/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * 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.
*
- * 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
+ * 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;
}
/**
- * restart search at given sequence and residue on alignment and (optionally) contained in selection
+ * restart search at given sequence and residue on alignment and (optionally)
+ * contained in selection
+ *
* @param alignment
* @param selectionGroup
* @param seqIndex
{
seq = (Sequence) alignment.getSequenceAt(seqIndex);
- if ((selection != null && selection.getSize()>0)
+ if ((selection != null && selection.getSize() > 0)
&& !selection.getSequences(null).contains(seq))
{
seqIndex++;
continue;
}
- if (resIndex<0) {
- resIndex=0;
+ if (resIndex < 0)
+ {
+ resIndex = 0;
if (regex.search(seq.getName()))
{
idMatch.addElement(seq);
if (!findAll)
{
// stop and return the match
- found=true;
+ found = true;
break;
}
}
{
resIndex = regex.matchedFrom();
- if ((selection != null && selection.getSize()>0)
+ if ((selection != null && selection.getSize() > 0)
&& ((resIndex + Integer.parseInt(spaces.elementAt(
resIndex).toString())) < selection.getStartRes()))
{
}
/**
- * 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;
- }
- } */
+ * 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)
{