本文整理汇总了Java中dr.evolution.util.Taxa.containsAll方法的典型用法代码示例。如果您正苦于以下问题：Java Taxa.containsAll方法的具体用法？Java Taxa.containsAll怎么用？Java Taxa.containsAll使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类dr.evolution.util.Taxa的用法示例。
在下文中一共展示了Taxa.containsAll方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: checkCompatibility
import dr.evolution.util.Taxa; //导入方法依赖的package包/类
protected boolean checkCompatibility(Taxa taxa) {
for (Taxa taxa2 : options.taxonSets) {
if (taxa2 != taxa && options.taxonSetsMono.get(taxa2)
&& options.taxonSetsTreeModel.get(taxa) == options.taxonSetsTreeModel.get(taxa2)) { // no matter if diff tree
if (taxa.containsAny(taxa2) && !taxa.containsAll(taxa2) && !taxa2.containsAll(taxa)) {
JOptionPane.showMessageDialog(frame,
"You cannot enforce monophyly on this " + TAXON.toLowerCase() + " \n" +
"because it is not compatible with another " + TAXON.toLowerCase() + ",\n" +
taxa2.getId() + ", for which monophyly is\n" + "enforced.",
"Warning",
JOptionPane.WARNING_MESSAGE);
return false;
}
}
}
return true;
}
示例2: writeSubTree
import dr.evolution.util.Taxa; //导入方法依赖的package包/类
private void writeSubTree(String treeId, String taxaId, Taxa taxa, PartitionTreeModel model, XMLWriter writer) {
Double height = options.taxonSetsHeights.get(taxa);
if (height == null) {
height = Double.NaN;
}
Attribute[] attributes = new Attribute[] {};
if (treeId != null) {
if (Double.isNaN(height)) {
attributes = new Attribute[] {
new Attribute.Default<String>(XMLParser.ID, treeId)
};
} else {
attributes = new Attribute[] {
new Attribute.Default<String>(XMLParser.ID, treeId),
new Attribute.Default<String>(CoalescentSimulatorParser.HEIGHT, "" + height)
};
}
} else {
if (!Double.isNaN(height)) {
attributes = new Attribute[] {
new Attribute.Default<String>(CoalescentSimulatorParser.HEIGHT, "" + height)
};
}
}
// construct a subtree
writer.writeOpenTag(
CoalescentSimulatorParser.COALESCENT_SIMULATOR,
attributes
);
List<Taxa> subsets = new ArrayList<Taxa>();
// Taxa remainingTaxa = new Taxa(taxa);
for (Taxa taxa2 : options.taxonSets) {
boolean sameTree = model.equals(options.taxonSetsTreeModel.get(taxa2));
boolean isMono = options.taxonSetsMono.get(taxa2);
boolean hasHeight = options.taxonSetsHeights.get(taxa2) != null;
boolean isSubset = taxa.containsAll(taxa2);
if (sameTree && (isMono || hasHeight) && taxa2 != taxa && isSubset) {
subsets.add(taxa2);
}
}
List<Taxa> toRemove = new ArrayList<Taxa>();
for (Taxa taxa3 : subsets) {
boolean isSubSubSet = false;
for (Taxa taxa4 : subsets) {
if (!taxa4.equals(taxa3) && taxa4.containsAll(taxa3)) {
isSubSubSet = true;
}
}
if (isSubSubSet) {
toRemove.add(taxa3);
}
}
subsets.removeAll(toRemove);
for (Taxa taxa5 : subsets) {
// remainingTaxa.removeTaxa(taxa5);
writeSubTree(null, null, taxa5, model, writer);
}
if (taxaId == null) {
writer.writeIDref(TaxaParser.TAXA, taxa.getId());
} else {
writer.writeIDref(TaxaParser.TAXA, taxaId);
}
writeInitialDemoModelRef(model, writer);
writer.writeCloseTag(CoalescentSimulatorParser.COALESCENT_SIMULATOR);
}
示例3: checkCompatibility
import dr.evolution.util.Taxa; //导入方法依赖的package包/类
protected boolean checkCompatibility(Taxa taxa) {
for (Taxa taxa2 : options.speciesSets) {
if (taxa2 != taxa && options.speciesSetsMono.get(taxa2)) {
