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A couple of small changes to internal node labelling #2

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A couple of small changes to internal node labelling #2

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712473d
Group names are now checked for length (<=2).
jergosh Sep 28, 2020
dcc6927
Nodes are now labelled from the root outwards to ensure labelling wor…
jergosh Sep 28, 2020
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10 changes: 9 additions & 1 deletion src/java/tdg09/Analyse.java
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Original file line number Diff line number Diff line change
Expand Up @@ -269,7 +269,15 @@ private void validate(Tree tree, Alignment alignment) {
System.out.printf("Alignment:\n SequenceCount: %s\n SiteCount: %s\n\n", alignment.getSequenceCount(), alignment.getSiteCount());
}

// 2. Check that all taxa have an assigned group and all groups are used
// 2. Check that group names have the right length
for (String group : options.groups) {
if (group.length() > 2) {
System.out.println("ERROR: Group names must be at most two characters long.");
System.exit(1);
}
}

// 3. Check that all taxa have an assigned group and all groups are used
List<String> taxa = Lists.newArrayList();
Set<String> usedGroups = Sets.newHashSet();

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5 changes: 5 additions & 0 deletions src/java/tdg09/trees/TreeNodeLabeller.java
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Expand Up @@ -12,6 +12,7 @@
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.Collections;

/**
* Takes a tree where taxa have been prefixed by a two-letter partition/group identifier and traverses the tree to
Expand Down Expand Up @@ -90,6 +91,10 @@ public SimpleTree label(Tree t) {
}

// now the only remaining unknown nodes are those that neighbour two different clades (and the root node)

// Iterate over unknownNodes in reverse to make sure the parent nodes are labelled before child nodes
Collections.reverse(unknownNodes);

for (Node n : unknownNodes) {
// the name of this hostshift node = parent node name (remember, could be the root node = leave unlabelled)
if (n.getParent() != null) {
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