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Merged
sbliven merged 9 commits into from
Jan 25, 2016
Merged

StructureIdentifier framework #376

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d4b0bba
Add substantially new unified class for identify structures: Structur…
sbliven Dec 10, 2015
10da1c2
Implement extension-based PDB/CIF filetype detection
sbliven Jan 15, 2016
de3e073
Adding URLIdentifier for files and URLs
sbliven Jan 15, 2016
9555a84
Fixing minor test failure
sbliven Jan 18, 2016
a5db930
Moving SCOP name guessing from AtomCache to StructureName
sbliven Jan 20, 2016
6017337
Add Structure.get/setStructureIdentifier methods
sbliven Jan 20, 2016
a62d45e
Changing many classes to use StructureIdentifier
sbliven Jan 20, 2016
1b11a48
Switching UserConfiguration to default to mmcif
sbliven Jan 20, 2016
1fa6f3d
Fix bug where an identifier's toString method differed from getIdenti…
sbliven Jan 21, 2016
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4 changes: 2 additions & 2 deletions biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java
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Expand Up @@ -130,9 +130,9 @@ public InputStream getInputStream(URL u)
return openCompressedURL(u);
} else if (magic == GZIP_MAGIC ) {
return openGZIPURL(u);
} else if ( u.toString().endsWith(".gz")) {
} else if ( u.getPath().endsWith(".gz")) {
return openGZIPURL(u);
} else if ( u.toString().endsWith(".Z")) {
} else if ( u.getPath().endsWith(".Z")) {
// unix compressed
return openCompressedURL(u);

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11 changes: 7 additions & 4 deletions ...ava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
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Expand Up @@ -126,6 +126,7 @@ public void testGetNrAtoms(){
assertEquals("did not find the expected number of Atoms (1087), but got " + length,1087,length);
}

@SuppressWarnings("deprecation")
public void testGetSubRanges() throws StructureException {
String range;
Structure substr;
Expand Down Expand Up @@ -230,13 +231,13 @@ public void testGetSubRanges() throws StructureException {
try {
range = "7-10";
substr = StructureTools.getSubRanges(structure2, range);
fail("Illegal range '"+range+"'. Should throw StructureException");
} catch(StructureException ex) {} //expected
fail("Illegal range '"+range+"'. Should throw IllegalArgumentException");
} catch(IllegalArgumentException ex) {} //expected
try {
range = "A7-10";
substr = StructureTools.getSubRanges(structure2, range);
fail("Illegal range '"+range+"'. Should throw StructureException");
} catch(StructureException ex) {} //expected
fail("Illegal range '"+range+"'. Should throw IllegalArgumentException");
} catch(IllegalArgumentException ex) {} //expected
}

public void testRevisedConvention() throws IOException, StructureException{
Expand Down Expand Up @@ -319,6 +320,7 @@ public void testRevisedConvention() throws IOException, StructureException{
* Test some subranges that we used to have problems with
* @throws StructureException
*/
@SuppressWarnings("deprecation")
public void testGetSubRangesExtended() throws StructureException {
String range;
Structure substr;
Expand Down Expand Up @@ -379,6 +381,7 @@ public void testGetSubRangesExtended() throws StructureException {
* Test insertion codes
* @throws StructureException
*/
@SuppressWarnings("deprecation")
public void testGetSubRangesInsertionCodes() throws StructureException {
String range;
Structure substr;
Expand Down
2 changes: 1 addition & 1 deletion ...va-integrationtest/src/test/java/org/biojava/nbio/structure/test/cath/CathDomainTest.java
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Expand Up @@ -36,6 +36,6 @@ public class CathDomainTest {
public void test() {
String id = "1qvrC03";
CathDomain domain = CathFactory.getCathDatabase().getDomainByCathId(id);
assertEquals("1qvr.C_332-400,C_514-540", domain.getIdentifier());
assertEquals("1qvr.C_332-400,C_514-540", domain.toCanonical().getIdentifier());
}
}
29 changes: 23 additions & 6 deletions biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentGui.java
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Expand Up @@ -22,8 +22,27 @@
*/
package org.biojava.nbio.structure.align.gui;

import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.io.File;
import java.io.IOException;

import javax.swing.AbstractAction;
import javax.swing.Action;
import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JMenuBar;
import javax.swing.JOptionPane;
import javax.swing.JProgressBar;
import javax.swing.JTabbedPane;

import org.biojava.nbio.structure.PassthroughIdentifier;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.StructureAlignmentFactory;
import org.biojava.nbio.structure.align.ce.AbstractUserArgumentProcessor;
Expand All @@ -34,10 +53,6 @@
import org.biojava.nbio.structure.gui.util.PDBUploadPanel;
import org.biojava.nbio.structure.gui.util.ScopSelectPanel;
import org.biojava.nbio.structure.gui.util.StructurePairSelector;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.io.File;

