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Add freeze methods to oboformat Clause and Frame. These methods
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(a) replace ArrayLists of size 0 with emptyList()
(b) replace ArrayLists of size 1 with singletonList()
(c) call trimToSize on ArrayLists of size >1.
Modifications automatically the relevant objects.

Add freezeFrames method to OBODoc, which will call freeze on all held frames.
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sesuncedu committed Aug 8, 2015
1 parent 113b626 commit 4b253bb
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Showing 3 changed files with 187 additions and 15 deletions.
147 changes: 134 additions & 13 deletions oboformat/src/main/java/org/obolibrary/oboformat/model/Clause.java
Original file line number Diff line number Diff line change
Expand Up @@ -2,23 +2,22 @@

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;

import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;

/** Clause */
public class Clause {

protected String tag;
@Nonnull
protected final List<Object> values = new ArrayList<>();
protected List<Object> values = new ArrayList<>();
@Nonnull
protected final Collection<Xref> xrefs = new ArrayList<>();
protected Collection<Xref> xrefs = new ArrayList<>();
@Nonnull
protected final Collection<QualifierValue> qualifierValues = new ArrayList<>();
protected Collection<QualifierValue> qualifierValues = new ArrayList<>();

/**
* @param tag
Expand Down Expand Up @@ -66,6 +65,64 @@ public Clause(@Nonnull OboFormatTag tag, String value) {
@Deprecated
public Clause() {}

/**
* freezing a clause signals that the clause has become quiescent, and that data structures can be adjusted to
* increase performance, or reduce memory consumption.
*/
void freeze() {
freezeValues();
freezeXrefs();
freezeQualifiers();
}

void freezeValues() {
switch (values.size()) {
case 0:
values = Collections.emptyList();
break;
case 1:
Object o = values.iterator().next();
values = Collections.singletonList(o);
break;
default:
((ArrayList) values).trimToSize();
}
}

void freezeXrefs() {
switch (xrefs.size()) {
case 0:
xrefs = Collections.emptyList();
break;
case 1:
Xref xref = xrefs.iterator().next();
xrefs = Collections.singletonList(xref);
break;
default:
if (values instanceof ArrayList) {
((ArrayList) values).trimToSize();
}
}
}

void freezeQualifiers() {
switch (qualifierValues.size()) {
case 0:
qualifierValues = Collections.emptyList();
break;
case 1:
QualifierValue qualifierValue = qualifierValues.iterator().next();
qualifierValues = Collections.singletonList(qualifierValue);
break;
default:
if (qualifierValues instanceof ArrayList) {
((ArrayList) qualifierValues).trimToSize();
}
}
}



/**
* @return tag
*/
Expand Down Expand Up @@ -94,24 +151,47 @@ public Collection<Object> getValues() {
* values
*/
public void setValues(@Nonnull Collection<Object> values) {
this.values.clear();
this.values.addAll(values);
if (!(this.values instanceof ArrayList)) {
switch (values.size()) {
case 0:
this.values = Collections.emptyList();
break;
case 1:
Object o = values.iterator().next();
this.values = Collections.singletonList(o);
break;
default:
this.values = new ArrayList<>(values);
}
} else {
this.values.clear();
this.values.addAll(values);
}
}

/**
* @param v
* v
*/
public void setValue(Object v) {
values.clear();
values.add(v);
if(values instanceof ArrayList) {
values.clear(); // TODO: Remove this line after profile gathering
values.add(v);
} else {
this.values = Collections.singletonList(v);
}
}

/**
* @param v
* v
*/
public void addValue(Object v) {
if (!(this.values instanceof ArrayList)) {
List<Object> newValues = new ArrayList<>(values.size() + 1);
newValues.addAll(this.values);
this.values = newValues;
}
values.add(v);
}

Expand Down Expand Up @@ -184,15 +264,34 @@ public Collection<Xref> getXrefs() {
* xrefs
*/
public void setXrefs(@Nonnull Collection<Xref> xrefs) {
this.xrefs.clear();
this.xrefs.addAll(xrefs);
if (!(this.xrefs instanceof ArrayList)) {
switch (xrefs.size()) {
case 0:
this.xrefs = Collections.emptyList();
break;
case 1:
Xref xref = xrefs.iterator().next();
this.xrefs = Collections.singletonList(xref);
break;
default:
this.xrefs = new ArrayList<>(xrefs);
}
} else {
this.xrefs.clear();
this.xrefs.addAll(xrefs);
}
}

