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org.biojava.nbio.structure.align.gui.DBResultTable Maven / Gradle / Ivy
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Nov 6, 2009
* Author: Andreas Prlic
*
*/
package org.biojava.nbio.structure.align.gui;
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.StructureAlignmentFactory;
import org.biojava.nbio.structure.align.ce.CeMain;
import org.biojava.nbio.structure.align.ce.CeParameters;
import org.biojava.nbio.structure.align.ce.CeParameters.ScoringStrategy;
import org.biojava.nbio.structure.align.ce.ConfigStrucAligParams;
import org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol;
import org.biojava.nbio.structure.align.model.AFPChain;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.structure.align.webstart.WebStartMain;
import org.biojava.nbio.structure.io.PDBFileReader;
import org.biojava.nbio.structure.io.StructureIOFile;
import javax.swing.*;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
import javax.swing.table.TableModel;
import javax.swing.table.TableRowSorter;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.*;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
public class DBResultTable implements ActionListener{
public static final String[] ceColumnNames = {"name1","tname2","score","z-score" ,"rmsd","len1","len2","cov1","cov2","%ID","Description",""};
public static final String[] fatColumnNames = {"name1","tname2","score","probability","rmsd","len1","len2","cov1","cov2","%ID","Description",""};
Object[][] data;
JTable table;
String oldName1;
String oldName2;
String algorithmName;
StructureAlignment algorithm;
boolean isCE = true;
UserConfiguration config;
AtomCache cache ;
String userPath ;
String userChain;
public static void main(String[] args){
String file = "/tmp/results_4hhb.A.out";
DBResultTable table = new DBResultTable();
UserConfiguration config = WebStartMain.getDefaultConfig();
table.show(new File(file),config);
}
public DBResultTable(){
oldName1 = "";
oldName2 = "";
userPath = null;
userChain = null;
}
public void show(BufferedReader in, UserConfiguration config) throws IOException{
String str;
List tmpdat = new ArrayList();
while ((str = in.readLine()) != null) {
if ( str.startsWith("#")) {
if ( str.startsWith("# algorithm:")) {
String[] spl = str.split(":");
if ( spl.length == 2) {
algorithmName = spl[1];
if (algorithmName.startsWith("jCE"))
isCE = true;
else
isCE = false;
}
initAlgorithm(algorithmName);
}
else if ( str.startsWith("#param:file1=")){
String path = str.substring(13);
userPath = path.trim();
}
else if ( str.startsWith("#param:chain1=")){
String chain = str.substring(14);
userChain = chain.trim();
}
else if ( str.startsWith("#param:scoring=")){
try {
String[] spl = str.split("=");
ScoringStrategy scoreS;
try {
// try to convert from integer score
int stratNum = Integer.parseInt(spl[1]);
ScoringStrategy[] vals = ScoringStrategy.values();
scoreS = vals[stratNum];//throws OutOfBounds if invalid; caught below
} catch(NumberFormatException e) {
scoreS = ScoringStrategy.valueOf(spl[1]); //
}
if (algorithm != null){
// scoring is a parameter of CE...
