+ *
* To read from an Illumina variant FASTQ sequence file:
*
* FastqReader reader = new IlluminaFastqReader(); @@ -31,30 +31,24 @@ * // ... * } *- * * - *
* To write to an Sanger variant FASTQ sequence file: *
* Collection<Fastq> fastq = ...;
* SangerFastqWriter writer = new SangerFastqWriter();
* writer.write(new File("sanger.fastq"), fastq);
*
- *
*
- * * For further documentation on the FASTQ sequence format, * its variants, and how they are handled in O|B|F projects, * see: - *
* - *
+ *
* The Sanger FASTQ file format for sequences
- * with quality scores, and the Solexa/Illumina FASTQ variants
+ * with quality scores, and the Solexa/Illumina FASTQ variants
* Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto (BioRuby),
- * Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS).
+ * Michael L. Heuer (BioJava) and Peter M. Rice (EMBOSS).
* Nucleic Acids Research, doi:10.1093/nar/gkp1137
- *
* Each alignment is described as a collection of: - *
* Neither removes this alignment from its previous ensemble, if any, nor
- * adds it to the new parent. Calling code should assure that links to
- * and from the ensemble are consistent and free of memory leaks.
+ * adds it to the new parent. Calling code should assure that links to and
+ * from the ensemble are consistent and free of memory leaks.
*
- * @param parent the parent MultipleAlignmentEnsemble.
+ * @param parent
+ * the parent MultipleAlignmentEnsemble.
* @see #getEnsemble()
*/
public void setEnsemble(MultipleAlignmentEnsemble parent);
@@ -82,7 +83,7 @@ public interface MultipleAlignment extends ScoresCache {
* Initializes the variable if it is null.
*
* @return List of BlockSets that describe the aligned residues of all the
- * structures.
+ * structures.
* @see #getBlocks()
* @see #setBlockSets(List)
*/
@@ -93,7 +94,8 @@ public interface MultipleAlignment extends ScoresCache {
* Throws an Exception if the index is out of bounds, like accessing a
* normal List.
*
- * @param index of the BlockSet
+ * @param index
+ * of the BlockSet
* @return BlockSets at the specified index
* @see #getBlocks()
* @see #getBlockSets()
@@ -103,16 +105,16 @@ public interface MultipleAlignment extends ScoresCache {
/**
* Sets the List of BlockSet List of the specified alignment.
*
- * @param blockSets the List of BlockSets that describe the aligned
- * residues.
+ * @param blockSets
+ * the List of BlockSets that describe the aligned residues.
* @see #getBlockSets()
*/
public void setBlockSets(List
* Recursively clears member BlockSets.
*/
public void clear();
/**
- * Return a summary of the MultipleAlignment, containing the structures,
- * the lengths and the cached scores. Can be used as a header for the
- * differnt display options.
+ * Return a summary of the MultipleAlignment, containing the structures, the
+ * lengths and the cached scores. Can be used as a header for the differnt
+ * display options.
*
* @return String header summary of the MultipleAlignment
*/
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
index 6f504bbd72..ea20b421e3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -35,17 +35,19 @@
* @since 4.1.0
*
*/
-public class MultipleAlignmentImpl extends AbstractScoresCache
-implements Serializable, MultipleAlignment, Cloneable {
+public class MultipleAlignmentImpl extends AbstractScoresCache implements
+ Serializable, MultipleAlignment, Cloneable {
private static final long serialVersionUID = 3432043794125805139L;
private MultipleAlignmentEnsemble parent;
private List
+ * For detailed explanation about the ECOD information see the original article
+ * at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256011.
+ *
* There must be at least Rmin residues different than null in every
- * alignment column.In case there is a column with more gaps than allowed it
- * will be shrinked (moved to freePool).
+ * alignment column. In case there is a column with more gaps than allowed
+ * it will be shrinked (moved to freePool).
*
* @return true if any columns has been shrinked and false otherwise
*/
@@ -805,15 +837,17 @@ private double probabilityFunction(double AS, int m, int maxIter) {
private void saveHistory(String folder) throws IOException {
String name = msa.getStructureIdentifier(0).getIdentifier();
- FileWriter writer = new FileWriter(folder + name + "-symm_optimization.csv");
- writer.append("Structure,Step,Repeat Length,RMSD,TM-Score\n");
+ FileWriter writer = new FileWriter(folder + name
+ + "-symm_opt.csv");
+ writer.append("Step,Time,RepeatLength,RMSD,TMscore,MCscore\n");
for (int i = 0; i < lengthHistory.size(); i++) {
- writer.append(name + ",");
writer.append(i * saveStep + ",");
+ writer.append(timeHistory.get(i) + ",");
writer.append(lengthHistory.get(i) + ",");
writer.append(rmsdHistory.get(i) + ",");
- writer.append(scoreHistory.get(i) + "\n");
+ writer.append(tmScoreHistory.get(i) + ",");
+ writer.append(mcScoreHistory.get(i) + "\n");
}
writer.flush();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
index e5e9a8d96c..fc0af1f14e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java
@@ -221,11 +221,12 @@ public Matrix4d getRepeatTransform(int repeat){
/**
* Return all symmetry axes of of the structure: the set of axes that
* describe all parts of the structure. This combines the elementary
- * axes to generate all possible axes.
- * Use this method to display the axes.
- *
+ * axes to generate all possible axes. The axes are returned in the repeat
+ * order.
+ * @deprecated because it does not work as expected for open symmetry
* @return axes all symmetry axes of the structure.
*/
+ @Deprecated
public List
+ * Cheng H, Schaeffer RD, Liao Y, et al.
+ * ECOD: An Evolutionary Classification of Protein Domains.
+ * Elofsson A, ed. PLoS Computational Biology. 2014;10(12):e1003926.
+ *
+ *
* @author Spencer Bliven
*
*/
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
index 4495496eb6..73e5f7db7f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
@@ -29,29 +29,29 @@
import java.util.Map.Entry;
import org.biojava.nbio.structure.align.util.UserConfiguration;
-import org.biojava.nbio.structure.cath.CathDatabase;
-import org.biojava.nbio.structure.cath.CathInstallation;
+import org.biojava.nbio.structure.cath.CathFactory;
import org.biojava.nbio.structure.scop.ScopFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
- * Controls global {@link CathDatabase CathDatabases} being used.
- * Implements a multiton pattern through {@link #getCathDatabase(String)},
- * and a singleton pattern through {@link #getCathDatabase()}.
+ * Controls global {@link EcodDatabase EcodDatabases} being used.
+ * Implements a multiton pattern through {@link #getEcodDatabase(String)},
+ * and a singleton pattern through {@link #getEcodDatabase()}.
* @author Spencer Bliven
* @see ScopFactory
- * @see CathInstallation
+ * @see CathFactory
+ * @see EcodInstallation
*/
public class EcodFactory {
- private static Logger logger = LoggerFactory.getLogger(EcodFactory.class);
-
- public static String DEFAULT_VERSION = EcodInstallation.DEFAULT_VERSION;
+ private static final Logger logger = LoggerFactory.getLogger(EcodFactory.class);
+
+ public static final String DEFAULT_VERSION = EcodInstallation.DEFAULT_VERSION;
private static Map