<commit_before>package org.biojava.bio.structure.align.gui;

import java.awt.BorderLayout;
import java.awt.Dimension;

import java.io.IOException;


import javax.swing.Box;

import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTabbedPane;
import javax.swing.JTextField;


import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.StructureException;
import org.biojava.bio.structure.StructureTools;

import org.biojava.bio.structure.align.util.UserConfiguration;
import org.biojava.bio.structure.align.webstart.WebStartMain;
import org.biojava.bio.structure.io.FileParsingParameters;
import org.biojava.bio.structure.io.MMCIFFileReader;
import org.biojava.bio.structure.io.PDBFileReader;
import org.biojava.bio.structure.io.StructureIOFile;
import org.biojava.bio.structure.gui.util.StructurePairSelector;


/** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
 * 
 * @author Andreas
 *
 */
public class SelectPDBPanel 
extends JPanel 
implements StructurePairSelector{

	boolean debug = true;
	
	JTextField f1;
	JTextField f2;
	JTextField c1;
	JTextField c2;
	JTextField r1;
	JTextField r2;

	UserConfiguration config;
	JTabbedPane configPane;

	/**
	 * 
	 */
	private static final long serialVersionUID = 4002475313717172193L;



	public SelectPDBPanel(){
		this(true);
	}
	public SelectPDBPanel(boolean show2PDBs) {	

		Box vBox = Box.createVerticalBox();

		JLabel help = new JLabel("Optional: specify chain ID or range.");
		Box hBox1 = Box.createHorizontalBox();
		hBox1.add(Box.createGlue());
		hBox1.add(help);
		vBox.add(hBox1);


		//pdbDir = new JTextField(20);

		int pdbfSize = 4;

		f1 = new JTextField(pdbfSize);
		c1 = new JTextField(1);
		r1 = new JTextField(5);
		Box p1 = getPDBFilePanel(1,f1,c1,r1);
		vBox.add(p1);

		f2 = new JTextField(pdbfSize);
		c2 = new JTextField(1);
		r2 = new JTextField(5);
		Box p2 = getPDBFilePanel(2, f2,c2,r2);

		if ( show2PDBs)
			vBox.add(p2);	

		//vBox.setBorder(BorderFactory.createLineBorder(Color.black));
		this.add(vBox);
	}

	public String getName1() {
		
		String chainId = c1.getText().trim();
		
		String name = f1.getText().trim(); 
		
		if ( ! chainId.equals("") ){
			name += "." + chainId;
		}
		return  name;
	}
	public String getName2() {
		String chainId = c2.getText().trim();
		
		String name = f2.getText().trim();
		
		if ( ! chainId.equals("") ){
			name += "." + chainId;
		}
		return  name;
	}
	public Structure getStructure1() throws StructureException{
		return fromPDB(f1,c1,r1);
	}

	public Structure getStructure2() throws StructureException{    
		return fromPDB(f2,c2,r2);
	}


	
	
	
	
	private Structure fromPDB(JTextField f, JTextField c,JTextField r) throws StructureException{
		String pdb = f.getText().trim();

		UserConfiguration config = WebStartMain.getWebStartConfig();
		
		if ( pdb.length() < 4) {
			f.setText("!!!");
			return null;
		}

		String chain = c.getText().trim();
		if ( debug )
			System.out.println("file :" + pdb + " " +  chain);


		String range = r.getText().trim();
		
		String fileFormat = config.getFileFormat();
		
		StructureIOFile reader = null;
		if ( fileFormat.equals(UserConfiguration.PDB_FORMAT)){
			PDBFileReader re = new PDBFileReader();
			
			reader = re;
		} else if ( fileFormat.equals(UserConfiguration.MMCIF_FORMAT)){						
			reader = new MMCIFFileReader();
			
		} else {
			throw new StructureException("Unkown file format " + fileFormat);
		}
		
		FileParsingParameters params = new FileParsingParameters();
        params.setAlignSeqRes(false);
		reader.setFileParsingParameters(params);
		
		reader.setPath(config.getPdbFilePath());
		
		reader.setPdbDirectorySplit(config.isSplit());
		
		reader.setAutoFetch(config.getAutoFetch());
		
	
		Structure structure ;
		try {
			structure = reader.getStructureById(pdb);
		} catch (IOException e) {
			throw new StructureException("Could not read structure " + pdb ,e);
		}


		//System.out.println(" got range: " + range);
		if ( range != null && ( ! range.equals(""))){
			Structure s = StructureTools.getSubRanges(structure, range);
			//System.out.println("got atoms: " + StructureTools.getAtomCAArray(s).length);
			return s;
		} 
		Structure s = StructureTools.getReducedStructure(structure,chain);
		//System.out.println("got atoms: " + StructureTools.getAtomCAArray(s).length);
		return s;

	}

	private Box getPDBFilePanel(int pos ,JTextField f, JTextField c, JTextField r){

		//JPanel panel = new JPanel();
		//panel.setBorder(BorderFactory.createLineBorder(Color.black));

		JLabel l01 = new JLabel("PDB code ");

		//panel.add(l01);
		Box hBox = Box.createHorizontalBox();
		hBox.add(Box.createGlue());
		hBox.add(l01);

		JLabel l11 = new JLabel(pos + ":");
		f.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
		f.setToolTipText("Provide 4-character PDB code here. Example: 4hhb");
		hBox.add(l11);
		hBox.add(Box.createVerticalGlue());
		hBox.add(f, BorderLayout.CENTER);
		hBox.add(Box.createGlue());

		//panel.add(hBox11);

		//Box hBox21 = Box.createHorizontalBox();
		JLabel l21 = new JLabel("Chain" + pos + ":");
		hBox.add(l21);

		c.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
		//hBox.add(Box.createGlue());
		hBox.add(c, BorderLayout.CENTER);

		String msg1 = "Both chainID and range specification are optional. If both are provided, range has preference.";
		l21.setToolTipText(msg1);
		c.setToolTipText(msg1);

		JLabel rangeL = new JLabel(" Range " + pos + ":");
		hBox.add(Box.createGlue());
		hBox.add(rangeL);
		r.setMaximumSize(new Dimension(Short.MAX_VALUE,30));

		// set help text:
		String msg ="Syntax example: A:407-495,A:582-686";
		rangeL.setToolTipText(msg);
		r.setToolTipText(msg);

		//hBox.add(Box.createGlue());
		hBox.add(r,BorderLayout.CENTER);

		//hBox21.add(Box.createGlue());

		//panel.add(hBox21);



		return hBox;
	}





}
<commit_msg>using the name that gets assigned by StructureTools.getSubRanges<commit_after>package org.biojava.bio.structure.align.gui;

import java.awt.BorderLayout;
import java.awt.Dimension;

import java.io.IOException;


import javax.swing.Box;

import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTabbedPane;
import javax.swing.JTextField;


import org.biojava.bio.structure.Structure;
import org.biojava.bio.structure.StructureException;
import org.biojava.bio.structure.StructureTools;

import org.biojava.bio.structure.align.util.UserConfiguration;
import org.biojava.bio.structure.align.webstart.WebStartMain;
import org.biojava.bio.structure.io.FileParsingParameters;
import org.biojava.bio.structure.io.MMCIFFileReader;
import org.biojava.bio.structure.io.PDBFileReader;
import org.biojava.bio.structure.io.StructureIOFile;
import org.biojava.bio.structure.gui.util.StructurePairSelector;


/** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
 * 
 * @author Andreas
 *
 */
public class SelectPDBPanel 
extends JPanel 
implements StructurePairSelector{

	boolean debug = true;
	
	JTextField f1;
	JTextField f2;
	JTextField c1;
	JTextField c2;
	JTextField r1;
	JTextField r2;

	UserConfiguration config;
	JTabbedPane configPane;

	/**
	 * 
	 */
	private static final long serialVersionUID = 4002475313717172193L;



	public SelectPDBPanel(){
		this(true);
	}
	public SelectPDBPanel(boolean show2PDBs) {	

		Box vBox = Box.createVerticalBox();

		JLabel help = new JLabel("Optional: specify chain ID or range.");
		Box hBox1 = Box.createHorizontalBox();
		hBox1.add(Box.createGlue());
		hBox1.add(help);
		vBox.add(hBox1);


		//pdbDir = new JTextField(20);

		int pdbfSize = 4;

		f1 = new JTextField(pdbfSize);
		c1 = new JTextField(1);
		r1 = new JTextField(5);
		Box p1 = getPDBFilePanel(1,f1,c1,r1);
		vBox.add(p1);

		f2 = new JTextField(pdbfSize);
		c2 = new JTextField(1);
		r2 = new JTextField(5);
		Box p2 = getPDBFilePanel(2, f2,c2,r2);

		if ( show2PDBs)
			vBox.add(p2);	

		//vBox.setBorder(BorderFactory.createLineBorder(Color.black));
		this.add(vBox);
	}

	public String getName1() {
		
		String chainId = c1.getText().trim();
		
		String name = f1.getText().trim(); 
		
		if ( ! chainId.equals("") ){
			name += "." + chainId;
		}
		return  name;
	}
	public String getName2() {
		String chainId = c2.getText().trim();
		
		String name = f2.getText().trim();
		
		if ( ! chainId.equals("") ){
			name += "." + chainId;
		}
		return  name;
	}
	public Structure getStructure1() throws StructureException{
		return fromPDB(f1,c1,r1);
	}

	public Structure getStructure2() throws StructureException{    
		return fromPDB(f2,c2,r2);
	}


	
	
	
	
	private Structure fromPDB(JTextField f, JTextField c,JTextField r) throws StructureException{
		String pdb = f.getText().trim();

		UserConfiguration config = WebStartMain.getWebStartConfig();
		
		if ( pdb.length() < 4) {
			f.setText("!!!");
			return null;
		}

		String chain = c.getText().trim();
		if ( debug )
			System.out.println("file :" + pdb + " " +  chain);


		String range = r.getText().trim();
		
		String fileFormat = config.getFileFormat();
		
		StructureIOFile reader = null;
		if ( fileFormat.equals(UserConfiguration.PDB_FORMAT)){
			PDBFileReader re = new PDBFileReader();
			
			reader = re;
		} else if ( fileFormat.equals(UserConfiguration.MMCIF_FORMAT)){						
			reader = new MMCIFFileReader();
			
		} else {
			throw new StructureException("Unkown file format " + fileFormat);
		}
		
		FileParsingParameters params = new FileParsingParameters();
        params.setAlignSeqRes(false);
		reader.setFileParsingParameters(params);
		
		reader.setPath(config.getPdbFilePath());
		
		reader.setPdbDirectorySplit(config.isSplit());
		
		reader.setAutoFetch(config.getAutoFetch());
		
	
		Structure structure ;
		try {
			structure = reader.getStructureById(pdb);
		} catch (IOException e) {
			throw new StructureException("Could not read structure " + pdb ,e);
		}


		//System.out.println(" got range: " + range);
		if ( range != null && ( ! range.equals(""))){
			if ( structure.getName() == null || structure.getName().equals(""))
				structure.setName(pdb);
			Structure s = StructureTools.getSubRanges(structure, range);
			//System.out.println("got atoms: " + StructureTools.getAtomCAArray(s).length);
			return s;
		} 
		Structure s = StructureTools.getReducedStructure(structure,chain);
		//System.out.println("got atoms: " + StructureTools.getAtomCAArray(s).length);
		if ( s.getName() == null || s.getName().equals(""))
			s.setName(pdb+"."+chain);
		return s;

	}

	private Box getPDBFilePanel(int pos ,JTextField f, JTextField c, JTextField r){

		//JPanel panel = new JPanel();
		//panel.setBorder(BorderFactory.createLineBorder(Color.black));

		JLabel l01 = new JLabel("PDB code ");

		//panel.add(l01);
		Box hBox = Box.createHorizontalBox();
		hBox.add(Box.createGlue());
		hBox.add(l01);

		JLabel l11 = new JLabel(pos + ":");
		f.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
		f.setToolTipText("Provide 4-character PDB code here. Example: 4hhb");
		hBox.add(l11);
		hBox.add(Box.createVerticalGlue());
		hBox.add(f, BorderLayout.CENTER);
		hBox.add(Box.createGlue());

		//panel.add(hBox11);

		//Box hBox21 = Box.createHorizontalBox();
		JLabel l21 = new JLabel("Chain" + pos + ":");
		hBox.add(l21);

		c.setMaximumSize(new Dimension(Short.MAX_VALUE,30));
		//hBox.add(Box.createGlue());
		hBox.add(c, BorderLayout.CENTER);

		String msg1 = "Both chainID and range specification are optional. If both are provided, range has preference.";
		l21.setToolTipText(msg1);
		c.setToolTipText(msg1);

		JLabel rangeL = new JLabel(" Range " + pos + ":");
		hBox.add(Box.createGlue());
		hBox.add(rangeL);
		r.setMaximumSize(new Dimension(Short.MAX_VALUE,30));

		// set help text:
		String msg ="Syntax example: A:407-495,A:582-686";
		rangeL.setToolTipText(msg);
		r.setToolTipText(msg);

		//hBox.add(Box.createGlue());
		hBox.add(r,BorderLayout.CENTER);

		//hBox21.add(Box.createGlue());

		//panel.add(hBox21);



		return hBox;
	}





}

{'fraction_non_alphanumeric': 0.14016578749058026, 'fraction_numerical': 0.019760529180272962, 'mean_word_length': 4.010067114093959, 'pattern_counts': {'":': 6, '<': 5, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3145741', 'n_tokens_mistral': 4699, 'n_tokens_neox': 4101, 'n_words': 823}