ConfigStrucAligParams params = algorithm.getParameters();
if ( params instanceof CeParameters){
CeParameters ceParams = (CeParameters) params;
ceParams.setScoringStrategy(scoreS);
}
}
} catch (IndexOutOfBoundsException e){
System.err.println("Unknown scoring strategy from line: " + str);
} catch (IllegalArgumentException e) {
System.err.println("Unknown scoring strategy from line: " + str);
} catch (Exception e) {
System.err.println("Unknown parameter can't read parameters from line: " + str);
e.printStackTrace();
}
}
continue;
}
String[] spl = str.split("\t");
if ( spl.length != ceColumnNames.length -1) {
System.err.println("wrong table width! " + spl.length + " should be: " + (ceColumnNames.length -1 ));
System.err.println(str);
continue;
}
tmpdat.add(spl);
}
in.close();
Object[][] d = new Object[tmpdat.size()][ceColumnNames.length + 1];
int i = -1;
for (String[] spl : tmpdat){
i++;
Object[] o = new Object[spl.length + 1];
for ( int j=0; j< spl.length;j++){
if (( j >= 2 && j <= 4)|| (j==9)) {
o[j] = Double.parseDouble(spl[j]);
} else if ( j >4 && j< 10) {
o[j] = Integer.parseInt(spl[j]);
} else {
o[j] = spl[j];
}
}
o[spl.length ] = "Align";
d[i] = o;
}
data = d;
String[] columnNames = ceColumnNames;
if ( ! isCE)
columnNames = fatColumnNames;
table = new JTable(data, columnNames);
TableRowSorter sorter = new MyTableRowSorter(table.getModel());
table.setRowSorter(sorter);
//table.setAutoCreateRowSorter(true);
JScrollPane scrollPane = new JScrollPane(table);
table.setFillsViewportHeight(true);
// take care of selections:
table.setSelectionMode( ListSelectionModel.SINGLE_INTERVAL_SELECTION);
table.getSelectionModel().addListSelectionListener(new RowListener());
JFrame f = new JFrame();
f.getContentPane().add(scrollPane);
f.pack();
f.setVisible(true);
}
public void show(File file, UserConfiguration config){
this.config = config;
cache = new AtomCache(config);
try {
BufferedReader in = new BufferedReader(new FileReader(file));
show(in, config);
} catch (IOException e) {
e.printStackTrace();
}
}
public void show(URL url, UserConfiguration config){
this.config = config;
cache = new AtomCache(config);
try {
BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));
show(in, config);
} catch (IOException e) {
e.printStackTrace();
}
}
private void initAlgorithm(String algorithmName) {
try {
algorithm = StructureAlignmentFactory.getAlgorithm(algorithmName);
} catch (Exception e){
e.printStackTrace();
System.err.println("Can't guess algorithm from output. Using jCE as default...");
try {
algorithm = StructureAlignmentFactory.getAlgorithm(CeMain.algorithmName);
} catch (Exception ex){
ex.printStackTrace();
return;
}
}
}
private void outputSelection() {
StringBuffer output = new StringBuffer();
output.append(String.format("Lead: %d, %d. ",
table.getSelectionModel().getLeadSelectionIndex(),
table.getColumnModel().getSelectionModel().
getLeadSelectionIndex()));
output.append("Rows:");
for (int c : table.getSelectedRows()) {
output.append(String.format(" %d", c));
}
output.append(". Columns:");
for (int c : table.getSelectedColumns()) {
output.append(String.format(" %d", c));
}
System.out.println(output.toString());
}
private class RowListener implements ListSelectionListener {
@Override
public void valueChanged(ListSelectionEvent event) {
if (event.getValueIsAdjusting()) {
return;
}
int row = table.getSelectionModel().getLeadSelectionIndex();
String name1 = (String)table.getValueAt(row, 0);
String name2 = (String)table.getValueAt(row, 1);
if ( name1.equals(oldName1) && oldName2.equals(name2)){
return;
}
System.out.println("recreating alignment of: " + name1 + " " + name2 + " using " + algorithmName);
outputSelection();
showAlignment(name1,name2);
oldName1 = name1;
oldName2 = name2;
}
}
private void showAlignment( String name1, String name2){
if ( algorithm == null) {
initAlgorithm(null);
}
try {
Structure structure1 = null;
if ( name1.equals("CUSTOM")) {
// user uploaded a custom PDB file...
structure1 = loadCustomStructure(userPath,userChain);
} else {
structure1 = cache.getStructure(name1);
}
Structure structure2 = cache.getStructure(name2);
Atom[] ca1;
Atom[] ca2;
ca1 = StructureTools.getRepresentativeAtomArray(structure1);
ca2 = StructureTools.getRepresentativeAtomArray(structure2);
AFPChain afpChain;
afpChain = algorithm.align(ca1, ca2);
afpChain.setName1(name1);
afpChain.setName2(name2);
StructureAlignmentJmol jmol = StructureAlignmentDisplay.display(afpChain,ca1,ca2);
//String result = afpChain.toFatcat(ca1, ca2);
//String rot = afpChain.toRotMat();
DisplayAFP.showAlignmentPanel(afpChain, ca1,ca2,jmol);
} catch (Exception e){
e.printStackTrace();
}
}
private Structure loadCustomStructure(String userPath2, String userChain2) throws StructureException{
StructureIOFile reader = new PDBFileReader();
Structure s = null;
try {
s = reader.getStructure(userPath2);
} catch (IOException e){
//e.printStackTrace();
throw new StructureException(e);
}
return StructureTools.getReducedStructure(s, userChain2);
}
@Override
public void actionPerformed(ActionEvent e) {
}
}
