upgrade FasterForest to 2.6.0 and fix GString compilation errors

Replace flat jar with local Maven repo dependency at correct path
(groupId/artifactId/version/). Fix GString-to-String type errors in
AnalyzeRoutine that broke compilation with @CompileStatic.
This commit is contained in:
rdk
2026-02-14 07:35:29 +01:00
parent 27caa5fe46
commit de75ac6be1
5 changed files with 37 additions and 3 deletions

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@@ -22,7 +22,7 @@ apply plugin: "com.github.ben-manes.versions" // ./gradlew dependencyUpdates
group = 'cz.siret'
version = '2.5.2-dev.6'
version = '2.5.2-dev.8'
description = 'Ligand binding site prediction based on machine learning.'
@@ -215,6 +215,7 @@ dependencies {
implementation 'org.openscience.cdk:cdk-silent:2.11' // for Atom class
implementation 'cz.cuni.cusbg:faster-molecular-surface:1.0'
implementation 'cz.siret.prank:FasterForest:2.6.0'
implementation 'nz.ac.waikato.cms.weka:weka-dev:3.9.6'

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@@ -0,0 +1,33 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<!-- This module was also published with a richer model, Gradle metadata, -->
<!-- which should be used instead. Do not delete the following line which -->
<!-- is to indicate to Gradle or any Gradle module metadata file consumer -->
<!-- that they should prefer consuming it instead. -->
<!-- do_not_remove: published-with-gradle-metadata -->
<modelVersion>4.0.0</modelVersion>
<groupId>cz.siret.prank</groupId>
<artifactId>FasterForest</artifactId>
<version>2.6.0</version>
<dependencies>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.18.0</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>nz.ac.waikato.cms.weka</groupId>
<artifactId>weka-dev</artifactId>
<version>3.9.6</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>com.carrotsearch</groupId>
<artifactId>hppc</artifactId>
<version>0.10.0</version>
<scope>runtime</scope>
</dependency>
</dependencies>
</project>

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@@ -181,7 +181,7 @@ class AnalyzeRoutine extends Routine {
String mmcifId = it.mmcifId
int nres = it.length
String chars = it.biojavaCodeCharString
csvRows.add("${item.label}, $nchains, $chainId, $mmcifId, $nres, $chars ")
csvRows.add("${item.label}, $nchains, $chainId, $mmcifId, $nres, $chars " as String)
}
}
String csv = "protein, n_chains, chain_id, mmcif_id, n_residues, residue_string\n" +
@@ -290,7 +290,7 @@ class AnalyzeRoutine extends Routine {
String chainIds = p.residueChains.collect { it.authorId }.join(" ")
int nres = p.residues.size()
int nlabres = s.total
csvRows.add("${item.label}, $nchains, $chainIds, $nres, $nlabres, ${s.positives}, ${s.negatives}, ${s.unlabeled}")
csvRows.add("${item.label}, $nchains, $chainIds, $nres, $nlabres, ${s.positives}, ${s.negatives}, ${s.unlabeled}" as String)
if (params.visualizations) {
new NewPymolRenderer("$outdir/visualizations", new RenderingModel(