import java.awt.*;
import java.net.URL;
import java.net.Socket;
import javax.swing.*;
import javax.swing.event.*;
import javax.swing.table.*;
import javax.swing.text.html.HTMLDocument;
import java.awt.event.*;
import java.util.BitSet;
import java.util.regex.*;
import java.io.*;
import java.util.List;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import components.TableSorter;
/**
* VarSifter is designed to read a flat file where a row contains a variant, and all sample info
* and allow sorting, and filtering of the data. This class is a wrapper that handles the GUI
* via Swing.
* @author Jamie K. Teer
*/
public class VarSifter extends JFrame implements ListSelectionListener, ActionListener, TableModelListener {
final static String version = "1.9";
final static String id = "$Id$";
final static int VARIANT_FILE = 0;
final static int GENE_FILTER_FILE = 1;
final static int BED_FILTER_FILE = 2;
final static int MAX_COLUMN_SIZE = 150;
public final static boolean isDebug = false;
//TODO will need to make this extendable
//final String[] sampleTableLabels = {"Sample", "Genotype", "Genotype score", "coverage"};
final Dimension dim = Toolkit.getDefaultToolkit().getScreenSize();
final int w = (int)dim.getWidth();
final int h = (int)dim.getHeight();
// Test using object[][], titles[]
private VarData vdat = null;
private JTable outTable;
private TableSorter sorter;
private JTable sampleTable;
private TableSorter sampleSorter;
//TODO: CONFIRM the values are needed here
//private String[] sampleTableLabels = {"Sample", "Genotype", "Genotype score", "coverage"};
private String[] sampleTableLabels;
private JScrollPane dataScroller;
private JScrollPane sampleScroller;
private ListSelectionModel lsm;
private JLabel lines = new JLabel();
private ConfigHandler opt;
private Map<String,String> bamList = null;
private JCheckBox dbsnp = new JCheckBox("dbID");
private JCheckBox mendRec = new JCheckBox("Hom. Recessive");
private JCheckBox mendDom = new JCheckBox("Dominant");
private JCheckBox mendBad = new JCheckBox("Inconsistent");
private JCheckBox mendCompHet = new JCheckBox("Mend. Compound Het");
private JCheckBox uniqInAff = new JCheckBox("Affected different from Norm");
private JCheckBox caseControl = new JCheckBox("Case / Control");
private JCheckBox filterFile = new JCheckBox("Include Gene File");
private JCheckBox notFilterFile = new JCheckBox("Exclude Gene File");
private JCheckBox bedFilterFile = new JCheckBox("Include Bed File Regions");
private JCheckBox customQuery = new JCheckBox("Custom Query");
private JCheckBox[] typeCBox;
private JCheckBox[] cBox = { dbsnp,
mendRec,
mendDom,
mendBad,
mendCompHet,
uniqInAff,
caseControl,
filterFile,
notFilterFile,
bedFilterFile,
customQuery
};
public final static int MENDHETREC = 4; //index of mendCompHet
public final static int CUSTOM = 10; //index of customQuery
private JMenuItem openItem;
private JMenuItem saveAsItem;
private JMenuItem saveViewItem;
private JMenuItem preferViewItem;
private JMenuItem sampleSettingsItem;
private JMenuItem exitItem;
private JMenuItem compHetViewItem;
private JMenuItem customQueryViewItem;
private JMenuItem sampleExportItem;
private JMenuItem aboutItem;
private JMenuItem docItem;
private JMenuItem troubleItem;
private JButton apply = new JButton("Apply Filter");
private JButton clear = new JButton("Clear All");
private JRadioButton showVar = new JRadioButton("Show Variants", true);
private JRadioButton showGene = new JRadioButton("Show Genes");
private JButton check = new JButton("Check");
private JButton filterFileButton = new JButton("Choose Gene File Filter");
private JButton bedFilterFileButton = new JButton("Choose Bed File Filter");
private JButton geneViewButton = new JButton("View Variants for Selected Gene");
private JButton prefApply = new JButton("Apply Preferences");
private JCheckBox compHetSamples = new JCheckBox("Show Sample Details");
private JButton compHetGeneViewButton = new JButton("View by Gene");
private JButton compHetPairViewButton = new JButton("View Pairs of Selected Position");
private JButton compHetAllButton = new JButton("View All Compound Hets");
private List<AbstractButton> listenerList = new ArrayList<AbstractButton>(20);
private MouseAdapter outTableMA;
private MouseAdapter sampleTableMA;
private JFrame compHetParent;
private JFrame customQueryParent;
private CustomQueryView cqPane;
private JFrame preferViewParent;
private int[] spinnerData = new int[5]; //Hold data for Spinner values (use int values from VarData)
private JLabel filterFileLabel = new JLabel("No Gene File Selected");
private JLabel bedFilterFileLabel = new JLabel("No Bed File Selected");
private JSpinner minAffSpinner = new JSpinner();
private JLabel affSpinnerLabel = new JLabel("Diff. in at least:");
private JTextField geneRegexField = new JTextField("");
private JTextField minMPGField = new JTextField(10);
private JTextField minMPGCovRatioField = new JTextField(10);
private JTextField genScoreThreshField = new JTextField(10);
private JTextField genScoreCovRatioThreshField = new JTextField(10);
private JSpinner caseSpinner = new JSpinner();
private JLabel caseSpinnerLabel = new JLabel("Var in cases (at least):");
private JSpinner controlSpinner = new JSpinner();
private JLabel controlSpinnerLabel = new JLabel("Var in controls (this or fewer):");
private JSpinner minMPGSpinner = new JSpinner();
private JSpinner minMPGCovRatioSpinner = new JSpinner();
private JLabel linesl = new JLabel("Number of Variant Positions: ");
final static String newLine = System.getProperty("line.separator");
private String geneFile = null;
private String bedFile = null;
private BitSet[] mask = new BitSet[2]; // holds { type filter mask (typeCBox), preset (cBox) }
private boolean isShowVar = true;
private DataFilter df = null;
public final static Pattern fDigits = Pattern.compile("^-?[0-9]+\\.[0-9]+(E-?[0-9]+)?$|^NaN$");
public final static Pattern emptyPat = Pattern.compile("emptyVS_.*tmp");
private final Pattern vcfPat = Pattern.compile("\\.vcf$");
private final Pattern gzPat = Pattern.compile("\\.gz$");
//Default score cutoff thresholds
protected static int SCORE_THRESH = 10;
protected static float SCORE_COV_THRESH = 0.5f;
private int minMPG = 0;
private float minMPGCovRatio = 0f;
private int genScoreThresh = SCORE_THRESH;
private float genScoreCovRatioThresh = SCORE_COV_THRESH;
private int IGVport = 60151;
private String IGVhost = "127.0.0.1";
private String geneDelim = ";";
private Map<String, Integer> typeMap;
private AbstractMapper[] annotMapper;
private AbstractMapper[] sampleMapper;
public final static String emptyHeader = "Chr\tLeftFlank\tRightFlank\tGene_name\ttype\tmuttype\tref_allele\tvar_allele";
public final static BitSet[] emptyBS = { new BitSet(), new BitSet() };
public final static int[] emptySpinnerData = {0,0,0,0,0};
/**
* Initiate GUI, instantiate VarData
* Constructor using FileName
*
* @param inFile path to input file (VS format)
*/
public VarSifter(String inFile) {
//initiate parent window
//super("VarSifter - " + inFile);
