/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.Hashtable;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
-import jalview.analysis.*;
-import jalview.util.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
public class SeqCigar extends CigarSimple
{
}
/**
+ *
+ * @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];
}
/**
{
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");
+ 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]));
+ 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,
boolean hasgaps = false;
if (seq == null)
{
- throw new Error("Implementation Error - _setSeq(null,...)");
+ throw new Error(MessageManager
+ .getString("error.implementation_error_set_seq_null"));
}
if (_s < 0)
{
- throw new Error("Implementation Error: _s=" + _s);
+ 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())
}
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);
}
// Check offsets
if (end > ds.getLength())
{
- throw new Error(
- "SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
+ throw new Error(MessageManager
+ .getString("error.implementation_error_seqcigar_possible"));
// end = ds.getLength();
}
* 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[])
{
super();
if (seq == null)
{
- throw new Error("Implementation Bug. Null seq !");
+ throw new Error(
+ MessageManager.getString("error.implmentation_bug_seq_null"));
}
if (operation.length != range.length)
{
- throw new 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(
- "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+ 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++)
{
char op = operation[j];
if (op != M && op != I && op != D)
{
- throw new Error("Implementation Bug. Cigar Operation '" + j
- + "' '" + op + "' not one of '" + M + "', '" + I
- + "', or '" + D + "'.");
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_bug_cigar_operation", new String[]
+ { Integer.valueOf(j).toString(),
+ Integer.valueOf(op).toString(),
+ Integer.valueOf(M).toString(),
+ Integer.valueOf(I).toString(),
+ Integer.valueOf(D).toString() }));
}
this.operation[i] = op;
this.range[i] = range[j];
this.length = 0;
if (_setSeq(seq, false, 0, 0))
{
- throw new Error(
- "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
+ throw new Error(MessageManager.getString(
+ "error.not_yet_implemented_cigar_object_from_cigar_string"));
}
}
}
* 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)
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)
* create a cigar string for given sequence
*
* @param seq
- * SequenceI
+ * SequenceI
*/
public SeqCigar(SequenceI seq)
{
super();
if (seq == null)
{
- throw new Error("Implementation error for new Cigar(SequenceI)");
+ throw new Error(MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, 0, 0);
// there is still work to do
* 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)
{
super();
if (seq == null)
{
- throw new Error("Implementation error for new Cigar(SequenceI)");
+ throw new Error(MessageManager
+ .getString("error.implementation_error_for_new_cigar"));
}
_setSeq(seq, false, start, end + 1);
// there is still work to do
* 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
+ * hiddenColumns.
*
* @param alseqs
- * SeqCigar[]
* @param gapCharacter
- * char
+ * @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}})
+ // endcol}, hidden regions {{start, end, col}})
if (gs_regions[i] == null)
{
- throw new Error("Implementation error: " + i
- + "'th sequence Cigar has no operations.");
+ throw new Error(MessageManager.formatMessage(
+ "error.implementation_error_cigar_seq_no_operations",
+ new String[]
+ { Integer.valueOf(i).toString() }));
}
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
- 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]));
+ 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());
}
{
// 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;
}
/**
- * non rigorous testing
- */
- /**
- *
- * @param seq
- * Sequence
- * @param ex_cs_gapped
- * String
- * @return String
+ * references to entities that this sequence cigar is associated with.
*/
- public static String testCigar_string(Sequence seq, String ex_cs_gapped)
+ private Hashtable selGroups = null;
+
+ public void setGroupMembership(Object group)
{
- SeqCigar c_sgapped = new SeqCigar(seq);
- String cs_gapped = c_sgapped.getCigarstring();
- if (!cs_gapped.equals(ex_cs_gapped))
+ if (selGroups == null)
{
- System.err.println("Failed getCigarstring: incorect string '"
- + cs_gapped + "' != " + ex_cs_gapped);
+ selGroups = new Hashtable();
}
- return cs_gapped;
+ selGroups.put(group, new int[0]);
}
- public static boolean testSeqRecovery(SeqCigar gen_sgapped,
- SequenceI s_gapped)
+ /**
+ * 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)
{
- // this is non-rigorous - start and end recovery is not tested.
- SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
- if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
+ if (selGroups != null && selGroups.containsKey(group))
{
- System.err.println("Couldn't reconstruct sequence.\n"
- + gen_sgapped_s.getSequenceAsString() + "\n"
- + s_gapped.getSequenceAsString());
- return false;
+ selGroups.remove(group);
+ return true;
}
- return true;
+ return false;
}
- public static void main(String argv[]) throws Exception
+ /**
+ * forget all associations for this sequence.
+ */
+ public void clearMemberships()
{
- String o_seq;
- Sequence s = new Sequence("MySeq",
- o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
- String orig_gapped;
- Sequence s_gapped = new Sequence(
- "MySeq",
- orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
- 39, 80);
- String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
- s_gapped.setDatasetSequence(s);
- String sub_gapped_s;
- Sequence s_subsequence_gapped = new Sequence(
- "MySeq",
- sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
- 43, 77);
-
- s_subsequence_gapped.setDatasetSequence(s);
- SeqCigar c_null = new SeqCigar(s);
- String cs_null = c_null.getCigarstring();
- if (!cs_null.equals("42M"))
- {
- System.err
- .println("Failed to recover ungapped sequence cigar operations:"
- + ((cs_null == "") ? "empty string" : cs_null));
- }
- testCigar_string(s_gapped, ex_cs_gapped);
- SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
- if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
- {
- System.err.println("Failed parseCigar(" + ex_cs_gapped
- + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
- + "'");
- }
- testSeqRecovery(gen_sgapped, s_gapped);
- // Test dataset resolution
- SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
- if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
+ if (selGroups != null)
{
- System.err
- .println("Failed recovery for subsequence of dataset sequence");
- }
- // width functions
- if (sub_gapped.getWidth() != sub_gapped_s.length())
- {
- System.err.println("Failed getWidth()");
+ selGroups.clear();
}
+ selGroups = null;
+ }
- sub_gapped.getFullWidth();
- if (sub_gapped.hasDeletedRegions())
- {
- System.err.println("hasDeletedRegions is incorrect.");
- }
- // Test start-end region SeqCigar
- SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
- if (sub_se_gp.getWidth() != 41)
- {
- System.err
- .println("SeqCigar(seq, start, end) not properly clipped alignsequence.");
- }
- System.out.println("Original sequence align:\n" + sub_gapped_s
- + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
- + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
- + sub_se_gp.getCigarstring() + "\n");
- SequenceI ssgp = sub_se_gp.getSeq('-');
- System.out.println("\t " + ssgp.getSequenceAsString());
- for (int r = 0; r < 10; r++)
- {
- sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
- int sl = sub_se_gp.getWidth();
- int st = sl - 1 - r;
- for (int rs = 0; rs < 10; rs++)
- {
- int e = st + rs;
- sub_se_gp.deleteRange(st, e);
- String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
- System.out.println(st + "," + e + "\t:" + ssgapedseq);
- st -= 3;
- }
- }
+ /**
+ *
+ * @return null or array of all associated entities
+ */
+ public Object[] getAllMemberships()
+ {
+ if (selGroups == null)
{
- SeqCigar[] set = new SeqCigar[]
- { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
- new SeqCigar(s_gapped) };
- Alignment al = new Alignment(set);
- for (int i = 0; i < al.getHeight(); i++)
- {
- System.out.println("" + al.getSequenceAt(i).getName() + "\t"
- + al.getSequenceAt(i).getStart() + "\t"
- + al.getSequenceAt(i).getEnd() + "\t"
- + al.getSequenceAt(i).getSequenceAsString());
- }
+ return null;
}
+ Object[] mmbs = new Object[selGroups.size()];
+ Enumeration en = selGroups.keys();
+ for (int i = 0; en.hasMoreElements(); i++)
{
- System.out.println("Gapped.");
- SeqCigar[] set = new SeqCigar[]
- { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
- new SeqCigar(s_gapped) };
- set[0].deleteRange(20, 25);
- Alignment al = new Alignment(set);
- for (int i = 0; i < al.getHeight(); i++)
- {
- System.out.println("" + al.getSequenceAt(i).getName() + "\t"
- + al.getSequenceAt(i).getStart() + "\t"
- + al.getSequenceAt(i).getEnd() + "\t"
- + al.getSequenceAt(i).getSequenceAsString());
- }
+ mmbs[i] = en.nextElement();
}
- // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
- // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
+ 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;
+ }
}