/**
* Gets background color for cell for row ic. Override it if you want to change the color from the
* default.
*/
public Color getBackgroundColorOfCell(int it, boolean selected) {
if (observedStates == null) {
doCalcs();
if (observedStates == null) return null;
}
if (observedStates.getParentData() != null) {
captureCharacterDataFromObservedStates();
Associable tInfo = data.getTaxaInfo(false);
NameReference genBankColor = NameReference.getNameReference("genbankcolor");
Object obj = tInfo.getAssociatedObject(genBankColor, it); // not saved to file
if (obj instanceof Color) return (Color) obj;
}
if (bits == null || it < 0 || it > bits.getSize()) return null;
String note = getNote(it);
if (selected) {
if (bits.isBitOn(it)) return ColorDistribution.darkGreen;
else return ColorDistribution.darkRed;
} else if (bits.isBitOn(it)) {
if (StringUtil.blank(note)) return ColorDistribution.veryLightGreen;
if (!(note.equalsIgnoreCase("x"))) return ColorDistribution.lightGreenYellowish;
return ColorDistribution.lightGreenYellow;
} else {
if (StringUtil.blank(note)) return ColorDistribution.brown;
if (!(note.equalsIgnoreCase("x"))) {
return Color.red;
}
return ColorDistribution.lightRed;
}
}
public String getStringForTaxon(int it) {
String note = getNote(it);
if (note != null) return note;
if (observedStates == null) doCalcs();
if (bits == null || it < 0 || it > bits.getSize()) return "?";
if (bits.isBitOn(it)) return "Yes";
else return "No Data";
}
public void readFrom(DataInput in) throws Exception {
status = in.readInt();
classname = Bits.readString(in);
name = Bits.readString(in);
start_time = in.readLong();
stop_time = in.readLong();
failure_type = Bits.readString(in);
failure_msg = Bits.readString(in);
stack_trace = Bits.readString(in);
}
public void writeTo(DataOutput out) throws Exception {
out.writeInt(status);
Bits.writeString(classname, out);
Bits.writeString(name, out);
out.writeLong(start_time);
out.writeLong(stop_time);
Bits.writeString(failure_type, out);
Bits.writeString(failure_msg, out);
Bits.writeString(stack_trace, out);
}
public void readFrom(DataInput in) throws Exception {
type = in.readByte();
switch (type) {
case DATA:
seqno = Bits.readLong(in);
conn_id = in.readShort();
first = in.readBoolean();
break;
case ACK:
seqno = Bits.readLong(in);
conn_id = in.readShort();
break;
case SEND_FIRST_SEQNO:
seqno = Bits.readLong(in);
break;
}
}
public void writeTo(DataOutput out) throws Exception {
out.writeByte(type);
switch (type) {
case DATA:
Bits.writeLong(seqno, out);
out.writeShort(conn_id);
out.writeBoolean(first);
break;
case ACK:
Bits.writeLong(seqno, out);
out.writeShort(conn_id);
break;
case SEND_FIRST_SEQNO:
Bits.writeLong(seqno, out);
break;
}
}
public final int size() {
int retval = Global.BYTE_SIZE; // type
switch (type) {
case DATA:
retval +=
Bits.size(seqno) // seqno
+ Global.SHORT_SIZE // conn_id
+ Global.BYTE_SIZE; // first
break;
case ACK:
retval += Bits.size(seqno) + Global.SHORT_SIZE; // conn_id
break;
case SEND_FIRST_SEQNO:
retval += Bits.size(seqno);
break;
}
return retval;
}
public void doCalcs() {
if (bits != null) bits.clearAllBits();
if (taxa == null) return;
if (bits == null) bits = new Bits(taxa.getNumTaxa());
else bits.resetSize(taxa.getNumTaxa());
if (observedStates == null) {
tInfo = null;
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
if (observedStates != null) {
captureCharacterDataFromObservedStates();
if (data != null) tInfo = data.getTaxaInfo(true);
}
}
if (observedStates == null) return;
