/*................................................................................................*/
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
addMenuItem("Directory for Sample Trees From Directory...", makeCommand("setDirPath", this));
fillerTasks = new Vector();
if (!MesquiteThread
.isScripting()) { // enclosed in conditional to avoid hiring query when opening file; should
// be handled by snapshot/doCommand when file is opened.
String directoryPath =
MesquiteFile.chooseDirectory(
"Choose directory containing tree files:",
previousDirectory); // MesquiteFile.saveFileAsDialog("Base name for files (files will
// be named <name>1.nex, <name>2.nex, etc.)", baseName);
if (StringUtil.blank(directoryPath)) { // TODO: clean this up?
return false;
} else {
directory = new File(directoryPath);
previousDirectory = directory.getParent();
if (directory.exists() && directory.isDirectory()) {
return hireFillers(directoryPath);
}
}
}
return true; // Add something to make sure directory paths are set up correctly, when not
// scripting...
}
/*................................................................................................*/
private boolean hireFillers(String directoryPath) {
String[] files = directory.list();
String treePath;
for (int i = 0; i < files.length; i++) {
if (files[i] != null) {
String fileLowerCase = files[i].toLowerCase();
if (fileLowerCase.endsWith(".nex") || fileLowerCase.endsWith(".nexus")) {
treePath = directoryPath + MesquiteFile.fileSeparator + files[i];
File treeFile = new File(treePath);
String treeFileName = treeFile.getName();
if (StringUtil.blank(treeFileName)) {
return false;
}
TreeBlockFiller newFiller;
newFiller =
(TreeBlockFiller)
hireNamedEmployee(TreeBlockFiller.class, "#SampleOneTreeFromFile"); // treePath);
if (newFiller != null) {
if (((SampleOneTreeFromFile) newFiller).setFilePath(treePath)
&& ((SampleOneTreeFromFile) newFiller).processFile()) {
fillerTasks.addElement(newFiller);
} else
Debugg.println(
"Filler "
+ i
+ " processFile = "
+ ((SampleOneTreeFromFile) newFiller).processFile());
}
}
}
}
return true;
}
/*.................................................................................................................*/
public void processOutputFiles(String jobURL) {
if (rootDir != null) {
downloadWorkingResults(jobURL, rootDir, true);
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;
}
}
}
}
}