public static void main(String[] args) {
javax.swing.SwingUtilities.invokeLater(
new Runnable() {
public void run() {
createAndShowGUI();
}
});
}
public static void main(String[] args) {
// Schedule a job for the event-dispatching thread:
// creating and showing this application's GUI.
javax.swing.SwingUtilities.invokeLater(
new Runnable() {
public void run() {
createAndShowGUI();
}
});
}
private void initColumnWidths(final JTable table) {
javax.swing.SwingUtilities.invokeLater(
new Runnable() {
public void run() {
table.getColumnModel().getColumn(0).setMaxWidth(100);
table.getColumnModel().getColumn(1).setPreferredWidth(150);
// table.getColumnModel().getColumn(2).setPreferredWidth(5);
// table.getColumnModel().getColumn(3).setPreferredWidth(5);
// table.getColumnModel().getColumn(4).setPreferredWidth(5);
// table.getColumnModel().getColumn(5).setPreferredWidth(5);
table.getColumnModel().getColumn(7).setPreferredWidth(175);
}
});
}
public static void main(String[] args) {
// Schedule a job for the event-dispatching thread:
// creating and showing this application's GUI.
javax.swing.SwingUtilities.invokeLater(
new Runnable() {
public void run() {
BearSweeper frame = new BearSweeper();
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.pack();
frame.setVisible(true);
}
});
}
public void run() {
String line;
String id = null;
config.refgenes = new ArrayList<RefGene>();
config.dbsnp = new ArrayList<dbSNP>();
try {
// System.err.println("quality read start"); // debug
boolean need_ruler_rebuild = false;
boolean need_title = false;
SAMRegion sr = null;
while (true) {
line = br.readLine();
if (line == null) break;
// EOF
String[] stuff = line.split("\t");
if (stuff[0].equals("sample2id")) {
Sample sample = Sample.get_sample(stuff[1]);
for (int i = 2; i < stuff.length; i++) {
config.read2sample.put(new String(stuff[i]), sample);
}
} else if (stuff[0].equals("consensus_label")) {
config.CONSENSUS_TAG = new String(stuff[1]);
} else if (stuff[0].equals("ruler_start")) {
config.ruler_start = Integer.parseInt(stuff[1]);
need_ruler_rebuild = true;
} else if (stuff[0].equals("title")) {
config.title = stuff[1];
need_title = true;
} else if (stuff[0].equals("refGene")) {
config.refgenes.add(new RefGene(stuff));
} else if (stuff[0].equals("dbsnp")) {
config.dbsnp.add(new dbSNP(stuff));
} else if (stuff[0].toUpperCase().indexOf("SAM_") == 0) {
// FUGLY
SAMResourceTags v = SAMResourceTags.valueOf(stuff[0].toUpperCase());
if (v.equals(SAMResourceTags.SAM_URL)) config.sams.add(new SAMResource());
config.sams.get(config.sams.size() - 1).import_data(v, stuff[1]);
} else if (stuff[0].equals("reference_sequence")) {
StringBuffer target_sequence = new StringBuffer();
while (true) {
line = br.readLine();
if (line.equals(">")) {
// config.target_sequence = target_sequence.toString().toCharArray();
config.target_sequence = target_sequence.toString().getBytes();
break;
} else {
target_sequence.append(line);
}
}
} else if (stuff[0].equals("target_region")) {
sr = new SAMRegion();
sr.tname = new String(stuff[1]);
sr.range = new Range(Integer.parseInt(stuff[2]), Integer.parseInt(stuff[3]));
// System.err.println("range " + sr.tname + " " + sr.range.start + " " + sr.range.end);
// // debug
} else {
System.err.println("error, don't recognize tag " + stuff[0]); // debug
}
}
if (config.ruler_start > 0) {
for (dbSNP snp : config.dbsnp) {
snp.consensus_adjust(config.ruler_start);
}
for (RefGene rg : config.refgenes) {
rg.consensus_adjust(config.ruler_start);
}
}
if (config.dbsnp != null) {
for (dbSNP snp : config.dbsnp) {
// System.err.println("adding snp at " + snp.start + " = " + (snp.start +
// config.ruler_start)); // debug
}
config.snp_config.snp_query = new dbSNPSet(config.dbsnp);
}
for (SAMResource sre : config.sams) {
sre.set_region(sr);
}
if (av != null) {
while (av.get_acepanel().is_built() == false) {
// spin until dependency built
try {
System.err.println("MarkupReader spin..."); // debug
Thread.sleep(50);
} catch (Exception e) {
}
}
PadMap pm = av.get_acepanel().get_assembly().get_padmap();
for (RefGene rg : config.refgenes) {
rg.consensus_setup(pm);
}
Runnable later;
if (need_title) {
// System.err.println("title="+config.title); // debug
later =
new Runnable() {
public void run() {
av.setTitle(config.title);
av.repaint();
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
if (need_ruler_rebuild) {
//
// ruler labeling has changed.
