Javadoc fix: <p>

josemduarte · josemduarte · commit 27a88ff9780f · 2025-01-03T10:45:17.000-08:00
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
@@ -30,7 +30,7 @@
 /**
  * This class is used to support the implementation of properties stated in IPeptideProperties.
  * It initializes several values that would be needed for the computation of properties such as
- * <p/>
+ * <p>
  * Molecular weight<br/>
  * Instability index<br/>
  * Hydropathy value<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
@@ -35,7 +35,7 @@
 /**
  * An interface to generate some basic physico-chemical properties of protein sequences.<br/>
  * The following properties could be generated:
- * <p/>
+ * <p>
  * Molecular weight<br/>
  * Absorbance<br/>
  * Extinction coefficient<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
@@ -28,7 +28,7 @@ public interface IProfeatProperties {
 	/**
 	 * Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf<br/>
 	 * An interface class to generate the properties of a protein sequence based on its converted attributes.<br/>
-	 * The seven different attributes are<p/>
+	 * The seven different attributes are<p>
 	 * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
 	 * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
 	 * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
@@ -28,7 +28,7 @@ public abstract class Convertor {
 	/**
 	 * Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf<br/>
 	 * An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.<br/>
-	 * The seven different attributes are<p/>
+	 * The seven different attributes are<p>
 	 * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
 	 * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
 	 * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
@@ -20,7 +20,7 @@
  */
 /**
  * Set of classes that enable the conversion protein sequences into various attributes.
- * The seven different attributes are<p/>
+ * The seven different attributes are<p>
  * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
  * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
  * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
@@ -58,7 +58,7 @@ private FlatFileCache(){
 
 	/**
 	 * The file is read and the bytes stored immediately.
-	 * <p/> 
+	 * <p> 
 	 * Once added, {@code fileToCache} can be modified or deleted and the cached values will not change.
 	 * @param key
 	 * @param fileToCache A readable file, of Integer.MAX bytes length or less.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
@@ -31,12 +31,13 @@
 import org.slf4j.LoggerFactory;
 
 
-/** A in memory cache using soft references. (can be garbage collected)
+/**
+ * An in memory cache using soft references. (can be garbage collected)
  * This code is based on: http://java-interview-faqs.blogspot.com/2008/09/building-faster-and-efficient-cache.html
- * <p/>
+ * <p>
  * Note that entrySet() is not implemented and therefore many methods such as keySet(),
  * containsKey(), values() etc do not work.
- * <p/>
+ * <p>
  * This class is therefore best used as a cache simply to put and get items by a known key
  */
 public class SoftHashMap<K, V> extends AbstractMap<K, V> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
@@ -113,7 +113,7 @@ public interface XMLWriter {
 	 * avoid namespaces that are used only in leaf-nodes of a tree being re-defined
 	 * every time they are used. The XMLWriter will generally try to use the
 	 * suggested prefix for this namespace, but there is no guarantee of this.
-	 * <p/>
+	 * <p>
 	 * 
 	 * In particular, if the namespace is already in use, the current prefix will still
 	 * be used. Similarly if the suggested prefix has already been used for another
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
@@ -26,7 +26,7 @@
 /**
  * Alignment request parameters accepted by QBlast service.<br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
- * <p/>
+ * <p>
  * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available output alignment types.
- * <p/>
+ * <p>
  * Values as used in QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available output formats.
- * <p/>
+ * <p>
  * Values are as used by QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
@@ -26,7 +26,7 @@
 /**
  * Output parameters accepted by QBlast service. <br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
- * <p/>
+ * <p>
  * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available blast programs.
- * <p/>
+ * <p>
  * Values are as used by QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
@@ -36,7 +36,7 @@
  * This class wraps a QBlast search request parameter {@code Map} by adding several convenient parameter addition
  * methods. Other QBlast URL API parameters should be added using
  * {@link #setAlignmentOption(BlastAlignmentParameterEnum, String)}
- * <p/>
+ * <p>
  * Required parameters are {@code PROGRAM} and {@code DATABASE}, other parameters are optional
  *
  * @author Sylvain Foisy, Diploide BioIT
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
@@ -119,7 +119,7 @@ public String getOutputFormat() {
 
 	/**
 	 * Sets the stream output format to get from the QBlast service
-	 * <p/>
+	 * <p>
 	 * If {@code HTML} format is selected, also adds the following parameters (which are removed if another output
 	 * format is chosen):
 	 *
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
@@ -248,7 +248,7 @@ public boolean isReady(String id) throws Exception {
 
 	/**
 	 * Checks for completion of request.
-	 * <p/>
+	 * <p>
 	 * If expected execution time (RTOE) is available for request, this method will always return false until that time
 	 * passes. This is done to prevent sending unnecessary requests to the server.
 	 *
@@ -307,7 +307,7 @@ public boolean isReady(String id, long present) throws Exception {
 	/**
 	 * Extracts the actual Blast report for given request id according to options provided in {@code outputProperties}
 	 * argument.
-	 * <p/>
+	 * <p>
 	 * If the results are not ready yet, sleeps until they are available. If sleeping is not desired, call this method
 	 * after {@code isReady} returns true
 	 *

Original file line number	Diff line number	Diff line change
`@@ -113,7 +113,7 @@ public interface XMLWriter {`
`113`	`113`	`* avoid namespaces that are used only in leaf-nodes of a tree being re-defined`
`114`	`114`	`* every time they are used. The XMLWriter will generally try to use the`
`115`	`115`	`* suggested prefix for this namespace, but there is no guarantee of this.`
`116`		`- * <p/>`
	`116`	`+ * <p>`
`117`	`117`	`*`
`118`	`118`	`* In particular, if the namespace is already in use, the current prefix will still`
`119`	`119`	`* be used. Similarly if the suggested prefix has already been used for another`
Original file line number	Diff line number	Diff line change
`@@ -26,7 +26,7 @@`
`26`	`26`	`/**`
`27`	`27`	`* Alignment request parameters accepted by QBlast service.<br/>`
`28`	`28`	`* Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.`
`29`		`- * <p/>`
	`29`	`+ * <p>`
`30`	`30`	`* Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>`
`31`	`31`	`*`
`32`	`32`	`* @author Gediminas Rimsa`
Original file line number	Diff line number	Diff line change
`@@ -25,7 +25,7 @@`
`25`	`25`
`26`	`26`	`/**`
`27`	`27`	`* Enum representing available output alignment types.`
`28`		`- * <p/>`
	`28`	`+ * <p>`
`29`	`29`	`* Values as used in QBlast URL API.`
`30`	`30`	`*`
`31`	`31`	`* @author Gediminas Rimsa`