apos){
this.apos = apos;
- if ( apos.size() == 0)
+ if (apos.isEmpty())
return;
AlignedPosition last = apos.get(apos.size()-1);
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
index de8df79dd8..7fbc64a3c1 100644
--- a/biojava-structure/pom.xml
+++ b/biojava-structure/pom.xml
@@ -4,7 +4,7 @@
biojava
org.biojava
- 7.2.0
+ 7.2.5-SNAPSHOT
biojava-structure
biojava-structure
@@ -51,13 +51,13 @@
org.biojava
biojava-alignment
- 7.2.0
+ 7.2.5-SNAPSHOT
compile
org.biojava
biojava-core
- 7.2.0
+ 7.2.5-SNAPSHOT
compile
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
index b0d7253507..bd5a01b885 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Author.java
@@ -62,7 +62,7 @@ public boolean equals(Object obj) {
if ((this.surname == null) ? (other.surname != null) : !this.surname.equals(other.surname)) {
return false;
}
- return !((this.initials == null) ? (other.initials != null) : !this.initials.equals(other.initials));
+ return (this.initials == null) ? other.initials == null : this.initials.equals(other.initials);
}
@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
index 2f534b2828..4e2d3e340a 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
@@ -424,7 +424,7 @@ public boolean isHeavyAtom() {
* @return true if Element is not Hydrogen and not Carbon.
*/
public boolean isHeteroAtom() {
- return !(this == C || this == H);
+ return this != C && this != H;
}
/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
index de8b5ca4d1..b4978fc582 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
@@ -21,8 +21,7 @@
package org.biojava.nbio.structure;
/**
- *
- * The type of entity (polymer, non-polymer, water, macrolide)
+ * The type of entity (polymer, non-polymer, water, macrolide, branched)
* as defined in the mmCIF dictionary:
*
* Entities are of four types: polymer, non-polymer, macrolide and water.
@@ -76,10 +75,8 @@ public enum EntityType {
/**
* @param entType the type of the Entity
*/
- private EntityType(String entType) {
-
+ EntityType(String entType) {
this.setEntityType(entType);
-
}
/**
@@ -101,19 +98,15 @@ private void setEntityType(String entityType) {
* Returns null if entityType is null or not one of the supported
* standard types.
*
- * @param entityType String value , should be one of "polymer","non-polymer","water","macrolide"
- * @return an EntityType object
+ * @param entityType should be one of "polymer", "non-polymer", "water", "macrolide", "branched" (case insensitive)
+ * @return an EntityType object or null if the input string doesn't correspond to a known entity
*/
- public static EntityType entityTypeFromString(String entityType)
- {
-
- if ( entityType == null)
+ public static EntityType entityTypeFromString(String entityType) {
+ if (entityType == null)
return null;
- for(EntityType et : EntityType.values())
- {
- if(entityType.equals(et.entityType))
- {
+ for(EntityType et : EntityType.values()) {
+ if (entityType.equalsIgnoreCase(et.entityType)) {
return et;
}
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
index 51d69234c7..05bd0ba859 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
@@ -178,10 +178,10 @@ public interface Structure extends Cloneable, Serializable {
/**
* Return number of chains of model.
*
- * @param modelnr an int specifying the number of the Model that should be used
+ * @param modelIdx an int specifying the index of the Model that should be used
* @return an int representing the number of Chains in this Model
*/
- int size(int modelnr);
+ int size(int modelIdx);
/**
* Return the number of models .
@@ -232,10 +232,10 @@ public interface Structure extends Cloneable, Serializable {
* Retrieve all Chains belonging to a model .
* @see #getChains(int modelnr)
*
- * @param modelnr an int
+ * @param modelIdx the model index
* @return a List object containing the Chains of Model nr. modelnr
*/
- List getModel(int modelnr);
+ List getModel(int modelIdx);
/**
* Retrieve all chains for the first model.
@@ -261,17 +261,17 @@ public interface Structure extends Cloneable, Serializable {
* Retrieve all chains of a model.
* @see #getModel
*
- * @param modelnr an int
+ * @param modelIdx the model index
* @return a List object containing the Chains of Model nr. modelnr
*/
- List getChains(int modelnr);
+ List getChains(int modelIdx);
/**
* Set the chains for a model
* @param chains the chains for a model
- * @param modelnr the number of the model
+ * @param modelIdx the model index
*/
- void setChains( int modelnr, List chains);
+ void setChains(int modelIdx, List chains);
/**
* Return all polymeric chains for the first model
@@ -315,7 +315,7 @@ public interface Structure extends Cloneable, Serializable {
/**
* Return all water chains for the given model index
- * @param modelIdx
+ * @param modelIdx the model index
* @return
* @since 5.0
*/
@@ -332,9 +332,9 @@ public interface Structure extends Cloneable, Serializable {
* Add a new chain to the model specified by the given index
*
* @param chain a Chain object
- * @param modelnr an int specifying to which model the Chain should be added
+ * @param modelIdx an int specifying to which model the Chain should be added
*/
- void addChain(Chain chain, int modelnr);
+ void addChain(Chain chain, int modelIdx);
/**
* Retrieve a chain by its index within the Structure .
