*/
package jalview.analysis;
+import java.util.Locale;
+
import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
{
doFind(theSearchString, matchCase, searchDescription, false,
ignoreHidden);
-
+
if (searchResults.isEmpty() && idMatches.isEmpty())
{
/*
idMatches = new ArrayList<>();
String searchString = matchCase ? theSearchString
- : theSearchString.toUpperCase();
+ : theSearchString.toUpperCase(Locale.ROOT);
Regex searchPattern = new Regex(searchString);
searchPattern.setIgnoreCase(!matchCase);
getSequence(ignoreHidden);
boolean found = false;
- while (!found || findAll)
+ while ((!found || findAll) && sequenceIndex < end)
{
found = findNextMatch(searchString, searchPattern, searchDescription,
ignoreHidden);
- if (sequenceIndex >= end)
- {
- break;
- }
}
}
/**
- * 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.
+ * 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
if (ignoreHidden)
{
seqString = getVisibleSequence(seq);
+ this.searchedSequenceStartPosition = 1;
}
else
{
}
/**
- * 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.
+ * 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.
+ * 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
*/
private String getVisibleSequence(SequenceI seq)
{
- int seqStartCol = seq.findIndex(seq.getStart());
- int seqEndCol = seq.findIndex(seq.getStart() + seq.getLength() - 1);
+ /*
+ * get start / end columns of sequence and convert to base 0
+ * (so as to match the visible column ranges)
+ */
+ 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<>();
* so add the range to the mapping being constructed
*/
int seqResFrom = seq.findPosition(range[0]);
- int seqResTo = seq.findPosition(range[1]);
+ int seqResTo = seqResFrom + ungapped.length() - 1;
fromRanges.add(new int[] { seqResFrom, seqResTo });
}
}
/**
* 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.
+ * 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 ignoreHidden
* @return
*/
- protected boolean findNextMatch(String searchString,
- Regex searchPattern, boolean matchDescription,
- boolean ignoreHidden)
+ protected boolean findNextMatch(String searchString, Regex searchPattern,
+ boolean matchDescription, boolean ignoreHidden)
{
if (residueIndex < 0)
{
* at start of sequence; try find by residue number, in sequence id,
* or (optionally) in sequence description
*/
- if (doNonMotifSearches(searchString, searchPattern,
- matchDescription))
+ if (doNonMotifSearches(searchString, searchPattern, matchDescription))
{
return true;
}
*/
int offset = searchPattern.matchedFrom();
int matchStartPosition = this.searchedSequenceStartPosition + offset;
- int matchEndPosition = matchStartPosition
- + searchPattern.charsMatched() - 1;
+ int matchEndPosition = matchStartPosition + searchPattern.charsMatched()
+ - 1;
/*
* update residueIndex to next position after the start of the match
* (findIndex returns a value base 1, columnIndex is held base 0)
*/
- residueIndex += offset + 1;
+ residueIndex = searchPattern.matchedFrom() + 1;
/*
* return false if the match is entirely in a hidden region
}
/**
- * 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).
+ * 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
*/
int[] truePositions = searchedSequenceMap
.locateInFrom(matchStartPosition, matchEndPosition);
- for (int i = 0; i < truePositions.length - 1; i += 2)
- {
- searchResults.addResult(seq, truePositions[i], truePositions[i + 1]);
- }
+ searchResults.addResult(seq, truePositions);
}
/**
* @param searchPattern
* @return
*/
- protected boolean searchSequenceDescription(SequenceI seq, Regex searchPattern)
+ protected boolean searchSequenceDescription(SequenceI seq,
+ Regex searchPattern)
{
String desc = seq.getDescription();
- if (desc != null && searchPattern.search(desc) && !idMatches.contains(seq))
+ if (desc != null && searchPattern.search(desc)
+ && !idMatches.contains(seq))
{
idMatches.add(seq);
return true;
/**
* 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.
+ * adds the position to the search results and returns true, else answers
+ * false.
*
* @param seq
* @param resNo
return true;
}
int col = seq.findIndex(res); // base 1
- return viewport.getAlignment().getHiddenColumns().isVisible(col - 1); // base 0
+ return viewport.getAlignment().getHiddenColumns().isVisible(col - 1); // base
+ // 0
}
@Override
git://source.jalview.org / jalview.git / blobdiff