Merge pull request #6 from ncats/encoding_param

Encoding param
ncats · Apr 27, 2023 · ed284ec · ed284ec
2 parents be5e503 + 8c094c2
commit ed284ec
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Showing 22 changed files with 48 additions and 19 deletions.
diff --git a/pom.xml b/pom.xml
@@ -99,6 +99,12 @@
             <groupId>uk.ac.cam.ch.opsin</groupId>
             <artifactId>opsin-core</artifactId>
             <version>2.6.0</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.apache.logging.log4j</groupId>
+					<artifactId>log4j-api</artifactId>
+				</exclusion>
+			</exclusions>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>

diff --git a/src/main/java/gov/nih/ncats/molwitch/ElementData.java b/src/main/java/gov/nih/ncats/molwitch/ElementData.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/datastores/ChemicalDataStore.java b/src/main/java/gov/nih/ncats/molwitch/datastores/ChemicalDataStore.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/datastores/FileChemicalDataStore.java b/src/main/java/gov/nih/ncats/molwitch/datastores/FileChemicalDataStore.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/datastores/SimpleChemicalDataStore.java b/src/main/java/gov/nih/ncats/molwitch/datastores/SimpleChemicalDataStore.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKey.java b/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKey.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2021 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyBag.java b/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyBag.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2022 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyUtil.java b/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyUtil.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2022 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/DefaultInchiKeyBag.java b/src/main/java/gov/nih/ncats/molwitch/inchi/DefaultInchiKeyBag.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2022 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/InchiKey.java b/src/main/java/gov/nih/ncats/molwitch/inchi/InchiKey.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2022 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/InchiKeyBag.java b/src/main/java/gov/nih/ncats/molwitch/inchi/InchiKeyBag.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2022 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/InchiUtil.java b/src/main/java/gov/nih/ncats/molwitch/inchi/InchiUtil.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2022 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/io/ChemicalReaderFactory.java b/src/main/java/gov/nih/ncats/molwitch/io/ChemicalReaderFactory.java
@@ -112,6 +112,16 @@ public static ChemicalReader newReader(InputStream in) throws IOException{
 		}
 		return new DefaultChemicalReader(factory.create(in));
 	}
+
+	public static ChemicalReader newReader(InputStream in, String encoding) throws IOException{
+		Objects.requireNonNull(in, "inputstream can not be null");
+		ChemicalImplFactory factory = ImplUtil.getChemicalImplFactory();
+		if(factory ==null) {
+			throw new IOException("could not find chemical factory");
+		}
+		return new DefaultChemicalReader(factory.create(in, encoding));
+	}
+
 	public static ChemicalReader newReader(String format, InputStream in) throws IOException{
 		Objects.requireNonNull(in, "inputstream can not be null");
 		ChemicalImplFactory factory = ImplUtil.getChemicalImplFactory(format);

diff --git a/src/main/java/gov/nih/ncats/molwitch/io/CtTableCleaner.java b/src/main/java/gov/nih/ncats/molwitch/io/CtTableCleaner.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/io/PushbackBufferedReader.java b/src/main/java/gov/nih/ncats/molwitch/io/PushbackBufferedReader.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/io/SdfUtil.java b/src/main/java/gov/nih/ncats/molwitch/io/SdfUtil.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/isotopes/ElementData.java b/src/main/java/gov/nih/ncats/molwitch/isotopes/ElementData.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/isotopes/Elements.java b/src/main/java/gov/nih/ncats/molwitch/isotopes/Elements.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImplFactory.java b/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImplFactory.java
@@ -181,6 +181,19 @@ public interface ChemicalImplFactory {
 	 * @throws IOException if there is a problem parsing the InputStream.
 	 */
 	ChemicalImplReader create(InputStream in) throws IOException;
+	/**
+	 * Parse the given {@link InputStream} and create all the {@link ChemicalImpl}s encoded inside it.
+	 * The file format of the streamed file is not provided so it could be any of the
+	 * standard cheminformatics file formats.
+	 *
+	 * @param in the {@link InputStream} to parse.
+	 * @param in the {@link String} to parse.
+	 *
+	 * @return a List of {@link ChemicalImpl}, will never be null, and shouldn't be empty.
+	 *
+	 * @throws IOException if there is a problem parsing the InputStream.
+	 */
+	ChemicalImplReader create(InputStream in, String encoding) throws IOException;
 	/**
 	 * Create a new {@link ChemicalImpl} object
 	 * that is doesn't have any atoms

diff --git a/src/test/java/CleanSdfTest.java b/src/test/java/CleanSdfTest.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2020 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/test/java/InchiKeyBagTest.java b/src/test/java/InchiKeyBagTest.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2021 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/test/java/InchiKeyTest.java b/src/test/java/InchiKeyTest.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2022 NIH/NCATS
+ * Copyright 2023 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.