/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * Jalview is free software: you can redistribute it and/or
+ * 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.datamodel;
+import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.Vector;
import jalview.analysis.*;
import jalview.util.*;
*/
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];
}
/**
{
return null;
}
- Object[] edit_result = getSequenceAndDeletions(refseq
- .getSequenceAsString(start, end), GapChar);
+ Object[] edit_result = getSequenceAndDeletions(
+ refseq.getSequenceAsString(start, end), GapChar);
if (edit_result == null)
{
throw new Error(
"Implementation Error - unexpected null from getSequenceAndDeletions");
}
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]));
+ seq = new Sequence(refseq.getName(), (String) edit_result[0],
+ 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
* prepends any 'D' operations needed to get to the first residue of seq.
*
* @param seq
- * SequenceI
+ * SequenceI
* @param initialDeletion
- * true to mark initial dataset sequence residues as deleted in
- * subsequence
+ * true to mark initial dataset sequence residues as deleted in
+ * subsequence
* @param _s
- * index of first position in seq
+ * index of first position in seq
* @param _e
- * index after last position in (possibly gapped) seq
+ * index after last position in (possibly gapped) seq
* @return true if gaps are present in seq
*/
private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
}
else
{
- ds = new Sequence(seq.getName(), ungapped, seq.getStart(), seq
- .getStart()
- + ungapped.length() - 1);
+ ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
+ seq.getStart() + ungapped.length() - 1);
// JBPNote: this would be consistent but may not be useful
// seq.setDatasetSequence(ds);
}
* to the seq.getStart()'th residue of the dataset seq resolved from seq.
*
* @param seq
- * SequenceI
+ * SequenceI
* @param operation
- * char[]
+ * char[]
* @param range
- * int[]
+ * int[]
*/
public SeqCigar(SequenceI seq, char operation[], int range[])
{
* add range matched residues to cigar string
*
* @param range
- * int
+ * int
*/
public void addMatch(int range)
{
* endpos column of seq.
*
* @param cigar
- * CigarBase
+ * CigarBase
* @param seq
- * SequenceI
+ * SequenceI
* @param startpos
- * int
+ * int
* @param endpos
- * int
+ * int
* @param initialDeletions
- * if true then initial deletions will be added from start of
- * seq to startpos
+ * if true then initial deletions will be added from start of seq to
+ * startpos
*/
protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
int startpos, int endpos, boolean initialDeletions)
* create a cigar string for given sequence
*
* @param seq
- * SequenceI
+ * SequenceI
*/
public SeqCigar(SequenceI seq)
{
* Create Cigar from a range of gaps and residues on a sequence object
*
* @param seq
- * SequenceI
+ * SequenceI
* @param start
- * int - first column in range
+ * int - first column in range
* @param end
- * int - last column in range
+ * int - last column in range
*/
public SeqCigar(SequenceI seq, int start, int end)
{
* will fix)
*
* @param seq
- * SequenceI object resolvable to a dataset sequence
+ * SequenceI object resolvable to a dataset sequence
* @param cigarString
- * String
+ * String
* @return Cigar
*/
public static SeqCigar parseCigar(SequenceI seq, String cigarString)
}
/**
- * createAlignment
+ * create an alignment from the given array of cigar sequences and gap
+ * character, and marking the given segments as visible in the given
+ * columselection.
*
* @param alseqs
- * SeqCigar[]
* @param gapCharacter
- * char
+ * @param colsel
+ * - columnSelection where hidden regions are marked
+ * @param segments
+ * - visible regions of alignment
* @return SequenceI[]
*/
public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
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}})
+ // endcol}, hidden regions {{start, end, col}})
if (gs_regions[i] == null)
{
throw new Error("Implementation error: " + i
+ "'th sequence Cigar has no operations.");
}
g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
- // visible
- // gapped
- // sequence
+ // visible
+ // gapped
+ // sequence
}
// Now account for insertions. (well - deletions)
// this is complicated because we must keep track of shifted positions in
insert[s] = gapCharacter;
}
int inspos = shifts.shift(region[2]); // resolve insertion position in
- // current alignment frame of
- // reference
+ // current alignment frame of
+ // reference
for (int s = 0; s < alseqs.length; s++)
{
if (s != i)
for (int l = inspos - g_seqs[s].length(); l > 0; l--)
{
g_seqs[s].append(gapCharacter); // to debug - use a diffferent
- // gap character here
+ // gap character here
}
}
g_seqs[s].insert(inspos, insert);
}
else
{
- g_seqs[s].insert(inspos, alseqs_string[i].substring(
- region[0], region[1] + 1));
+ g_seqs[s].insert(inspos,
+ alseqs_string[i].substring(region[0], region[1] + 1));
}
}
shifts.addShift(region[2], insert.length); // update shift in
- // alignment frame of
- // reference
+ // alignment frame of
+ // reference
if (segments == null)
{
// add a hidden column for this deletion
{
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]));
+ 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]));
seqs[i].setDatasetSequence(ref);
seqs[i].setDescription(ref.getDescription());
}
/**
*
* @param seq
- * Sequence
+ * Sequence
* @param ex_cs_gapped
- * String
+ * String
* @return String
*/
public static String testCigar_string(Sequence seq, String ex_cs_gapped)
// System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
}
+ /**
+ * references to entities that this sequence cigar is associated with.
+ */
+ private Hashtable selGroups = null;
+
+ public void setGroupMembership(Object group)
+ {
+ if (selGroups == null)
+ {
+ selGroups = new Hashtable();
+ }
+ selGroups.put(group, new int[0]);
+ }
+
+ /**
+ * Test for and if present remove association to group.
+ *
+ * @param group
+ * @return true if group was associated and it was removed
+ */
+ public boolean removeGroupMembership(Object group)
+ {
+ if (selGroups != null && selGroups.containsKey(group))
+ {
+ selGroups.remove(group);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * forget all associations for this sequence.
+ */
+ public void clearMemberships()
+ {
+ if (selGroups != null)
+ {
+ selGroups.clear();
+ }
+ selGroups = null;
+ }
+
+ /**
+ *
+ * @return null or array of all associated entities
+ */
+ public Object[] getAllMemberships()
+ {
+ if (selGroups == null)
+ {
+ return null;
+ }
+ Object[] mmbs = new Object[selGroups.size()];
+ Enumeration en = selGroups.keys();
+ for (int i = 0; en.hasMoreElements(); i++)
+ {
+ mmbs[i] = en.nextElement();
+ }
+ return mmbs;
+ }
+
+ /**
+ * Test for group membership
+ *
+ * @param sgr
+ * - a selection group or some other object that may be associated
+ * with seqCigar
+ * @return true if sgr is associated with this seqCigar
+ */
+ public boolean isMemberOf(Object sgr)
+ {
+ return (selGroups != null) && selGroups.get(sgr) != null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff