import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Range;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.VisibleContigsIterator;
import jalview.util.Comparison;
+import jalview.util.MapList;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
import com.stevesoft.pat.Regex;
/*
* sequences matched by id or description
*/
- private Vector<SequenceI> idMatches;
+ private List<SequenceI> idMatches;
/*
* the viewport to search over
private int sequenceIndex;
/*
- * column position in sequence to search from, base 0
- * - absolute column number including any hidden columns
- * (position after start of last match for a repeat search)
+ * position offset in sequence to search from, base 0
+ * (position after start of last match for a 'find next')
*/
- private int columnIndex;
+ private int residueIndex;
+
+ /*
+ * the true sequence position of the start of the
+ * last sequence searched (when 'ignore hidden regions' does not apply)
+ */
+ private int searchedSequenceStartPosition;
+
+ /*
+ * when 'ignore hidden regions' applies, this holds the mapping from
+ * the visible sequence positions (1, 2, ...) to true sequence positions
+ */
+ private MapList searchedSequenceMap;
+
+ private String seqToSearch;
/**
* Constructor for searching a viewport
{
this.viewport = av;
this.sequenceIndex = 0;
- this.columnIndex = -1;
+ this.residueIndex = -1;
}
@Override
public void findAll(String theSearchString, boolean matchCase,
- boolean searchDescription)
+ boolean searchDescription, boolean ignoreHidden)
{
/*
* search from the start
*/
sequenceIndex = 0;
- columnIndex = -1;
+ residueIndex = -1;
- doFind(theSearchString, matchCase, searchDescription, true);
+ doFind(theSearchString, matchCase, searchDescription, true,
+ ignoreHidden);
/*
* reset to start for next search
*/
sequenceIndex = 0;
- columnIndex = -1;
+ residueIndex = -1;
}
@Override
public void findNext(String theSearchString, boolean matchCase,
- boolean searchDescription)
+ boolean searchDescription, boolean ignoreHidden)
{
- doFind(theSearchString, matchCase, searchDescription, false);
+ doFind(theSearchString, matchCase, searchDescription, false,
+ ignoreHidden);
if (searchResults.isEmpty() && idMatches.isEmpty())
{
* search failed - reset to start for next search
*/
sequenceIndex = 0;
- columnIndex = -1;
+ residueIndex = -1;
}
}
* @param matchCase
* @param searchDescription
* @param findAll
+ * @param ignoreHidden
*/
protected void doFind(String theSearchString, boolean matchCase,
- boolean searchDescription, boolean findAll)
+ boolean searchDescription, boolean findAll, boolean ignoreHidden)
{
+ searchResults = new SearchResults();
+ idMatches = new ArrayList<>();
+
String searchString = matchCase ? theSearchString
: theSearchString.toUpperCase();
Regex searchPattern = new Regex(searchString);
searchPattern.setIgnoreCase(!matchCase);
- searchResults = new SearchResults();
- idMatches = new Vector<>();
-
SequenceGroup selection = viewport.getSelectionGroup();
if (selection != null && selection.getSize() < 1)
{
AlignmentI alignment = viewport.getAlignment();
int end = alignment.getHeight();
- while (sequenceIndex < end)
+ getSequence(ignoreHidden);
+
+ boolean found = false;
+ while ((!found || findAll) && sequenceIndex < end)
{
- SequenceI seq = alignment.getSequenceAt(sequenceIndex);
- boolean found = findNextMatch(seq, searchString, searchPattern,
- searchDescription);
- if (found && !findAll)
+ found = findNextMatch(searchString, searchPattern, searchDescription,
+ ignoreHidden);
+ }
+ }
+
+ /**
+ * Calculates and saves the sequence string to search. The string is restricted
+ * to the current selection region if there is one, and is saved with all gaps
+ * removed.
+ * <p>
+ * If there are hidden columns, and option {@ignoreHidden} is selected, then
+ * only visible positions of the sequence are included, and a mapping is also
+ * constructed from the returned string positions to the true sequence
+ * positions.
