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Miscellaneous and minor enhancements #995

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Merged
josemduarte merged 3 commits into from
Nov 8, 2021
Merged

Miscellaneous and minor enhancements #995

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9da6f27
AutoUnboxing instead of deprecated constructor
aalhossary Nov 7, 2021
419d5f0
Minor Miscellaneous formatting and import
aalhossary Nov 7, 2021
d62c7e6
Handling a missed corner case
aalhossary Nov 7, 2021
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2 changes: 1 addition & 1 deletion biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
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Expand Up @@ -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;
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5 changes: 5 additions & 0 deletions biojava-core/src/test/java/org/biojava/nbio/core/util/FileDownloadUtilsTest.java
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Expand Up @@ -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));
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16 changes: 9 additions & 7 deletions biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
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Expand Up @@ -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;


Expand Down Expand Up @@ -1931,7 +1931,7 @@ private void pdb_ATOM_Handler(String line) {



}
}


private Group getCorrectAltLocGroup( Character altLoc,
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