public class SAMSequenceDictionary
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Field and Description |
---|---|
static java.util.List<java.lang.String> |
DEFAULT_DICTIONARY_EQUAL_TAG |
static long |
serialVersionUID |
Constructor and Description |
---|
SAMSequenceDictionary() |
SAMSequenceDictionary(java.util.List<SAMSequenceRecord> list) |
Modifier and Type | Method and Description |
---|---|
void |
addSequence(SAMSequenceRecord sequenceRecord) |
SAMSequenceRecord |
addSequenceAlias(java.lang.String originalName,
java.lang.String altName)
Add an alias to a SAMSequenceRecord.
|
void |
assertSameDictionary(SAMSequenceDictionary that)
Non-comprehensive
equals(Object) -assertion: instead of calling SAMSequenceRecord.equals(Object) on constituent
SAMSequenceRecord s in this dictionary against its pair in the target dictionary, in order, call
SAMSequenceRecord.isSameSequence(SAMSequenceRecord) . |
boolean |
equals(java.lang.Object o)
returns true if the two dictionaries are the same, aliases are NOT considered
|
long |
getReferenceLength() |
SAMSequenceRecord |
getSequence(int sequenceIndex) |
SAMSequenceRecord |
getSequence(java.lang.String name) |
int |
getSequenceIndex(java.lang.String sequenceName) |
java.util.List<SAMSequenceRecord> |
getSequences() |
int |
hashCode() |
boolean |
isEmpty() |
boolean |
isSameDictionary(SAMSequenceDictionary that)
Non-comprehensive
equals(Object) -validation: instead of calling SAMSequenceRecord.equals(Object) on constituent
SAMSequenceRecord s in this dictionary against its pair in the target dictionary, in order, call
SAMSequenceRecord.isSameSequence(SAMSequenceRecord) . |
java.lang.String |
md5()
return a MD5 sum for ths dictionary, the checksum is re-computed each
time this method is called.
|
static SAMSequenceDictionary |
mergeDictionaries(SAMSequenceDictionary dict1,
SAMSequenceDictionary dict2,
java.util.List<java.lang.String> tagsToMatch)
Will merge dictionaryTags from two dictionaries into one focusing on merging the tags rather than the sequences.
|
void |
setSequences(java.util.List<SAMSequenceRecord> list)
Replaces the existing list of SAMSequenceRecords with the given list.
|
int |
size() |
java.lang.String |
toString() |
public static final long serialVersionUID
public static final java.util.List<java.lang.String> DEFAULT_DICTIONARY_EQUAL_TAG
public SAMSequenceDictionary()
public SAMSequenceDictionary(java.util.List<SAMSequenceRecord> list)
public java.util.List<SAMSequenceRecord> getSequences()
public SAMSequenceRecord getSequence(java.lang.String name)
public void setSequences(java.util.List<SAMSequenceRecord> list)
list
- This value is used directly, rather than being copied.public void addSequence(SAMSequenceRecord sequenceRecord)
public SAMSequenceRecord getSequence(int sequenceIndex)
public int getSequenceIndex(java.lang.String sequenceName)
public int size()
public long getReferenceLength()
public boolean isEmpty()
public void assertSameDictionary(SAMSequenceDictionary that)
equals(Object)
-assertion: instead of calling SAMSequenceRecord.equals(Object)
on constituent
SAMSequenceRecord
s in this dictionary against its pair in the target dictionary, in order, call
SAMSequenceRecord.isSameSequence(SAMSequenceRecord)
.
Aliases are ignored.java.lang.AssertionError
- When the dictionaries are not the same, with some human-readable information as to whypublic boolean isSameDictionary(SAMSequenceDictionary that)
equals(Object)
-validation: instead of calling SAMSequenceRecord.equals(Object)
on constituent
SAMSequenceRecord
s in this dictionary against its pair in the target dictionary, in order, call
SAMSequenceRecord.isSameSequence(SAMSequenceRecord)
.that
- SAMSequenceDictionary
to compare againstpublic boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public SAMSequenceRecord addSequenceAlias(java.lang.String originalName, java.lang.String altName)
1,chr1,chr01,01,CM000663,NC_000001.10
e.g:
MT,chrM
originalName
- existing contig namealtName
- new contig namepublic java.lang.String md5()
md5( (seq1.md5_if_available) + ' '+(seq2.name+seq2.length) + ' '+...)
public int hashCode()
hashCode
in class java.lang.Object
public java.lang.String toString()
toString
in class java.lang.Object
public static SAMSequenceDictionary mergeDictionaries(SAMSequenceDictionary dict1, SAMSequenceDictionary dict2, java.util.List<java.lang.String> tagsToMatch)
dict1
- first dictionarydict2
- first dictionarytagsToMatch
- list of tags that must be equal if present in both sequence. Must contain MD, and LN