X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2FAlignment.html;fp=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2FAlignment.html;h=c8137d3928b1dffe4aaaed2fd015f331147584e6;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/dm_javadoc/compbio/data/sequence/Alignment.html b/website/dm_javadoc/compbio/data/sequence/Alignment.html new file mode 100644 index 0000000..c8137d3 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Alignment.html @@ -0,0 +1,403 @@ + + + + + + +Alignment + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class Alignment

+
+java.lang.Object
+  extended by compbio.data.sequence.Alignment
+
+
+
+
@Immutable
+public final class Alignment
extends java.lang.Object
+ + +

+Multiple sequence alignment. + + Does not give any guarantees on the content of individual FastaSequece + records. It does not guarantee neither the uniqueness of the names of + sequences nor it guarantees the uniqueness of the sequences. +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
See Also:
FastaSequence, +AlignmentMetadata
+
+ +

+ + + + + + + + + + + + + + +
+Constructor Summary
Alignment(java.util.List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
Alignment(java.util.List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(java.lang.Object obj) + +
+          Please note that this implementation does not take the order of sequences + into account!
+ AlignmentMetadatagetMetadata() + +
+           
+ java.util.List<FastaSequence>getSequences() + +
+           
+ intgetSize() + +
+           
+ inthashCode() + +
+           
+ java.lang.StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Alignment

+
+public Alignment(java.util.List<FastaSequence> sequences,
+                 Program program,
+                 char gapchar)
+
+
+
Parameters:
sequences -
program -
gapchar -
+
+
+ +

+Alignment

+
+public Alignment(java.util.List<FastaSequence> sequences,
+                 AlignmentMetadata metadata)
+
+
+
Parameters:
sequences -
metadata -
+
+ + + + + + + + +
+Method Detail
+ +

+getSequences

+
+public java.util.List<FastaSequence> getSequences()
+
+
+ +
Returns:
list of FastaSequence records
+
+
+
+ +

+getSize

+
+public int getSize()
+
+
+ +
Returns:
a number of sequence in the alignment
+
+
+
+ +

+getMetadata

+
+public AlignmentMetadata getMetadata()
+
+
+ +
Returns:
AlignmentMetadata object
+
+
+
+ +

+toString

+
+public java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(java.lang.Object obj)
+
+
Please note that this implementation does not take the order of sequences + into account! +

+

+
Overrides:
equals in class java.lang.Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + +