/*................................................................................................*/
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;
}
/*................................................................................................*/
private TreeVector fillBlock(Taxa taxa) { // TODO: fill in
TreeVector filledVector = new TreeVector(taxa);
int vectorTreeCount = 0;
for (int fillers = 0; fillers < fillerTasks.size(); fillers++) {
if (fillerTasks.get(fillers) instanceof SampleOneTreeFromFile) {
((SampleOneTreeFromFile) fillerTasks.get(fillers))
.resetTreesToSample(); // One unnecessary resetting of bits on first call
TreeVector tempTreeVector = new TreeVector(taxa);
((TreeBlockFiller) fillerTasks.get(fillers)).fillTreeBlock(tempTreeVector, 1);
if (tempTreeVector.getNumberOfTrees() < 1) {
logln(
"Not enough trees were supplied by "
+ ((TreeBlockFiller) fillerTasks.get(fillers)).getName()
+ "; "
+ tempTreeVector.getNumberOfTrees()
+ " provided, one requested.");
;
}
if (tempTreeVector.getNumberOfTrees() > 0) {
int treeCount = 0;
while (treeCount < 1
&& treeCount
< tempTreeVector
.getNumberOfTrees()) { // Check so we don't ask for more trees that are there.
filledVector.addElement(tempTreeVector.getTree(treeCount), false);
if (filledVector != null && tempTreeVector != null) {
if (filledVector.getTree(vectorTreeCount) != null
&& tempTreeVector.getName() != null) {
if (filledVector.getTree(vectorTreeCount).getName() != null)
logln(
filledVector.getTree(vectorTreeCount).getName()
+ " added from "
+ tempTreeVector.getName());
}
}
treeCount++;
vectorTreeCount++;
}
}
tempTreeVector.dispose(); // disposed to reduce memory demands
// (fillerTask.get(fillers)).
}
}
return filledVector;
}
/*.................................................................................................................*/
public TreeDisplayExtra createTreeDisplayExtra(TreeDisplay treeDisplay) {
PAdjustToolExtra newPj = new PAdjustToolExtra(this, treeDisplay);
extras.addElement(newPj);
return newPj;
}