/*
* (non-Javadoc)
*
* @see org.bigwiv.blastgraph.command.Command#concreteExecute()
*/
@Override
public void concreteExecute() {
String curPath = Global.getAppPath(this.getClass());
File mclGraphFile = new File(curPath + File.separator + "mcl_graph_file");
File mclClustFile =
new File(
curPath
+ File.separator
+ "out.mcl_graph_file.I"
+ ("" + inflation).replace(".", "").substring(0, 2));
// System.out.println(mclClustFile);
try {
ArrayList<ValueEdge> edges = new ArrayList<ValueEdge>(Global.graph.getEdges());
BufferedWriter bw;
bw = new BufferedWriter(new FileWriter(mclGraphFile));
Global.WORK_STATUS.setMessage("");
Global.WORK_STATUS.setMessage("Stage1: Generating Tabular Format...");
for (ValueEdge valueEdge : edges) {
Pair<HitVertex> pair = Global.graph.getEndpoints(valueEdge);
HitVertex hv1 = pair.getFirst();
HitVertex hv2 = pair.getSecond();
double weight = 0;
if (weightType == EVALUE_WEIGHT) {
double evalue = valueEdge.getExpectValue();
if (evalue >= lowCutoff) {
weight = 0;
} else if (evalue < highCutoff) {
weight = -Math.log10(highCutoff);
} else {
weight = -Math.log10(evalue);
}
} else if (weightType == SCORE_WEIGHT) {
double score = valueEdge.getScore();
if (score <= lowCutoff) {
weight = 0;
} else if (score > highCutoff) {
weight = highCutoff;
} else {
weight = score;
}
} else if (weightType == SCORE_DENSITY_WEIGHT) {
double scoreDensity = Global.graph.getScoreDensity(valueEdge);
if (scoreDensity <= lowCutoff) {
weight = 0;
} else if (scoreDensity > highCutoff) {
weight = highCutoff;
} else {
weight = scoreDensity;
}
}
bw.write(hv1.getId() + "\t" + hv2.getId() + "\t" + weight + "\n");
}
// store single vertices
for (HitVertex hv : Global.graph.getVertices()) {
if (Global.graph.getInEdges(hv).size() == 0)
bw.write(hv.getId() + "\t" + hv.getId() + "\t" + 10 + "\n");
}
bw.close();
Global.WORK_STATUS.setMessage("Stage1 Complete");
Global.WORK_STATUS.setMessage("");
String mclCmd;
String cmdPath = Global.SETTING.get("MCL_PATH");
if (cmdPath != null && (new File(cmdPath).isDirectory())) {
mclCmd = cmdPath + File.separator + "mcl";
} else {
mclCmd = "mcl";
}
ProcessBuilder pb =
new ProcessBuilder(mclCmd, "mcl_graph_file", "--abc", "-I", "" + inflation);
// System.out.println(pb.command().toString());
pb.redirectErrorStream(true);
pb.directory(new File(curPath));
Process p = pb.start();
Global.WORK_STATUS.setMessage("Stage2: Markov Clustering...");
BufferedInputStream in = new BufferedInputStream(p.getInputStream());
BufferedReader inBr = new BufferedReader(new InputStreamReader(in));
String lineStr;
while ((lineStr = inBr.readLine()) != null) {
// System.out.println(lineStr);
Global.WORK_STATUS.setMessage(lineStr);
}
if (p.waitFor() != 0) {
if (p.exitValue() == 1)
// System.err.println("Failed to run mcl!");
Global.WORK_STATUS.setError("Failed to run mcl!");
}
inBr.close();
in.close();
Global.WORK_STATUS.setMessage("Stage2 Complete");
mclGraphFile.delete();
Global.WORK_STATUS.setMessage("");
Global.WORK_STATUS.setMessage("Stage3: Regenerating SubGraphs...");
BufferedReader br = new BufferedReader(new FileReader(mclClustFile));
String line = br.readLine();
BlastGraph<HitVertex, ValueEdge> tempGraph = new BlastGraph<HitVertex, ValueEdge>();
int count = 0;
while (line != null && !line.equals("")) {
String[] ids = line.split("\t");
// set to store vertices
Set<HitVertex> hvs2 = new HashSet<HitVertex>();
// get and add vertices into hvs by GI in ids
for (int i = 0; i < ids.length; i++) {
hvs2.add(Global.graph.getVertex(ids[i]));
}
tempGraph.union(FilterUtils.createInducedSubgraph(hvs2, Global.graph));
line = br.readLine();
Global.WORK_STATUS.setMessage("Subgraph: " + (++count));
}
br.close();
mclClustFile.delete();
Global.graph.copy(tempGraph);
Global.WORK_STATUS.setMessage("Stage3 Complete");
Global.WORK_STATUS.setMessage("");
Global.WORK_STATUS.setMessage("Markov Clustering Complete");
// System.out.println(curPath);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
@Override
public void actionPerformed(ActionEvent e) {
int index = valueComboBox.getSelectedIndex();
int index2 = methodComboBox.getSelectedIndex();
if (!plot2dPanel.getPlots().isEmpty()) {
plot2dPanel.getPlots().clear();
}
// System.out.println("changed: " + index + " " + index2);
Vector vector = new Vector();
if (index == 0) {
Collection<HitVertex> hvs = graph.getVertices();
for (HitVertex hitVertex : hvs) {
vector.add((double) hitVertex.getLength());
}
} else if (index == 1) {
Collection<ValueEdge> ves = graph.getEdges();
for (ValueEdge ve : ves) {