@@ -348,10 +348,10 @@ public interface Structure extends Cloneable, Serializable {
* Retrieve a chain by its indices within the Structure and model.
*
* @param chainIndex the index of the desired chain in the structure
- * @param modelnr the model the desired chain is in
+ * @param modelIdx the model index
* @return a Chain object
*/
- Chain getChainByIndex(int modelnr, int chainIndex);
+ Chain getChainByIndex(int modelIdx, int chainIndex);
/**
* Check if a chain with the chainId aymId is contained in this structure.
@@ -394,11 +394,11 @@ public interface Structure extends Cloneable, Serializable {
* considers only model nr X. count starts with 0.
* @param authId the chain name of the chain to use
* @param pdbResnum the PDB residue number of the requested group
- * @param modelnr the number of the model to use
+ * @param modelIdx the model index
* @return Group the requested Group
* @throws StructureException
*/
- Group findGroup(String authId, String pdbResnum, int modelnr) throws StructureException;
+ Group findGroup(String authId, String pdbResnum, int modelIdx) throws StructureException;
/**
* Retrieve a Chain (polymeric, non-polymeric or water) based on
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index ae00c8f7f3..0a697e2d7b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -123,20 +123,15 @@ public Structure clone() {
n.setDBRefs(this.getDBRefs());
n.setSites(getSites());
-
// go through each chain and clone chain
for (int i=0;i cloned_model = new ArrayList<>();
for (int j=0;j models.size())
- throw new StructureException(" no model nr " + modelnr +
+ if ( modelIdx > models.size())
+ throw new StructureException(" no model nr " + modelIdx +
" in this structure. (contains "+models.size()+")");
-
// first we need to gather all groups with the author id chainName: polymers, non-polymers and waters
- Chain polyChain = getPolyChainByPDB(chainName, modelnr);
+ Chain polyChain = getPolyChainByPDB(chainName, modelIdx);
if(polyChain != null) {
- List groups = new ArrayList<>();
-
- groups.addAll(polyChain.getAtomGroups());
+ List groups = new ArrayList<>(polyChain.getAtomGroups());
// there can be more than one non-poly chain for a given author id
- for (Chain chain: getNonPolyChainsByPDB(chainName, modelnr)) {
+ for (Chain chain: getNonPolyChainsByPDB(chainName, modelIdx)) {
groups.addAll(chain.getAtomGroups());
}
- Chain water = getWaterChainByPDB(chainName, modelnr);
+ Chain water = getWaterChainByPDB(chainName, modelIdx);
if (water!=null)
groups.addAll(water.getAtomGroups());
-
-
// now iterate over all groups
// in order to find the amino acid that has this pdbRenum.
@@ -254,13 +243,12 @@ public void setStructureIdentifier(StructureIdentifier structureIdentifier) {
/** {@inheritDoc} */
@Override
public void addChain(Chain chain) {
- int modelnr = 0 ;
- addChain(chain,modelnr);
+ addChain(chain, 0);
}
/** {@inheritDoc} */
@Override
- public void addChain(Chain chain, int modelnr) {
+ public void addChain(Chain chain, int modelIdx) {
// if model has not been initialized, init it!
chain.setStructure(this);
if (models.isEmpty()) {
@@ -271,37 +259,25 @@ public void addChain(Chain chain, int modelnr) {
models.add(model);
} else {
- Model model = models.get(modelnr);
+ Model model = models.get(modelIdx);
model.addChain(chain);
}
-
-
-
}
-
-
/** {@inheritDoc} */
@Override
public Chain getChainByIndex(int number) {
-
- int modelnr = 0 ;
-
- return getChainByIndex(modelnr,number);
+ return getChainByIndex(0, number);
}
/** {@inheritDoc} */
@Override
- public Chain getChainByIndex(int modelnr,int number) {
-
- Model model = models.get(modelnr);
-
+ public Chain getChainByIndex(int modelIdx, int number) {
+ Model model = models.get(modelIdx);
return model.getChains().get(number);
}
-
-
/** {@inheritDoc} */
@Override
public void addModel(List modelChains){
@@ -313,16 +289,12 @@ public void addModel(List modelChains){
models.add(model);
}
-
/** {@inheritDoc} */
@Override
public void setChains(List chains){
-
- setModel(0,chains);
+ setModel(0, chains);
}
-
-
/** {@inheritDoc} */
@Override
public void setModel(int position, List modelChains){
@@ -333,8 +305,6 @@ public void setModel(int position, List modelChains){
c.setStructure(this);
//System.out.println("model size:" + models.size());
-
-
Model model = new Model();
model.setChains(modelChains);
@@ -345,12 +315,9 @@ public void setModel(int position, List modelChains){
}
}
- /** String representation.
- *
- */
@Override
public String toString(){
- String newline = System.getProperty("line.separator");
+ String newline = System.lineSeparator();
StringBuilder str = new StringBuilder();
str.append("structure ");
str.append(name);
@@ -384,17 +351,13 @@ public String toString(){
List hgr = cha.getAtomGroups(GroupType.HETATM);
List ngr = cha.getAtomGroups(GroupType.NUCLEOTIDE);
-
-
-
str.append("chain ")
.append(j).append(": asymId:")
.append(cha.getId())
.append(" authId:")
.append(cha.getName()).append(" ");
-
- if ( cha.getEntityInfo() != null){
+ if (cha.getEntityInfo() != null){
EntityInfo comp = cha.getEntityInfo();
String molName = comp.getDescription();
if ( molName != null){
@@ -406,7 +369,6 @@ public String toString(){
.append(")");
}
-
str.append(newline);
str.append(" length SEQRES: ").append(cha.getSeqResLength());
str.append(" length ATOM: ").append(cha.getAtomLength());
@@ -425,32 +387,21 @@ public String toString(){
str.append(mol).append(newline);
}
-
return str.toString() ;
}
@Override
public int size() {
- int modelnr = 0 ;
-
if (!models.isEmpty()) {
- return models.get(modelnr).getPolyChains().size();
- }
- else {
+ return models.get(0).getPolyChains().size();
+ } else {
return 0 ;
}
-
}
- /** return number of chains of model.
- *
- */
@Override
- public int size(int modelnr) { return models.get(modelnr).size(); }
+ public int size(int modelIdx) { return models.get(modelIdx).size(); }
- // some NMR stuff :
-
- /** return number of models. */
@Override
public int nrModels() {
return models.size() ;
@@ -520,16 +471,15 @@ public List getChains(int modelIdx){
/** {@inheritDoc} */
@Override
public List getChains(){
- if (models.size()==0) {
+ if (models.isEmpty()) {
return new ArrayList<>(0);
}
return getChains(0);
-
}
@Override
public List getPolyChains() {
- if (models.size()==0) {
+ if (models.isEmpty()) {
return new ArrayList<>(0);
}
return getPolyChains(0);
@@ -542,7 +492,7 @@ public List getPolyChains(int modelIdx) {
@Override
public List getNonPolyChains() {
- if (models.size()==0) {
+ if (models.isEmpty()) {
return new ArrayList<>(0);
}
return getNonPolyChains(0);
@@ -555,7 +505,7 @@ public List getNonPolyChains(int modelIdx) {
@Override
public List getWaterChains() {
- if (models.size()==0) {
+ if (models.isEmpty()) {
return new ArrayList<>(0);
}
return getWaterChains(0);
@@ -566,55 +516,46 @@ public List getWaterChains(int modelIdx) {
return models.get(modelIdx).getWaterChains();
}
-
-
/** {@inheritDoc} */
@Override
- public void setChains(int modelnr, List chains){
+ public void setChains(int modelIdx, List chains){
for (Chain c: chains){
c.setStructure(this);
}
- if (models.size()>modelnr) {
- models.remove(modelnr);
+ if (models.size()> modelIdx) {
+ models.remove(modelIdx);
}
Model model = new Model();
model.setChains(chains);
- models.add(modelnr, model);
-
+ models.add(modelIdx, model);
}
- /** Retrieve all Chains belonging to a model .
- *
- * @param modelnr an int
- * @return a List object
+ /**
+ * {@inheritDoc}
*/
@Override
- public List getModel(int modelnr) {
-
- return models.get(modelnr).getChains();
+ public List getModel(int modelIdx) {
+ if (models.isEmpty()) return new ArrayList<>();
+ return models.get(modelIdx).getChains();
}
/** {@inheritDoc} */
@Override
- public Chain getChain(String asymId, int modelnr) {
-
- List chains = getChains(modelnr);
+ public Chain getChain(String asymId, int modelIdx) {
+ List chains = getChains(modelIdx);
for (Chain c : chains) {
if (c.getId().equals(asymId)) {
return c;
}
}
return null;
-
}
/** {@inheritDoc} */
@Override
public Chain getChain(String asymId) {
-
return getChain(asymId,0);
-
}
@Override
@@ -625,6 +566,8 @@ public Chain getPolyChain(String asymId) {
@Override
public Chain getPolyChain(String asymId, int modelIdx) {
+ if (models.isEmpty()) return null;
+
Model model = models.get(modelIdx);
if (model==null) {
return null;
@@ -637,7 +580,6 @@ public Chain getPolyChain(String asymId, int modelIdx) {
return null;
}
-
@Override
public Chain getNonPolyChain(String asymId) {
return getNonPolyChain(asymId, 0);
@@ -655,7 +597,6 @@ public Chain getNonPolyChain(String asymId, int modelIdx) {
if (c.getId().equals(asymId))
return c;
}
-
return null;
}
@@ -693,7 +634,6 @@ public List getNonPolyChainsByPDB(String authId, int modelIdx) {
return chains;
}
-
List nonpolyChains = model.getNonPolyChains();
for (Chain c : nonpolyChains){
if (c.getName().equals(authId))
@@ -708,7 +648,6 @@ public Chain getWaterChain(String asymId) {
return getWaterChain(asymId, 0);
}
-
@Override
public Chain getWaterChain(String asymId, int modelIdx) {
Model model = models.get(modelIdx);
@@ -729,7 +668,6 @@ public Chain getWaterChainByPDB(String authId) {
return getWaterChainByPDB(authId, 0);
}
-
@Override
public Chain getWaterChainByPDB(String authId, int modelIdx) {
Model model = models.get(modelIdx);
@@ -745,8 +683,6 @@ public Chain getWaterChainByPDB(String authId, int modelIdx) {
return null;
}
-
-
/** {@inheritDoc} */
@Override
public String toPDB() {
@@ -835,7 +771,6 @@ public EntityInfo getEntityById(int entityId) {
return null;
}
-
/** {@inheritDoc} */
@Override
public List getDBRefs() {
@@ -855,7 +790,6 @@ public void setDBRefs(List dbrefs) {
this.dbrefs = dbrefs;
}
-
/** {@inheritDoc} */
@Override
public PDBHeader getPDBHeader() {
@@ -872,7 +806,6 @@ public void setPDBHeader(PDBHeader pdbHeader){
@Override
public List getSSBonds(){
return ssbonds;
-
}
/** {@inheritDoc} */
@@ -882,9 +815,7 @@ public void setSSBonds(List ssbonds){
}
/**
- * Adds a single disulfide Bond to this structure
- *
- * @param ssbond the SSBond.
+ * {@inheritDoc}
*/
@Override
public void addSSBond(Bond ssbond){
@@ -892,10 +823,7 @@ public void addSSBond(Bond ssbond){
}
/**
- * Return whether or not the entry has an associated journal article
- * or publication. The JRNL section is not mandatory and thus may not be
- * present.
- * @return flag if a JournalArticle could be found.
+ * R{@inheritDoc}
*/
@Override
public boolean hasJournalArticle() {
@@ -903,9 +831,7 @@ public boolean hasJournalArticle() {
}
/**
- * get the associated publication as defined by the JRNL records in a PDB
- * file.
- * @return a JournalArticle
+ * {@inheritDoc}
*/
@Override
public JournalArticle getJournalArticle() {
@@ -913,9 +839,7 @@ public JournalArticle getJournalArticle() {
}
/**
- * set the associated publication as defined by the JRNL records in a PDB
- * file.
- * @param journalArticle the article
+ * {@inheritDoc}
*/
@Override
public void setJournalArticle(JournalArticle journalArticle) {
@@ -923,29 +847,21 @@ public void setJournalArticle(JournalArticle journalArticle) {
}
/**
- * @return the sites contained in this structure
+ * {@inheritDoc}
*/
-
@Override
public List getSites() {
return sites;
}
/**
- * @param sites the sites to set in the structure
+ * {@inheritDoc}
*/
-
@Override
public void setSites(List sites) {
this.sites = sites;
}
- /** Caution: we should probably remove this to avoid confusion. Currently this is always an empty list!
- *
- * @return a list of Groups listed in the HET records - this will not
- * include any waters.
- */
-
/**
* Sets a flag to indicate if this structure is a biological assembly
* @param biologicalAssembly true if biological assembly, otherwise false
@@ -1026,19 +942,17 @@ public void setPDBCode(String pdb_id){
pdbId = new PdbId(pdb_id);
}
}
-
-
- /** {@inheritDoc}
- * @since 6.0.0
- * */
+ /**
+ * {@inheritDoc}
+ **/
public PdbId getPdbId() {
return this.pdbId;
}
- /** {@inheritDoc}
- * @since 6.0.0
- * */
+ /**
+ * {@inheritDoc}
+ **/
public void setPdbId(PdbId pdbId) {
this.pdbId = pdbId;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
index 373bcf1611..0933198d7b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ClusterAltAligs.java
@@ -102,7 +102,7 @@ public static void cluster(AlternativeAlignment[] aligs, int cutoff){
}
clusters.add(currentCluster);
- if ( remainList.size() == 0) {
+ if ( remainList.isEmpty()) {
break;
}
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
index 6c045ba48e..83f16b7982 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -1450,7 +1450,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
//afpChain.setTotalRmsdOpt(rmsd);
//System.out.println("rmsd: " + rmsd);
- if(!(nAtom= strLen * 0.95 && !isRmsdLenAssigned) {
rmsdLen=rmsd;
isRmsdLenAssigned=true;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
index 4f57161268..cab98b0113 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -1455,7 +1455,7 @@ private int optimizeSuperposition(AFPChain afpChain, int nse1, int nse2, int str
//afpChain.setTotalRmsdOpt(rmsd);
//System.out.println("rmsd: " + rmsd);
- if(!(nAtom= strLen * 0.95 && !isRmsdLenAssigned) {
rmsdLen=rmsd;
isRmsdLenAssigned=true;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
index e0423b6f8f..43da1d7c06 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -127,7 +127,7 @@ public void setAlignRes(List> alignRes) {
public int length() {
if (alignRes == null)
return 0;
- if (alignRes.size() == 0)
+ if (alignRes.isEmpty())
return 0;
return alignRes.get(0).size();
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
index cbbb3ae895..344ee3c239 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
@@ -179,7 +179,7 @@ public int size() {
// Get the size from the variables that can contain the information
if (parent != null)
return parent.size();
- else if (getBlocks().size() == 0) {
+ else if (getBlocks().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty BlockSet: number of Blocks == 0.");
} else
@@ -194,7 +194,7 @@ public int getCoreLength() {
}
protected void updateLength() {
- if (getBlocks().size() == 0) {
+ if (getBlocks().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty BlockSet: number of Blocks == 0.");
}
@@ -207,7 +207,7 @@ protected void updateLength() {
}
protected void updateCoreLength() {
- if (getBlocks().size() == 0) {
+ if (getBlocks().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty BlockSet: number of Blocks == 0.");
}
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 738eee30c5..06c93a4403 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
@@ -207,7 +207,7 @@ public int getCoreLength() {
* lengths.
*/
protected void updateLength() {
- if (getBlockSets().size() == 0) {
+ if (getBlockSets().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty MultipleAlignment: blockSets size == 0.");
} // Otherwise try to calculate it from the BlockSet information
@@ -223,7 +223,7 @@ protected void updateLength() {
* BlockSet core lengths.
*/
protected void updateCoreLength() {
- if (getBlockSets().size() == 0) {
+ if (getBlockSets().isEmpty()) {
throw new IndexOutOfBoundsException(
"Empty MultipleAlignment: blockSets size == 0.");
} // Otherwise try to calculate it from the BlockSet information
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index 052f147fc6..29c7012801 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -153,7 +153,7 @@ public MultipleMcOptimizer(MultipleAlignment seedAln,
for (Block b : toDelete) {
for (BlockSet bs : msa.getBlockSets()) {
bs.getBlocks().remove(b);
- if (bs.getBlocks().size() == 0)
+ if (bs.getBlocks().isEmpty())
emptyBs.add(bs);
}
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
index 7ac77a602e..fe1c9c411b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/quaternary/QsAlignResult.java
@@ -117,7 +117,7 @@ public void setSubunitMap(Map subunitMap) {
"Subunit Map index higher than Subunit List size.");
// Update the relation enum
- if (subunitMap.size() == 0) {
+ if (subunitMap.isEmpty()) {
relation = QsRelation.DIFFERENT;
} else if (subunitMap.keySet().size() == subunits1.size()) {
if (subunitMap.values().size() == subunits2.size()) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 1435191c2c..71b8a3da22 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -228,7 +228,7 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
throws StructureException, IOException {
return getBiologicalAssembly(new PdbId(pdbId), bioAssemblyId, multiModel);
}
-
+
/**
* Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the
* assembly from the biounit annotations found in {@link Structure#getPDBHeader()}
@@ -284,7 +284,7 @@ public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean m
asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
- if (transformations == null || transformations.size() == 0) {
+ if (transformations == null || transformations.isEmpty()) {
throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId);
}
@@ -339,7 +339,7 @@ public Structure getBiologicalAssembly(String pdbId, boolean multiModel) throws
asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
- if (transformations == null || transformations.size() == 0) {
+ if (transformations == null || transformations.isEmpty()) {
throw new StructureException("Could not load transformations to recreate biological assembly id " + bioAssemblyId + " of " + pdbId);
}
@@ -385,7 +385,7 @@ public List getBiologicalAssemblies(String pdbId, boolean multiModel)
List transformations =
asymUnit.getPDBHeader().getBioAssemblies().get(bioAssemblyId).getTransforms();
- if (transformations == null || transformations.size() == 0) {
+ if (transformations == null || transformations.isEmpty()) {
logger.info("Could not load transformations to recreate biological assembly id {} of {}. Assembly " +
"id will be missing in biological assemblies.", bioAssemblyId, pdbId);
continue;
@@ -807,7 +807,7 @@ public Structure getStructureForPdbId(String id) throws IOException, StructureEx
public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
if (pdbId == null)
return null;
-
+
while (checkLoading(pdbId)) {
// waiting for loading to be finished...
try {
@@ -833,7 +833,7 @@ public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException {
return loadStructureFromCifByPdbId(new PdbId(pdbId));
}
-
+
protected Structure loadStructureFromCifByPdbId(PdbId pdbId) throws IOException {
logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path);
Structure s;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
index 4fe19aca58..a68019efb7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/ZipChemCompProvider.java
@@ -120,7 +120,7 @@ public ChemComp getChemComp(String recordName) {
}
// If a null record or an empty chemcomp, return a default ChemComp and blacklist.