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
setBounds(0, (h/8), (w/2), (h/2));
//Load config file
opt = parseConfig();
if (inFile == null) {
try {
File emptyFile = File.createTempFile("emptyVS_", null, null);
emptyFile.deleteOnExit();
PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(emptyFile)));
pw.println(emptyHeader);
pw.close();
inFile = emptyFile.toString();
}
catch (IOException ioe) {
VarSifter.showError("<html>Could not write to Java temp directory.<p>To avoid this error again, " +
"either allow write permission in the Java temp directory,<p>" +
"or open a file from the commandline:<p>java -jar VarSifter[version].jar [your data file]</html>");
System.out.println(ioe);
System.exit(1);
}
}
if (emptyPat.matcher(inFile).find()) {
this.setTitle("VarSifter - No file loaded yet");
}
else {
this.setTitle("VarSifter - " + inFile);
}
outTable = new JTable();
sampleTable = new JTable();
redrawOutTable(inFile);
initTable();
if (emptyPat.matcher(inFile).find()) {
VarSifter.showMessage(VSMessages.welcome);
}
}
/**
* Constructor using VarData object
*
* @param vdatTemp VarData object
*/
public VarSifter(VarData vdatTemp) {
super("VarSifter SubSet");
setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
setBounds(w-(3* w/4), (h/2), (w/2), (h/2));
//setBounds(0, (h/4), (w/2), (h/2));
vdat = vdatTemp;
String[] sampValName = vdat.returnSampleValueNames();
sampleTableLabels = new String[sampValName.length + 1];
sampleTableLabels[0] = "Sample";
System.arraycopy(sampValName, 0, sampleTableLabels, 1, sampValName.length);
outTable = new JTable();
sampleTable = new JTable();
redrawOutTable(null);
initTable();
}
/**
* Handle Actions
*
* @param e resulting from clicking a button, menuitem
*/
public void actionPerformed(ActionEvent e) {
Object es = e.getSource();
if (es == apply || es == geneRegexField) {
sorter.setTableHeader(null); //Must do this to avoid memory leak
mask = getFilterMask();
if (showVar.isSelected()) {
isShowVar = true;
linesl.setText("Number of Variant Positions: ");
}
else if (showGene.isSelected()) {
isShowVar = false;
linesl.setText("Number of Genes: ");
}
spinnerData[vdat.AFF_NORM_PAIR] = ((Integer)minAffSpinner.getValue()).intValue();
spinnerData[vdat.CASE] = ((Integer)caseSpinner.getValue()).intValue();
spinnerData[vdat.CONTROL] = ((Integer)controlSpinner.getValue()).intValue();
spinnerData[vdat.MIN_MPG] = ((Integer)minMPGSpinner.getValue()).intValue();
spinnerData[vdat.MIN_MPG_COV] = ((Integer)minMPGCovRatioSpinner.getValue()).intValue();
df = new DataFilter(mask, geneFile, bedFile, spinnerData, getRegex(), minMPG, minMPGCovRatio, genScoreThresh, geneDelim);
vdat.filterData(df);
redrawOutTable(null);
}
else if (es == clear) {
for (JCheckBox cb : typeCBox) {
cb.setSelected(false);
}
for (JCheckBox cb : cBox) {
cb.setSelected(false);
}
geneRegexField.setText("");
}
else if (es == filterFileButton) {
String temp = openData(GENE_FILTER_FILE);
if (temp != null) {
geneFile = temp;
}
}
else if (es == bedFilterFileButton) {
String temp = openData(BED_FILTER_FILE);
if (temp != null) {
bedFile = temp;
}
}
else if (es == geneViewButton) {
//Use this button to return a VarSifter view of one gene
String geneRegex = "";
if (isShowVar) {
int dataRowIndex = sorter.modelIndex(outTable.getSelectedRow());
String geneName = vdat.returnDataValueAt(dataRowIndex, "Gene_name");
geneRegex = "^" + geneName + "$";
}
else {
try {
geneRegex = "^" + (String)outTable.getValueAt(outTable.getSelectedRow(), 0) + "$";
}
catch (ClassCastException cce) {
showError(VSMessages.geneNotFoundError);
return;
}
}
vdat.filterData(new DataFilter(emptyBS, null, null, spinnerData, geneRegex, minMPG, minMPGCovRatio, genScoreThresh, geneDelim));
VarData tempVdat = vdat.returnSubVarData(vdat, null);
VarSifter vs = new VarSifter(tempVdat);
//Must return the filtered state to what it was, to avoid data mapping errors!
vdat.filterData(df);
}
else if (es == openItem) {
String fName = openData(VARIANT_FILE);
// If a new data file is loaded, we need to clear out the current data
if (fName != null) {
//Clear listeners
registerActionListeners(listenerList, false);
listenerList.clear();
geneRegexField.removeActionListener(this);
outTable.removeMouseListener(outTableMA);
sampleTable.removeMouseListener(sampleTableMA);
//lsm.removeListSelectionListener(this);
//Clear JFrames
customQueryParent.dispose();
compHetParent.dispose();
preferViewParent.dispose();
dispose();
//Reinitialize, load data
frameInit();
redrawOutTable(fName);
initTable();
}
}
else if (es == saveAsItem) {
saveData(null, true);
}
else if (es == saveViewItem) {
saveData(null, false);
}
else if (es == preferViewItem) {
preferViewParent.setVisible(true);
}
else if (es == sampleSettingsItem) {
SampleSettingsDialog ssd = new SampleSettingsDialog(vdat);
ssd.runDialog();
maskCBox();
drawMinAffSpinner();
drawCaseControlSpinner();
//Fire list selection to update names
lsm.setSelectionInterval(outTable.getSelectedRow(), outTable.getSelectedRow() + 1);
}
else if (es == prefApply) {
try {
int mM = Integer.parseInt(minMPGField.getText());
float mMCR = Float.parseFloat(minMPGCovRatioField.getText());
int gST = Integer.parseInt(genScoreThreshField.getText());
float gSCRT = Float.parseFloat(genScoreCovRatioThreshField.getText());
minMPG = mM;
minMPGCovRatio = mMCR;
genScoreThresh = gST;
genScoreCovRatioThresh = gSCRT;
sampleTable.setDefaultRenderer(Object.class, new SampleScoreRenderer(genScoreCovRatioThresh));
sampleTable.setDefaultRenderer(Number.class, new SampleScoreRenderer(genScoreCovRatioThresh));
sampleTable.setDefaultRenderer(Float.class, new SampleScoreRenderer(genScoreCovRatioThresh));
}
catch (NumberFormatException nfe) {
showError("<html>You have entered an inappropriate number!<p>Please use an integer for Genotype Score "
+ "and a floating point number for Score / Coverage Ratio.</html>");
System.out.println(nfe);
}
}
else if (es == exitItem) {
processWindowEvent(new WindowEvent(this, WindowEvent.WINDOW_CLOSING));
}
else if (es == compHetViewItem) {
compHetParent.setVisible(true);
}
else if (es == customQueryViewItem) {
customQueryParent.setVisible(true);
}
else if (es == compHetGeneViewButton) {
String geneRegex = "";
int indexIndex = ((Integer)typeMap.get("Index")).intValue();
int mendHetRecIndex = ((Integer)typeMap.get("MendHetRec")).intValue();
int dataRowIndex = sorter.modelIndex(outTable.getSelectedRow());
String geneName = vdat.returnDataValueAt(dataRowIndex, "Gene_name");
if (isShowVar) {
geneRegex = "^" + geneName + "$";
}
else {
try {
geneRegex = "^" + (String)outTable.getValueAt(outTable.getSelectedRow(), 0) + "$";
}
catch (ClassCastException cce) {
showError(VSMessages.geneNotFoundError);
return;
}
}
BitSet[] tempBS = { mask[0], (BitSet)(mask[1].clone()) };
tempBS[1].set(MENDHETREC);
vdat.filterData(new DataFilter(tempBS, geneFile, bedFile, spinnerData, geneRegex, minMPG, minMPGCovRatio, genScoreThresh, geneDelim));
int temp[][] = vdat.returnOutData();
//Must return the filtered state to what it was, to avoid data mapping errors!
