/**
* A request for the MesquiteModule to perform a command. It is passed two strings, the name of
* the command and the arguments. This should be overridden by any module that wants to respond to
* a command.
*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(MesquiteModule.class, null, null, commandName, "paint")) {
MesquiteInteger io = new MesquiteInteger(0);
int column = MesquiteInteger.fromString(arguments, io);
int row = MesquiteInteger.fromString(arguments, io);
if (MesquiteInteger.isCombinable(row)) {
if (!MesquiteLong.isCombinable(currentColor)) removeColor(row, true);
else setColor(row, (int) currentColor);
}
} else if (checker.compare(
this.getClass(),
"Sets the color to be used to paint cells",
"[name of color]",
commandName,
"setColor")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
removeColor.setValue(false);
currentColor = bc;
savedColor = bc;
colorString = "Color " + ColorDistribution.standardColorNames.getValue(bc);
}
} else if (checker.compare(
this.getClass(),
"Sets the color of selected taxa",
"[name of color]",
commandName,
"setColorSelected")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
for (int it = 0; it < taxa.getNumTaxa(); it++) if (taxa.getSelected(it)) setColor(it, bc);
}
} else if (checker.compare(
this.getClass(), "Removes color from all the cells", null, commandName, "removeAllColor")) {
removeAllColor(true);
} else if (checker.compare(
this.getClass(),
"Sets the paint brush so that it removes colors from any cells touched",
null,
commandName,
"removeColor")) {
if (StringUtil.blank(arguments)) removeColor.setValue(!removeColor.getValue());
else removeColor.toggleValue(parser.getFirstToken(arguments));
if (removeColor.getValue()) {
colorString = "Remove color";
currentColor = MesquiteLong.unassigned;
} else {
colorString = "Color " + ColorDistribution.standardColorNames.getValue((int) currentColor);
currentColor = savedColor;
}
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public int[] getTaxonNumberTranslation(Taxa taxa) {
int max = -1;
for (int it = 0; it < taxa.getNumTaxa(); it++) {
long translateNumber = getTaxonNumberInTree(taxa, it);
if (MesquiteLong.isCombinable(translateNumber) && translateNumber > max) {
max = (int) translateNumber;
}
}
int[] translate = new int[max + 1];
for (int it = 0; it < data.getNumTaxa(); it++) {
long translateNumber = getTaxonNumberInTree(taxa, it);
if (MesquiteLong.isCombinable(translateNumber) && translateNumber >= 0) {
translate[(int) translateNumber] = it;
}
}
return translate;
}
/*.................................................................................................................*/
public void processOutputFiles() {
if (outputFileProcessor != null && outputFilePaths != null && lastModified != null) {
String[] paths = outputFileProcessor.modifyOutputPaths(outputFilePaths);
for (int i = 0; i < paths.length && i < lastModified.length; i++) {
File file = new File(paths[i]);
long lastMod = file.lastModified();
if (!MesquiteLong.isCombinable(lastModified[i]) || lastMod > lastModified[i]) {
outputFileProcessor.processOutputFile(paths, i);
lastModified[i] = lastMod;
}
}
}
}
/**
* This processes information about the files contained in either the results or working directory
* of a job.
*/
public CipresJobFile[] processFilesDocument(Document cipresResponseDoc) {
Element jobfiles = cipresResponseDoc.getRootElement().element("jobfiles");
if (jobfiles == null) return null;
List tools = jobfiles.elements("jobfile");
int count = 0;
for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
Element nextTool = (Element) iter.next();
count++;
}
if (count == 0) return null;
CipresJobFile[] cipresJobFile = new CipresJobFile[count];
count = 0;
for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
Element nextJob = (Element) iter.next();
if (nextJob != null) {
if (cipresJobFile[count] == null) cipresJobFile[count] = new CipresJobFile();
Element jobFileElement = nextJob.element("downloadUri");
String fileInfo = null;
if (jobFileElement != null) {
fileInfo = jobFileElement.elementText("url");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setDownloadURL(fileInfo);
}
fileInfo = jobFileElement.elementText("title");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setDownloadTitle(fileInfo);
}
}
fileInfo = nextJob.elementText("dateModified");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setLastModified(fileInfo);
}
fileInfo = nextJob.elementText("filename");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setFileName(fileInfo);
}
fileInfo = nextJob.elementText("length");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setLength(MesquiteLong.fromString(fileInfo));
}
count++;
}
}
return cipresJobFile;
}