+ * <p>
+ * Note we have to do this each time {@code findNext} or {@code findAll} is
+ * called, in case the alignment, selection group or hidden columns have
+ * changed. In particular, if the sequence at offset {@code sequenceIndex} in
+ * the alignment is (no longer) in the selection group, search is advanced to
+ * the next sequence that is.
+ * <p>
+ * Sets sequence string to the empty string if there are no more sequences (in
+ * selection group if any) at or after {@code sequenceIndex}.
+ * <p>
+ * Returns true if a sequence could be found, false if end of alignment was
+ * reached
+ *
+ * @param ignoreHidden
+ * @return
+ */
+ private boolean getSequence(boolean ignoreHidden)
+ {
+ AlignmentI alignment = viewport.getAlignment();
+ if (sequenceIndex >= alignment.getHeight())
+ {
+ seqToSearch = "";
+ return false;
+ }
+ SequenceI seq = alignment.getSequenceAt(sequenceIndex);
+ SequenceGroup selection = viewport.getSelectionGroup();
+ if (selection != null && !selection.contains(seq))
+ {
+ if (!nextSequence(ignoreHidden))
{
- return;
+ return false;
}
- if (!found)
+ seq = alignment.getSequenceAt(sequenceIndex);
+ }
+
+ String seqString = null;
+ if (ignoreHidden)
+ {
+ seqString = getVisibleSequence(seq);
+ this.searchedSequenceStartPosition = 1;
+ }
+ else
+ {
+ int startCol = 0;
+ int endCol = seq.getLength() - 1;
+ this.searchedSequenceStartPosition = seq.getStart();
+ if (selection != null)
{
- sequenceIndex++;
- columnIndex = -1;
+ startCol = selection.getStartRes();
+ endCol = Math.min(endCol, selection.getEndRes());
+ this.searchedSequenceStartPosition = seq.findPosition(startCol);
}
+ seqString = seq.getSequenceAsString(startCol, endCol + 1);
}
+
+ /*
+ * remove gaps; note that even if this leaves an empty string, we 'search'
+ * the sequence anyway (for possible match on name or description)
+ */
+ String ungapped = AlignSeq.extractGaps(Comparison.GapChars, seqString);
+ this.seqToSearch = ungapped;
+
+ return true;
}
/**
- * Answers the start-end column range of the visible region of
- * <code>sequence</code> starting at or after the given <code>column</code>.
- * If there are no hidden columns, this just returns the remaining width of
- * the sequence. The range is restricted to the current <code>selection</code>
- * if there is one. Answers null if there are no visible columns at or after
- * <code>column</code>.
+ * Returns a string consisting of only the visible residues of {@code seq} from
+ * alignment column {@ fromColumn}, restricted to the current selection region
+ * if there is one.
+ * <p>
+ * As a side-effect, also computes the mapping from the true sequence positions
+ * to the positions (1, 2, ...) of the returned sequence. This is to allow
+ * search matches in the visible sequence to be converted to sequence positions.
+ *
+ * @param seq
+ * @return
*/
- protected Range getNextVisibleSequenceRegion(SequenceI sequence,
- int column)
+ private String getVisibleSequence(SequenceI seq)
{
- int seqColStart = column;
- int seqColEnd = sequence.getLength() - 1;
-
/*
- * restrict search to (next) visible column region,
- * in case there are hidden columns
+ * get start / end columns of sequence and convert to base 0
+ * (so as to match the visible column ranges)
*/
- AlignmentI alignment = viewport.getAlignment();
- VisibleContigsIterator visibleRegions = alignment.getHiddenColumns()
- .getVisContigsIterator(column, alignment.getWidth(),
- false);
- int[] visible = visibleRegions.hasNext() ? visibleRegions.next() : null;
- if (visible == null)
- {
- columnIndex = seqColEnd + 1;
- return null;
- }
- seqColStart = Math.max(seqColStart, visible[0]);
- seqColEnd = Math.min(seqColEnd, visible[1]);
+ int seqStartCol = seq.findIndex(seq.getStart()) - 1;
+ int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1) - 1;
+ Iterator<int[]> visibleColumns = viewport.getViewAsVisibleContigs(true);
+ StringBuilder visibleSeq = new StringBuilder(seqEndCol - seqStartCol);
+ List<int[]> fromRanges = new ArrayList<>();
- /*
- * restrict search to selected region if there is one
- */
- SequenceGroup selection = viewport.getSelectionGroup();
- if (selection != null)
+ while (visibleColumns.hasNext())
{
- int selectionStart = selection.getStartRes();
- int selectionEnd = selection.getEndRes();
