/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
}
/**
+ *
+ * @param column
+ * @return position in sequence for column (or -1 if no match state exists)
+ */
+ public int findPosition(int column)
+ {
+ int w = 0, ew, p = refseq.findPosition(start);
+ if (column < 0)
+ {
+ return -1;
+ }
+ if (range != null)
+ {
+ for (int i = 0; i < length; i++)
+ {
+ if (operation[i] == M || operation[i] == D)
+ {
+ p += range[i];
+ }
+ if (operation[i] == M || operation[i] == I)
+ {
+ ew = w + range[i];
+ if (column < ew)
+ {
+ if (operation[i] == I)
+ {
+ return -1;
+ }
+ return p - (ew - column);
+ }
+ w = ew;
+ }
+ }
+ }
+ return -1;
+ }
+
+ /**
* Returns sequence as a string with cigar operations applied to it
*
* @return String
*/
+ @Override
public String getSequenceString(char GapChar)
{
- return (length == 0) ? "" : (String) getSequenceAndDeletions(
- refseq.getSequenceAsString(start, end), GapChar)[0];
+ return (length == 0) ? ""
+ : (String) getSequenceAndDeletions(
+ refseq.getSequenceAsString(start, end), GapChar)[0];
}
/**
refseq.getSequenceAsString(start, end), GapChar);
if (edit_result == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
}
int bounds[] = (int[]) edit_result[1];
seq = new Sequence(refseq.getName(), (String) edit_result[0],
- refseq.getStart() + start + bounds[0], refseq.getStart()
- + start + ((bounds[2] == 0) ? -1 : bounds[2]));
+ refseq.getStart() + start + bounds[0], refseq.getStart() + start
+ + ((bounds[2] == 0) ? -1 : bounds[2]));
seq.setDescription(refseq.getDescription());
int sstart = seq.getStart(), send = seq.getEnd();
// seq.checkValidRange(); probably not needed
boolean hasgaps = false;
if (seq == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_set_seq_null"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_set_seq_null"));
}
if (_s < 0)
{
- throw new Error(MessageManager.formatMessage(
- "error.implementation_error_s", new String[] { Integer
- .valueOf(_s).toString() }));
+ throw new Error(MessageManager
+ .formatMessage("error.implementation_error_s", new String[]
+ { Integer.valueOf(_s).toString() }));
}
String seq_string = seq.getSequenceAsString();
if (_e == 0 || _e < _s || _e > seq_string.length())
// Check offsets
if (end > ds.getLength())
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_seqcigar_possible"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_seqcigar_possible"));
// end = ds.getLength();
}
}
if (operation.length != range.length)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_bug_cigar_operation_list_range_list"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_bug_cigar_operation_list_range_list"));
}
if (operation != null)
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(
- MessageManager
- .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+ throw new Error(MessageManager.getString(
+ "error.not_yet_implemented_cigar_object_from_cigar_string"));
}
for (int i = this.length, j = 0; j < operation.length; i++, j++)
{
if (op != M && op != I && op != D)
{
throw new Error(MessageManager.formatMessage(
- "error.implementation_bug_cigar_operation", new String[] {
- Integer.valueOf(j).toString(),
+ "error.implementation_bug_cigar_operation", new String[]
+ { Integer.valueOf(j).toString(),
Integer.valueOf(op).toString(),
Integer.valueOf(M).toString(),
Integer.valueOf(I).toString(),
this.length = 0;
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(
- MessageManager
- .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
+ throw new Error(MessageManager.getString(
+ "error.not_yet_implemented_cigar_object_from_cigar_string"));
}
}
}
while (p <= endpos)
{
- boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
- .getCharAt(p)) : true;
+ boolean isGap = (p < res)
+ ? jalview.util.Comparison.isGap(seq.getCharAt(p))
+ : true;
if ((startpos <= p) && (p <= endpos))
{
if (isGap)
super();
if (seq == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_for_new_cigar"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, 0, 0);
// there is still work to do
super();
if (seq == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_for_new_cigar"));
+ throw new Error(MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, start, end + 1);
// there is still work to do
/**
* create an alignment from the given array of cigar sequences and gap
* character, and marking the given segments as visible in the given
- * columselection.
+ * hiddenColumns.
*
* @param alseqs
* @param gapCharacter
- * @param colsel
- * - columnSelection where hidden regions are marked
+ * @param hidden
+ * - hiddenColumns where hidden regions are marked
* @param segments
* - visible regions of alignment
* @return SequenceI[]
*/
public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
- char gapCharacter, ColumnSelection colsel, int[] segments)
+ char gapCharacter, HiddenColumns hidden, int[] segments)
{
SequenceI[] seqs = new SequenceI[alseqs.length];
StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
Object[] gs_regions = new Object[alseqs.length];
for (int i = 0; i < alseqs.length; i++)
{
- alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
- alseqs[i].start, alseqs[i].end);
+ alseqs_string[i] = alseqs[i].getRefSeq()
+ .getSequenceAsString(alseqs[i].start, alseqs[i].end);
gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
gapCharacter); // gapped sequence, {start, start col, end.
// endcol}, hidden regions {{start, end, col}})
{
throw new Error(MessageManager.formatMessage(
"error.implementation_error_cigar_seq_no_operations",
- new String[] { Integer.valueOf(i).toString() }));
+ new String[]
+ { Integer.valueOf(i).toString() }));
}
g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
// visible
if (segments == null)
{
// add a hidden column for this deletion
- colsel.hideColumns(inspos, inspos + insert.length - 1);
+ hidden.hideColumns(inspos, inspos + insert.length - 1);
}
}
}
int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
SequenceI ref = alseqs[i].getRefSeq();
seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
- ref.getStart() + alseqs[i].start + bounds[0], ref.getStart()
- + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
+ ref.getStart() + alseqs[i].start + bounds[0],
+ ref.getStart() + alseqs[i].start
+ + (bounds[2] == 0 ? -1 : bounds[2]));
seqs[i].setDatasetSequence(ref);
seqs[i].setDescription(ref.getDescription());
+ SeqsetUtils.SeqCharacterUnhash(seqs[i],alseqs[i].seqProps);
}
if (segments != null)
{
{
// int start=shifts.shift(segments[i]-1)+1;
// int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
- colsel.hideColumns(segments[i + 1], segments[i + 1]
- + segments[i + 2] - 1);
+ hidden.hideColumns(segments[i + 1],
+ segments[i + 1] + segments[i + 2] - 1);
}
}
return seqs;
git://source.jalview.org / jalview.git / blobdiff