vdat.filterData(df);
if (temp.length > 0) {
String[] index = new String[temp.length];
for (int i=0; i<temp.length; i++) {
index[i] = annotMapper[indexIndex].getString(temp[i][indexIndex]) + ","
+ annotMapper[mendHetRecIndex].getString(temp[i][mendHetRecIndex]);
}
CompHetView c = new CompHetView(index, vdat, compHetSamples.isSelected());
}
else {
showError("Gene does not have any compound heterozygous positions.");
}
}
else if (es == compHetPairViewButton) {
if (isShowVar) {
int dataRowIndex = sorter.modelIndex(outTable.getSelectedRow());
String mhrString = vdat.returnDataValueAt(dataRowIndex, "MendHetRec");
if (mhrString.equals("0,")) {
showError("This variant is not in a compound heterozygous pair.");
}
else {
String index = vdat.returnDataValueAt(dataRowIndex, "Index");
index += ("," + mhrString);
CompHetView c = new CompHetView(index, vdat, compHetSamples.isSelected());
}
}
else {
showError("Not available for \"Show Gene\" view - please re-filter with \"Show Variants\"");
}
}
else if (es == compHetAllButton) {
int indexIndex = ((Integer)typeMap.get("Index")).intValue();
int mendHetRecIndex = ((Integer)typeMap.get("MendHetRec")).intValue();
String geneRegex = (getRegex() == null) ? "." : getRegex();
BitSet[] tempBS = { mask[0], (BitSet)(mask[1].clone()) };
tempBS[1].set(MENDHETREC);
vdat.filterData(new DataFilter(tempBS, geneFile, bedFile, spinnerData, geneRegex, minMPG, minMPGCovRatio, genScoreThresh, geneDelim));
int temp[][] = vdat.returnOutData();
//Must return the filtered state to what it was, to avoid data mapping errors!
vdat.filterData(df);
if (temp.length > 0) {
String[] index = new String[temp.length];
for (int i=0; i<temp.length; i++) {
index[i] = annotMapper[indexIndex].getString(temp[i][indexIndex]) + ","
+ annotMapper[mendHetRecIndex].getString(temp[i][mendHetRecIndex]);
}
CompHetView c = new CompHetView(index, vdat, compHetSamples.isSelected());
}
else {
showError("No compound heterozygous positions. Check your filters!");
}
}
else if (es == sampleExportItem) {
SampleExporter se = new SampleExporter(vdat);
File fcFile;
String fileName;
String outLine;
int ovwResult = JOptionPane.YES_OPTION;
JFileChooser fc = new JFileChooser(System.getProperty("user.dir"));
fc.setDialogTitle("Save Sample Export File As");
int fcReturn = fc.showSaveDialog(VarSifter.this);
if (fcReturn == JFileChooser.APPROVE_OPTION) {
fcFile = fc.getSelectedFile();
fileName = fcFile.getAbsolutePath();
if (fcFile.exists()) {
ovwResult = JOptionPane.showConfirmDialog(null, fileName + " already exists. " +
"Do you want to overwrite it?", "Overwrite Warning",
JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
}
if (ovwResult == JOptionPane.YES_OPTION) {
try {
PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(fcFile)));
pw.println(se.getHeader());
while ((outLine = se.getNextVariant()) != null) {
pw.println(outLine);
}
pw.close();
if (pw.checkError()) {
showError("Error Detected writing sample export file! File NOT saved!");
System.out.println("Error Detected writing sample export file");
}
else {
System.out.println("File " + fileName + " written");
}
}
catch (IOException ioe) {
showError("File write error: " + ioe.getMessage());
}
}
else {
System.out.println(fileName + " not overwritten");
}
}
else {
System.out.println("Sample Export NOT saved!");
}
}
else if (es == aboutItem) {
JTextArea tPane = new JTextArea("VarSifter v" + version + "\n" +
"Jamie K. Teer, 2010\n\n" + VSMessages.govWork + "\n" + id +
"\n\n--------------------------------------------------------" +
"\n\nThis program uses the JTable sorting class TableSorter.java from Sun\n" +
"and must include the following copyright notification:\n\n" +
VSMessages.sunCopyright + "\n" + VSMessages.sunDisclaimer);
JScrollPane sPane = new JScrollPane(tPane);
sPane.setPreferredSize(new Dimension(600,600));
JOptionPane.showMessageDialog(null, sPane, "About VarSifter", JOptionPane.PLAIN_MESSAGE);
}
else if (es == docItem) {
Font f = new Font(Font.SANS_SERIF, Font.PLAIN, 12);
java.net.URL dURL = getClass().getResource("misc/doc.html");
JEditorPane dPane = null;
try {
dPane = new JEditorPane(dURL);
}
catch (IOException ioe) {
showError("<html>This is embarassing - the Documentation page could not be loaded.<p>"
+ "Please see the online documentation to answer your questions.");
ioe.printStackTrace();
}
String css = "body { font-family: " + f.getFamily() + "; " + "font-size: " + f.getSize() + "pt; }";
((HTMLDocument)dPane.getDocument()).getStyleSheet().addRule(css);
dPane.setEditable(false);
JScrollPane sPane = new JScrollPane(dPane);
sPane.setPreferredSize(new Dimension(600,800));
JOptionPane.showMessageDialog(null, sPane, "VarSifter Documentation", JOptionPane.PLAIN_MESSAGE);
}
else if (es == troubleItem) {
//Font f = UIManager.getFont("TextArea.font");
Font f = new Font(Font.SANS_SERIF, Font.PLAIN, 12);
java.net.URL tsURL = getClass().getResource("misc/trouble.html");
JEditorPane tsPane = null;
try {
tsPane = new JEditorPane(tsURL);
}
catch (IOException ioe) {
showError("<html>This is embarassing - the TroubleShooting page could not be loaded.<p>"
+ "Please see the online documentation to answer your questions.");
ioe.printStackTrace();
}
//tsPane.setFont(f);
String css = "body { font-family: " + f.getFamily() + "; " + "font-size: " + f.getSize() + "pt; }";
((HTMLDocument)tsPane.getDocument()).getStyleSheet().addRule(css);
tsPane.setEditable(false);
JScrollPane sPane = new JScrollPane(tsPane);
sPane.setPreferredSize(new Dimension(600,800));
JOptionPane.showMessageDialog(null, sPane, "TroubleShooting", JOptionPane.PLAIN_MESSAGE);
}
else if (es == check) {
int row = outTable.getSelectedRow();
int col = outTable.getSelectedColumn();
int sRow = sampleTable.getSelectedRow();
int sCol = sampleTable.getSelectedColumn();
System.out.println("Ann: " + row + "\t" + col + "\t" + outTable.getValueAt(row,col).getClass() +
"\t" + outTable.getColumnClass(col));
System.out.println("Sample: " + sRow + "\t" + sCol + "\t" + sampleTable.getValueAt(sRow,sCol).getClass() +
"\t" + sampleTable.getColumnClass(sCol));
}
}
/**
* Handle List Actions
*
* @param e - changing the choice on the top table
*/
public void valueChanged(ListSelectionEvent e) {
ListSelectionModel lsme = (ListSelectionModel)e.getSource();
//May remove this test if its the only List Action
if ( e.getSource() == lsm && lsme.getValueIsAdjusting() == false) {
int rowIndex = outTable.getSelectedRow();
if (rowIndex < 0) {
rowIndex = 0;
}
int dataIndex = sorter.modelIndex(rowIndex);
sampleSorter.setTableHeader(null); //Do this to avoid a memory leak
if (isShowVar) {
sampleSorter = new TableSorter((new SampleTableModel(vdat.returnSample(dataIndex),
sampleTableLabels, vdat )));
sampleTable.setModel(sampleSorter);
sampleSorter.setTableHeader(sampleTable.getTableHeader());
}
else {
sampleSorter = new TableSorter((new SampleTableModel(new int[0][], null, vdat)));
sampleTable.setModel(sampleSorter);
}
outTable.setRowSelectionInterval(rowIndex,rowIndex);
initColSizes(sampleTable, (SampleTableModel)((TableSorter)sampleTable.getModel()).getTableModel() );
}
}
/**
* Handle Table Actions
*
* @param e (changing a value in the table)
*/
public void tableChanged(TableModelEvent e) {
if (e.getSource().getClass() == VarTableModel.class) {
int row = e.getFirstRow();
int lastRow = e.getLastRow();
int col = e.getColumn();
