-package jalview.analysis;\r
-import java.util.Vector;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class Finder {\r
- /**\r
- * Implements the search algorithms for the Find dialog box.\r
- */\r
- SearchResults searchResults;\r
- AlignmentI alignment;\r
- jalview.datamodel.SequenceGroup selection=null;\r
- Vector idMatch=null;\r
- boolean caseSensitive=false;\r
- boolean findAll=false;\r
- com.stevesoft.pat.Regex regex=null;\r
- /**\r
- * hold's last-searched position between calles to find(false)\r
- */\r
- int seqIndex=0,resIndex=0;\r
- public Finder(AlignmentI alignment, SequenceGroup selection) {\r
- this.alignment=alignment;\r
- this.selection = selection;\r
- }\r
-\r
- public Finder(AlignmentI alignment, SequenceGroup selectionGroup, int seqIndex, int resIndex) {\r
- this(alignment, selectionGroup);\r
- this.seqIndex=seqIndex;\r
- this.resIndex=resIndex;\r
- }\r
-\r
- public boolean find(String searchString) {\r
- boolean hasResults=false;\r
- if(!caseSensitive)\r
- searchString = searchString.toUpperCase();\r
- regex = new com.stevesoft.pat.Regex(searchString);\r
- searchResults = new SearchResults();\r
- idMatch = new Vector();\r
- Sequence seq;\r
- String item = null;\r
- boolean found = false;\r
-\r
- ////// is the searchString a residue number?\r
- try\r
- {\r
- int res = Integer.parseInt(searchString);\r
- found = true;\r
- if (selection == null || selection.getSize() < 1)\r
- {\r
- seq = (Sequence) alignment.getSequenceAt(0);\r
- }\r
- else\r
- {\r
- seq = (Sequence) (selection.getSequenceAt(0));\r
- }\r
-\r
- searchResults.addResult(seq, res, res);\r
- hasResults=true;\r
- }\r
- catch (NumberFormatException ex)\r
- {\r
- }\r
-\r
- ///////////////////////////////////////////////\r
-\r
- int end = alignment.getHeight();\r
-\r
-\r
- if (selection != null)\r
- {\r
- if ((selection.getSize() < 1) ||\r
- ((selection.getEndRes() - selection.getStartRes()) < 2))\r
- {\r
- selection = null;\r
- }\r
- }\r
-\r
- while (!found && (seqIndex < end))\r
- {\r
- seq = (Sequence) alignment.getSequenceAt(seqIndex);\r
-\r
- if ((selection != null) && !selection.getSequences(null).contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
-\r
- continue;\r
- }\r
-\r
- item = seq.getSequenceAsString();\r
- // JBPNote - check if this toUpper which is present in the application implementation makes a difference\r
- //if(!caseSensitive)\r
- // item = item.toUpperCase();\r
-\r
- if ((selection != null) &&\r
- (selection.getEndRes() < alignment.getWidth()-1))\r
- {\r
- item = item.substring(0, selection.getEndRes() + 1);\r
- }\r
-\r
- ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not\r
- StringBuffer noGapsSB = new StringBuffer();\r
- int insertCount = 0;\r
- Vector spaces = new Vector();\r
-\r
- for (int j = 0; j < item.length(); j++)\r
- {\r
- if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
- {\r
- noGapsSB.append(item.charAt(j));\r
- spaces.addElement(new Integer(insertCount));\r
- }\r
- else\r
- {\r
- insertCount++;\r
- }\r
- }\r
-\r
- String noGaps = noGapsSB.toString();\r
-\r
- for (int r = resIndex; r < noGaps.length(); r++)\r
- {\r
-\r
- if (regex.searchFrom(noGaps, r))\r
- {\r
- resIndex = regex.matchedFrom();\r
-\r
- if ((selection != null) &&\r
- ((resIndex +\r
- Integer.parseInt(spaces.elementAt(resIndex).toString())) < selection.getStartRes()))\r
- {\r
- continue;\r
- }\r
-\r
-\r
- int sres = seq.findPosition(resIndex +\r
- Integer.parseInt(spaces.elementAt(resIndex)\r
- .toString()));\r
- int eres = seq.findPosition(regex.matchedTo() - 1 +\r
- Integer.parseInt(spaces.elementAt(regex.matchedTo() -\r
- 1).toString()));\r
-\r
- searchResults.addResult(seq, sres, eres);\r
- hasResults=true;\r
- if (!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
-\r
- break;\r
- }\r
-\r
- r = resIndex;\r
- }\r
- else\r
- {\r
- break;\r
- }\r
- }\r
-\r
- if (!found)\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- }\r
- }\r
-\r
- for (int id = 0; id < alignment.getHeight(); id++)\r
- {\r
- if (regex.search(alignment.getSequenceAt(id).getName()))\r
- {\r
- idMatch.addElement(alignment.getSequenceAt(id));\r
- hasResults=true;\r
- }\r
- }\r
- return hasResults;\r
- }\r
- /**\r
- * @return the alignment\r
- */\r
- public AlignmentI getAlignment() {\r