//
later =
new Runnable() {
public void run() {
// av.get_acepanel().get_canvas().build_ruler();
if (config.start_unpadded_offset != 0) {
AcePanel ap = av.get_acepanel();
PadMap pm = ap.get_assembly().get_padmap();
int upo = (config.start_unpadded_offset - config.ruler_start) + 1;
// +1: convert to 1-based offset
int po = pm.get_unpadded_to_padded(upo);
System.err.println("upo=" + upo + " po=" + po); // debug
SNPList sl = new SNPList();
sl.addElement(new SNP(po, 0.0));
ap.ace.set_snps(sl);
ap.get_canvas().center_on(po);
ap.get_canvas().repaint();
}
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
if (config.enable_exon_navigation) {
if (false) {
System.err.println("DEBUG: exon nav disabled");
} else {
av.get_acepanel().init_exon_navigation();
}
}
av.get_acepanel().get_assembly().build_summary_info();
// group samples by tumor/normal, if applicable
// av.repaint();
later =
new Runnable() {
public void run() {
av.repaint();
}
};
javax.swing.SwingUtilities.invokeLater(later);
}
// System.err.println("quality read end"); // debug
} catch (Exception e) {
e.printStackTrace(); // debug
}
}
/** @throws Exception */
private static void displayStats() throws Exception {
String[][] statsList = getCounters();
ManagedObjectReference hostmor = getHostByHostName(hostname);
if (hostmor == null) {
System.out.println("Host Not Found");
return;
}
Object property;
ArrayList props = (ArrayList) getDynamicProperty(perfManager, "perfCounter");
if (props != null && props.size() > 0) {
property = props.get(0);
} else {
property = null;
}
// ArrayOfPerfCounterInfo arrayCounter = (ArrayOfPerfCounterInfo) property;
ArrayList counterInfoList = new ArrayList();
counterInfoList.add(property);
List<PerfMetricId> midVector = new ArrayList<PerfMetricId>();
List<String> statNames = new ArrayList<String>();
for (int i = 0; i < statsList.length; i++) {
PerfCounterInfo counterInfo =
getCounterInfo(counterInfoList, statsList[i][0], statsList[i][1]);
if (counterInfo == null) {
System.out.println(
"Warning: Unable to find stat " + statsList[i][0] + " " + statsList[i][1]);
continue;
}
String counterName = counterInfo.getNameInfo().getLabel();
statNames.add(counterName);
PerfMetricId pmid = new PerfMetricId();
pmid.setCounterId(counterInfo.getKey());
pmid.setInstance("");
midVector.add(pmid);
}
List<PerfMetricId> midList = new ArrayList<PerfMetricId>(midVector);
Collections.copy(midList, midVector);
PerfQuerySpec spec = new PerfQuerySpec();
spec.setEntity(hostmor);
GregorianCalendar startTime = new GregorianCalendar();
startTime.add(Calendar.SECOND, -60);
XMLGregorianCalendar starttimexmlgc =
DatatypeFactory.newInstance().newXMLGregorianCalendar(startTime);
// spec.setStartTime(starttimexmlgc);
spec.getMetricId().addAll(midList);
spec.setIntervalId(new Integer(20));
querySpec = spec;
final List<String> statNames2 = statNames;
javax.swing.SwingUtilities.invokeLater(
new Runnable() {
public void run() {
createAndShowGUI("VM Name", statNames2);
}
});
Timer timer = new Timer(true);
timer.schedule(
new TimerTask() {
public void run() {
refreshStats();
}
},
1000,
21000);
}