/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.io.vamsas;
/*
* (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