VarTableModel model = (VarTableModel)e.getSource();
Object data = model.getValueAt(row, col);
vdat.setData(row, col, (String)data);
}
}
/**
* Determine which boxes are checked
*
* @return Array of BitSets describing which boxes are checked
*/
private BitSet[] getFilterMask() {
BitSet[] m = new BitSet[2];
m[0] = new BitSet(typeCBox.length);
for (int i=0; i < typeCBox.length; i++) {
if (typeCBox[i].isSelected()) {
m[0].set(i);
}
}
m[1] = new BitSet(cBox.length);
for (int i=0; i < cBox.length; i++) {
if (cBox[i].isSelected()) {
m[1].set(i);
}
}
return m;
}
/**
* Sets fitted column sizes
*
* @param table the JTable holding the data
* @param model the VarTableModel holding the data
*/
public void initColSizes(JTable table, VarTableModel model) {
TableColumn col = null;
Component comp = null;
int headerWidth = 0;
int cellWidth = 0;
Object[] largestInCol = model.getLargestInColumn();
TableCellRenderer headerRenderer = table.getTableHeader().getDefaultRenderer();
for (int i=0; i < largestInCol.length; i++) {
col = table.getColumnModel().getColumn(i);
comp = headerRenderer.getTableCellRendererComponent(
table, col.getHeaderValue(), false, false, 0, 0);
headerWidth = comp.getPreferredSize().width;
if (headerWidth > MAX_COLUMN_SIZE) {
headerWidth = MAX_COLUMN_SIZE;
}
comp = table.getDefaultRenderer(model.getColumnClass(i)).getTableCellRendererComponent(
table, largestInCol[i], false, false, 0, i);
cellWidth = comp.getPreferredSize().width;
if (cellWidth > MAX_COLUMN_SIZE) {
cellWidth = MAX_COLUMN_SIZE;
}
col.setPreferredWidth( (Math.max(headerWidth, cellWidth) + 25) );
}
}
/**
* Initialize Table
*
*/
private void initTable() {
JPanel pane = new JPanel();
pane.setLayout(new BorderLayout());
pane.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
ToolTipManager.sharedInstance().setInitialDelay(1250);
ToolTipManager.sharedInstance().setReshowDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
//Menu
JMenuBar mBar = new JMenuBar();
JMenu fileMenu = new JMenu("File");
JMenu viewMenu = new JMenu("View");
JMenu toolMenu = new JMenu("Tools");
JMenu helpMenu = new JMenu("Help");
openItem = new JMenuItem("Open File");
saveAsItem = new JMenuItem("Save File As");
saveViewItem = new JMenuItem("Save Current View As");
preferViewItem = new JMenuItem("Preferences");
sampleSettingsItem = new JMenuItem("Sample Settings");
exitItem = new JMenuItem("Exit");
compHetViewItem = new JMenuItem("Viewing Compound Hets");
customQueryViewItem = new JMenuItem("Custom Query");
sampleExportItem = new JMenuItem("Export Samples");
aboutItem = new JMenuItem("About VarSifter");
docItem = new JMenuItem("VarSifter Documentation");
troubleItem = new JMenuItem("TroubleShooting");
fileMenu.add(openItem);
fileMenu.add(saveAsItem);
fileMenu.add(saveViewItem);
fileMenu.add(preferViewItem);
fileMenu.add(sampleSettingsItem);
fileMenu.add(exitItem);
viewMenu.add(compHetViewItem);
viewMenu.add(customQueryViewItem);
toolMenu.add(sampleExportItem);
helpMenu.add(aboutItem);
helpMenu.add(docItem);
helpMenu.add(troubleItem);
mBar.add(fileMenu);
mBar.add(viewMenu);
mBar.add(toolMenu);
mBar.add(helpMenu);
setJMenuBar(mBar);
drawMinAffSpinner();
drawCaseControlSpinner();
drawMinMPGSampleSpinner();
drawMinMPGCovRatioSampleSpinner();
outTable.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
outTable.setRowSelectionInterval(0,0);
outTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
DefaultTableCellRenderer tcr = new DefaultTableCellRenderer();
tcr.setHorizontalAlignment(SwingConstants.CENTER);
outTable.setDefaultRenderer(String.class, tcr);
outTable.setDefaultRenderer(Float.class, new FloatScoreRenderer(6));
lsm = outTable.getSelectionModel();
lsm.addListSelectionListener(this);
//IGV double click listener of outTable
// (courtesy of Timothy Gall)
outTableMA = new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() == 2) {
int dataRowIndex = sorter.modelIndex(outTable.getSelectedRow());
//IGV connection check
try {
Socket igvSocket = new Socket(IGVhost, IGVport);
PrintWriter igvOut = new PrintWriter(igvSocket.getOutputStream(),true);
BufferedReader igvIn = new BufferedReader(new InputStreamReader(igvSocket.getInputStream()));
igvOut.println("goto " + vdat.returnDataValueAt(dataRowIndex, "Chr") + ":"
+ String.valueOf(Integer.valueOf(vdat.returnDataValueAt(dataRowIndex, "LeftFlank")) + 1));
String response = igvIn.readLine();
System.out.println("IGV message: " +response);
igvSocket.close();
} catch (IOException igvExcept) {
System.out.println("igvException");
VarSifter.showError("IGV reported an error (or may not be opened!)");
}
}
}
};
outTable.addMouseListener(outTableMA);
// End IGV outTable listener
dataScroller = new JScrollPane(outTable,
ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
dataScroller.setPreferredSize(new Dimension((w/2), (h/4)));
if (sampleSorter != null) {
sampleSorter.setTableHeader(null); //Do this to avoid memory leak
}
sampleSorter = new TableSorter( new SampleTableModel(vdat.returnSample(outTable.getSelectedRow()),
sampleTableLabels, vdat ));
sampleTable.setModel(sampleSorter);
sampleSorter.setTableHeader(sampleTable.getTableHeader());
sampleTable.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
sampleScroller = new JScrollPane(sampleTable,
ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
sampleScroller.setPreferredSize(new Dimension((w/2), 80));
sampleScroller.setAlignmentY(Component.TOP_ALIGNMENT);
sampleTable.setDefaultRenderer(Object.class, new SampleScoreRenderer(genScoreCovRatioThresh));
sampleTable.setDefaultRenderer(Number.class, new SampleScoreRenderer(genScoreCovRatioThresh));
sampleTable.setDefaultRenderer(Float.class, new SampleScoreRenderer(genScoreCovRatioThresh));
initColSizes(sampleTable, (SampleTableModel)((TableSorter)sampleTable.getModel()).getTableModel() );
//IGV double click listener of sampleTable
//(courtesy of Timothy Gall)
sampleTableMA = new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
if (e.getClickCount() == 2) {
String selectedSample = sampleTable.getValueAt(sampleTable.getSelectedRow(), 0).toString();
String line = null;
if (opt.exists("IGV_bampath")) {
line = opt.get("IGV_bampath");
line += selectedSample + ".bam";
}
else if (opt.exists("IGV_bamlist")) {
if (bamList == null) {
bamList = new HashMap<String,String>();
String blLine;
try {
BufferedReader br = new BufferedReader(new FileReader(opt.get("IGV_bamlist")));
while ( (blLine = br.readLine()) != null) {
String[] kv = blLine.split("=",2);
bamList.put(kv[0], kv[1]);
}
br.close();
}
catch (IOException ioe) {
System.err.println("Error parsing IGV_bamlist!");
System.err.println(ioe);
showError("Error parsing IGV_bamlist! File may not be accessible - check console.");
}
}
if (bamList.containsKey(selectedSample)) {
line = bamList.get(selectedSample);
}
else {
showError("<html>Selected sample " + selectedSample + " not in bamList "
+ opt.get("IGV_bamlist") + "<p>IGV cannot load this sample.</html>");
System.err.println("Selected sample " + selectedSample + " not in bamList "
+ opt.get("IGV_bamlist"));
}
}
else {
System.err.println("No way to identify bamfile - set option in VarSifter.config");
}
if (line != null && new File(line).exists()) {
//IGV connection check
try {
System.out.println("Loading: " + line);
Socket igvSocket = new Socket(IGVhost, IGVport);
