/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.analysis;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.*;
+import java.util.Vector;
public class Finder
{
boolean caseSensitive = false;
+ private boolean includeDescription = false;
+
boolean findAll = false;
com.stevesoft.pat.Regex regex = null;
/**
* hold's last-searched position between calles to find(false)
*/
- int seqIndex = 0, resIndex = 0;
+ int seqIndex = 0, resIndex = -1;
public Finder(AlignmentI alignment, SequenceGroup selection)
{
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)
{
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;
-
- // //// is the searchString a residue number?
- try
- {
- int res = Integer.parseInt(searchString);
- found = true;
- if (selection == null || selection.getSize() < 1)
- {
- seq = (Sequence) alignment.getSequenceAt(0);
- }
- else
- {
- seq = (Sequence) (selection.getSequenceAt(0));
- }
-
- searchResults.addResult(seq, res, res);
- hasResults = true;
- } catch (NumberFormatException ex)
- {
- }
+ int end = alignment.getHeight();
// /////////////////////////////////////////////
- int end = alignment.getHeight();
-
if (selection != null)
{
if ((selection.getSize() < 1)
{
seq = (Sequence) alignment.getSequenceAt(seqIndex);
- if ((selection != null)
+ if ((selection != null && selection.getSize() > 0)
&& !selection.getSequences(null).contains(seq))
{
seqIndex++;
- resIndex = 0;
+ 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);
+ // possibly a residue number - check if valid for seq
+ if (seq.getEnd() >= res)
+ {
+ searchResults.addResult(seq, res, res);
+ hasResults = true;
+ // resIndex=seq.getLength();
+ // seqIndex++;
+ if (!findAll)
+ {
+ found = true;
+ break;
+ }
+ }
+ } catch (NumberFormatException ex)
+ {
+ }
+ if (regex.search(seq.getName()))
+ {
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
+ }
+
+ if (isIncludeDescription() && seq.getDescription() != null
+ && regex.search(seq.getDescription()))
+ {
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
+ }
+ }
item = seq.getSequenceAsString();
- if (!caseSensitive)
- item = item.toUpperCase();
if ((selection != null)
&& (selection.getEndRes() < alignment.getWidth() - 1))
{
resIndex = regex.matchedFrom();
- if ((selection != null)
+ if ((selection != null && selection.getSize() > 0)
&& ((resIndex + Integer.parseInt(spaces.elementAt(
resIndex).toString())) < selection.getStartRes()))
{
continue;
}
-
+ // if invalid string used, then regex has no matched to/from
int sres = seq
.findPosition(resIndex
+ Integer.parseInt(spaces.elementAt(resIndex)
if (!found)
{
seqIndex++;
- resIndex = 0;
+ resIndex = -1;
}
}
- for (int id = 0; id < alignment.getHeight(); id++)
- {
- if (regex.search(alignment.getSequenceAt(id).getName()))
- {
- idMatch.addElement(alignment.getSequenceAt(id));
- hasResults = true;
- }
- }
+ /**
+ * 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; } }
+ */
return hasResults;
}
/**
* @param alignment
- * the alignment to set
+ * the alignment to set
*/
public void setAlignment(AlignmentI alignment)
{
/**
* @param caseSensitive
- * the caseSensitive to set
+ * the caseSensitive to set
*/
public void setCaseSensitive(boolean caseSensitive)
{
/**
* @param findAll
- * the findAll to set
+ * the findAll to set
*/
public void setFindAll(boolean findAll)
{
/**
* @param selection
- * the selection to set
+ * the selection to set
*/
public void setSelection(jalview.datamodel.SequenceGroup selection)
{
/**
* @param resIndex
- * the resIndex to set
+ * the resIndex to set
*/
public void setResIndex(int resIndex)
{
/**
* @param seqIndex
- * the seqIndex to set
+ * the seqIndex to set
*/
public void setSeqIndex(int seqIndex)
{
this.seqIndex = seqIndex;
}
+
+ public boolean isIncludeDescription()
+ {
+ return includeDescription;
+ }
+
+ public void setIncludeDescription(boolean includeDescription)
+ {
+ this.includeDescription = includeDescription;
+ }
}
git://source.jalview.org / jalview.git / blobdiff