/**
* Reads a microarray data file with the BicOverlapper format, that is: organism/chip col1 col2
* ... colN row1 exp11 exp12 ... exp1N ... rowM expM1 expM2 ... expMN
*/
public void readMicroarray(File file, Session sesion, MicroarrayRequester mr) throws Exception {
int skipColumns = 1;
int skipRows = 1;
double t1 = System.currentTimeMillis();
double t2 = System.currentTimeMillis();
MicroarrayData md =
new MicroarrayData(file, false, skipRows, skipColumns, 1, mr, sesion.getAnalysis(), sesion);
sesion.setMicroarrayData(md);
t1 = System.currentTimeMillis();
System.out.println("Time to load microarray data: " + (t1 - t2) / 1000 + " seconds");
t2 = System.currentTimeMillis();
System.out.println("Time to load fichero: " + (t2 - t1) / 1000 + " seconds");
}
/** Reads a Transcription Regulatory Network in GML or Syntren's XML format */
public void readTRN(String path, File fichero, Session sesion, String fileType)
throws FileNotFoundException, IOException {
BufferedReader in = new BufferedReader(new FileReader(fichero));
String variable = null;
BicOverlapperWindow window = sesion.getMainWindow();
JDesktopPane desktop = sesion.getDesktop();
variable = in.readLine();
// En función de esto determinamos qué es:
// 1) Un fichero de tabla xml como los que usa Javi (usamos su método de
// lectura) a DatosFile
// 2) Un grafo xml de los que usamos nosotros, usamos nuestro parser a
// TRN Data
// 3) Un fichero txt de los que usamos para los resultados de
// biclustering, usamos
// nuestro lector a BubbleData
BufferedReader in2 = in; // Para no estropear lo que se lea de in
NetworkData trnd = null;
if (variable.contains("GeneNetwork")) {
trnd = new NetworkData(getPath(path)); // Syntren format
} else if (variable.contains("?xml")) {
String linea2 = in2.readLine();
if (linea2.contains("graphml")) {
trnd = new NetworkData(getPath(path)); // GraphML
}
} else {
trnd = new NetworkData(getPath(path));
}
in.close();
in2.close();
if (sesion.getMicroarrayData() != null) { // Set ids equivalent to the
// session ids
for (int i = 0; i < trnd.getGraph().getNodeCount(); i++) {
Node n = trnd.getGraph().getNode(i);
n.setInt("id", sesion.getMicroarrayData().getGeneId(n.getString("name").trim()));
}
} else {
for (int i = 0; i < trnd.getGraph().getNodeCount(); i++) {
Node n = trnd.getGraph().getNode(i);
n.setInt("id", i);
}
}
boolean error = false; // TODO: check possible errors
if (!error) {
window.getViewMenu().setEnabled(true);
window.getMenuViewTRN().setEnabled(true);
if (path != null && path.length() > 0) {
try {
BufferedWriter pathWriter =
new BufferedWriter(
new FileWriter(
sesion.getReader().getPath("es/usal/bicoverlapper/data/networkPath.txt")));
pathWriter.write(path);
pathWriter.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
if (window.getActiveWorkDesktop() == null)
window.addWorkDesktop(new WorkDesktop(desktop, sesion));
else {
JDesktopPane p = window.getActiveWorkDesktop().getPanel();
// Carlos
/*
* String
* title=window.getDesktop().getTitleAt(window.getDesktop(
* ).getSelectedIndex()); if(title.contains(".bic") ||
* title.contains(".tmp")) { if(title.endsWith(".bic") ||
* title.endsWith(".tmp")) { if(title.contains("|"))
* title=title.substring(0, title.lastIndexOf("|")).trim(); else
* title=""; } } title=title+" | "+fichero.getName();
* window.getDesktop
* ().setTitleAt(window.getDesktop().getSelectedIndex(), title);
* p.setName(title);
*/
// Carlos
String title = window.getTitle();
if (title.contains(".bic") || title.contains(".tmp")) {
if (title.endsWith(".bic") || title.endsWith(".tmp")) {
if (title.contains("|")) title = title.substring(0, title.lastIndexOf("|")).trim();
else title = "";
}
}
title = title + " | " + fichero.getName();
window.setTitle(title);
p.setName(title);
}
}
sesion.setTRNData(trnd);
}
public void readBiclusterResults(String path, String fileName, String file, Session sesion) {
BicOverlapperWindow window = sesion.getMainWindow();
JDesktopPane desktop = sesion.getDesktop();
boolean error = false;
try {
BubbleData bd = new BubbleData(file, sesion.getMicroarrayData(), sesion);
bd.getGraph().getNodes().getClientProperty("name");
sesion.setBubbleData(bd);
sesion.setBiclusterDataFile(file);
sesion.setBubbleDataLoaded(true); // TODO para que sea true de verdad
sesion.setBiclusterDataStatus(true);
} catch (FileNotFoundException e1) {
JOptionPane.showMessageDialog(
null, "File not found: " + file, "Error", JOptionPane.ERROR_MESSAGE);
error = true;
} catch (IOException e2) {
JOptionPane.showMessageDialog(
null, "I/O Error " + e2.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
error = true;
} catch (Exception e3) {
JOptionPane.showMessageDialog(
null, "Format error " + e3.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
error = true;
}
if (!error) {
window.getViewMenu().setEnabled(true);
window.getMenuViewOverlapper().setEnabled(true);
window.getMenuViewBubbles().setEnabled(true);
if (path != null && path.length() > 0) {
try {
BufferedWriter pathWriter =
new BufferedWriter(
new FileWriter(
sesion.getReader().getPath("es/usal/bicoverlapper/data/groupsPath.txt")));
pathWriter.write(path);
pathWriter.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
if (window.getActiveWorkDesktop() == null)
window.addWorkDesktop(new WorkDesktop(desktop, sesion));
else {
JDesktopPane p = window.getActiveWorkDesktop().getPanel();
// Carlos
/*
* String
* title=window.getDesktop().getTitleAt(window.getDesktop(
* ).getSelectedIndex()); if(title.contains(".bic") ||
* title.contains(".tmp")) { if(title.endsWith(".bic") ||
* title.endsWith(".tmp")) { if(title.contains("|"))
* title=title.substring(0, title.lastIndexOf("|")).trim(); else
* title=""; } } title=title+" | "+fileName;
* //window.getDesktop().setTitleAt(0,
* p.getName()+" | "+fileName);
* //p.setName(p.getName()+" | "+fileName);
* window.getDesktop().setTitleAt
* (window.getDesktop().getSelectedIndex(), title);
* p.setName(title);
*/
// Carlos
String title = window.getTitle();
if (title.contains(".bic") || title.contains(".tmp")) {
if (title.endsWith(".bic") || title.endsWith(".tmp")) {
if (title.contains("|")) title = title.substring(0, title.lastIndexOf("|")).trim();
else title = "";
}
}
title = title + " | " + fileName;
window.setTitle(title);
p.setName(title);
// Carlos
// window.setTitle(window.getTitle() + " | " + fileName);
}
}
}