if (ve.getExpectValue() == 0) {
vector.add(-200.0);
} else {
vector.add(Math.log10(ve.getExpectValue()));
}
}
} else if (index == 2) {
Collection<ValueEdge> ves = graph.getEdges();
for (ValueEdge ve : ves) {
vector.add(graph.getCoverage(ve));
}
} else if (index == 3) {
Collection<ValueEdge> ves = graph.getEdges();
for (ValueEdge ve : ves) {
vector.add(graph.getCoverage2(ve));
}
} else if (index == 4) {
Collection<ValueEdge> ves = graph.getEdges();
for (ValueEdge ve : ves) {
vector.add(graph.getScoreDensity(ve));
}
} else if (index == 5) {
Collection<ValueEdge> ves = graph.getEdges();
for (ValueEdge ve : ves) {
vector.add(graph.getPercentageIdentity(ve));
}
} else if (index == 6) {
Collection<ValueEdge> ves = graph.getEdges();
for (ValueEdge ve : ves) {
vector.add(graph.getPercentagePositive(ve));
}
} else if (index == 7) {
final BlastGraph<HitVertex, ValueEdge> tmpGraph = new BlastGraph<HitVertex, ValueEdge>();
tmpGraph.copy(graph);
ArrayList<ValueEdge> ves = new ArrayList<ValueEdge>(tmpGraph.getEdges());
vertexCount = new double[ves.size()];
values = new double[ves.size()];
Collections.sort(
ves,
new Comparator<ValueEdge>() {
@Override
public int compare(ValueEdge arg0, ValueEdge arg1) {
// from biggest to smallest
if (arg0.getExpectValue() < arg1.getExpectValue()) {
return 1;
} else if (arg0.getExpectValue() > arg1.getExpectValue()) {
return -1;
} else {
return 0;
}
}
});
for (int i = 0; i < ves.size(); i++) {
ValueEdge ve = ves.get(i);
if (ve.getExpectValue() == 0) {
values[i] = -200.0;
} else {
values[i] = Math.log10(ve.getExpectValue());
}
// values[i] = ve.getExpectValue();
tmpGraph.removeEdge(ve);
tmpGraph.generateSubSet();
vertexCount[i] = tmpGraph.getSubSet().get(0).size();
// System.out.println(values[i] + ": " + vertexCount[i]);
}
} else if (index == 8) {
final BlastGraph<HitVertex, ValueEdge> tmpGraph = new BlastGraph<HitVertex, ValueEdge>();
tmpGraph.copy(graph);
ArrayList<ValueEdge> ves = new ArrayList<ValueEdge>(tmpGraph.getEdges());
vertexCount = new double[ves.size()];
values = new double[ves.size()];
Collections.sort(
ves,
new Comparator<ValueEdge>() {
@Override
public int compare(ValueEdge arg0, ValueEdge arg1) {
// from smallest to biggest
if (tmpGraph.getCoverage(arg0) > tmpGraph.getCoverage(arg1)) {
return 1;
} else if (tmpGraph.getCoverage(arg0) < tmpGraph.getCoverage(arg1)) {
return -1;
} else {
return 0;
}
}
});
for (int i = 0; i < ves.size(); i++) {
ValueEdge ve = ves.get(i);
values[i] = tmpGraph.getCoverage(ve);
tmpGraph.removeEdge(ve);
tmpGraph.generateSubSet();
vertexCount[i] = tmpGraph.getSubSet().get(0).size();
// System.out.println(values[i] + ": " + vertexCount[i]);
}
} else {
final BlastGraph<HitVertex, ValueEdge> tmpGraph = new BlastGraph<HitVertex, ValueEdge>();
tmpGraph.copy(graph);
ArrayList<ValueEdge> ves = new ArrayList<ValueEdge>(tmpGraph.getEdges());
vertexCount = new double[ves.size()];
values = new double[ves.size()];
Collections.sort(
ves,
new Comparator<ValueEdge>() {
@Override
public int compare(ValueEdge arg0, ValueEdge arg1) {
// from smallest to biggest
if (tmpGraph.getCoverage2(arg0) > tmpGraph.getCoverage2(arg1)) {
return 1;
} else if (tmpGraph.getCoverage2(arg0) < tmpGraph.getCoverage2(arg1)) {
return -1;
} else {
return 0;
}
}
});
for (int i = 0; i < ves.size(); i++) {
ValueEdge ve = ves.get(i);
values[i] = tmpGraph.getCoverage2(ve);
tmpGraph.removeEdge(ve);
tmpGraph.generateSubSet();
vertexCount[i] = tmpGraph.getSubSet().get(0).size();
// System.out.println(values[i] + ": " + vertexCount[i]);
}
}
double[] array = new double[vector.size()];
for (int i = 0; i < vector.size(); i++) {
array[i] = (Double) vector.get(i);
}
Arrays.sort(array);
double[] arrayIndex = new double[array.length];
for (int i = 0; i < arrayIndex.length; i++) {
arrayIndex[i] = i + 1;
}
// System.out.println(array[1]);
if (index2 == 0) {
// if (valueComboBox.getItemCount() == items.length) {
// addAdditional();
// }
if (index < items.length) {
plot2dPanel.addLinePlot("Array", array, arrayIndex);
} else {
// System.out.println(values.length + " " + vertexCount.length);
plot2dPanel.addLinePlot("vertexCount", values, vertexCount);
}
plot2dPanel.repaint();
} else if (index2 == 1) {
// try {
// Image image = bsTool.getHistogram(array);
// statisticsPanel.setImage(image);
// statisticsPanel.repaint();
// this.pack();
// } catch (IOException e) {
// e.printStackTrace();
// }
// if (valueComboBox.getItemCount() > items.length) {
// removeAdditional();
// }
plot2dPanel.addHistogramPlot("Array", array, 20);
plot2dPanel.repaint();
}
}