PrintWriter igvOut = new PrintWriter(igvSocket.getOutputStream(),true);
BufferedReader igvIn = new BufferedReader(new InputStreamReader(igvSocket.getInputStream() ) );
igvOut.println("load " + line);
String response = igvIn.readLine();
System.out.println(response);
igvSocket.close();
} catch (IOException igvExcept) {
System.out.println("igvException");
VarSifter.showError("IGV reported an error (or may not be opened!)");
}
}
else {
showError("File " + line + " does not exist - cannot load in IGV.");
}
}
}
};
sampleTable.addMouseListener(sampleTableMA);
//End IGV sampleTable listener
//Sample display
JPanel samplePane = new JPanel();
samplePane.setLayout(new BoxLayout(samplePane, BoxLayout.X_AXIS));
samplePane.add(sampleScroller);
//Filters
JPanel filtPane = new JPanel();
filtPane.setLayout(new BoxLayout(filtPane, BoxLayout.Y_AXIS));
JPanel includePane = new JPanel();
includePane.setLayout(new BoxLayout(includePane, BoxLayout.Y_AXIS));
includePane.setBorder(BorderFactory.createLineBorder(Color.black));
for (JCheckBox cb : typeCBox) {
includePane.add(cb);
}
JPanel excludePane = new JPanel();
excludePane.setLayout(new BoxLayout(excludePane, BoxLayout.Y_AXIS));
excludePane.setBorder(BorderFactory.createLineBorder(Color.black));
excludePane.add(dbsnp);
excludePane.add(notFilterFile);
JPanel sampleFiltPane = new JPanel();
sampleFiltPane.setLayout(new BoxLayout(sampleFiltPane, BoxLayout.Y_AXIS));
sampleFiltPane.setBorder(BorderFactory.createLineBorder(Color.black));
sampleFiltPane.add(mendRec);
sampleFiltPane.add(mendDom);
sampleFiltPane.add(mendBad);
sampleFiltPane.add(mendCompHet);
sampleFiltPane.add(filterFile);
sampleFiltPane.add(bedFilterFile);
sampleFiltPane.add(uniqInAff);
JPanel affSpinnerPane = new JPanel();
affSpinnerPane.setLayout(new BoxLayout(affSpinnerPane, BoxLayout.X_AXIS));
affSpinnerPane.setAlignmentX(Component.LEFT_ALIGNMENT);
affSpinnerPane.add(Box.createRigidArea(new Dimension(15,0)));
affSpinnerPane.add(affSpinnerLabel);
affSpinnerPane.add(minAffSpinner);
sampleFiltPane.add(affSpinnerPane);
JPanel casePane = new JPanel();
casePane.setLayout(new BoxLayout(casePane, BoxLayout.X_AXIS));
casePane.setAlignmentX(Component.LEFT_ALIGNMENT);
casePane.add(Box.createRigidArea(new Dimension(15,0)));
casePane.add(caseSpinnerLabel);
casePane.add(caseSpinner);
JPanel controlPane = new JPanel();
controlPane.setLayout(new BoxLayout(controlPane, BoxLayout.X_AXIS));
controlPane.setAlignmentX(Component.LEFT_ALIGNMENT);
controlPane.add(Box.createRigidArea(new Dimension(15,0)));
controlPane.add(controlSpinnerLabel);
controlPane.add(controlSpinner);
sampleFiltPane.add(caseControl);
sampleFiltPane.add(casePane);
sampleFiltPane.add(controlPane);
sampleFiltPane.add(customQuery);
JPanel regexPane = new JPanel();
regexPane.setLayout(new BoxLayout(regexPane, BoxLayout.Y_AXIS));
regexPane.add(new JLabel("Search gene names for:"));
geneRegexField.setMaximumSize( new Dimension( (int)geneRegexField.getMaximumSize().getWidth(),
(int)geneRegexField.getMinimumSize().getHeight()));
regexPane.add(geneRegexField);
JPanel fFiltPane = new JPanel();
fFiltPane.setLayout(new BoxLayout(fFiltPane, BoxLayout.Y_AXIS));
fFiltPane.add(filterFileLabel);
fFiltPane.add(filterFileButton);
JPanel bFiltPane = new JPanel();
bFiltPane.setLayout(new BoxLayout(bFiltPane, BoxLayout.Y_AXIS));
bFiltPane.add(bedFilterFileLabel);
bFiltPane.add(bedFilterFileButton);
JPanel showPane = new JPanel();
showPane.setLayout(new BoxLayout(showPane, BoxLayout.X_AXIS));
showPane.setBorder(BorderFactory.createLineBorder(Color.black));
showPane.setAlignmentX(Component.LEFT_ALIGNMENT);
ButtonGroup showGroup = new ButtonGroup();
showGroup.add(showVar);
showGroup.add(showGene);
showPane.add(showVar);
showPane.add(showGene);
filtPane.add(new JLabel("Include:"));
filtPane.add(includePane);
filtPane.add(Box.createRigidArea(new Dimension(0,15)));
filtPane.add(new JLabel("Exclude:"));
filtPane.add(excludePane);
filtPane.add(Box.createRigidArea(new Dimension(0,15)));
filtPane.add(new JLabel("Include:"));
filtPane.add(sampleFiltPane);
filtPane.add(Box.createRigidArea(new Dimension(0,15)));
filtPane.add(regexPane);
filtPane.add(Box.createRigidArea(new Dimension(0,15)));
filtPane.add(showPane);
filtPane.add(Box.createRigidArea(new Dimension(0,15)));
filtPane.add(Box.createVerticalGlue());
filtPane.add(fFiltPane);
filtPane.add(Box.createRigidArea(new Dimension(0,10)));
filtPane.add(bFiltPane);
filtPane.add(Box.createRigidArea(new Dimension(0,10)));
filtPane.add(geneViewButton);
if (isDebug) {
filtPane.add(Box.createRigidArea(new Dimension(0,10)));
filtPane.add(check); //TESTING
}
JScrollPane filtScroll = new JScrollPane(filtPane,
ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED,
ScrollPaneConstants.HORIZONTAL_SCROLLBAR_AS_NEEDED);
filtScroll.setBorder(null);
//Stats (line count)
apply.setMnemonic(KeyEvent.VK_F);
JPanel stats = new JPanel();
stats.setLayout(new BoxLayout(stats, BoxLayout.X_AXIS));
stats.setBorder(BorderFactory.createEmptyBorder(10,0,0,0));
stats.add(linesl);
stats.add(lines);
stats.add(Box.createHorizontalGlue());
stats.add(apply);
stats.add(Box.createRigidArea(new Dimension(15,0)));
stats.add(clear);
stats.add(Box.createRigidArea(new Dimension(21,0)));
JPanel tablePanel = new JPanel();
tablePanel.setLayout(new BoxLayout(tablePanel, BoxLayout.Y_AXIS));
tablePanel.setPreferredSize(new Dimension((w/2), (h/3)));
tablePanel.setBorder(BorderFactory.createEmptyBorder(0,0,0,10));
tablePanel.add(dataScroller);
tablePanel.add(Box.createRigidArea(new Dimension(0,15)));
tablePanel.add(samplePane);
//Icons
setIconImage(createImageIcon("images/vs.png", "VarSifter").getImage());
apply.setIcon(createImageIcon("images/sift_a.png", "Sift variants"));
//Listener Registration
listenerList.add(apply);
listenerList.add(clear);
listenerList.add(openItem);
listenerList.add(saveAsItem);
listenerList.add(saveViewItem);
listenerList.add(preferViewItem);
listenerList.add(sampleSettingsItem);
listenerList.add(prefApply);
listenerList.add(compHetViewItem);
listenerList.add(customQueryViewItem);
listenerList.add(sampleExportItem);
listenerList.add(exitItem);
listenerList.add(aboutItem);
listenerList.add(docItem);
listenerList.add(troubleItem);
listenerList.add(check);
listenerList.add(filterFileButton);
listenerList.add(bedFilterFileButton);
listenerList.add(geneViewButton);
registerActionListeners(listenerList, true);
geneRegexField.addActionListener(this);
//Disable unused buttons
filterFile.setEnabled(false);
notFilterFile.setEnabled(false);
bedFilterFile.setEnabled(false);
if (vdat.returnParent() != null) {
geneViewButton.setVisible(false);
}
compHetGeneViewButton.setEnabled(false);
maskCBox();
//ToolTips
apply.setToolTipText("Execute the query using all checked filters");
clear.setToolTipText("Unset all filters");
includePane.setToolTipText("Variants meeting these conditions will be displayed");
excludePane.setToolTipText("Variants meeting these conditions will NOT be displayed");
sampleFiltPane.setToolTipText("Variants meeting these conditions will be displayed");
showVar.setToolTipText("Annotation Panel will show each variant");
showGene.setToolTipText("Annotation Panel will show each gene, and the number of variants in that gene.");
filterFileButton.setToolTipText("<html>Select a file of gene names for filtering.<p>"
+ "Remember to check the \"Include/Exclude Gene File\" filter box!");
