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Version 1.0.0 release
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@pennatula
pennatula committed Jun 13, 2014
1 parent 61e9e66 commit 3b165c3
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Showing 17 changed files with 1,024 additions and 717 deletions.
Binary file removed dist/PathSBML.jar_1.0.0.jar
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6 changes: 3 additions & 3 deletions src/org/pathvisio/sbml/Activator.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
// PathVisio,
// a tool for data visualization and analysis using Biological Pathways
// Copyright 2006-2014 BiGCaT Bioinformatics
// PathSBML Plugin
// SBML Plugin for PathVisio.
// Copyright 2013 developed for Google Summer of Code
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
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186 changes: 142 additions & 44 deletions src/org/pathvisio/sbml/BioModelPanel.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
// PathVisio,
// a tool for data visualization and analysis using Biological Pathways
// Copyright 2006-2009 BiGCaT Bioinformatics
// PathSBML Plugin
// SBML Plugin for PathVisio.
// Copyright 2013 developed for Google Summer of Code
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
Expand All @@ -14,6 +14,7 @@
// See the License for the specific language governing permissions and
// limitations under the License.
//

package org.pathvisio.sbml;

import java.awt.Component;
Expand Down Expand Up @@ -49,6 +50,7 @@
import javax.swing.SwingWorker;
import javax.swing.border.Border;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableModel;
import javax.swing.table.TableRowSorter;

import org.pathvisio.core.debug.Logger;
Expand All @@ -67,14 +69,15 @@
* @author anwesha
* @version 1.0.0
*/
@SuppressWarnings("serial")
public class BioModelPanel extends JPanel {

SBMLPlugin plugin;

static Border etch = BorderFactory.createEtchedBorder();
private JComboBox clientDropdown;
private JTable resultTable;
private JScrollPane resultspane;
JScrollPane resultspane;

private JRadioButton Browse;
private JRadioButton All;
Expand All @@ -90,6 +93,9 @@ public class BioModelPanel extends JPanel {
private JTextField taxonomyId;
private JButton search;

/**
* @param plugin
*/
public BioModelPanel(final SBMLPlugin plugin) {

this.plugin = plugin;
Expand All @@ -114,13 +120,13 @@ public BioModelPanel(final SBMLPlugin plugin) {
group2.add(NonCurated);

// biomodel search terms
bioModelName = new JTextField();
chebiId = new JTextField();
uniprotId = new JTextField();
pubTitId = new JTextField();
personName = new JTextField();
goId = new JTextField();
taxonomyId = new JTextField();
setBioModelName(new JTextField());
setChebiId(new JTextField());
setUniprotId(new JTextField());
setPubTitId(new JTextField());
setPersonName(new JTextField());
setGoId(new JTextField());
setTaxonomyId(new JTextField());

//tooltips for browse buttons and search choice button
All.setToolTipText("Browse all submitted models at Biomodels");
Expand All @@ -130,13 +136,13 @@ public BioModelPanel(final SBMLPlugin plugin) {
Search.setToolTipText("Choose to browse models in Biomodels");

//tooltips for all the search boxes
bioModelName.setToolTipText("Tip:Use Biomodel name (e.g.:'Tyson1991 - Cell Cycle 6 var')");
pubTitId.setToolTipText("Tip:Use publication name(e.g.:'sbml')");
chebiId.setToolTipText("Tip:Use Chebi id (e.g.:'24996')");
personName.setToolTipText("Tip:Use person/encoder name (e.g.:'Rainer','Nicolas')");
uniprotId.setToolTipText("Tip:Use Uniprot id (e.g.:'P04637','P10113')");
goId.setToolTipText("Tip:Use GO id (e.g.:'0006915')");
taxonomyId.setToolTipText("Tip:Use Taxonomy id (e.g.:'9606')");
getBioModelName().setToolTipText("Tip:Use Biomodel name (e.g.:'Tyson1991 - Cell Cycle 6 var')");
getPubTitId().setToolTipText("Tip:Use publication name(e.g.:'sbml')");
getChebiId().setToolTipText("Tip:Use Chebi id (e.g.:'24996')");
getPersonName().setToolTipText("Tip:Use person/encoder name (e.g.:'Rainer','Nicolas')");
getUniprotId().setToolTipText("Tip:Use Uniprot id (e.g.:'P04637','P10113')");
getGoId().setToolTipText("Tip:Use GO id (e.g.:'0006915')");
getTaxonomyId().setToolTipText("Tip:Use Taxonomy id (e.g.:'9606')");

