Skip to content

fix: Phmmer enhance e-value handling to support both number and string types #52

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
sreenathnair wants to merge 1 commit into
base: master
Choose a base branch
from
Open

fix: Phmmer enhance e-value handling to support both number and string types #52

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
30 changes: 25 additions & 5 deletions sequence/phmmer/src/main/java/uk/co/flax/biosolr/pdbe/phmmer/Alignment.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import javax.json.JsonArray;
import javax.json.JsonObject;
import javax.json.JsonValue;

public class Alignment {

Expand Down Expand Up @@ -60,18 +61,37 @@ public Alignment(JsonObject hit) {
species = hit.getString("species");
description = hit.getString("desc");
score = Double.parseDouble(hit.getString("score"));
eValue = Double.parseDouble(hit.getString("evalue"));

JsonValue eValueJSON = hit.get("evalue");

if (eValueJSON.getValueType() == JsonValue.ValueType.NUMBER) {
eValue = hit.getJsonNumber("evalue").doubleValue();
} else if (eValueJSON.getValueType() == JsonValue.ValueType.STRING) {
eValue = Double.parseDouble(hit.getString("evalue"));
}

JsonArray domains = hit.getJsonArray("domains");
for (int i = 0; i < domains.size(); ++i) {
JsonObject domain = domains.getJsonObject(i);

// skip insignificant matches (by ind. eValue)
eValueInd = Double.parseDouble(domain.getString("ievalue"));
JsonValue eValue = domain.get("ievalue");
if (eValue.getValueType() == JsonValue.ValueType.NUMBER) {
eValueInd = domain.getJsonNumber("ievalue").doubleValue();
} else if (eValue.getValueType() == JsonValue.ValueType.STRING) {
eValueInd = Double.parseDouble(domain.getString("ievalue"));
}

if (eValueInd >= SIGNIFICANCE_THRESHOLD) continue;

eValueCond = Double.parseDouble(domain.getString("cevalue"));


JsonValue ceValue = domain.get("cevalue");

if (ceValue.getValueType() == JsonValue.ValueType.NUMBER) {
eValueCond = domain.getJsonNumber("cevalue").doubleValue();
} else if (ceValue.getValueType() == JsonValue.ValueType.STRING) {
eValueCond = Double.parseDouble(domain.getString("cevalue"));
}

querySequence = domain.getString("alimodel");
querySequenceStart = domain.getInt("alihmmfrom");
querySequenceEnd = domain.getInt("alihmmto");
Expand Down