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sblivensbliven
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Remove trailing spaces from java files
find . -iname '*.java' -exec gsed -ri 's/\s+$//' '{}' ';'
1 parent af1e287 commit 405b005

275 files changed

Lines changed: 1969 additions & 1970 deletions

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‎biojava-aa-prop/pom.xml‎

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@@ -29,7 +29,7 @@
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</excludes>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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</descriptorRefs>
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<fileSets>
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<fileSet>
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<!-- TODO: use expresssions instead: ${project.build.sourceDirectory},
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<!-- TODO: use expresssions instead: ${project.build.sourceDirectory},
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etc -->
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<directory>${project.basedir}/src</directory>
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<useDefaultExcludes>true</useDefaultExcludes>
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<dependency>
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<groupId>org.apache.logging.log4j</groupId>
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<artifactId>log4j-core</artifactId>
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</dependency>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/AminoAcidProperties.java‎

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@@ -35,12 +35,12 @@ public class AminoAcidProperties {
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private static final Set<String> posChargedAAs = Stream.of("K", "R", "H").collect(Collectors.toSet());
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private static final Set<String> polarAAs = Stream.of("D", "E", "K", "R", "H", "N", "Q", "S", "T", "Y")
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.collect(Collectors.toSet());
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/**
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* At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
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* At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
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* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
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*
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* @param aa The one-letter amino acid code
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*
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* @param aa The one-letter amino acid code
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* @return true if amino acid is charged
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*/
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public static final boolean isCharged(char aa) {
@@ -52,12 +52,12 @@ else if (posChargedAAs.contains(String.valueOf(aa))) {
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}
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return false;
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}
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/**
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* Returns the charge of amino acid. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
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* Returns the charge of amino acid. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
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* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
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*
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* @param aa The one-letter amino acid code
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*
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* @param aa The one-letter amino acid code
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* @return the charge of amino acid (1 if positively charged, -1 if negatively charged, 0 if not charged)
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*/
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public static final int getChargeOfAminoAcid(char aa) {
@@ -69,11 +69,11 @@ else if (posChargedAAs.contains(String.valueOf(aa))) {
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}
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return 0;
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}
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/**
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* There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
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*
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* @param aa The one-letter amino acid code
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*
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* @param aa The one-letter amino acid code
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* @return true if amino acid is polar
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*/
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public static final boolean isPolar(char aa) {
@@ -82,10 +82,10 @@ public static final boolean isPolar(char aa) {
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}
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return false;
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}
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/**
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* There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
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*
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*
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* @param aa The one-letter amino acid code
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* @return the polarity of amino acid (1 if polar, 0 if not polar)
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*/

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java‎

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@@ -555,12 +555,12 @@ public static final Map<Character, Double> getAACompositionChar(String sequence)
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}
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return aaChar2Composition;
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}
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/**
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* Returns the array of charges of each amino acid in a protein. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
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* Returns the array of charges of each amino acid in a protein. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
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* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
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*
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* @param sequence
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*
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* @param sequence
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* a protein sequence consisting of non-ambiguous characters only
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* @return the array of charges of amino acids in the protein (1 if amino acid is positively charged, -1 if negatively charged, 0 if not charged)
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*/
@@ -572,15 +572,15 @@ public static final int[] getChargesOfAminoAcids(String sequence) {
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}
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return charges;
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}
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/**
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* Returns the array of polarity values of each amino acid in a protein sequence.
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*
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* @param sequence
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* a protein sequence consisting of non-ambiguous characters only
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*
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* @param sequence
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* a protein sequence consisting of non-ambiguous characters only
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* @return the array of polarity of amino acids in the protein (1 if amino acid is polar, 0 if not)
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*/
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public static final int[] getPolarityOfAminoAcids(String sequence) {
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public static final int[] getPolarityOfAminoAcids(String sequence) {
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int[] polarity = new int[sequence.length()];
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for ( int i=0; i < sequence.length(); i++ ) {
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char aa = sequence.toCharArray()[i];

‎biojava-alignment/pom.xml‎

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@@ -24,7 +24,7 @@
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<build>
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<plugins>
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<!-- Excluding demo package is required for avoiding namespace clashes
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<!-- Excluding demo package is required for avoiding namespace clashes
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(demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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</excludes>
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</configuration>
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</plugin>
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</plugins>
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</build>
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<dependencies>
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<groupId>org.biojava.thirdparty</groupId>
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<artifactId>forester</artifactId>
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</dependency>
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<!-- logging dependencies (managed by parent pom, don't set versions or
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<!-- logging dependencies (managed by parent pom, don't set versions or
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scopes here) -->
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<dependency>
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<groupId>org.slf4j</groupId>

‎biojava-core/pom.xml‎

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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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</plugin>
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</plugins>
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</build>
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<dependencies>

‎biojava-core/src/main/java/demo/ParseFastaFileDemo.java‎

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}
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/**
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/**
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* e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
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* and pass in path to local location of file
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*

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java‎

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@@ -442,7 +442,7 @@ public int getNumGapPositions() {
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@Override
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public double getCoverage() {
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double coverage = getLength() - getNumGapPositions();
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return coverage / getOriginalSequence().getLength();
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}

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java‎

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@@ -92,17 +92,17 @@ enum Step { COMPOUND, GAP }
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* @return number of gaps in the sequence
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*/
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int getNumGaps();
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/**
97-
* Returns number of gap positions (gap openings and extensions) in the sequence. This could be determined from the {@link Location}
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* Returns number of gap positions (gap openings and extensions) in the sequence. This could be determined from the {@link Location}
9898
* information or from gap {@link Compound}s, which may not necessarily result in the same number.
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*
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* @return number of gap positions in the sequence
101101
*/
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int getNumGapPositions();
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/**
105-
* Returns the coverage, as a fraction between 0 and 1, of this {@link AlignedSequence} with respect to the original sequence.
105+
* Returns the coverage, as a fraction between 0 and 1, of this {@link AlignedSequence} with respect to the original sequence.
106106
* This is equivalent to ({@link #getLength()} - {@link #getNumGapPositions()}) / getOriginalSequence().getLength().
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*
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* @return coverage of the original sequence by the aligned sequence

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java‎

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@@ -96,7 +96,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
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* @return the number of identical indices
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*/
9898
int getNumIdenticals();
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100100
/**
101101
* Returns the percentage of identity between the two sequences in the alignment as a fraction between 0 and 1.
102102
*

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java‎

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@@ -133,7 +133,7 @@ public void setVersion(Integer version) {
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/**
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* In case if {@link #getID() } in not unique keeps the alternative id, eg. NCBI GI number.
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*
136+
*
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* This may null.
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*
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* @return

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