- if (cc == null || (null == cc.getName() && cc.getAtoms().size() == 0)) {
+ if (cc == null || (null == cc.getName() && cc.getAtoms().isEmpty())) {
s_logger.info("Unable to find or download {} - excluding from future searches.", recordName);
unavailable.add(recordName);
return getEmptyChemComp(recordName);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
index 9a87e92f88..87c3c06e3c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java
@@ -331,7 +331,7 @@ public boolean mergeIdenticalByEntityId(SubunitCluster other) {
}
}
- if (thisAligned.size() == 0 && otherAligned.size() == 0) {
+ if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
logger.warn("No equivalent aligned atoms found between SubunitClusters {}-{} via entity SEQRES alignment. Is FileParsingParameters.setAlignSeqRes() set?", thisName, otherName);
}
@@ -507,27 +507,24 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
}
}
- AFPChain afp = aligner.align(this.subunits.get(this.representative)
- .getRepresentativeAtoms(),
- other.subunits.get(other.representative)
- .getRepresentativeAtoms());
+ AFPChain afp = aligner.align(this.subunits.get(this.representative).getRepresentativeAtoms(),
+ other.subunits.get(other.representative).getRepresentativeAtoms());
+ String pairName = this.subunits.get(this.representative).getName() + "-" + other.subunits.get(other.representative).getName();
if (afp.getOptLength() < 1) {
// alignment failed (eg if chains were too short)
throw new StructureException(
- String.format("Subunits failed to align using %s", params.getSuperpositionAlgorithm()));
+ String.format("Subunits %s failed to align using %s", pairName, params.getSuperpositionAlgorithm()));
}
// Convert AFPChain to MultipleAlignment for convenience
MultipleAlignment msa = new MultipleAlignmentEnsembleImpl(
afp,
this.subunits.get(this.representative).getRepresentativeAtoms(),
- other.subunits.get(other.representative)
- .getRepresentativeAtoms(), false)
- .getMultipleAlignment(0);
+ other.subunits.get(other.representative).getRepresentativeAtoms(),
+ false).getMultipleAlignment(0);
- double structureCoverage = Math.min(msa.getCoverages().get(0), msa
- .getCoverages().get(1));
+ double structureCoverage = Math.min(msa.getCoverages().get(0), msa.getCoverages().get(1));
if(params.isUseStructureCoverage() && structureCoverage < params.getStructureCoverageThreshold()) {
return false;
@@ -543,8 +540,7 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
return false;
}
- logger.info(String.format("SubunitClusters are structurally similar with "
- + "%.2f RMSD %.2f coverage", rmsd, structureCoverage));
+ logger.info("SubunitClusters {} are structurally similar with [ {} ] RMSD and [ {} ] coverage", pairName, String.format("%.2f", rmsd), String.format("%.2f", structureCoverage));
// Merge clusters
List> alignedRes = msa.getBlock(0).getAlignRes();
@@ -565,13 +561,18 @@ public boolean mergeStructure(SubunitCluster other, SubunitClustererParameters p
// Only consider residues that are part of the SubunitCluster
if (this.subunitEQR.get(this.representative).contains(thisIndex)
- && other.subunitEQR.get(other.representative).contains(
- otherIndex)) {
+ && other.subunitEQR.get(other.representative).contains(otherIndex)) {
thisAligned.add(thisIndex);
otherAligned.add(otherIndex);
}
}
+ // this can happen in very rare cases, e.g. 9y9z when merging E_1 into the cluster D_1, OM_1, Y_1
+ if (thisAligned.isEmpty() && otherAligned.isEmpty()) {
+ logger.warn("No equivalent aligned atoms found between SubunitClusters {} via structure alignment. Will not merge the second one into the first.", pairName);
+ return false;
+ }
+
updateEquivResidues(other, thisAligned, otherAligned);
this.method = SubunitClustererMethod.STRUCTURE;
@@ -602,18 +603,12 @@ private void updateEquivResidues(SubunitCluster other, List thisAligned
Collections.sort(otherRemove);
Collections.reverse(otherRemove);
- for (int t = 0; t < thisRemove.size(); t++) {
- for (List eqr : this.subunitEQR) {
- int column = thisRemove.get(t);
- eqr.remove(column);
- }
+ for (int column : thisRemove) {
+ this.subunitEQR.forEach(eqr -> eqr.remove(column));
}
- for (int t = 0; t < otherRemove.size(); t++) {
- for (List eqr : other.subunitEQR) {
- int column = otherRemove.get(t);
- eqr.remove(column);
- }
+ for (int column : otherRemove) {
+ other.subunitEQR.forEach(eqr -> eqr.remove(column));
}
// The representative is the longest sequence
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
index 6295f8fdf0..fa63b96d96 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitClusterer.java
@@ -58,7 +58,7 @@ public static Stoichiometry cluster(Structure structure,
public static Stoichiometry cluster(List subunits, SubunitClustererParameters params) {
List clusters = new ArrayList<>();
- if (subunits.size() == 0)
+ if (subunits.isEmpty())
return new Stoichiometry(clusters);
// First generate a new cluster for each Subunit
@@ -83,8 +83,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara
}
} catch (CompoundNotFoundException e) {
- logger.warn("Could not merge by Sequence. {}",
- e.getMessage());
+ logger.info("Could not merge by Sequence. {}", e.getMessage());
}
}
}
@@ -100,7 +99,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara
clusters.remove(c2);
}
} catch (StructureException e) {
- logger.warn("Could not merge by Structure. {}", e.getMessage());
+ logger.info("Could not merge by Structure. {}", e.getMessage());
}
}
}
@@ -112,8 +111,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara
try {
clusters.get(c).divideInternally(params);
} catch (StructureException e) {
- logger.warn("Error analyzing internal symmetry. {}",
- e.getMessage());
+ logger.info("Error analyzing internal symmetry. {}", e.getMessage());
}
}
@@ -125,8 +123,7 @@ public static Stoichiometry cluster(List subunits, SubunitClustererPara
if (clusters.get(c1).mergeStructure(clusters.get(c2), params))
clusters.remove(c2);
} catch (StructureException e) {
- logger.warn("Could not merge by Structure. {}",
- e.getMessage());
+ logger.info("Could not merge by Structure. {}", e.getMessage());
}
}
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
index 8cfd032daa..5a6e69c4cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/MomentsOfInertia.java
@@ -72,7 +72,7 @@ public void addPoint(Point3d point, double mass) {
public Point3d getCenterOfMass() {
- if (points.size() == 0) {
+ if (points.isEmpty()) {
throw new IllegalStateException(
"MomentsOfInertia: no points defined");
}
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
index 176459bbf2..58e4ee6625 100644
--- 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
@@ -1970,7 +1970,7 @@ private Group getCorrectAltLocGroup( Character altLoc,
// build it up.
if ( groupCode3.equals(currentGroup.getPDBName())) {
- if ( currentGroup.getAtoms().size() == 0) {
+ if ( currentGroup.getAtoms().isEmpty()) {
//System.out.println("current group is empty " + current_group + " " + altLoc);
return currentGroup;
}
@@ -2762,7 +2762,7 @@ private void makeCompounds(List compoundList,
}
// System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
// since we're starting again from the first compound, reset it here
- if ( entities.size() == 0){
+ if ( entities.isEmpty()){
current_compound = new EntityInfo();
} else {
current_compound = entities.get(0);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
index 826d9588ef..7e9d8ad7ac 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
@@ -308,7 +308,12 @@ public void accept(WrappedAtom wrappedAtom) {
}
}
labelEntityId.add(entityId);
- labelSeqId.add(seqId);
+ // see https://github.com/biojava/biojava/issues/1116
+ if (chain.getEntityInfo().getType() == EntityType.POLYMER) {
+ labelSeqId.add(seqId);
+ } else {
+ labelSeqId.markNextNotPresent();
+ }
String insCode = "";
if (group.getResidueNumber().getInsCode() != null) {
insCode = Character.toString(group.getResidueNumber().getInsCode());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
index c610c05f2b..67514edd84 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -1161,7 +1161,7 @@ public void finish() {
currentModel.add(currentChain);
}
} else if (!params.isHeaderOnly()) {
- logger.warn("current chain is null at end of document.");
+ logger.warn("No chains were instantiated after parsing the whole CIF document. This could be due to the atom_site category being absent");
}
allModels.add(currentModel);
@@ -1297,17 +1297,21 @@ public void finish() {
SeqMisMatch seqMisMatch = new SeqMisMatchImpl();
seqMisMatch.setDetails(structRefSeqDif.getDetails().get(rowIndex));
- String insCode = structRefSeqDif.getPdbxPdbInsCode().get(rowIndex);
+ String insCode = null;
+ if (structRefSeqDif.getPdbxPdbInsCode().isDefined()) {
+ insCode = structRefSeqDif.getPdbxPdbInsCode().get(rowIndex);
if ("?".equals(insCode)) {
- insCode = null;
+ insCode = null;
+ }
}
seqMisMatch.setInsCode(insCode);
seqMisMatch.setOrigGroup(structRefSeqDif.getDbMonId().get(rowIndex));
seqMisMatch.setPdbGroup(structRefSeqDif.getMonId().get(rowIndex));
- seqMisMatch.setPdbResNum(structRefSeqDif.getPdbxAuthSeqNum().get(rowIndex));
- seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex));
+ seqMisMatch.setPdbResNum(structRefSeqDif.getPdbxAuthSeqNum().isDefined()? structRefSeqDif.getPdbxAuthSeqNum().get(rowIndex):null);
+ seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);
seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));
+ if (!structRefSeqDif.getPdbxPdbStrandId().isDefined()) continue;
String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);
List seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>());
seqMisMatches.add(seqMisMatch);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
index c2830c1685..21ef8bb64c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -396,7 +396,7 @@ private Group getCorrectAltLocGroup(Character altLoc) {
}
// no matching altLoc group found.
// build it up.
- if (group.getAtoms().size() == 0) {
+ if (group.getAtoms().isEmpty()) {
return group;
}
Group altLocG = (Group) group.clone();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 7c359121de..8f76b2ae61 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -55,7 +55,7 @@ public static boolean isUnaryExpression(String expression) {
if (first < 0 || last < 0) {
return true;
}
- return ! (first == 0 && last > first);
+ return first != 0 || last <= first;
}
public static List parseUnaryOperatorExpression(String operatorExpression) {
@@ -279,7 +279,7 @@ public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,
return centroid;
}
- if ( transformations.size() == 0) {
+ if ( transformations.isEmpty()) {
return Calc.getCentroid(atoms).getCoords();
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
index c6ec6bc8ff..9edb8f404c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -205,7 +205,7 @@ private void addChainMultiModel(Structure s, Chain newChain, String transformId)
// multi-model bioassembly
- if ( modelIndex.size() == 0)
+ if (modelIndex.isEmpty())
modelIndex.add("PLACEHOLDER FOR ASYM UNIT");
int modelCount = modelIndex.indexOf(transformId);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
index 7732c04b80..42191d682d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucTools.java
@@ -57,7 +57,7 @@ public static List getSecStrucInfo(Structure s) {
Group g = iter.next();
if (g.hasAminoAtoms()) {
Object p = g.getProperty(Group.SEC_STRUC);
- if (!(p == null)) {
+ if (p != null) {
SecStrucInfo ss = (SecStrucInfo) p;
listSSI.add(ss);
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
index ff9c77cf13..cd16aa5f87 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -64,7 +64,7 @@ public Map getInteractingRepeatUnits() {
private void run() {
this.repeatUnitCenters = calcRepeatUnitCenters();
- if (this.repeatUnitCenters.size() == 0) {
+ if (this.repeatUnitCenters.isEmpty()) {