/** A JFrame that allows to trigger a pairwise structure alignment,
* either from files in a directory,
Expand Down Expand Up @@ -368,8 +383,8 @@ private void calcAlignment() {
String name2 = "custom2";

if ( pos == 0){
name1 = tab1.getName1();
name2 = tab1.getName2();
name1 = tab1.getName1().getIdentifier();
name2 = tab1.getName2().getIdentifier();
} else {
name1 = s1.getName();
name2 = s2.getName();
Expand All @@ -389,6 +404,8 @@ private void calcAlignment() {
drawer.start();
} catch (StructureException e){
JOptionPane.showMessageDialog(null,"Could not align structures. Exception: " + e.getMessage());
} catch (IOException e) {
JOptionPane.showMessageDialog(null,"Could not align structures. Exception: " + e.getMessage());
}

}
Expand Down
7 changes: 4 additions & 3 deletions ...ructure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentCalc.java
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Expand Up @@ -28,6 +28,7 @@
import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.MultipleStructureAligner;
import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
Expand All @@ -49,7 +50,7 @@ public class MultipleAlignmentCalc implements AlignmentCalculationRunnable {
private static final Logger logger =
LoggerFactory.getLogger(MultipleAlignmentCalc.class);

private List<String> names;
private List<StructureIdentifier> names;
private List<Structure> structures;

private MultipleAlignmentGUI parent;
Expand All @@ -63,7 +64,7 @@ public class MultipleAlignmentCalc implements AlignmentCalculationRunnable {
* @param names
*/
public MultipleAlignmentCalc(MultipleAlignmentGUI parent,
List<Structure> structures, List<String> names) {
List<Structure> structures, List<StructureIdentifier> names) {

this.parent= parent;
this.structures = structures;
Expand All @@ -84,7 +85,7 @@ public void run() {
}

MultipleAlignment msa = algorithm.align(atomArrays);
msa.getEnsemble().setStructureNames(names);
msa.getEnsemble().setStructureIdentifiers(names);

MultipleAlignmentDisplay.display(msa);

Expand Down
7 changes: 4 additions & 3 deletions ...tructure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MultipleAlignmentGUI.java
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Expand Up @@ -40,6 +40,7 @@

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.align.MultipleStructureAligner;
import org.biojava.nbio.structure.align.StructureAlignment;
import org.biojava.nbio.structure.align.StructureAlignmentFactory;
Expand Down Expand Up @@ -291,11 +292,11 @@ private void calcAlignment() {
return;
}

List<String> names = tab.getNames();
List<StructureIdentifier> names = tab.getNames();

String message = "aligning: ";
for (String name:names){
message += name + " ";
for (StructureIdentifier name:names){
message += name.getIdentifier() + " ";
}
System.out.println(message);

Expand Down
132 changes: 41 additions & 91 deletions biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
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Expand Up @@ -20,20 +20,25 @@
*/
package org.biojava.nbio.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.nbio.structure.ResidueRange;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.SubstructureIdentifier;
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.gui.util.StructurePairSelector;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.MMCIFFileReader;
import org.biojava.nbio.structure.io.PDBFileReader;
import org.biojava.nbio.structure.io.StructureProvider;

import javax.swing.*;
import java.awt.*;
import java.io.IOException;


/** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
Expand Down Expand Up @@ -100,101 +105,46 @@ public SelectPDBPanel(boolean show2PDBs) {
this.add(vBox);
}

public String getName1() {

public StructureIdentifier getName1() {
String pdbId = f1.getText().trim();
String chainId = c1.getText().trim();

String name = f1.getText().trim();

if ( ! chainId.equals("") ){
name += "." + chainId;
String range = r1.getText().trim();