bedFilterFileButton.setToolTipText("<html>Select a file with BED format regions for filtering.<p>"
+ "Remember to check the \"Include Bed File Regions\" filter box!");
geneViewButton.setToolTipText("Open a new window showing all variants for the highlighted gene");
pane.add(tablePanel, BorderLayout.CENTER);
pane.add(filtScroll, BorderLayout.LINE_END);
pane.add(stats, BorderLayout.PAGE_END);
add(pane);
pack();
setVisible(true);
//Initialize (but don't display) compHetPane
JPanel compHetPane = new JPanel();
compHetPane.setLayout(new BoxLayout(compHetPane, BoxLayout.Y_AXIS));
compHetPane.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
JPanel buttonPane = new JPanel();
buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.Y_AXIS));
buttonPane.add(new JLabel("Choose Compound Het View:"));
buttonPane.add(Box.createRigidArea(new Dimension(0,15)));
buttonPane.add(compHetSamples);
buttonPane.add(Box.createRigidArea(new Dimension(0,10)));
buttonPane.add(compHetGeneViewButton);
buttonPane.add(Box.createRigidArea(new Dimension(0,10)));
buttonPane.add(compHetPairViewButton);
buttonPane.add(Box.createRigidArea(new Dimension(0,10)));
buttonPane.add(compHetAllButton);
compHetGeneViewButton.addActionListener(this);
compHetPairViewButton.addActionListener(this);
compHetAllButton.addActionListener(this);
compHetPane.add(buttonPane);
compHetParent = new JFrame("Compound Het View");
compHetParent.add(compHetPane);
compHetParent.pack();
//compHetParent.setVisible(true);
//Initialize (but don't display) preferViewPane
JPanel preferViewPane = new JPanel();
preferViewParent = new JFrame("Preferences");
preferViewPane.setLayout(new BoxLayout(preferViewPane, BoxLayout.Y_AXIS));
preferViewPane.setBorder(BorderFactory.createEmptyBorder(10,10,10,10));
setJComponentSize(minMPGField);
setJComponentSize(minMPGCovRatioField);
setJComponentSize(genScoreThreshField);
setJComponentSize(genScoreCovRatioThreshField);
minMPGField.setText(Integer.toString(minMPG));
minMPGCovRatioField.setText(Float.toString(minMPGCovRatio));
genScoreThreshField.setText(Integer.toString(genScoreThresh));
genScoreCovRatioThreshField.setText(Float.toString(genScoreCovRatioThresh));
JPanel minMPGPane = new JPanel();
minMPGPane.setLayout(new BoxLayout(minMPGPane, BoxLayout.X_AXIS));
minMPGPane.add(new JLabel("Minimum Genotype Score: "));
minMPGPane.add(minMPGField);
minMPGPane.add(new JLabel(" in at least "));
minMPGPane.add(minMPGSpinner);
minMPGPane.add(new JLabel(" samples."));
JPanel minMPGCovRatioPane = new JPanel();
minMPGCovRatioPane.setLayout(new BoxLayout(minMPGCovRatioPane, BoxLayout.X_AXIS));
minMPGCovRatioPane.add(new JLabel("Minimum (Genotype Score / coverage) ratio: "));
minMPGCovRatioPane.add(minMPGCovRatioField);
minMPGCovRatioPane.add(new JLabel(" in at least "));
minMPGCovRatioPane.add(minMPGCovRatioSpinner);
minMPGCovRatioPane.add(new JLabel(" samples."));
JPanel preferFilterPane = new JPanel();
preferFilterPane.setLayout(new BoxLayout(preferFilterPane, BoxLayout.Y_AXIS));
preferFilterPane.setBorder(BorderFactory.createLineBorder(Color.black));
preferFilterPane.setAlignmentX(Component.LEFT_ALIGNMENT);
preferFilterPane.add(Box.createRigidArea(new Dimension(0,15)));
preferFilterPane.add(minMPGPane);
preferFilterPane.add(Box.createRigidArea(new Dimension(0,10)));
preferFilterPane.add(minMPGCovRatioPane);
preferFilterPane.add(Box.createRigidArea(new Dimension(0,10)));
JPanel preferSettingsPane = new JPanel();
preferSettingsPane.setLayout(new BoxLayout(preferSettingsPane, BoxLayout.Y_AXIS));
preferSettingsPane.setBorder(BorderFactory.createLineBorder(Color.black));
preferSettingsPane.setAlignmentX(Component.LEFT_ALIGNMENT);
preferSettingsPane.add(Box.createRigidArea(new Dimension(0,15)));
preferSettingsPane.add(new JLabel("Genotype Score Threshold for Aff/Norm, Case/Control filters:"));
preferSettingsPane.add(genScoreThreshField);
preferSettingsPane.add(Box.createRigidArea(new Dimension(0,10)));
preferSettingsPane.add(new JLabel("Genotype Score / Coverage Ratio Threshold for low-lighting:"));
preferSettingsPane.add(genScoreCovRatioThreshField);
preferSettingsPane.add(Box.createRigidArea(new Dimension(0,10)));
preferViewPane.add(new JLabel("Choose minimum scores for general filtering:"));
preferViewPane.add(preferFilterPane);
preferViewPane.add(Box.createRigidArea(new Dimension(0,15)));
preferViewPane.add(new JLabel("Choose minimum scores for certain filters and for lowlighting:"));
preferViewPane.add(preferSettingsPane);
preferViewPane.add(Box.createRigidArea(new Dimension(0,15)));
preferViewPane.add(prefApply);
preferViewParent.add(preferViewPane);
preferViewParent.pack();
//preferViewParent.setVisible(true);
initCustomQueryParent();
}
/**
* Redraw Table
*
* @param newData VS file
*/
private void redrawOutTable(String newData) {
if (newData != null) {
vdat = getNewVarData(newData);
String[] sampValName = vdat.returnSampleValueNames();
sampleTableLabels = new String[sampValName.length + 1];
sampleTableLabels[0] = "Sample";
System.arraycopy(sampValName, 0, sampleTableLabels, 1, sampValName.length);
typeMap = null;
}
if (typeMap == null) {
typeMap = vdat.returnDataTypeAt();
annotMapper = vdat.returnAnnotMap();
sampleMapper = vdat.returnSampleMap();
String[] types = annotMapper[typeMap.get("type")].getSortedEntries();
typeCBox = new JCheckBox[types.length];
for (int i=0; i<types.length; i++) {
typeCBox[i] = new JCheckBox(types[i]);
}
maskCBox();
mask = getFilterMask();
clear.doClick();
drawMinAffSpinner();
drawCaseControlSpinner();
drawMinMPGSampleSpinner();
drawMinMPGCovRatioSampleSpinner();
df = new DataFilter(mask, geneFile, bedFile, spinnerData, getRegex(), minMPG, minMPGCovRatio, genScoreThresh, geneDelim);
}
if (sorter != null) {
sorter.setTableHeader(null); //Must do this to avoid memory leak
}
int geneNameIndex = ((Integer)typeMap.get("Gene_name")).intValue();
if (isShowVar) {
sorter = new TableSorter( new VarTableModel(vdat.returnOutData(),
vdat.returnDataNames(),
annotMapper,
vdat ));
}
else {
AbstractMapper[] geneMap = { annotMapper[geneNameIndex], new IntMapper() };
sorter = new TableSorter( new VarTableModel(vdat.returnGeneData(),
vdat.returnGeneNames(),
geneMap,
vdat ));
}
//TableListener to detect data changes added in redrawOutTable(String)
((VarTableModel)sorter.getTableModel()).addTableModelListener(this);
outTable.setModel(sorter);
sorter.setTableHeader(outTable.getTableHeader());
initColSizes(outTable, (VarTableModel)((TableSorter)outTable.getModel()).getTableModel() );
lines.setText(Integer.toString(outTable.getRowCount()));
outTable.requestFocusInWindow();
}
/**
* Initialize the Custom Query Window
*/
private void initCustomQueryParent() {
//Initialize (but don't display) customQueryParent
try {
customQueryParent = new JFrame("Custom Query");
cqPane = new CustomQueryView(vdat, this);
JPanel customQueryPane = new JPanel();
customQueryPane.setPreferredSize(new Dimension(w/2, h/2));
customQueryPane.setLayout(new BoxLayout(customQueryPane, BoxLayout.Y_AXIS));
customQueryPane.setBorder(BorderFactory.createEmptyBorder(6,6,6,6));
customQueryPane.add(cqPane);
customQueryParent.add(customQueryPane);
customQueryParent.pack();
//customQueryParent.setVisible(true);
}
catch (NoClassDefFoundError e) {
showError("<html>Required JUNG files are not in the same directory as the VarSifter.jar file."
