Skip to content

Commit

Permalink
....
Browse files Browse the repository at this point in the history
  • Loading branch information
@jrobinso
jrobinso committed Oct 7, 2024
1 parent 04b5e89 commit 95f0408
Show file tree
Hide file tree
Showing 4 changed files with 156 additions and 130 deletions.
2 changes: 2 additions & 0 deletions src/main/java/org/broad/igv/encode/EncodeTableModel.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,8 @@ public void setValueAt(Object value, int row, int col) {
fireTableCellUpdated(row, col);
}



public List<EncodeFileRecord> getRecords() {
return records;
}
Expand Down
194 changes: 99 additions & 95 deletions src/main/java/org/broad/igv/encode/EncodeTrackChooser.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,7 @@
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.action.BrowseEncodeAction;
import org.broad.igv.util.FileUtils;
import org.broad.igv.util.Pair;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
Expand All @@ -68,18 +69,31 @@ public class EncodeTrackChooser extends org.broad.igv.ui.IGVDialog {
private static Map<String, EncodeTrackChooser> instanceMap = Collections.synchronizedMap(new HashMap<>());
private static NumberFormatter numberFormatter = new NumberFormatter();

private JButton cancelButton;
private JPanel dialogPane;
private JPanel contentPanel;
private JScrollPane scrollPane1;
private JTable table;
private JPanel filterPanel;
private JLabel filterLabel;
private JTextField filterTextField;
private JLabel rowCountLabel;
private JPanel buttonBar;
private JButton okButton;
private static String ENCODE_HOST = "https://www.encodeproject.org";
private static Set<String> filteredColumns = new HashSet(Arrays.asList("ID", "Assembly", "HREF", "path"));

private static List<String> filteredExtensions = Arrays.asList("tsv", "tsv.gz");

private static Map<String, String> speciesNames = Map.of(
"ce10", "Caenorhabditis elegans",
"ce11", "Caenorhabditis elegans",
"dm3", "Drosophila melanogaster",
"dm6", "Drosophila melanogaster",
"GRCh38", "Homo sapiens",
"hg19", "Homo sapiens",
"mm10", "Mus musculus",
"mm9", "Mus musculus"
);

static HashSet<String> ucscSupportedGenomes = new HashSet<>(Arrays.asList("hg19", "mm9"));
static HashSet<String> supportedGenomes = new HashSet<>(
Arrays.asList("ce10", "ce11", "dm3", "dm6", "GRCh38", "hg19", "mm10", "mm9"));



JTable table;
JTextField filterTextField;
JLabel rowCountLabel;
EncodeTableModel model;
private boolean canceled;

Expand All @@ -105,37 +119,38 @@ public synchronized static EncodeTrackChooser getInstance(String genomeId, Brows
Frame parent = IGV.hasInstance() ? IGV.getInstance().getMainFrame() : null;
final List<String> headings = records.getFirst();
final List<EncodeFileRecord> rows = records.getSecond();
instance = new EncodeTrackChooser(parent, new EncodeTableModel(headings, rows));
final String title = getDialogTitle(genomeId, type);
instance = new EncodeTrackChooser(parent, new EncodeTableModel(headings, rows), title);
instanceMap.put(key, instance);
}

return instance;
}

static HashSet<String> ucscSupportedGenomes = new HashSet<>(Arrays.asList("hg19", "mm9"));
private static String getDialogTitle(String genomeId, BrowseEncodeAction.Type type) {

if (type == BrowseEncodeAction.Type.UCSC) {
return "ENCODE data hosted at UCSC (2012)";
} else {
switch (type) {
case SIGNALS_CHIP:
return "ENCODE CHiP Seq - Signals";
case SIGNALS_OTHER:
return "ENCODE Non CHiP Data - Signals";
default:
return "ENCODE";
}
}
}

public static boolean genomeSupportedUCSC(String genomeId) {
return genomeId != null && ucscSupportedGenomes.contains(getEncodeGenomeID(genomeId));
}

static HashSet<String> supportedGenomes = new HashSet<>(
Arrays.asList("ce10", "ce11", "dm3", "dm6", "GRCh38", "hg19", "mm10", "mm9"));

public static boolean genomeSupported(String genomeId) {
return genomeId != null && supportedGenomes.contains(getEncodeGenomeID(genomeId));
}

private static Map<String, String> speciesNames = Map.of(
"ce10", "Caenorhabditis elegans",
"ce11", "Caenorhabditis elegans",
"dm3", "Drosophila melanogaster",
"dm6", "Drosophila melanogaster",
"GRCh38", "Homo sapiens",
"hg19", "Homo sapiens",
"mm10", "Mus musculus",
"mm9", "Mus musculus"
);


private static String getEncodeGenomeID(String genomeId) {
switch (genomeId) {
Expand Down Expand Up @@ -185,18 +200,6 @@ private static InputStream getStreamFor(String genomeId, BrowseEncodeAction.Type
}
}

/*
* rowHandler: row => {
* const name = constructName(row)
* const url = `https://www.encodeproject.org${row['HREF']}`
* const color = colorForTarget(row['Target'])
* return {name, url, color}
* }
*/

private static String ENCODE_HOST = "https://www.encodeproject.org";
private static Set<String> filteredColumns = new HashSet(Arrays.asList("ID", "Assembly", "HREF", "path"));

private static Pair parseRecords(InputStream is, BrowseEncodeAction.Type type, String genomeId) throws IOException {

BufferedReader reader = new BufferedReader(new InputStreamReader(is));
Expand All @@ -213,6 +216,10 @@ private static Pair parseRecords(InputStream is, BrowseEncodeAction.Type type, S
String[] tokens = Globals.tabPattern.split(nextLine, -1);
String path = type == BrowseEncodeAction.Type.UCSC ? tokens[pathColumn] : ENCODE_HOST + tokens[pathColumn];

if(filteredExtensions.stream().anyMatch(e -> path.endsWith(e))) {
continue;
}

Map<String, String> attributes = new LinkedHashMap<>();
for (int i = 0; i < headers.length; i++) {
String value = i < tokens.length ? tokens[i] : "";
Expand All @@ -239,17 +246,17 @@ private static String shortenField(String value, String genomeId) {
}


private EncodeTrackChooser(Frame owner, EncodeTableModel model) {
private EncodeTrackChooser(Frame owner, EncodeTableModel model, String title) {
super(owner);
setTitle(title);
this.model = model;
setModal(true);
initComponents();
initComponents(owner);
init(model);
}

private void init(final EncodeTableModel model) {
setModal(true);
setTitle("Encode Production Data");

table.setAutoCreateRowSorter(true);
table.setModel(model);
Expand Down Expand Up @@ -427,106 +434,103 @@ public boolean include(Entry value) {
}


private void initComponents() {

dialogPane = new JPanel();
contentPanel = new JPanel();
scrollPane1 = new JScrollPane();
table = new JTable();
filterPanel = new JPanel();
filterLabel = new JLabel();
filterTextField = new JTextField();
rowCountLabel = new JLabel();
buttonBar = new JPanel();
okButton = new JButton();
cancelButton = new JButton();

getRootPane().setDefaultButton(okButton);
private void initComponents(Frame owner) {

final String filterToolTip = "Enter multiple filter strings separated by commas. e.g. GM12878, ChipSeq";
filterLabel.setToolTipText(filterToolTip);
filterTextField.setToolTipText(filterToolTip);
// All this to have tool tip text!
table = new JTable() {
@Override
public String getToolTipText(MouseEvent e) {
java.awt.Point p = e.getPoint();
int rowIndex = rowAtPoint(p);
int colIndex = columnAtPoint(p);
int realColumnIndex = convertColumnIndexToModel(colIndex);
if (realColumnIndex > 0) {
return getModel().getValueAt(rowIndex, realColumnIndex).toString();
}
return null;
}
};

//======== this ========
//======== outer content pane ========
Container contentPane = getContentPane();
contentPane.setLayout(new BorderLayout());

//======== dialogPane ========

JPanel dialogPane = new JPanel();
dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
dialogPane.setLayout(new BorderLayout());

//======== contentPanel ========

//======== main content panel ========
JPanel contentPanel = new JPanel();
contentPanel.setLayout(new BorderLayout(0, 10));

//======== scrollPane1 ========

JScrollPane scrollPane1 = new JScrollPane();
scrollPane1.setViewportView(table);

contentPanel.add(scrollPane1, BorderLayout.CENTER);

//======== panel1 ========

//---- Filter panel ----
JPanel filterPanel = new JPanel();
filterPanel.setLayout(new JideBoxLayout(filterPanel, JideBoxLayout.X_AXIS, 5));

//---- label1 ----
filterLabel.setText("Filter:");
JLabel filterLabel = new JLabel("Filter:");
final String filterToolTip = "Enter multiple filter strings separated by commas. e.g. GM12878, ChipSeq";
filterLabel.setToolTipText(filterToolTip);
filterPanel.add(filterLabel, JideBoxLayout.FIX);

//---- filterTextField ----
filterTextField = new JTextField();
filterTextField.setToolTipText(filterToolTip);
filterPanel.add(filterTextField, JideBoxLayout.VARY);

rowCountLabel = new JLabel();
rowCountLabel.setHorizontalAlignment(JLabel.RIGHT);
JPanel sillyPanel = new JPanel();
sillyPanel.setLayout(new JideBoxLayout(sillyPanel, JideBoxLayout.X_AXIS, 0));
sillyPanel.setPreferredSize(new Dimension(100, 28));
sillyPanel.add(rowCountLabel, JideBoxLayout.VARY);

filterPanel.add(sillyPanel, JideBoxLayout.FIX);
JPanel rowCountPanel = new JPanel();
rowCountPanel.setLayout(new JideBoxLayout(rowCountPanel, JideBoxLayout.X_AXIS, 0));
rowCountPanel.setPreferredSize(new Dimension(100, 28));
rowCountPanel.add(rowCountLabel, JideBoxLayout.VARY);
filterPanel.add(rowCountPanel, JideBoxLayout.FIX);

contentPanel.add(filterPanel, BorderLayout.NORTH);

dialogPane.add(contentPanel, BorderLayout.CENTER);

//======== buttonBar ========

JPanel buttonBar = new JPanel();
buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0));
buttonBar.setLayout(new GridBagLayout());
((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 85, 80};
((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{1.0, 0.0, 0.0};

//---- okButton ----
okButton.setText("Load");
okButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
loadButtonActionPerformed(e);
}
});
JButton okButton = new JButton("Load");
getRootPane().setDefaultButton(okButton);
okButton.addActionListener(e -> loadButtonActionPerformed(e));
buttonBar.add(okButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 5), 0, 0));

//---- cancelButton ----
cancelButton.setText("Cancel");
cancelButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
cancelButtonActionPerformed(e);
}
});
JButton cancelButton = new JButton("Cancel");
cancelButton.addActionListener(e -> cancelButtonActionPerformed(e));

buttonBar.add(cancelButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
new Insets(0, 0, 0, 0), 0, 0));

dialogPane.add(buttonBar, BorderLayout.SOUTH);

contentPane.add(dialogPane, BorderLayout.CENTER);
setSize(700, 620);

Rectangle ownerBounds = owner.getBounds();
setSize(ownerBounds.width, 620);
setLocationRelativeTo(getOwner());
}


/**
* Main function for testing only
*
* @param args
* @throws IOException
*/
public static void main(String[] args) throws IOException {
getInstance("hg19", BrowseEncodeAction.Type.UCSC).setVisible(true);
}
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/broad/igv/ui/IGVMenuBar.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -418,7 +418,7 @@ private void addEncodeItems(List<JComponent> menuItems, String genomeId) {
menuItems.add(separator);

JLabel encodeLabel = new JLabel(" ENCODE");
encodeLabel.setForeground(Color.BLUE);
encodeLabel.setFont(encodeLabel.getFont().deriveFont(Font.BOLD));
menuItems.add(encodeLabel);

// Post 2012 ENCODE menu
Expand All @@ -431,7 +431,7 @@ private void addEncodeItems(List<JComponent> menuItems, String genomeId) {
encodeMenuItems.add(otherSignalsItem);

JMenuItem otherItem = new JMenuItem();
otherItem.setAction(new BrowseEncodeAction("Peaks and Other", 0, BrowseEncodeAction.Type.OTHER, igv));
otherItem.setAction(new BrowseEncodeAction("Other (peaks, calls, ...)", 0, BrowseEncodeAction.Type.OTHER, igv));
encodeMenuItems.add(otherItem);

for(JComponent item : encodeMenuItems) {
Expand Down
Loading

0 comments on commit 95f0408

Please sign in to comment.