// Prefer range over chain
if( ! range.isEmpty() ) {
return new SubstructureIdentifier(pdbId, ResidueRange.parseMultiple(range));
} else if ( ! chainId.isEmpty() ){
return new SubstructureIdentifier(pdbId, ResidueRange.parseMultiple(chainId));
}
return name;
return new SubstructureIdentifier(pdbId);
}
public String getName2() {
public StructureIdentifier getName2() {
String pdbId = f2.getText().trim();
String chainId = c2.getText().trim();

String name = f2.getText().trim();

if ( ! chainId.equals("") ){
name += "." + chainId;
String range = r2.getText().trim();

// Prefer range over chain
if( ! range.isEmpty() ) {
return new SubstructureIdentifier(pdbId, ResidueRange.parseMultiple(range));
} else if ( ! chainId.isEmpty() ){
return new SubstructureIdentifier(pdbId, ResidueRange.parseMultiple(chainId));
}
return name;
return new SubstructureIdentifier(pdbId);
}
@Override
public Structure getStructure1() throws StructureException{
return fromPDB(f1,c1,r1);
public Structure getStructure1() throws StructureException, IOException{
return getStructure(getName1());
}

@Override
public Structure getStructure2() throws StructureException{
return fromPDB(f2,c2,r2);
public Structure getStructure2() throws StructureException, IOException{
return getStructure(getName2());
}






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

private Structure getStructure(StructureIdentifier name) throws IOException, StructureException {
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();

StructureProvider reader = null;
if ( fileFormat.equals(UserConfiguration.PDB_FORMAT)){
PDBFileReader re = new PDBFileReader(config.getPdbFilePath());
re.setFetchBehavior(config.getFetchBehavior());
reader = re;
} else if ( fileFormat.equals(UserConfiguration.MMCIF_FORMAT)){
MMCIFFileReader re = new MMCIFFileReader(config.getPdbFilePath());
re.setFetchBehavior(config.getFetchBehavior());
reader = re;
} else {
throw new StructureException("Unkown file format " + fileFormat);
}

FileParsingParameters params = new FileParsingParameters();
params.setAlignSeqRes(false);
reader.setFileParsingParameters(params);


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;

AtomCache cache = new AtomCache(config);
return cache.getStructure(name);
}

private Box getPDBFilePanel(int pos ,JTextField f, JTextField c, JTextField r){
Expand Down
9 changes: 6 additions & 3 deletions ...re-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
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Expand Up @@ -46,6 +46,7 @@
import org.biojava.nbio.structure.PDBHeader;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.align.gui.MenuCreator;
import org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay;
import org.biojava.nbio.structure.align.gui.MultipleAlignmentGUI;
Expand Down Expand Up @@ -181,7 +182,7 @@ public void actionPerformed(ActionEvent e) {

for (int str=0; str<multAln.size(); str++){
JCheckBox structureSelection = new JCheckBox(
multAln.getEnsemble().getStructureNames().get(str));
multAln.getEnsemble().getStructureIdentifiers().get(str).getIdentifier());
hBox0.add(structureSelection);
hBox0.add(Box.createGlue());
structureSelection.setSelected(true);
Expand Down Expand Up @@ -334,6 +335,7 @@ public void itemStateChanged(ItemEvent e) {
resetDisplay();
}

@Override
protected void initCoords(){
try {
if ( multAln == null ){
Expand All @@ -348,8 +350,8 @@ protected void initCoords(){
String title = multAln.getEnsemble().getAlgorithmName() +
" V." +multAln.getEnsemble().getVersion() + " : ";

for (String name:multAln.getEnsemble().getStructureNames()){
title += name + " ";
for (StructureIdentifier name:multAln.getEnsemble().getStructureIdentifiers()){
title += name.getIdentifier() + " ";
}
Structure artificial = MultipleAlignmentDisplay.
getAlignedStructure(transformedAtoms);
Expand Down Expand Up @@ -534,6 +536,7 @@ private static void printJmolScript4Block(Atom[] atoms,
jmol.append(buf);
}

@Override
public void resetDisplay() {

if (multAln != null && transformedAtoms != null) {
Expand Down
1 change: 0 additions & 1 deletion biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/ScopSelectPanel.java
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Expand Up @@ -137,7 +137,6 @@ private Structure getStructure(String domainID) throws StructureException{
//String cacheLocation = config.getPdbFilePath();

AtomCache cache = new AtomCache(config);
cache.setStrictSCOP(false);

Structure s = null;
try {
Expand Down
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