+ "<p>Disabling custom querying.");
customQueryViewItem.setEnabled(false);
customQuery.setEnabled(false);
e.printStackTrace();
}
}
/**
* Disable unused CheckBoxes
*
*/
private void maskCBox() {
if (typeMap.containsKey("dbID")) {
dbsnp.setEnabled(true);
}
else {
dbsnp.setEnabled(false);
dbsnp.setSelected(false);
}
if (typeMap.containsKey("MendHomRec")) {
mendRec.setEnabled(true);
}
else {
mendRec.setEnabled(false);
mendRec.setSelected(false);
}
if (typeMap.containsKey("MendHetRec")) {
mendCompHet.setEnabled(true);
compHetGeneViewButton.setEnabled(true);
compHetPairViewButton.setEnabled(true);
compHetAllButton.setEnabled(true);
}
else {
mendCompHet.setEnabled(false);
mendCompHet.setSelected(false);
compHetGeneViewButton.setEnabled(false);
compHetPairViewButton.setEnabled(false);
compHetAllButton.setEnabled(false);
}
if (typeMap.containsKey("MendDom")) {
mendDom.setEnabled(true);
}
else {
mendDom.setEnabled(false);
mendDom.setSelected(false);
}
if (typeMap.containsKey("MendInconsis")) {
mendBad.setEnabled(true);
}
else {
mendBad.setEnabled(false);
mendBad.setSelected(false);
}
if (vdat.countSampleType(vdat.AFF_NORM_PAIR) == 0) {
uniqInAff.setEnabled(false);
uniqInAff.setSelected(false);
minAffSpinner.setEnabled(false);
affSpinnerLabel.setEnabled(false);
}
else {
uniqInAff.setEnabled(true);
minAffSpinner.setEnabled(true);
affSpinnerLabel.setEnabled(true);
}
if (vdat.countSampleType(vdat.CASE) == 0) {
caseControl.setEnabled(false);
caseControl.setSelected(false);
caseSpinner.setEnabled(false);
caseSpinnerLabel.setEnabled(false);
}
else {
caseControl.setEnabled(true);
caseSpinner.setEnabled(true);
caseSpinnerLabel.setEnabled(true);
}
if (vdat.countSampleType(vdat.CONTROL) == 0) {
//caseControl.setEnabled(false);
caseControl.setSelected(false);
controlSpinner.setEnabled(false);
controlSpinnerLabel.setEnabled(false);
}
else {
//caseControl.setEnabled(true);
controlSpinner.setEnabled(true);
controlSpinnerLabel.setEnabled(true);
}
}
/**
* get regex or null if nothing
*
*/
private String getRegex() {
if (geneRegexField.getText().equals("")) {
return null;
}
else {
return geneRegexField.getText();
}
}
/**
* Determine what type of file to interpret, call the correct VarData object
*/
private VarData getNewVarData(String in) {
VarData v = null;
if (vcfPat.matcher(in).find()) {
v = new VCFVarData(in);
}
else if (gzPat.matcher(in).find()) {
VarSifter.showError("Cannot read .gz files. Please uncompress and load the uncompressed file.");
System.exit(1);
}
else {
v = new VarData(in);
}
return v;
}
/**
* initialize minAffSpinner
*
*/
private void drawMinAffSpinner() {
if (vdat.countSampleType(vdat.AFF_NORM_PAIR) > 0) {
minAffSpinner.setModel(new SpinnerNumberModel(1, 1, vdat.countSampleType(vdat.AFF_NORM_PAIR), 1));
}
setJComponentSize(minAffSpinner);
spinnerData[vdat.AFF_NORM_PAIR] = ((Integer)minAffSpinner.getValue()).intValue();
}
/**
* initialize case, control spinners
*
*/
private void drawCaseControlSpinner() {
int caseCount = vdat.countSampleType(vdat.CASE);
int controlCount = vdat.countSampleType(vdat.CONTROL);
if (caseCount > 0) {
caseSpinner.setModel(new SpinnerNumberModel(1, 0, caseCount, 1));
}
if (controlCount > 0) {
controlSpinner.setModel(new SpinnerNumberModel(0, 0, controlCount, 1));
}
setJComponentSize(caseSpinner);
setJComponentSize(controlSpinner);
spinnerData[vdat.CASE] = ((Integer)caseSpinner.getValue()).intValue();
spinnerData[vdat.CONTROL] = ((Integer)controlSpinner.getValue()).intValue();
}
/**
* Initialize minMPG sample Spinner
*/
private void drawMinMPGSampleSpinner() {
int count = vdat.countSampleType(vdat.MIN_MPG);
if (count > 0) {
minMPGSpinner.setModel(new SpinnerNumberModel(0, 0, count, 1));
}
setJComponentSize(minMPGSpinner);
spinnerData[vdat.MIN_MPG] = ((Integer)minMPGSpinner.getValue()).intValue();
}
/**
* Initialize minMPGCovRatio sample Spinner
*/
private void drawMinMPGCovRatioSampleSpinner() {
int count = vdat.countSampleType(vdat.MIN_MPG_COV);
if (count > 0) {
minMPGCovRatioSpinner.setModel(new SpinnerNumberModel(0, 0, count, 1));
}
setJComponentSize(minMPGCovRatioSpinner);
spinnerData[vdat.MIN_MPG_COV] = ((Integer)minMPGCovRatioSpinner.getValue()).intValue();
}
/**
* Create an ImageIcon from a path relative to this class.
* @param path Relative path of image file.
* @param desc Assistive tech description
* @return ImageIcon or null if path invalid.