// browse biomodel action
Action browseBioModelAction = new AbstractAction("browseBioModels") {
Expand Down Expand Up @@ -242,37 +248,37 @@ public void actionPerformed(ActionEvent e) {
cc2.gridx = 1;
cc2.gridy = 0;
cc2.gridwidth =2;
searchOptBox.add(bioModelName, cc2);
searchOptBox.add(getBioModelName(), cc2);
cc2.fill = GridBagConstraints.HORIZONTAL;
cc2.gridx = 1;
cc2.gridy = 1;
cc2.gridwidth =2;
searchOptBox.add(pubTitId,cc2);
searchOptBox.add(getPubTitId(),cc2);
cc2.fill = GridBagConstraints.HORIZONTAL;
cc2.gridx = 1;
cc2.gridy = 2;
cc2.gridwidth =2;
searchOptBox.add(chebiId,cc2);
searchOptBox.add(getChebiId(),cc2);
cc2.fill = GridBagConstraints.HORIZONTAL;
cc2.gridx = 1;
cc2.gridy = 3;
cc2.gridwidth =2;
searchOptBox.add(personName,cc2);
searchOptBox.add(getPersonName(),cc2);
cc2.fill = GridBagConstraints.HORIZONTAL;
cc2.gridx = 1;
cc2.gridy = 4;
cc2.gridwidth =2;
searchOptBox.add(uniprotId,cc2);
searchOptBox.add(getUniprotId(),cc2);
cc2.fill = GridBagConstraints.HORIZONTAL;
cc2.gridx = 1;
cc2.gridy = 5;
cc2.gridwidth =2;
searchOptBox.add(goId,cc2);
searchOptBox.add(getGoId(),cc2);
cc2.fill = GridBagConstraints.HORIZONTAL;
cc2.gridx = 1;
cc2.gridy = 6;
cc2.gridwidth =2;
searchOptBox.add(taxonomyId,cc2);
searchOptBox.add(getTaxonomyId(),cc2);
cc2.fill = GridBagConstraints.HORIZONTAL;
cc2.gridx = 1;
cc2.gridy = 7;
Expand Down Expand Up @@ -414,7 +420,8 @@ public void mouseClicked(MouseEvent e) {
* @throws InterruptedException
* @throws ExecutionException
*/
private void browse(final String command) throws RemoteException, InterruptedException,
void browse(final String command) throws RemoteException,
InterruptedException,
ExecutionException {

String clientName = clientDropdown.getSelectedItem().toString();
Expand Down Expand Up @@ -506,7 +513,7 @@ else if(pk.isCancelled())

resultTable.setModel(new ResultTableModel(sw.get(), clientName));
resultTable
.setRowSorter(new TableRowSorter(resultTable.getModel()));
.setRowSorter(new TableRowSorter<TableModel>(resultTable.getModel()));
}


Expand All @@ -517,17 +524,17 @@ else if(pk.isCancelled())
* @throws InterruptedException
* @throws ExecutionException
*/
private void search() throws RemoteException, InterruptedException,
void search() throws RemoteException, InterruptedException,
ExecutionException {

// search terms typed in the search boxes are trimmed and stored in the following respective variables.
final String sbmlName = bioModelName.getText().trim();
final String sbmlPub = pubTitId.getText().trim();
final String sbmlChebi = chebiId.getText().trim();
final String sbmlPerson = personName.getText().trim();
final String sbmlUniprot = uniprotId.getText().trim();
final String sbmlGo = goId.getText().trim();
final String sbmlTaxonomy = taxonomyId.getText().trim();
final String sbmlName = getBioModelName().getText().trim();
final String sbmlPub = getPubTitId().getText().trim();
final String sbmlChebi = getChebiId().getText().trim();
final String sbmlPerson = getPersonName().getText().trim();
final String sbmlUniprot = getUniprotId().getText().trim();
final String sbmlGo = getGoId().getText().trim();
final String sbmlTaxonomy = getTaxonomyId().getText().trim();

if (!(sbmlPub.isEmpty()&&sbmlName.isEmpty()&&sbmlChebi.isEmpty()&&sbmlPerson.isEmpty()&&sbmlUniprot.isEmpty()&&sbmlGo.isEmpty()&&sbmlTaxonomy.isEmpty())) {
String clientName = clientDropdown.getSelectedItem().toString();
Expand All @@ -552,7 +559,7 @@ protected String[] doInBackground() throws Exception {
String[] results7 = null;
try {
// getting the models id by name.
if(!bioModelName.getText().equalsIgnoreCase(""))
if(!getBioModelName().getText().equalsIgnoreCase(""))
{
results1 = client.getModelsIdByName(sbmlName);

Expand All @@ -565,7 +572,7 @@ protected String[] doInBackground() throws Exception {
}

//getting the models id by publication title or id.
if(!pubTitId.getText().equalsIgnoreCase(""))
if(!getPubTitId().getText().equalsIgnoreCase(""))
{
results2= client.getModelsIdByPublication(sbmlPub);
if(results2!=null){
Expand All @@ -577,7 +584,7 @@ protected String[] doInBackground() throws Exception {
}

//getting models id by chebi id.
if(!chebiId.getText().equalsIgnoreCase(""))
if(!getChebiId().getText().equalsIgnoreCase(""))
{
results3= client.getModelsIdByChEBIId(sbmlChebi);
if(results3!=null){
Expand All @@ -589,7 +596,7 @@ protected String[] doInBackground() throws Exception {
}

//getting models id by person or encoder or author name.
if(!personName.getText().equalsIgnoreCase(""))
if(!getPersonName().getText().equalsIgnoreCase(""))
{
results4= client.getModelsIdByPerson(sbmlPerson);
if(results4!=null){
Expand All @@ -601,7 +608,7 @@ protected String[] doInBackground() throws Exception {
}

//getting models id by uniprot id.
if(!uniprotId.getText().equalsIgnoreCase(""))
if(!getUniprotId().getText().equalsIgnoreCase(""))
{
results5= client.getModelsIdByUniprot(sbmlUniprot);
if(results5!=null){
Expand All @@ -613,7 +620,7 @@ protected String[] doInBackground() throws Exception {
}

//getting models id by go id.
if(!goId.getText().equalsIgnoreCase(""))
if(!getGoId().getText().equalsIgnoreCase(""))
{
results6 = client.getModelsIdByGOId(sbmlGo);

Expand All @@ -626,7 +633,7 @@ protected String[] doInBackground() throws Exception {
}

//getting models id by taxonomy id.
if(!taxonomyId.getText().equalsIgnoreCase(""))
if(!getTaxonomyId().getText().equalsIgnoreCase(""))
{
results7 = client.getModelsIdByTaxonomyId(sbmlTaxonomy);

Expand Down Expand Up @@ -675,15 +682,15 @@ else if(pk.isCancelled())

resultTable.setModel(new ResultTableModel(sw.get(), clientName));
resultTable
.setRowSorter(new TableRowSorter(resultTable.getModel()));
.setRowSorter(new TableRowSorter<TableModel>(resultTable.getModel()));
} else {
JOptionPane.showMessageDialog(null, "Please Enter a Search Query",
"ERROR", JOptionPane.ERROR_MESSAGE);
}
}

//enable search
private void enableFrame(JPanel container, boolean enable) {
void enableFrame(JPanel container, boolean enable) {
Component[] components = container.getComponents();
for (Component component : components) {
component.setEnabled(enable);
Expand All @@ -692,6 +699,97 @@ private void enableFrame(JPanel container, boolean enable) {
}
}
}
/**
* @return the pubTitId
*/
public JTextField getPubTitId() {
return pubTitId;
}

/**
* @param pubTitId the pubTitId to set
*/
public void setPubTitId(JTextField pubTitId) {
this.pubTitId = pubTitId;
}
/**
* @return the bioModelName
*/
public JTextField getBioModelName() {
return bioModelName;
}

/**
* @param bioModelName the bioModelName to set
*/
public void setBioModelName(JTextField bioModelName) {
this.bioModelName = bioModelName;
}
/**
* @return the chebiId
*/
public JTextField getChebiId() {
return chebiId;
}

/**
* @param chebiId the chebiId to set
*/
public void setChebiId(JTextField chebiId) {
this.chebiId = chebiId;
}
/**
* @return the personName
*/
public JTextField getPersonName() {
return personName;
}

/**
* @param personName the personName to set
*/
public void setPersonName(JTextField personName) {
this.personName = personName;
}
/**
* @return the goId
*/
public JTextField getGoId() {
return goId;
}

/**
* @param goId the goId to set
*/
public void setGoId(JTextField goId) {
this.goId = goId;
}
/**
* @return the taxonomyId
*/
public JTextField getTaxonomyId() {
return taxonomyId;
}

/**
* @param taxonomyId the taxonomyId to set
*/
public void setTaxonomyId(JTextField taxonomyId) {
this.taxonomyId = taxonomyId;
}
/**
* @return the uniprotId
*/
public JTextField getUniprotId() {
return uniprotId;
}

/**
* @param uniprotId the uniprotId to set
*/
public void setUniprotId(JTextField uniprotId) {
this.uniprotId = uniprotId;
}
/**
* This class creates the result table model
* based on the results.
Expand Down
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