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Updates #8

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Updates #8

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8930234
New CDK and Cytoscape versions
egonw Mar 24, 2022
a6d5f7f
Replaced some Guava with modern Java
egonw Mar 24, 2022
d2928a5
Updated the Bnd tool, to fix a build error
egonw Mar 24, 2022
dc110e7
Bumped the version number
egonw Mar 24, 2022
a63931f
Duh. It did not include the shared objects
egonw May 18, 2022
fb0b7c9
Don't try to layout when the compoundType is null
egonw May 18, 2022
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123 changes: 34 additions & 89 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,18 +4,20 @@
<properties>
<bundle.symbolicName>chemViz2</bundle.symbolicName>
<bundle.namespace>edu.ucsf.rbvi.chemViz2.internal</bundle.namespace>
<cytoscape.api.version>3.5.0</cytoscape.api.version>
<cytoscape.api.version>3.9.0</cytoscape.api.version>

<maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version>
<maven-bundle-plugin.version>5.1.2</maven-bundle-plugin.version>
<osgi.api.version>4.2.0</osgi.api.version>
<cdk.version>2.7.1</cdk.version>
<jna-inchi.version>1.1</jna-inchi.version>
</properties>

<groupId>edu.ucsf.rbvi</groupId>
<artifactId>chemViz2</artifactId>
<packaging>bundle</packaging>
<name>${bundle.symbolicName}</name>

<version>1.1.1</version>
<version>1.2.0</version>

<build>
<plugins>
Expand Down Expand Up @@ -93,28 +95,6 @@
<enabled>true</enabled>
</releases>
</repository>
<!-- repository>
<id>ebi-repo</id>
<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
<releases>
<enabled>true</enabled>
</releases>
</repository -->
<repository>
<id>jni-inchi</id>
<name>JNI-InChI Maven Repository</name>
<url>http://jni-inchi.sourceforge.net/m2repo</url>
<releases>
<enabled>true</enabled>
</releases>
</repository>
<repository>
<id>jnati</id>
<url>http://jnati.sourceforge.net/m2repo</url>
<releases>
<enabled>true</enabled>
</releases>
</repository>
</repositories>

<dependencies>
Expand Down Expand Up @@ -190,6 +170,11 @@
<version>1.11.11</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>31.1-jre</version>
</dependency>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.core</artifactId>
Expand All @@ -200,122 +185,107 @@
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-interfaces</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-core</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-smiles</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-smarts</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-inchi</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-qsar</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-qsarmolecular</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-render</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-renderbasic</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-renderextra</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-renderawt</artifactId>
<version>1.5.14</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-smsd</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-builder3d</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-fingerprint</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-silent</artifactId>
<version>1.5.14</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<!--dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-depict</artifactId>
<version>1.5.12</version>
<optional>true</optional>
</dependency-->
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-legacy</artifactId>
<version>1.5.14</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>net.sf.jnati</groupId>
<artifactId>jnati-core</artifactId>
<version>0.4</version>
<version>${cdk.version}</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>io.github.dan2097</groupId>
<artifactId>jna-inchi-api</artifactId>
<version>${jna-inchi.version}</version>
</dependency>
<dependency>
<groupId>net.sf.jnati</groupId>
<artifactId>jnati-deploy</artifactId>
<version>0.4</version>
<optional>true</optional>
<groupId>io.github.dan2097</groupId>
<artifactId>jna-inchi-all</artifactId>
<version>${jna-inchi.version}</version>
</dependency>
<!-- These dependencies cause real problems for JNI-INCHI -->
<dependency>
<groupId>xom</groupId>
<artifactId>xom</artifactId>
<version>1.2.5</version>
<version>1.3.7</version>
<scope>provided</scope>
</dependency>
<dependency>
Expand All @@ -336,37 +306,12 @@
<version>2.4</version>
<optional>true</optional>
</dependency>

<!-- dependency>
<groupId>xalan</groupId>
<artifactId>xalan</artifactId>
<version>2.7.0</version>
<scope>provided</scope>
</dependency -->
<dependency>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
<version>1.3.03</version>
<scope>provided</scope>
</dependency>
<!-- dependency>
<groupId>net.sf.jnati</groupId>
<artifactId>jnati-deploy</artifactId>
<version>0.4</version>
<optional>true</optional>
</dependency -->
<dependency>
<groupId>net.sf.jni-inchi</groupId>
<artifactId>jni-inchi</artifactId>
<version>0.9-SNAPSHOT</version>
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.0</version>
<optional>true</optional>
</dependency>
</dependencies>

</project>
25 changes: 13 additions & 12 deletions src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/Depiction.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,28 +18,29 @@
*/
package edu.ucsf.rbvi.chemViz2.internal.depict;

import com.google.common.base.Charsets;
import org.openscience.cdk.renderer.RendererModel;
import org.openscience.cdk.renderer.elements.Bounds;
import org.openscience.cdk.renderer.elements.IRenderingElement;
import org.openscience.cdk.renderer.font.AWTFontManager;
import org.openscience.cdk.renderer.generators.BasicSceneGenerator;
import org.openscience.cdk.renderer.visitor.IDrawVisitor;
import static edu.ucsf.rbvi.chemViz2.internal.depict.DepictionGenerator.AUTOMATIC;

import javax.imageio.ImageIO;
import java.awt.geom.AffineTransform;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Locale;

import static edu.ucsf.rbvi.chemViz2.internal.depict.DepictionGenerator.AUTOMATIC;
import javax.imageio.ImageIO;

import org.openscience.cdk.renderer.RendererModel;
import org.openscience.cdk.renderer.elements.Bounds;
import org.openscience.cdk.renderer.elements.IRenderingElement;
import org.openscience.cdk.renderer.font.AWTFontManager;
import org.openscience.cdk.renderer.generators.BasicSceneGenerator;
import org.openscience.cdk.renderer.visitor.IDrawVisitor;

/**
* Base class of a pre-rendered depiction. The class allows introspection of
Expand Down Expand Up @@ -212,11 +213,11 @@ public final List<String> listFormats() {
*/
public final void writeTo(String fmt, OutputStream out) throws IOException {
if (fmt.equalsIgnoreCase(SVG_FMT)) {
out.write(toSvgStr().getBytes(Charsets.UTF_8));
out.write(toSvgStr().getBytes(StandardCharsets.UTF_8));
} else if (fmt.equalsIgnoreCase(PS_FMT)) {
out.write(toEpsStr().getBytes(Charsets.UTF_8));
out.write(toEpsStr().getBytes(StandardCharsets.UTF_8));
} else if (fmt.equalsIgnoreCase(PDF_FMT)) {
out.write(toPdfStr().getBytes(Charsets.UTF_8));
out.write(toPdfStr().getBytes(StandardCharsets.UTF_8));
} else {
ImageIO.write(toImg(), fmt, out);
}
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/SvgDrawVisitor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -353,7 +353,7 @@ private void visit(String id, String cls, LineElement elem) {
private void visit(MarkedElement elem) {
String id = elem.getId();
List<String> classes = elem.getClasses();
String cls = classes.isEmpty() ? null : Joiner.on(" ").join(classes);
String cls = classes.isEmpty() ? null : String.join(" ", classes);

IRenderingElement marked = elem.element();

Expand Down
10 changes: 5 additions & 5 deletions src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
import org.cytoscape.model.CyNetwork;

import edu.ucsf.rbvi.chemViz2.internal.view.ViewUtils;
import io.github.dan2097.jnainchi.InchiStatus;

import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.CDKConstants;
Expand All @@ -41,8 +42,6 @@
import org.openscience.cdk.tools.CDKHydrogenAdder;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

import net.sf.jniinchi.INCHI_RET;

/**
* The Compound class provides the main interface to molecule compounds. A
* given node or edge in Cytoscape could have multiple Compounds, either
Expand Down Expand Up @@ -201,6 +200,7 @@ public IAtomContainer getMolecule3D() {

public void layoutStructure() {
if (!laidOut) {
if (compoundType == null) {} else
if (compoundType.equals(CompoundType.MOLECULE)) {
if (iMolecule == null)
return;
Expand Down Expand Up @@ -394,10 +394,10 @@ private String convertInchiToSmiles(String inchi) {
InChIToStructure intostruct = factory.getInChIToStructure(inchi, SilentChemObjectBuilder.getInstance());

// Get the structure
INCHI_RET ret = intostruct.getReturnStatus();
if (ret == INCHI_RET.WARNING) {
InchiStatus ret = intostruct.getStatus();
if (ret == InchiStatus.WARNING) {
logger.warn("InChI warning: " + intostruct.getMessage());
} else if (ret != INCHI_RET.OKAY) {
} else if (ret != InchiStatus.SUCCESS) {
logger.warn("Structure generation failed: " + ret.toString()
+ " [" + intostruct.getMessage() + "]");
return null;
Expand Down