return;
}
this.repeatUnits = calcRepeatUnits();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index 70b69afe14..1490d27036 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -98,7 +98,7 @@ public void complete() {
public String getPointGroup() {
if (modified) {
- if (rotations.size() == 0) {
+ if (rotations.isEmpty()) {
return "C1";
}
complete();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
index 37a44be7ac..b1566a6d2f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
@@ -305,7 +305,7 @@ private boolean isSpherical() {
* @return null if invalid, or a rotation if valid
*/
private Rotation isValidPermutation(List permutation) {
- if (permutation.size() == 0) {
+ if (permutation.isEmpty()) {
return null;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
index d13fa4db16..a449771b58 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
@@ -145,7 +145,7 @@ private void completeRotationGroup() {
}
private boolean isValidPermutation(List permutation) {
- if (permutation.size() == 0) {
+ if (permutation.isEmpty()) {
return false;
}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
index 2d9b1d6dca..25d37693fb 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/DistanceBox.java
@@ -166,7 +166,7 @@ private List getBoxTwo(long location) {
}
// ensure that boxTwo has no empty element by copying from tempBox of defined size
List boxTwo = null;
- if (tempBox.size() == 0) {
+ if (tempBox.isEmpty()) {
boxTwo = Collections.emptyList();
} else if (tempBox.size() == 1) {
boxTwo = Collections.singletonList(tempBox.get(0));
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
index cff84c70f8..852d213bb9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SpaceGroup.java
@@ -645,10 +645,10 @@ public List getTransfAlgebraic() {
public void setTransfAlgebraic(List transfAlgebraic) {
//System.out.println("setting transfAlgebraic " + transfAlgebraic);
- if ( transformations == null || transformations.size() == 0)
+ if ( transformations == null || transformations.isEmpty())
transformations = new ArrayList(transfAlgebraic.size());
- if ( this.transfAlgebraic == null || this.transfAlgebraic.size() == 0)
+ if ( this.transfAlgebraic == null || this.transfAlgebraic.isEmpty())
this.transfAlgebraic = new ArrayList<>(transfAlgebraic.size());
for ( String transf : transfAlgebraic){
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
index 8eee2ee49d..88f901cdea 100644
--- a/biojava-survival/pom.xml
+++ b/biojava-survival/pom.xml
@@ -4,7 +4,7 @@
org.biojava
biojava
- 7.2.0
+ 7.2.5-SNAPSHOT
biojava-survival
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
index c4578f1c8b..144942a809 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
@@ -76,7 +76,7 @@ private void paintTable(Graphics g) {
sfiHashMap = sfi.getStrataInfoHashMap();
}
- if(sfiHashMap.size() == 0)
+ if(sfiHashMap.isEmpty())
return;
//int height = this.getHeight();
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
index a242020712..7e960b4445 100644
--- a/biojava-ws/pom.xml
+++ b/biojava-ws/pom.xml
@@ -3,7 +3,7 @@
biojava
org.biojava
- 7.2.0
+ 7.2.5-SNAPSHOT
biojava-ws
biojava-ws
@@ -19,7 +19,7 @@
org.biojava
biojava-core
- 7.2.0
+ 7.2.5-SNAPSHOT
compile
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
index 3304e78d4f..373b78cd0a 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java
@@ -140,7 +140,7 @@ public int compareTo(HmmerResult o) {
return(me.getSqFrom().compareTo(other.getSqFrom()));
}
private boolean emptyDomains(HmmerResult o) {
- if ( o.getDomains() == null || o.getDomains().size() == 0)
+ if ( o.getDomains() == null || o.getDomains().isEmpty())
return true;
return false;
}
diff --git a/pom.xml b/pom.xml
index 84774f7281..e9f246202b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
org.biojava
biojava
pom
- 7.2.0
+ 7.2.5-SNAPSHOT
biojava
BioJava is an open-source project dedicated to providing a Java framework for processing biological
data. It provides analytical and statistical routines, parsers for common file formats and allows the
@@ -44,14 +44,14 @@
2.23.1
5.10.1
ciftools-java
- 5.0.1
+ 7.0.1
scm:git:git://github.com/biojava/biojava.git
scm:git:git@github.com:biojava/biojava.git
https://github.com/biojava/biojava
- biojava-7.2.0
+ HEAD
-
+
- org.sonatype.plugins
- nexus-staging-maven-plugin
- 1.6.13
+ org.sonatype.central
+ central-publishing-maven-plugin
+ 0.8.0
true
- ossrh
- https://oss.sonatype.org/
- true
+
+ central
+
+
+ true
+
+ published
-[](https://github.com/biojava/biojava/releases/tag/biojava-7.1.4) [](https://github.com/biojava/biojava/blob/master/LICENSE) [](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+[](https://github.com/biojava/biojava/releases/tag/biojava-7.2.4) [](https://github.com/biojava/biojava/blob/master/LICENSE) [](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
BioJava is an open-source project dedicated to providing a Java framework for **processing biological data**. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -29,7 +29,7 @@ If you are using Maven you can add the BioJava repository by adding the followin