/*
* (non-Javadoc)
- *
+ *
* @see jalview.io.vamsas.DatastoreItem#addFromDocument()
*/
@Override
/*
* (non-Javadoc)
- *
+ *
* @see jalview.io.vamsas.DatastoreItem#conflict()
*/
@Override
/*
* (non-Javadoc)
- *
+ *
* @see jalview.io.vamsas.DatastoreItem#update()
*/
@Override
/*
* (non-Javadoc)
- *
+ *
* @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
*/
@Override
// TODO: Tree.updateFromDoc
/*
* TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
- *
+ *
* // make a new tree Object[] idata =
* recoverInputData(tree.getProvenance()); try { if (idata != null &&
* idata[0] != null) { inputData = (AlignmentView) idata[0]; } ntree =
/**
* correctly creates provenance for trees calculated on an alignment by
* jalview.
- *
+ *
* @param jal
* @param tp
* @return
/**
* look up SeqCigars in an existing alignment.
- *
+ *
* @param jal
* @param sequences
* @return vector of alignment sequences in order of SeqCigar array (but
System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
Vector alsq = new Vector();
List<SequenceI> jalsqs;
- synchronized (jalsqs=jal.getSequences())
- {for (SequenceI asq:jalsqs)
+ synchronized (jalsqs = jal.getSequences())
{
- for (int t = 0; t < sequences.length; t++)
+ for (SequenceI asq : jalsqs)
{
- if (tseqs[t] != null
- && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
- .getDatasetSequence()))
- // && tseqs[t].getStart()>=asq.getStart() &&
- // tseqs[t].getEnd()<=asq.getEnd())
+ for (int t = 0; t < sequences.length; t++)
{
- tseqs[t] = null;
- alsq.add(asq);
+ if (tseqs[t] != null
+ && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
+ .getDatasetSequence()))
+ // && tseqs[t].getStart()>=asq.getStart() &&
+ // tseqs[t].getEnd()<=asq.getEnd())
+ {
+ tseqs[t] = null;
+ alsq.add(asq);
+ }
}
}
- }}
+ }
if (alsq.size() < sequences.length)
Cache.log
.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
}
/**
- *
+ *
* Update jalview newick representation with TreeNode map
- *
+ *
* @param tp
* the treepanel that this tree is bound to.
*/
// / TODO: refactor to vamsas :start
/**
* construct treenode mappings for mapped sequences
- *
+ *
* @param ntree
* @param newick
* @return
/**
* call to match up Treenode specs to NJTree parsed from document object.
- *
+ *
* @param nodespec
* @param leaves
* as returned from NJTree.findLeaves( .., ..) ..
// todo: end refactor to vamsas library
/**
* add jalview object to vamsas document
- *
+ *
*/
@Override
public void addToDocument()
/**
* note: this function assumes that all sequence and alignment objects
* referenced in input data has already been associated with jalview objects.
- *
+ *
* @param tp
* @param alignFrame
* @return Object[] { AlignmentView, AlignmentI - reference alignment for