- if (selectionStart > seqColEnd || selectionEnd < seqColStart)
+ int[] range = visibleColumns.next();
+ if (range[0] > seqEndCol)
+ {
+ // beyond the end of the sequence
+ break;
+ }
+ if (range[1] < seqStartCol)
+ {
+ // before the start of the sequence
+ continue;
+ }
+ String subseq = seq.getSequenceAsString(range[0], range[1] + 1);
+ String ungapped = AlignSeq.extractGaps(Comparison.GapChars, subseq);
+ visibleSeq.append(ungapped);
+ if (!ungapped.isEmpty())
{
/*
- * sequence region doesn't overlap selection region
+ * visible region includes at least one non-gap character,
+ * so add the range to the mapping being constructed
*/
- columnIndex = seqColEnd + 1;
- return null;
+ int seqResFrom = seq.findPosition(range[0]);
+ int seqResTo = seqResFrom + ungapped.length() - 1;
+ fromRanges.add(new int[] { seqResFrom, seqResTo });
}
- seqColStart = Math.max(seqColStart, selectionStart);
- seqColEnd = Math.min(seqColEnd, selectionEnd);
}
- return new Range(seqColStart, seqColEnd);
+ /*
+ * construct the mapping
+ * from: visible sequence positions 1..length
+ * to: true residue positions of the alignment sequence
+ */
+ List<int[]> toRange = Arrays
+ .asList(new int[]
+ { 1, visibleSeq.length() });
+ searchedSequenceMap = new MapList(fromRanges, toRange, 1, 1);
+
+ return visibleSeq.toString();
}
/**
- * Finds the next match in the given sequence, starting at column at
- * <code>columnIndex</code>. Answers true if a match is found, else false. If
- * a match is found, <code>columnIndex</code> is advanced to the column after
- * the start of the matched region, ready for a search from the next position.
+ * Advances the search to the next sequence in the alignment. Sequences not in
+ * the current selection group (if there is one) are skipped. The (sub-)sequence
+ * to be searched is extracted, gaps removed, and saved, or set to null if there
+ * are no more sequences to search.
+ * <p>
+ * Returns true if a sequence could be found, false if end of alignment was
+ * reached
*
- * @param seq
+ * @param ignoreHidden
+ */
+ private boolean nextSequence(boolean ignoreHidden)
+ {
+ sequenceIndex++;
+ residueIndex = -1;
+
+ return getSequence(ignoreHidden);
+ }
+
+ /**
+ * Finds the next match in the given sequence, starting at offset
+ * {@code residueIndex}. Answers true if a match is found, else false.
+ * <p>
+ * If a match is found, {@code residueIndex} is advanced to the position after
+ * the start of the matched region, ready for the next search.
+ * <p>
+ * If no match is found, {@code sequenceIndex} is advanced ready to search the
+ * next sequence.
+ *
+ * @param seqToSearch
* @param searchString
* @param searchPattern
* @param matchDescription
+ * @param ignoreHidden
* @return
*/
- protected boolean findNextMatch(SequenceI seq, String searchString,
- Regex searchPattern, boolean matchDescription)
+ protected boolean findNextMatch(String searchString,
+ Regex searchPattern, boolean matchDescription,
+ boolean ignoreHidden)
{
- SequenceGroup selection = viewport.getSelectionGroup();
- if (selection != null && !selection.contains(seq))
- {
- /*
- * this sequence is not in the selection - advance to next sequence
- */
- return false;
- }
-
- if (columnIndex < 0)
+ if (residueIndex < 0)
{
/*
* at start of sequence; try find by residue number, in sequence id,
* or (optionally) in sequence description
*/
- if (doNonMotifSearches(seq, searchString, searchPattern,
+ if (doNonMotifSearches(searchString, searchPattern,
matchDescription))
{
return true;
/*
* search for next match in sequence string
*/
- int end = seq.getLength();
- while (columnIndex < end)
+ int end = seqToSearch.length();
+ while (residueIndex < end)
{
- if (searchNextVisibleRegion(seq, searchPattern))
+ boolean matched = searchPattern.searchFrom(seqToSearch, residueIndex);
+ if (matched)
{
- return true;
+ if (recordMatch(searchPattern, ignoreHidden))
+ {
+ return true;
+ }
+ }
+ else
+ {
+ residueIndex = Integer.MAX_VALUE;
}
- }
- return false;
- }
-
- /**
- * Searches the sequence, starting from <code>columnIndex</code>, and adds the
- * next match (if any) to <code>searchResults</code>. The search is restricted
- * to the next visible column region, and to the <code>selection</code> region
- * if there is one. Answers true if a match is added, else false.