if (taxa.containsAny(taxa2) && !taxa.containsAll(taxa2) && !taxa2.containsAll(taxa)) {
JOptionPane.showMessageDialog(frame,
"You cannot enforce monophyly on this " + TAXON.toLowerCase() + " \n" +
"because it is not compatible with another " + TAXON.toLowerCase() + ",\n" +
taxa2.getId() + ", for which monophyly is\n" + "enforced.",
"Warning",
JOptionPane.WARNING_MESSAGE);
return false;
}
}
}
return true;
}
示例4: checkCompatibility
import dr.evolution.util.Taxa; //导入方法依赖的package包/类
private boolean checkCompatibility(Taxa taxa) {
for (Taxa taxa2 : options.taxonSets) {
if (taxa2 != taxa && options.taxonSetsMono.get(taxa2)) {
if (taxa.containsAny(taxa2) && !taxa.containsAll(taxa2) && !taxa2.containsAll(taxa)) {
JOptionPane.showMessageDialog(frame,
"You cannot enforce monophyly on this taxon set \n" +
"because it is not compatible with another taxon \n" +
"set, " + taxa2.getId() + ", for which monophyly is\n" +
"enforced.",
"Warning",
JOptionPane.WARNING_MESSAGE);
return false;
}
}
}
return true;
}
示例5: isMaximal
import dr.evolution.util.Taxa; //导入方法依赖的package包/类
private boolean isMaximal(List<Taxa> taxa, int k) {
final Taxa tk = taxa.get(k);
for (int i = 0; i < taxa.size(); ++i) {
if (i != k) {
final Taxa ti = taxa.get(i);
if (ti.containsAll(tk)) {
return false;
}
}
}
return true;
}
示例6: writeSubTree
import dr.evolution.util.Taxa; //导入方法依赖的package包/类
private void writeSubTree(String treeId, String taxaId, Taxa taxa, PartitionTreeModel model, XMLWriter writer) {
Double height = options.taxonSetsHeights.get(taxa);
if (height == null) {
height = Double.NaN;
}
Attribute[] attributes = new Attribute[] {};
if (treeId != null) {
if (Double.isNaN(height)) {
attributes = new Attribute[] {
new Attribute.Default<String>(XMLParser.ID, treeId)
};
} else {
attributes = new Attribute[] {
new Attribute.Default<String>(XMLParser.ID, treeId),
new Attribute.Default<String>(NewCoalescentSimulatorParser.HEIGHT, "" + height)
};
}
} else {
if (!Double.isNaN(height)) {
attributes = new Attribute[] {
new Attribute.Default<String>(NewCoalescentSimulatorParser.HEIGHT, "" + height)
};
}
}
// construct a subtree
writer.writeOpenTag(
NewCoalescentSimulatorParser.COALESCENT_SIMULATOR,
attributes
);
List<Taxa> subsets = new ArrayList<Taxa>();
// Taxa remainingTaxa = new Taxa(taxa);
for (Taxa taxa2 : options.taxonSets) {
boolean sameTree = model.equals(options.taxonSetsTreeModel.get(taxa2));
boolean isMono = options.taxonSetsMono.get(taxa2);
boolean hasHeight = options.taxonSetsHeights.get(taxa2) != null;
boolean isSubset = taxa.containsAll(taxa2);
if (sameTree && (isMono || hasHeight) && taxa2 != taxa && isSubset) {
subsets.add(taxa2);
}
}
List<Taxa> toRemove = new ArrayList<Taxa>();
for (Taxa taxa3 : subsets) {
boolean isSubSubSet = false;
for (Taxa taxa4 : subsets) {
if (!taxa4.equals(taxa3) && taxa4.containsAll(taxa3)) {
isSubSubSet = true;
}
}
if (isSubSubSet) {
toRemove.add(taxa3);
}
}
subsets.removeAll(toRemove);
for (Taxa taxa5 : subsets) {
// remainingTaxa.removeTaxa(taxa5);
writeSubTree(null, null, taxa5, model, writer);
}
if (taxaId != null) {
writer.writeIDref(TaxaParser.TAXA, taxa.getId());
} else {
writer.writeIDref(TaxaParser.TAXA, taxaId);
}
writeInitialDemoModelRef(model, writer);
writer.writeCloseTag(NewCoalescentSimulatorParser.COALESCENT_SIMULATOR);
}