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it)) bits.setBit(it);
}
}
public int getElementType() {
return Bits.maskBits(getLayoutHelper() >> LH_ELEMENT_TYPE_SHIFT, 0xFF);
}
public int getLog2ElementSize() {
return Bits.maskBits(getLayoutHelper() >> LH_LOG2_ELEMENT_SIZE_SHIFT, 0xFF);
}
public long getArrayHeaderInBytes() {
return Bits.maskBits(getLayoutHelper() >> LH_HEADER_SIZE_SHIFT, 0xFF);
}
public void testRandom() throws Exception {
int num = atLeast(2);
for (int iter = 0; iter < num; iter++) {
if (VERBOSE) {
System.out.println("TEST: iter=" + iter);
}
Directory dir = newDirectory();
IndexWriter w =
new IndexWriter(
dir,
newIndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer(random()))
.setMergePolicy(NoMergePolicy.COMPOUND_FILES));
_TestUtil.keepFullyDeletedSegments(w);
Map<BytesRef, List<Integer>> docs = new HashMap<BytesRef, List<Integer>>();
Set<Integer> deleted = new HashSet<Integer>();
List<BytesRef> terms = new ArrayList<BytesRef>();
int numDocs = _TestUtil.nextInt(random(), 1, 100 * RANDOM_MULTIPLIER);
Document doc = new Document();
Field f = newStringField("field", "", Field.Store.NO);
doc.add(f);
Field id = newStringField("id", "", Field.Store.NO);
doc.add(id);
boolean onlyUniqueTerms = random().nextBoolean();
if (VERBOSE) {
System.out.println("TEST: onlyUniqueTerms=" + onlyUniqueTerms + " numDocs=" + numDocs);
}
Set<BytesRef> uniqueTerms = new HashSet<BytesRef>();
for (int i = 0; i < numDocs; i++) {
if (!onlyUniqueTerms && random().nextBoolean() && terms.size() > 0) {
// re-use existing term
BytesRef term = terms.get(random().nextInt(terms.size()));
docs.get(term).add(i);
f.setStringValue(term.utf8ToString());
} else {
String s = _TestUtil.randomUnicodeString(random(), 10);
BytesRef term = new BytesRef(s);
if (!docs.containsKey(term)) {
docs.put(term, new ArrayList<Integer>());
}
docs.get(term).add(i);
terms.add(term);
uniqueTerms.add(term);
f.setStringValue(s);
}
id.setStringValue("" + i);
w.addDocument(doc);
if (random().nextInt(4) == 1) {
w.commit();
}
if (i > 0 && random().nextInt(20) == 1) {
int delID = random().nextInt(i);
deleted.add(delID);
w.deleteDocuments(new Term("id", "" + delID));
if (VERBOSE) {
System.out.println("TEST: delete " + delID);
}
}
}
if (VERBOSE) {
List<BytesRef> termsList = new ArrayList<BytesRef>(uniqueTerms);
Collections.sort(termsList, BytesRef.getUTF8SortedAsUTF16Comparator());
System.out.println("TEST: terms in UTF16 order:");
for (BytesRef b : termsList) {
System.out.println(" " + UnicodeUtil.toHexString(b.utf8ToString()) + " " + b);
for (int docID : docs.get(b)) {
if (deleted.contains(docID)) {
System.out.println(" " + docID + " (deleted)");
} else {
System.out.println(" " + docID);
}
}
}
}
IndexReader reader = w.getReader();
w.close();
if (VERBOSE) {
System.out.println("TEST: reader=" + reader);
}
Bits liveDocs = MultiFields.getLiveDocs(reader);
for (int delDoc : deleted) {
assertFalse(liveDocs.get(delDoc));
}
for (int i = 0; i < 100; i++) {
BytesRef term = terms.get(random().nextInt(terms.size()));
if (VERBOSE) {
System.out.println(
"TEST: seek term=" + UnicodeUtil.toHexString(term.utf8ToString()) + " " + term);
}
DocsEnum docsEnum = _TestUtil.docs(random(), reader, "field", term, liveDocs, null, 0);
assertNotNull(docsEnum);
for (int docID : docs.get(term)) {
if (!deleted.contains(docID)) {
assertEquals(docID, docsEnum.nextDoc());
}
}
assertEquals(DocIdSetIterator.NO_MORE_DOCS, docsEnum.nextDoc());
}
reader.close();
dir.close();
}
}