Skip to content

Commit c34385a

Browse files
andreasprlicandreasprlic
committed
Merge branch 'master' of github.com:biojava/biojava
* 'master' of github.com:biojava/biojava: (211 commits) TestSuperPosition now tests rmsd of non-centered points. Documentation and minor fix Redo the PR #576 re-use code into a method Fix bug in centroid calculation SuperPositionSVD #588 Simple integration test for superposition methods More complete test Inserts space when altLoc is null, so that the rest of fields are properly aligned. FileConvert fix - added empty space if altLoc is null. Fixing hard biounits test. Small fix in Chain docs. Cleanup whitespace Solving a compilation problem, making Grid usable for Point3d #545 Some more work towards #545, some cleanup Issue #582 and some more work towards #545 Add constructors for the MMTFFilereader Added caching functionality for MMTF Address jose comment on #558 Also get short name when getting other protein aliases Fix bug with dihedral axis calculation #558 Fix bug in superposeAndTransform method SuperPositions Remove tests that require String comparisons with floats ...
2 parents 1937027 + 42724d1 commit c34385a

File tree

196 files changed

+27332
-25744
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

196 files changed

+27332
-25744
lines changed

‎.travis.yml‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,4 +2,5 @@ language: java
22
jdk:
33
- oraclejdk8
44
sudo: false
5-
5+
#after_success:
6+
# - mvn clean cobertura:cobertura coveralls:report

‎biojava-aa-prop/src/test/resources/log4j2.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
</Console>
77
</appenders>
88
<loggers>
9-
<root level="info">
9+
<root level="warn">
1010
<appender-ref ref="Console"/>
1111
</root>
1212
</loggers>

‎biojava-alignment/pom.xml‎

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -73,10 +73,5 @@
7373
<groupId>org.apache.logging.log4j</groupId>
7474
<artifactId>log4j-core</artifactId>
7575
</dependency>
76-
<dependency>
77-
<groupId>org.biojava</groupId>
78-
<artifactId>biojava-phylo</artifactId>
79-
<version>5.0.0-SNAPSHOT</version>
80-
</dependency>
8176
</dependencies>
8277
</project>

biojava-phylo/src/main/java/demo/DemoDistanceTree.java renamed to biojava-alignment/src/main/java/demo/DemoDistanceTree.java

File renamed without changes.

biojava-phylo/src/main/java/org/biojava/nbio/phylo/Comparison.java renamed to biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java

File renamed without changes.

biojava-phylo/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java renamed to biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java

Lines changed: 1 addition & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -391,7 +391,7 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix pamMLdi
391391
// Need to import PAM1 matrix to biojava TODO
392392
//SubstitutionMatrix<AminoAcidCompound> PAM1 = SubstitutionMatrixHelper.getPAM250();
393393

394-
return null;
394+
throw new IllegalStateException("PAM ML distance calculation not implemented!");
395395
}
396396

397397
/**
@@ -447,18 +447,4 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix structu
447447
return DM;
448448
}
449449

450-
/**
451-
* The joint sequence-structure distance (d<sub>SS</sub>) is a combination
452-
* of the sequence-based and the structure-based distances.
453-
*
454-
* @param rmsdMat
455-
* RMSD matrix for all structure pairs (symmetric matrix)
456-
* @return DistanceMatrix
457-
*/
458-
public static <C extends Sequence<D>, D extends Compound> DistanceMatrix jointSeqStrucDistance(
459-
double[][] rmsdMat) {
460-
// TODO
461-
return null;
462-
}
463-
464450
}

biojava-phylo/src/main/java/org/biojava/nbio/phylo/DistanceTreeEvaluator.java renamed to biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceTreeEvaluator.java

File renamed without changes.

biojava-phylo/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java renamed to biojava-alignment/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java

File renamed without changes.

biojava-phylo/src/main/java/org/biojava/nbio/phylo/TreeConstructor.java renamed to biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeConstructor.java

File renamed without changes.

biojava-phylo/src/main/java/org/biojava/nbio/phylo/TreeConstructorType.java renamed to biojava-alignment/src/main/java/org/biojava/nbio/phylo/TreeConstructorType.java

File renamed without changes.

0 commit comments

Comments
 (0)