			//update current directory
			f.setFileChooserSource(getPhyTree.getCurrentDirectory());
			
			Tree t = ParseNewickTree(TreeFile);
			setCurrentParsedTree(t);

			//add + update, if the tree is new.
			if (!LoadedPhyTrees.contains(TreeFile) && t != null){
				
				//update catalog
				CurrentParsedTree = t;				//Tree
				ParsedPhyTrees.add(t);				//LinkedList<Tree>
				LoadedPhyTrees.add(0,TreeFile);		//LinkedList<File>
				FilePath = TreeFile;				//Path
						
				//update GUI
				menuLoadedPhyTrees.removeAllItems();
				String[] PhyTrees = getLoadedPhyTrees();
				for (String s : PhyTrees){
					menuLoadedPhyTrees.addItem(s);
				}
				
				//update OS
				f.getOS().getParsedPhyTrees().add(t);
				f.getOS().getLoadedPhyTrees().add(0, TreeFile);
				
			}
		}
	}
	
	//retrieve the current parsed phylogenetic tree
	public Tree getCurrentParsedTree() {
		return CurrentParsedTree;
	}

	public void setCurrentParsedTree(Tree currentParsedTree) {
		CurrentParsedTree = currentParsedTree;
	}

	public JRadioButton getRadCladogram() {
		return radCladogram;
	}

	public JRadioButton getRadPhylogram() {
		return radPhylogram;
	}

	public JCheckBox getChkDashed() {
		return chkDashed;
	}

	public JCheckBox getChkWeights() {
		return chkWeights;
	}

	public LinkedList<Tree> getParsedPhyTrees() {
		return ParsedPhyTrees;
	}

	public void setParsedPhyTrees(LinkedList<Tree> parsedPhyTrees) {
		ParsedPhyTrees = parsedPhyTrees;
	}

	public void setLoadedPhyTrees(LinkedList<File> loadedPhyTrees) {
		LoadedPhyTrees = loadedPhyTrees;
	}

	public File getFilePath() {
		return FilePath;
	}

	public void setFilePath(File filePath) {
		FilePath = filePath;
	}

	public JComboBox<String> getMenuLoadedPhyTrees() {
		return menuLoadedPhyTrees;
	}

	public void setMenuLoadedPhyTrees(JComboBox<String> menuLoadedPhyTrees) {
		this.menuLoadedPhyTrees = menuLoadedPhyTrees;
	}

	public JRadioButton getRadSpecies() {
		return radSpecies;
	}

	public void setRadSpecies(JRadioButton radSpecies) {
		this.radSpecies = radSpecies;
	}

	public JRadioButton getRadGene() {
		return radGene;
	}

	public void setRadGene(JRadioButton radGene) {
		this.radGene = radGene;
	}

}