- *
- * @param seq
- * @param searchPattern
- * @return
- */
- protected boolean searchNextVisibleRegion(SequenceI seq, Regex searchPattern)
- {
- Range visible = getNextVisibleSequenceRegion(seq, columnIndex);
- if (visible == null)
- {
- return false;
- }
- String seqString = seq.getSequenceAsString(visible.start, visible.end + 1);
- String noGaps = AlignSeq.extractGaps(Comparison.GapChars, seqString);
-
- if (searchPattern.search(noGaps))
- {
- int sequenceStartPosition = seq.findPosition(visible.start);
- recordMatch(seq, searchPattern, sequenceStartPosition);
- return true;
- }
- else
- {
- /*
- * no match - advance columnIndex past this visible region
- * so the next visible region (if any) is searched next
- */
- columnIndex = visible.end + 1;
}
+ nextSequence(ignoreHidden);
return false;
}
/**
* Adds the match held in the <code>searchPattern</code> Regex to the
* <code>searchResults</code>, unless it is a subregion of the last match
- * recorded. <code>columnIndex</code> is advanced to the position after the
+ * recorded. <code>residueIndex</code> is advanced to the position after the
* start of the matched region, ready for the next search. Answers true if a
* match was added, else false.
+ * <p>
+ * Matches that lie entirely within hidden regions of the alignment are not
+ * added.
*
- * @param seq
* @param searchPattern
- * @param firstResiduePosition
+ * @param ignoreHidden
* @return
*/
- protected boolean recordMatch(SequenceI seq, Regex searchPattern,
- int firstResiduePosition)
+ protected boolean recordMatch(Regex searchPattern, boolean ignoreHidden)
{
+ SequenceI seq = viewport.getAlignment().getSequenceAt(sequenceIndex);
+
/*
- * get start/end of the match in sequence coordinates
+ * convert start/end of the match to sequence coordinates
*/
int offset = searchPattern.matchedFrom();
- int matchStartPosition = firstResiduePosition + offset;
+ int matchStartPosition = this.searchedSequenceStartPosition + offset;
int matchEndPosition = matchStartPosition
+ searchPattern.charsMatched() - 1;
/*
- * update columnIndex to next column after the start of the match
+ * update residueIndex to next position after the start of the match
* (findIndex returns a value base 1, columnIndex is held base 0)
*/
- columnIndex = seq.findIndex(matchStartPosition);
+ residueIndex += offset + 1;
+
+ /*
+ * return false if the match is entirely in a hidden region
+ */
+ if (allHidden(seq, matchStartPosition, matchEndPosition))
+ {
+ return false;
+ }
/*
* check that this match is not a subset of the previous one (JAL-2302)
if (lastMatch == null || !lastMatch.contains(seq, matchStartPosition,
matchEndPosition))
{
- searchResults.addResult(seq, matchStartPosition, matchEndPosition);
+ addMatch(seq, matchStartPosition, matchEndPosition, ignoreHidden);
return true;
}
}
/**
+ * Adds one match to the stored list. If hidden residues are being skipped, then
+ * the match may need to be split into contiguous positions of the sequence (so
+ * it does not include skipped residues).