- return alignment;\r
- }\r
- /**\r
- * @param alignment the alignment to set\r
- */\r
- public void setAlignment(AlignmentI alignment) {\r
- this.alignment = alignment;\r
- }\r
- /**\r
- * @return the caseSensitive\r
- */\r
- public boolean isCaseSensitive() {\r
- return caseSensitive;\r
- }\r
- /**\r
- * @param caseSensitive the caseSensitive to set\r
- */\r
- public void setCaseSensitive(boolean caseSensitive) {\r
- this.caseSensitive = caseSensitive;\r
- }\r
- /**\r
- * @return the findAll\r
- */\r
- public boolean isFindAll() {\r
- return findAll;\r
- }\r
- /**\r
- * @param findAll the findAll to set\r
- */\r
- public void setFindAll(boolean findAll) {\r
- this.findAll = findAll;\r
- }\r
- /**\r
- * @return the selection\r
- */\r
- public jalview.datamodel.SequenceGroup getSelection() {\r
- return selection;\r
- }\r
- /**\r
- * @param selection the selection to set\r
- */\r
- public void setSelection(jalview.datamodel.SequenceGroup selection) {\r
- this.selection = selection;\r
- }\r
- /**\r
- * @return the idMatch\r
- */\r
- public Vector getIdMatch() {\r
- return idMatch;\r
- }\r
- /**\r
- * @return the regex\r
- */\r
- public com.stevesoft.pat.Regex getRegex() {\r
- return regex;\r
- }\r
- /**\r
- * @return the searchResults\r
- */\r
- public SearchResults getSearchResults() {\r
- return searchResults;\r
- }\r
-\r
- /**\r
- * @return the resIndex\r
- */\r
- public int getResIndex() {\r
- return resIndex;\r
- }\r
-\r
- /**\r
- * @param resIndex the resIndex to set\r
- */\r
- public void setResIndex(int resIndex) {\r
- this.resIndex = resIndex;\r
- }\r
-\r
- /**\r
- * @return the seqIndex\r
- */\r
- public int getSeqIndex() {\r
- return seqIndex;\r
- }\r
-\r
- /**\r
- * @param seqIndex the seqIndex to set\r
- */\r
- public void setSeqIndex(int seqIndex) {\r
- this.seqIndex = seqIndex;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+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 java.util.List;
+import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * Implements the search algorithm for the Find dialog
+ */
+public class Finder implements FinderI
+{
+ /*
+ * matched residue locations
+ */
+ private SearchResultsI searchResults;
+
+ /*
+ * sequences matched by id or description
+ */
+ private Vector<SequenceI> idMatches;
+
+ /*
+ * the viewport to search over
+ */
+ private AlignViewportI viewport;
+
+ /*
+ * sequence index in alignment to search from
+ */
+ 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)
+ */
+ private int columnIndex;
+
+ /**
+ * Constructor for searching a viewport
+ *
+ * @param av
+ */
+ public Finder(AlignViewportI av)
+ {
+ this.viewport = av;
+ this.sequenceIndex = 0;
+ this.columnIndex = -1;
+ }
+
+ @Override
+ public void findAll(String theSearchString, boolean matchCase,
+ boolean searchDescription)
+ {
+ /*
+ * search from the start
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
+
+ doFind(theSearchString, matchCase, searchDescription, true);
+
+ /*
+ * reset to start for next search
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
+ }
+
+ @Override
+ public void findNext(String theSearchString, boolean matchCase,
+ boolean searchDescription)
+ {
+ doFind(theSearchString, matchCase, searchDescription, false);
+
+ if (searchResults.isEmpty() && idMatches.isEmpty())
+ {
+ /*
+ * search failed - reset to start for next search
+ */
+ sequenceIndex = 0;
+ columnIndex = -1;
+ }
+ }
+
+ /**
+ * Performs a 'find next' or 'find all'
+ *
+ * @param theSearchString
+ * @param matchCase
+ * @param searchDescription
+ * @param findAll
+ */
+ protected void doFind(String theSearchString, boolean matchCase,
+ boolean searchDescription, boolean findAll)
+ {
+ 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)
+ {
+ selection = null; // ? ignore column-only selection
+ }
+
+ AlignmentI alignment = viewport.getAlignment();
+ int end = alignment.getHeight();
+
+ while (sequenceIndex < end)
+ {
+ SequenceI seq = alignment.getSequenceAt(sequenceIndex);
+ boolean found = findNextMatch(seq, searchString, searchPattern,
+ searchDescription);
+ if (found && !findAll)
+ {
+ return;
+ }
+ if (!found)
+ {
+ sequenceIndex++;
+ columnIndex = -1;
+ }
+ }
+ }
+
+ /**
+ * 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>.