*/
private ImageIcon createImageIcon(String path, String desc) {
java.net.URL url = getClass().getResource(path);
if (url != null) {
return new ImageIcon(url, desc);
}
else {
showError("Couldn't find icon path: " + path);
return null;
}
}
/**
* Add or remove Action Listeners
* @param inList A Set of AbstractButtons to add/remove
* @param doAdd Add if true, remove if false
*/
private void registerActionListeners(List<AbstractButton> inList, boolean doAdd) {
if (doAdd) {
//Add listener
for (AbstractButton ab : inList) {
ab.addActionListener(this);
}
}
else {
//Remove listener
for (AbstractButton ab : inList) {
ab.removeActionListener(this);
}
}
}
/**
* Display error as dialog
*
* @param err An error message to display as a MessageDialog
*/
public static void showError(String err) {
JOptionPane.showMessageDialog(null, err, "Error!", JOptionPane.ERROR_MESSAGE);
}
/**
* Display message as dialog
*
* @param mess A message to display
*/
public static void showMessage(String mess) {
JOptionPane.showMessageDialog(null, mess, "VarSifter Message", JOptionPane.INFORMATION_MESSAGE);
}
/**
* Set the "checked" status of the fixed checkboxes
* @param index The 0-based index of the desired JCheckBox in cBox
* @param val True or false (should be box be checked)
*/
public void setCBoxChecked(int index, boolean val) {
cBox[index].setSelected(val);
}
/**
* Set Component size
* @param comp Component for which to modify size
*/
protected static void setJComponentSize(JComponent comp) {
Dimension d = comp.getPreferredSize();
d.width = 60;
comp.setPreferredSize(d);
comp.setMaximumSize(comp.getPreferredSize());
}
/**
* Open data
*
* @param openType Type of file to open
* @return Absolute path to file
*/
private String openData(int openType) {
File fcFile;
String fileName;
String[] dTitle = { "Open variant list",
"Open gene filter list",
"Open bed filter list"
};
JFileChooser fc = new JFileChooser(System.getProperty("user.dir"));
fc.setDialogTitle(dTitle[openType]);
int fcReturnVal = fc.showOpenDialog(VarSifter.this);
if (fcReturnVal == JFileChooser.APPROVE_OPTION) {
fcFile = fc.getSelectedFile();
fileName = fcFile.getAbsolutePath();
}
else {
System.out.println("No File opened.");
if (vdat == null) {
showError("No file specified. Please specify a file to open.");
System.out.println("No file specified. Please specify a file to open.");
System.exit(0);
}
return null;
}
System.out.println(fileName);
if (openType == VARIANT_FILE) {
VarSifter.this.setTitle("VarSifter - " + fileName);
}
else if (openType == GENE_FILTER_FILE) {
filterFileLabel.setText(fileName);
filterFile.setEnabled(true);
notFilterFile.setEnabled(true);
}
else if (openType == BED_FILTER_FILE) {
bedFilterFileLabel.setText(fileName);
bedFilterFile.setEnabled(true);
}
return fileName;
}
/**
* Save data, either in place, or as new
*
* @param fileName Name of file to save to or null to open a FileChooser
* @param saveAll Save all variants (or the selected subset, if false)
*/
private void saveData(String fileName, boolean saveAll) {
File fcFile;
int ovwResult = JOptionPane.YES_OPTION;
if (fileName == null) {
JFileChooser fc = new JFileChooser(System.getProperty("user.dir"));
fc.setDialogTitle("Save File As");
int fcReturnVal = fc.showSaveDialog(VarSifter.this);
if (fcReturnVal == JFileChooser.APPROVE_OPTION) {
fcFile = fc.getSelectedFile();
fileName = fcFile.getAbsolutePath();
}
else {
System.out.println("File NOT SAVED!!!");
return;
}
}
else {
fcFile = new File(System.getProperty("user.dir") + fileName);
fileName = fcFile.getAbsolutePath();
}
if (fcFile.exists()) {
ovwResult = JOptionPane.showConfirmDialog(null, fileName + " already exists. " +
"Do you want to overwrite it?", "Overwrite Warning",
JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
}
if (ovwResult == JOptionPane.YES_OPTION) {
try {
if (saveAll) {
// Remove all filters so all data included. MUST reset filter after writing!!
vdat.filterData(new DataFilter(emptyBS, null, null, emptySpinnerData, null, 0, 0, 0, geneDelim));
}
PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter(fcFile)));
String[] dataNames = vdat.returnDataNames();
String[] sampleNamesOrig = vdat.returnSampleNamesOrig();
String[] sampleNames = vdat.returnSampleNames();
String[] sampleValueName = vdat.returnSampleValueNames();
String[] commentList = vdat.returnCommentList();
//comments
for (String c : commentList) {
pw.println(c);
}
//header
StringBuilder outString = new StringBuilder(100);
for (int j=0; j < dataNames.length; j++) {
outString.append(dataNames[j] + "\t");
}
for (int j=0; j < sampleNamesOrig.length; j++) {
outString.append(sampleNamesOrig[j] + "\t");
}
outString.deleteCharAt(outString.length() - 1 );
pw.println(outString.toString());
int[][] outData = vdat.returnOutData();
for (int i=0; i < outData.length; i++) {
outString = new StringBuilder(100);
// append Annotatations to outString
for (int j=0; j < dataNames.length; j++) {
outString.append(annotMapper[j].getString(outData[i][j]) + "\t");
}
// append sample info to outString
int[][] outSamples = vdat.returnSample(i);
for (int j=0; j < sampleNames.length; j++) {
for (int k=0; k < sampleValueName.length; k++) {
outString.append(sampleMapper[k].getString(outSamples[j][k+1]) + "\t");
}
}
outString.deleteCharAt(outString.length() - 1);
pw.println(outString.toString());
}
if (saveAll) {
//Must return the filtered state to what it was, to avoid data mapping errors!
vdat.filterData(df);
}
pw.close();
if (pw.checkError()) {
showError("Error Detected writing file! File NOT saved!");
System.out.println("Error Detected writing file!");
}
else {
System.out.println("File " + fileName + " written");
}
}
catch (IOException ioe) {
JOptionPane.showMessageDialog(null, "File write error: " + ioe.getMessage(),
"Error", JOptionPane.ERROR_MESSAGE);
}
}
else {
System.out.println(fileName + " not overwritten!");
}
}
/**
* Load config file and populate ConfigHandler
* @return ConfigHanlder containing configfile info
*/
private ConfigHandler parseConfig() {
URL cDir = getClass().getProtectionDomain().getCodeSource().getLocation();
File cPath = new File(cDir.getFile());
//System.out.println(cPath);
if (! cPath.isDirectory() ) {
cPath = cPath.getParentFile();
}
ConfigHandler cTemp = new ConfigHandler(cPath.getAbsolutePath() + "/VarSifter.config");
if (cTemp.exists("IGV_port")) {
Integer i = cTemp.getInteger("IGV_port");
if (i != null) {
IGVport = i.intValue();
}
}
if (cTemp.exists("IGV_host")) {
IGVhost = cTemp.get("IGV_host");
}
if (cTemp.exists("Min_GenScore")) {
Integer i = cTemp.getInteger("Min_GenScore");
if (i != null) {
minMPG = i;
}
}
if (cTemp.exists("Min_GenCovRatio")) {
Float f = cTemp.getFloat("Min_GenCovRatio");
if (f != null) {
minMPGCovRatio = f;
}
}
if (cTemp.exists("GenScoreThresh")) {
Integer i = cTemp.getInteger("GenScoreThresh");
if (i != null) {
genScoreThresh = i;
}
}
if (cTemp.exists("LowLightCutoff")) {
Float f = cTemp.getFloat("LowLightCutoff");
if (f != null) {
genScoreCovRatioThresh = f;
}
}
if (cTemp.exists("GeneDelim")) {
geneDelim = cTemp.get("Gene_Delim");
}
return cTemp;
}
public static void main(final String args[]) {
SwingUtilities.invokeLater(new Runnable() {
public void run() {
VarSifter v;
if (args.length > 0) {
v = new VarSifter(args[0]);
}
else {
v = new VarSifter((String)null);
}
}
});
}
}