+ *
+ * @param seq
+ * @param matchStartPosition
+ * @param matchEndPosition
+ * @param ignoreHidden
+ */
+ private void addMatch(SequenceI seq, int matchStartPosition,
+ int matchEndPosition, boolean ignoreHidden)
+ {
+ if (!ignoreHidden)
+ {
+ /*
+ * simple case
+ */
+ searchResults.addResult(seq, matchStartPosition, matchEndPosition);
+ return;
+ }
+
+ /*
+ * get start-end contiguous ranges in underlying sequence
+ */
+ int[] truePositions = searchedSequenceMap
+ .locateInFrom(matchStartPosition, matchEndPosition);
+ searchResults.addResult(seq, truePositions);
+ }
+
+ /**
+ * Returns true if all residues are hidden, else false
+ *
+ * @param seq
+ * @param fromPos
+ * @param toPos
+ * @return
+ */
+ private boolean allHidden(SequenceI seq, int fromPos, int toPos)
+ {
+ if (!viewport.hasHiddenColumns())
+ {
+ return false;
+ }
+ for (int res = fromPos; res <= toPos; res++)
+ {
+ if (isVisible(seq, res))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
* Does searches other than for residue patterns. Currently this includes
* <ul>
* <li>find residue by position (if search string is a number)</li>
* </ul>
* Answers true if a match is found, else false.
*
- * @param seq
* @param searchString
* @param searchPattern
* @param includeDescription
* @return
*/
- protected boolean doNonMotifSearches(SequenceI seq, String searchString,
+ protected boolean doNonMotifSearches(String searchString,
Regex searchPattern, boolean includeDescription)
{
+ SequenceI seq = viewport.getAlignment().getSequenceAt(sequenceIndex);
+
/*
* position sequence search to start of sequence
*/
- columnIndex = 0;
-
- if (searchForResidueNumber(seq, searchString))
+ residueIndex = 0;
+ try
{
- return true;
+ int res = Integer.parseInt(searchString);
+ return searchForResidueNumber(seq, res);
+ } catch (NumberFormatException ex)
+ {
+ // search pattern is not a number
}
+
if (searchSequenceName(seq, searchPattern))
{
return true;
String desc = seq.getDescription();
if (desc != null && searchPattern.search(desc) && !idMatches.contains(seq))
{
- idMatches.addElement(seq);
+ idMatches.add(seq);
return true;
}
return false;
{
if (searchPattern.search(seq.getName()) && !idMatches.contains(seq))
{
- idMatches.addElement(seq);
+ idMatches.add(seq);
return true;
}
return false;
}
/**
- * Tries to interpret the search string as a residue position, and if valid,
- * adds the position to the search results and returns true, else answers
- * false
+ * If the residue position is valid for the sequence, and in a visible column,
+ * adds the position to the search results and returns true, else answers false.
+ *
+ * @param seq
+ * @param resNo
+ * @return
*/
- protected boolean searchForResidueNumber(SequenceI seq, String searchString)
+ protected boolean searchForResidueNumber(SequenceI seq, int resNo)
{
- try
+ if (seq.getStart() <= resNo && seq.getEnd() >= resNo)
{
- int res = Integer.parseInt(searchString);
- if (seq.getStart() <= res && seq.getEnd() >= res)
+ if (isVisible(seq, resNo))
{
- searchResults.addResult(seq, res, res);
+ searchResults.addResult(seq, resNo, resNo);
return true;
}
- } catch (NumberFormatException ex)
- {
}
return false;
}
- /* (non-Javadoc)
- * @see jalview.analysis.FinderI#getIdMatch()
+ /**
+ * Returns true if the residue is in a visible column, else false
+ *
+ * @param seq
+ * @param res
+ * @return
*/
+ private boolean isVisible(SequenceI seq, int res)
+ {
+ if (!viewport.hasHiddenColumns())
+ {
+ return true;
+ }
+ int col = seq.findIndex(res); // base 1
+ return viewport.getAlignment().getHiddenColumns().isVisible(col - 1); // base 0
+ }
+
@Override
- public Vector<SequenceI> getIdMatches()
+ public List<SequenceI> getIdMatches()
{
return idMatches;
}
- /* (non-Javadoc)
- * @see jalview.analysis.FinderI#getSearchResults()
- */
@Override
public SearchResultsI getSearchResults()
{
git://source.jalview.org / jalview.git / blobdiff