+ */
+ protected Range getNextVisibleSequenceRegion(SequenceI sequence,
+ int column)
+ {
+ int seqColStart = column;
+ int seqColEnd = sequence.getLength() - 1;
+
+ /*
+ * restrict search to (next) visible column region,
+ * in case there are hidden columns
+ */
+ 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]);
+
+ /*
+ * restrict search to selected region if there is one
+ */
+ SequenceGroup selection = viewport.getSelectionGroup();
+ if (selection != null)
+ {
+ int selectionStart = selection.getStartRes();
+ int selectionEnd = selection.getEndRes();
+ if (selectionStart > seqColEnd || selectionEnd < seqColStart)
+ {
+ /*
+ * sequence region doesn't overlap selection region
+ */
+ columnIndex = seqColEnd + 1;
+ return null;
+ }
+ seqColStart = Math.max(seqColStart, selectionStart);
+ seqColEnd = Math.min(seqColEnd, selectionEnd);
+ }
+
+ return new Range(seqColStart, seqColEnd);
+ }
+
+ /**
+ * 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.
+ *
+ * @param seq
+ * @param searchString
+ * @param searchPattern
+ * @param matchDescription
+ * @return
+ */
+ protected boolean findNextMatch(SequenceI seq, String searchString,
+ Regex searchPattern, boolean matchDescription)
+ {
+ 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)
+ {
+ /*
+ * at start of sequence; try find by residue number, in sequence id,
+ * or (optionally) in sequence description
+ */
+ if (doNonMotifSearches(seq, searchString, searchPattern,
+ matchDescription))
+ {
+ return true;
+ }
+ }
+
+ /*
+ * search for next match in sequence string
+ */
+ int end = seq.getLength();
+ while (columnIndex < end)
+ {
+ if (searchNextVisibleRegion(seq, searchPattern))
+ {
+ return true;
+ }
+ }
+ 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;
+ }
+
+ 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
+ * start of the matched region, ready for the next search. Answers true if a
+ * match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @param firstResiduePosition
+ * @return
+ */
+ protected boolean recordMatch(SequenceI seq, Regex searchPattern,
+ int firstResiduePosition)
+ {
+ /*
+ * get start/end of the match in sequence coordinates
+ */
+ int offset = searchPattern.matchedFrom();
+ int matchStartPosition = firstResiduePosition + offset;
+ int matchEndPosition = matchStartPosition
+ + searchPattern.charsMatched() - 1;
+
+ /*
+ * update columnIndex to next column after the start of the match
+ * (findIndex returns a value base 1, columnIndex is held base 0)
+ */
+ columnIndex = seq.findIndex(matchStartPosition);
+
+ /*
+ * check that this match is not a subset of the previous one (JAL-2302)
+ */
+ List<SearchResultMatchI> matches = searchResults.getResults();
+ SearchResultMatchI lastMatch = matches.isEmpty() ? null
+ : matches.get(matches.size() - 1);
+
+ if (lastMatch == null || !lastMatch.contains(seq, matchStartPosition,
+ matchEndPosition))
+ {
+ searchResults.addResult(seq, matchStartPosition, matchEndPosition);
+ return true;
+ }
+
+ return false;
+ }
+
+ /**
+ * Does searches other than for residue patterns. Currently this includes
+ * <ul>
+ * <li>find residue by position (if search string is a number)</li>
+ * <li>match search string to sequence id</li>
+ * <li>match search string to sequence description (optional)</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,
+ Regex searchPattern, boolean includeDescription)
+ {
+ /*
+ * position sequence search to start of sequence
+ */
+ columnIndex = 0;
+
+ if (searchForResidueNumber(seq, searchString))
+ {
+ return true;
+ }
+ if (searchSequenceName(seq, searchPattern))
+ {
+ return true;
+ }
+ if (includeDescription && searchSequenceDescription(seq, searchPattern))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Searches for a match with the sequence description, and if found, adds the
+ * sequence to the list of match ids (but not as a duplicate). Answers true if
+ * a match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
+ */
+ protected boolean searchSequenceDescription(SequenceI seq, Regex searchPattern)
+ {
+ String desc = seq.getDescription();
+ if (desc != null && searchPattern.search(desc) && !idMatches.contains(seq))
+ {
+ idMatches.addElement(seq);
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Searches for a match with the sequence name, and if found, adds the
+ * sequence to the list of match ids (but not as a duplicate). Answers true if
+ * a match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
+ */
+ protected boolean searchSequenceName(SequenceI seq, Regex searchPattern)
+ {
+ if (searchPattern.search(seq.getName()) && !idMatches.contains(seq))
+ {
+ idMatches.addElement(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
+ */
+ protected boolean searchForResidueNumber(SequenceI seq, String searchString)
+ {
+ try
+ {
+ int res = Integer.parseInt(searchString);
+ if (seq.getStart() <= res && seq.getEnd() >= res)
+ {
+ searchResults.addResult(seq, res, res);
+ return true;
+ }
+ } catch (NumberFormatException ex)
+ {
+ }
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.analysis.FinderI#getIdMatch()
+ */
+ @Override
+ public Vector<SequenceI> getIdMatches()
+ {
+ return idMatches;
+ }
+
+ /* (non-Javadoc)
+ * @see jalview.analysis.FinderI#getSearchResults()
+ */
+ @Override
+ public SearchResultsI getSearchResults()
+ {
+ return searchResults;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff