From f27656357cdc14bd9261fd1e3a7d9d76edc2d260 Mon Sep 17 00:00:00 2001
From: worku005 <dirk-jan.vanworkum@wur.nl>
Date: Fri, 27 Sep 2024 09:24:29 +0200
Subject: [PATCH] also update frequency property on nucleotide nodes
---
.../construction/build_pangenome/GenomeLayer.java | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/src/main/java/nl/wur/bif/pantools/construction/build_pangenome/GenomeLayer.java b/src/main/java/nl/wur/bif/pantools/construction/build_pangenome/GenomeLayer.java
index 85aeeecf7..1b09464a4 100644
--- a/src/main/java/nl/wur/bif/pantools/construction/build_pangenome/GenomeLayer.java
+++ b/src/main/java/nl/wur/bif/pantools/construction/build_pangenome/GenomeLayer.java
@@ -1341,8 +1341,6 @@ public class GenomeLayer {
targetNode = createNewNodeGfa(edge.getTarget(), new int[]{genomeNr, sequenceNr, pathPosition}, index, nodeCache);
createNewRelationshipGfa(sourceNode, edge.getType(), edge.getSourceEndOnTarget(), targetNode, origin, pathPosition, trsc);
sourceNode = targetNode;
-
- //TODO: update the localization information in the edge to the next node
}
// connect the last node to the sequence node with FF
@@ -1374,6 +1372,7 @@ public class GenomeLayer {
newNode.setProperty("address", address);
newNode.setProperty("length", node.getLength());
newNode.setProperty("frequencies", new long[GENOME_DB.num_genomes + 1]);
+ newNode.setProperty("frequency", 0);
newNode.setProperty("sequence", node.getSequence());
num_bases += node.getLength();
@@ -1438,6 +1437,15 @@ public class GenomeLayer {
frequencies[address[0]]++;
newNode.setProperty("frequencies", frequencies);
+ // update the frequency property of the node
+ final long frequency = Arrays.stream(frequencies).sum();
+ newNode.setProperty("frequency", frequency);
+
+ // update global highest_frequency integer
+ if (frequency > highest_frequency) {
+ highest_frequency = frequency;
+ }
+
// return the new node
return newNode;
}
--
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