/**
* @param xref
* xref
*/
public void addXref(Xref xref) {
if (!(xrefs instanceof ArrayList)) {
List<Xref> newXrefs = new ArrayList<>(xrefs.size() + 1);
newXrefs.addAll(xrefs);
this.xrefs = newXrefs;
}
xrefs.add(xref);
}

Expand All @@ -209,15 +308,36 @@ public Collection<QualifierValue> getQualifierValues() {
* qualifierValues
*/
public void setQualifierValues(@Nonnull Collection<QualifierValue> qualifierValues) {
this.qualifierValues.clear();
this.qualifierValues.addAll(qualifierValues);
if (!(this.qualifierValues instanceof ArrayList)) {
switch (qualifierValues.size()) {
case 0:
this.qualifierValues = Collections.emptyList();
break;
case 1:
QualifierValue qualifierValue = qualifierValues.iterator().next();
this.qualifierValues = Collections.singletonList(qualifierValue);
break;
default:
this.qualifierValues = new ArrayList<>(qualifierValues);
}
} else {
this.qualifierValues.clear();
this.qualifierValues.addAll(qualifierValues);
}
}


/**
* @param qv
* qv
*/
public void addQualifierValue(QualifierValue qv) {
if (!(qualifierValues instanceof ArrayList)) {
List<QualifierValue> newQualifierValues = new ArrayList<>(qualifierValues.size() + 1);
newQualifierValues.addAll(qualifierValues);
this.qualifierValues = newQualifierValues;
}

qualifierValues.add(qv);
}

Expand Down Expand Up @@ -327,4 +447,5 @@ public boolean equals(Object obj) {
*/
return collectionsEquals(qualifierValues, other.getQualifierValues());
}

}
33 changes: 31 additions & 2 deletions oboformat/src/main/java/org/obolibrary/oboformat/model/Frame.java
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,11 @@

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;

import javax.annotation.Nonnull;
import javax.annotation.Nullable;

import org.obolibrary.obo2owl.OboInOwlCardinalityTools;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;

Expand Down Expand Up @@ -52,6 +51,33 @@ protected final void init() {
clauses = new ArrayList<>();
}

/**
* freezing a frame signals that a frame has become quiescent, and that data structures can be adjusted to
* increase performance or reduce memory consumption. If a frozen frame is subsequently modified it will be thawed
* as necessary.
*/
public void freeze() {
if (clauses.isEmpty()) {
clauses = Collections.emptyList();
return;
}

for (Clause clause : clauses) {
clause.freeze();
}

if (clauses.size() == 1) {
clauses = Collections.singletonList(clauses.iterator().next());
return;
}

if (clauses instanceof ArrayList<?>) {
ArrayList<?> arrayList = (ArrayList<?>) clauses;
arrayList.trimToSize();
}

}

/**
* @return the type
*/
Expand Down Expand Up @@ -154,6 +180,9 @@ public void setClauses(Collection<Clause> clauses) {
* the clause
*/
public void addClause(Clause cl) {
if (!(clauses instanceof ArrayList)) {
clauses = new ArrayList<>(clauses.size()+1);
}
clauses.add(cl);
}

Expand Down
22 changes: 22 additions & 0 deletions oboformat/src/main/java/org/obolibrary/oboformat/model/OBODoc.java
Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,28 @@ public Collection<Frame> getInstanceFrames() {
return instanceFrameMap.values();
}

/**
* Freezing an OBODoc signals that the document has become quiescent, and that the system may optimize data
* structures for performance or space.
*/

public void freezeFrames() {
headerFrame.freeze();
freezeFrameMap(termFrameMap);
freezeFrameMap(typedefFrameMap);
freezeFrameMap(instanceFrameMap);
for (Frame frame : annotationFrames) {
frame.freeze();
}

}

private static void freezeFrameMap(Map<String, Frame> frameMap) {
for (Frame frame : frameMap.values()) {
frame.freeze();
}
}

/**
* @param id
* the id
Expand Down

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