+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
package jalview.analysis;
-import java.util.Vector;
+
+import java.util.*;
import jalview.datamodel.*;
-public class Finder {
- /**
- * Implements the search algorithms for the Find dialog box.
- */
- SearchResults searchResults;
- AlignmentI alignment;
- jalview.datamodel.SequenceGroup selection=null;
- Vector idMatch=null;
- boolean caseSensitive=false;
- boolean findAll=false;
- com.stevesoft.pat.Regex regex=null;
- public Finder(AlignmentI alignment, SequenceGroup selection) {
- this.alignment=alignment;
- this.selection = selection;
+public class Finder
+{
+ /**
+ * Implements the search algorithms for the Find dialog box.
+ */
+ SearchResults searchResults;
+
+ AlignmentI alignment;
+
+ jalview.datamodel.SequenceGroup selection = null;
+
+ Vector idMatch = null;
+
+ boolean caseSensitive = false;
+
+ boolean findAll = false;
+
+ com.stevesoft.pat.Regex regex = null;
+
+ /**
+ * hold's last-searched position between calles to find(false)
+ */
+ int seqIndex = 0, resIndex = -1;
+
+ public Finder(AlignmentI alignment, SequenceGroup selection)
+ {
+ this.alignment = alignment;
+ this.selection = selection;
+ }
+
+ /**
+ * restart search at given sequence and residue on alignment and (optionally)
+ * contained in selection
+ *
+ * @param alignment
+ * @param selectionGroup
+ * @param seqIndex
+ * @param resIndex
+ */
+ public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
+ int seqIndex, int resIndex)
+ {
+ this(alignment, selectionGroup);
+ this.seqIndex = seqIndex;
+ this.resIndex = resIndex;
+ }
+
+ public boolean find(String searchString)
+ {
+ boolean hasResults = false;
+ if (!caseSensitive)
+ {
+ searchString = searchString.toUpperCase();
+ }
+ regex = new com.stevesoft.pat.Regex(searchString);
+ regex.setIgnoreCase(!caseSensitive);
+ searchResults = new SearchResults();
+ idMatch = new Vector();
+ Sequence seq;
+ String item = null;
+ boolean found = false;
+ int end = alignment.getHeight();
+
+
+ // /////////////////////////////////////////////
+
+ if (selection != null)
+ {
+ if ((selection.getSize() < 1)
+ || ((selection.getEndRes() - selection.getStartRes()) < 2))
+ {
+ selection = null;
+ }
}
- public boolean find(String searchString) {
- boolean hasResults=false;
- if(!caseSensitive)
- searchString = searchString.toUpperCase();
- regex = new com.stevesoft.pat.Regex(searchString);
- searchResults = new SearchResults();
- idMatch = new Vector();
- Sequence seq;
- int seqIndex=0,resIndex=0;
- String item = null;
- boolean found = false;
-
- ////// is the searchString a residue number?
+
+ while (!found && (seqIndex < end))
+ {
+ seq = (Sequence) alignment.getSequenceAt(seqIndex);
+
+ if ((selection != null && selection.getSize() > 0)
+ && !selection.getSequences(null).contains(seq))
+ {
+ seqIndex++;
+ resIndex = -1;
+
+ continue;
+ }
+ if (resIndex < 0)
+ {
+ resIndex = 0;
+ // test for one off matches - sequence position and sequence ID
+ // //// is the searchString a residue number?
try
{
- int res = Integer.parseInt(searchString);
- found = true;
- if (selection == null || selection.getSize(false) < 1)
- {
- seq = (Sequence) alignment.getSequenceAt(0);
- }
- else
- {
- seq = (Sequence) (selection.getSequenceAt(0));
- }
-
+ int res = Integer.parseInt(searchString);
+ // possibly a residue number - check if valid for seq
+ if (seq.getEnd() >= res)
+ {
searchResults.addResult(seq, res, res);
- hasResults=true;
+ hasResults = true;
+ //resIndex=seq.getLength();
+ // seqIndex++;
+ if (!findAll) {
+ found = true;
+ break;
+ }
+ }
+ } catch (NumberFormatException ex)
+ {
}
- catch (NumberFormatException ex)
+
+ if (regex.search(seq.getName()))
{
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
}
+ }
+ item = seq.getSequenceAsString();
- ///////////////////////////////////////////////
+ if ((selection != null)
+ && (selection.getEndRes() < alignment.getWidth() - 1))
+ {
+ item = item.substring(0, selection.getEndRes() + 1);
+ }
- int end = alignment.getHeight();
+ // /Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
+ StringBuffer noGapsSB = new StringBuffer();
+ int insertCount = 0;
+ Vector spaces = new Vector();
-
- if (selection != null)
+ for (int j = 0; j < item.length(); j++)
+ {
+ if (!jalview.util.Comparison.isGap(item.charAt(j)))
{
- if ((selection.getSize(false) < 1) ||
- ((selection.getEndRes() - selection.getStartRes()) < 2))
- {
- selection = null;
- }
+ noGapsSB.append(item.charAt(j));
+ spaces.addElement(new Integer(insertCount));
}
-
- while (!found && (seqIndex < end))
+ else
{
- seq = (Sequence) alignment.getSequenceAt(seqIndex);
+ insertCount++;
+ }
+ }
- if ((selection != null) && !selection.getSequences(false).contains(seq))
- {
- seqIndex++;
- resIndex = 0;
+ String noGaps = noGapsSB.toString();
- continue;
- }
+ for (int r = resIndex; r < noGaps.length(); r++)
+ {
- item = seq.getSequenceAsString();
- // JBPNote - check if this toUpper which is present in the application implementation makes a difference
- //if(!caseSensitive)
- // item = item.toUpperCase();
+ if (regex.searchFrom(noGaps, r))
+ {
+ resIndex = regex.matchedFrom();
- if ((selection != null) &&
- (selection.getEndRes() < alignment.getWidth()-1))
- {
- item = item.substring(0, selection.getEndRes() + 1);
- }
-
- ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
- StringBuffer noGapsSB = new StringBuffer();
- int insertCount = 0;
- Vector spaces = new Vector();
-
- for (int j = 0; j < item.length(); j++)
- {
- if (!jalview.util.Comparison.isGap(item.charAt(j)))
- {
- noGapsSB.append(item.charAt(j));
- spaces.add(new Integer(insertCount));
- }
- else
- {
- insertCount++;
- }
- }
+ if ((selection != null && selection.getSize() > 0)
+ && ((resIndex + Integer.parseInt(spaces.elementAt(
+ resIndex).toString())) < selection.getStartRes()))
+ {
+ continue;
+ }
- String noGaps = noGapsSB.toString();
-
- for (int r = resIndex; r < noGaps.length(); r++)
- {
-
- if (regex.searchFrom(noGaps, r))
- {
- resIndex = regex.matchedFrom();
-
- if ((selection != null) &&
- ((resIndex +
- Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
- {
- continue;
- }
-
-
- int sres = seq.findPosition(resIndex +
- Integer.parseInt(spaces.elementAt(resIndex)
- .toString()));
- int eres = seq.findPosition(regex.matchedTo() - 1 +
- Integer.parseInt(spaces.elementAt(regex.matchedTo() -
- 1).toString()));
-
- searchResults.addResult(seq, sres, eres);
- hasResults=true;
- if (!findAll)
- {
- // thats enough, break and display the result
- found = true;
- resIndex++;
-
- break;
- }
-
- r = resIndex;
- }
- else
- {
- break;
- }
- }
+ int sres = seq
+ .findPosition(resIndex
+ + Integer.parseInt(spaces.elementAt(resIndex)
+ .toString()));
+ int eres = seq.findPosition(regex.matchedTo()
+ - 1
+ + Integer.parseInt(spaces
+ .elementAt(regex.matchedTo() - 1).toString()));
- if (!found)
- {
- seqIndex++;
- resIndex = 0;
- }
- }
+ searchResults.addResult(seq, sres, eres);
+ hasResults = true;
+ if (!findAll)
+ {
+ // thats enough, break and display the result
+ found = true;
+ resIndex++;
+
+ break;
+ }
- for (int id = 0; id < alignment.getHeight(); id++)
+ r = resIndex;
+ }
+ else
{
- if (regex.search(alignment.getSequenceAt(id).getName()))
- {
- idMatch.add(alignment.getSequenceAt(id));
- hasResults=true;
- }
+ break;
}
- return hasResults;
- }
- /**
- * @return the alignment
- */
- public AlignmentI getAlignment() {
- return alignment;
- }
- /**
- * @param alignment the alignment to set
- */
- public void setAlignment(AlignmentI alignment) {
- this.alignment = alignment;
- }
- /**
- * @return the caseSensitive
- */
- public boolean isCaseSensitive() {
- return caseSensitive;
- }
- /**
- * @param caseSensitive the caseSensitive to set
- */
- public void setCaseSensitive(boolean caseSensitive) {
- this.caseSensitive = caseSensitive;
- }
- /**
- * @return the findAll
- */
- public boolean isFindAll() {
- return findAll;
- }
- /**
- * @param findAll the findAll to set
- */
- public void setFindAll(boolean findAll) {
- this.findAll = findAll;
- }
- /**
- * @return the selection
- */
- public jalview.datamodel.SequenceGroup getSelection() {
- return selection;
- }
- /**
- * @param selection the selection to set
- */
- public void setSelection(jalview.datamodel.SequenceGroup selection) {
- this.selection = selection;
- }
- /**
- * @return the idMatch
- */
- public Vector getIdMatch() {
- return idMatch;
- }
- /**
- * @return the regex
- */
- public com.stevesoft.pat.Regex getRegex() {
- return regex;
+ }
+
+ if (!found)
+ {
+ seqIndex++;
+ resIndex = -1;
+ }
}
+
/**
- * @return the searchResults
+ * We now search the Id string in the main search loop. for (int id = 0; id
+ * < alignment.getHeight(); id++) { if
+ * (regex.search(alignment.getSequenceAt(id).getName())) {
+ * idMatch.addElement(alignment.getSequenceAt(id)); hasResults = true; } }
*/
- public SearchResults getSearchResults() {
- return searchResults;
- }
+ return hasResults;
+ }
+
+ /**
+ * @return the alignment
+ */
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ /**
+ * @param alignment
+ * the alignment to set
+ */
+ public void setAlignment(AlignmentI alignment)
+ {
+ this.alignment = alignment;
+ }
+
+ /**
+ * @return the caseSensitive
+ */
+ public boolean isCaseSensitive()
+ {
+ return caseSensitive;
+ }
+
+ /**
+ * @param caseSensitive
+ * the caseSensitive to set
+ */
+ public void setCaseSensitive(boolean caseSensitive)
+ {
+ this.caseSensitive = caseSensitive;
+ }
+
+ /**
+ * @return the findAll
+ */
+ public boolean isFindAll()
+ {
+ return findAll;
+ }
+
+ /**
+ * @param findAll
+ * the findAll to set
+ */
+ public void setFindAll(boolean findAll)
+ {
+ this.findAll = findAll;
+ }
+
+ /**
+ * @return the selection
+ */
+ public jalview.datamodel.SequenceGroup getSelection()
+ {
+ return selection;
+ }
+
+ /**
+ * @param selection
+ * the selection to set
+ */
+ public void setSelection(jalview.datamodel.SequenceGroup selection)
+ {
+ this.selection = selection;
+ }
+
+ /**
+ * @return the idMatch
+ */
+ public Vector getIdMatch()
+ {
+ return idMatch;
+ }
+
+ /**
+ * @return the regex
+ */
+ public com.stevesoft.pat.Regex getRegex()
+ {
+ return regex;
+ }
+
+ /**
+ * @return the searchResults
+ */
+ public SearchResults getSearchResults()
+ {
+ return searchResults;
+ }
+
+ /**
+ * @return the resIndex
+ */
+ public int getResIndex()
+ {
+ return resIndex;
+ }
+
+ /**
+ * @param resIndex
+ * the resIndex to set
+ */
+ public void setResIndex(int resIndex)
+ {
+ this.resIndex = resIndex;
+ }
+
+ /**
+ * @return the seqIndex
+ */
+ public int getSeqIndex()
+ {
+ return seqIndex;
+ }
+
+ /**
+ * @param seqIndex
+ * the seqIndex to set
+ */
+ public void setSeqIndex(int seqIndex)
+ {
+ this.seqIndex = seqIndex;
+ }
}
git://source.jalview.org / jalview.git / blobdiff