/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.ws;\r
\r
DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry\r
.getDBRef(), new String[]\r
{ dbSource });\r
+ if (entryRefs == null)\r
+ {\r
+ System.err\r
+ .println("Dud dbSource string ? no entryrefs selected for "\r
+ + dbSource + " on " + entry.getName());\r
+ continue;\r
+ }\r
for (int j = 0; j < entryRefs.length; j++)\r
{\r
String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();\r
// absStart+sequence.getStart()+entrySeq.length()-1},\r
// new int[] { entry.getStart(), entry.getEnd() }, 1, 1);\r
// relocate local features for updated start\r
- if (updateRefFrame) {\r
+ if (updateRefFrame)\r
+ {\r
if (sequence.getSequenceFeatures() != null)\r
{\r
- SequenceFeature[] sf = sequence.getSequenceFeatures();\r
- int start = sequence.getStart();\r
- int end = sequence.getEnd();\r
- int startShift = 1 - absStart - start; // how much the features are\r
- // to be shifted by\r
- for (int sfi = 0; sfi < sf.length; sfi++)\r
- {\r
- if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)\r
+ SequenceFeature[] sf = sequence.getSequenceFeatures();\r
+ int start = sequence.getStart();\r
+ int end = sequence.getEnd();\r
+ int startShift = 1 - absStart - start; // how much the features\r
+ // are\r
+ // to be shifted by\r
+ for (int sfi = 0; sfi < sf.length; sfi++)\r
{\r
- // shift feature along by absstart\r
- sf[sfi].setBegin(sf[sfi].getBegin() + startShift);\r
- sf[sfi].setEnd(sf[sfi].getEnd() + startShift);\r
+ if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)\r
+ {\r
+ // shift feature along by absstart\r
+ sf[sfi].setBegin(sf[sfi].getBegin() + startShift);\r
+ sf[sfi].setEnd(sf[sfi].getEnd() + startShift);\r
+ }\r
}\r
}\r
- }\r
}\r
}\r
\r
sequence.setStart(absStart);\r
sequence.setEnd(absEnd);\r
// search for alignment sequences to update coordinate frame for\r
- for (int alsq = 0; alsq<alseqs.length; alsq++)\r
+ for (int alsq = 0; alsq < alseqs.length; alsq++)\r
{\r
- if (alseqs[alsq].getDatasetSequence()==sequence)\r
+ if (alseqs[alsq].getDatasetSequence() == sequence)\r
{\r
String ngAlsq = AlignSeq.extractGaps("-. ",\r
alseqs[alsq].getSequenceAsString()).toUpperCase();\r
int oldstrt = alseqs[alsq].getStart();\r
- alseqs[alsq].setStart(sequence.getSequenceAsString().toUpperCase().indexOf(ngAlsq)+sequence.getStart());\r
- if (oldstrt != alseqs[alsq].getStart()) {\r
- alseqs[alsq].setEnd(ngAlsq.length()+alseqs[alsq].getStart()-1);\r
+ alseqs[alsq].setStart(sequence.getSequenceAsString()\r
+ .toUpperCase().indexOf(ngAlsq)\r
+ + sequence.getStart());\r
+ if (oldstrt != alseqs[alsq].getStart())\r
+ {\r
+ alseqs[alsq].setEnd(ngAlsq.length()\r
+ + alseqs[alsq].getStart() - 1);\r
}\r
}\r
}\r
- // TODO: search for all other references to this dataset sequence, and update start/end\r
- // TODO: update all AlCodonMappings which involve this alignment sequence (e.g. Q30167 cdna translation from exon2 product (vamsas demo)\r
+ // TODO: search for all other references to this dataset sequence, and\r
+ // update start/end\r
+ // TODO: update all AlCodonMappings which involve this alignment\r
+ // sequence (e.g. Q30167 cdna translation from exon2 product (vamsas\r
+ // demo)\r
}\r
// and remove it from the rest\r
// TODO: decide if we should remove annotated sequence from set\r
git://source.jalview.org / jalview.git / blobdiff