Merge pull request #995 from aalhossary/master

josemduarte · web-flow · commit baefba4b3e6e · 2021-11-08T10:21:40.000-08:00
Miscellaneous and minor enhancements
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -200,7 +200,7 @@ public static String toUnixPath(String path) {
 	public static String expandUserHome(String file) {
 		// replace any / with the proper separator (/ or \ for Linux and Windows respectively).
 		file = file.replaceAll("/", "\\"+File.separator); //The "\\" is to escape the separator if needed.
-		if (file.startsWith("~" + File.separator)) {
+		if (file.startsWith("~") && (file.length() == 1 || File.separator.equals(file.substring(1, 2)))) {
 			file = System.getProperty("user.home") + file.substring(1);
 		}
 		return file;
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java
@@ -131,6 +131,11 @@ void unixPathReturnedUnchanged(){
     class ExpandUserHome {
         String currUserHome = System.getProperty("user.home");
         @Test
+        void minimalPath (){
+        	String path="~";
+        	assertEquals(currUserHome, FileDownloadUtils.expandUserHome(path));
+        }
+        @Test
         void simplePath (){
             String path="~/sequence.gb";
             assertEquals(currUserHome+File.separator+"sequence.gb", FileDownloadUtils.expandUserHome(path));
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
@@ -20,19 +20,21 @@
  */
 package org.biojava.nbio.phosphosite;
 
-import org.biojava.nbio.structure.align.util.AtomCache;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.*;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.StandardCopyOption;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.stream.Collectors;
-import java.util.stream.Stream;
+
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -1726,7 +1726,7 @@ private void  pdb_ATOM_Handler(String line)	{
 		startOfMolecule = false;
 
 
-		Character altLoc   = new Character(line.substring (16, 17).charAt(0));
+		Character altLoc   = line.substring (16, 17).charAt(0);
 		Group altGroup = null;
 
 
@@ -1931,7 +1931,7 @@ private void  pdb_ATOM_Handler(String line)	{
 
 
 
-			}
+	}
 
 
 	private Group getCorrectAltLocGroup( Character altLoc,

Original file line number	Diff line number	Diff line change
`@@ -200,7 +200,7 @@ public static String toUnixPath(String path) {`
`200`	`200`	`public static String expandUserHome(String file) {`
`201`	`201`	`// replace any / with the proper separator (/ or \ for Linux and Windows respectively).`
`202`	`202`	`file = file.replaceAll("/", "\\"+File.separator); //The "\\" is to escape the separator if needed.`
`203`		`- if (file.startsWith("~" + File.separator)) {`
	`203`	`+ if (file.startsWith("~") && (file.length() == 1 \|\| File.separator.equals(file.substring(1, 2)))) {`
`204`	`204`	`file = System.getProperty("user.home") + file.substring(1);`
`205`	`205`	`}`
`206`	`206`	`return file;`