/*\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 2.5)\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.io.vamsas;\r
\r
public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,\r
DataSetAnnotations dseta, SequenceI dsSeq)\r
{\r
- super(vamsasAppDatastore, dseta, jalview.datamodel.SequenceFeature.class);\r
+ super(vamsasAppDatastore, dseta,\r
+ jalview.datamodel.SequenceFeature.class);\r
this.dsSeq = dsSeq;\r
doJvUpdate();\r
}\r
public void addFromDocument()\r
{\r
DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
- if (dsa.getSeqRefCount()!=1)\r
+ if (dsa.getSeqRefCount() != 1)\r
{\r
- Cache.log.warn("Not binding "+dsa.getVorbaId()+" to Sequence Feature - has multiple dataset sequence references.");\r
+ Cache.log\r
+ .warn("Not binding "\r
+ + dsa.getVorbaId()\r
+ + " to Sequence Feature - has multiple dataset sequence references.");\r
return;\r
}\r
jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;\r
DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;\r
jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);\r
- replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature to newly created feature\r
+ replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature\r
+ // to newly created feature\r
dsSeq.addSequenceFeature(sf); // add new imported feature\r
- addToDocument(); // and create a new feature in the document \r
+ addToDocument(); // and create a new feature in the document\r
}\r
\r
public void updateToDoc()\r
}\r
\r
}\r
+\r
public void updateFromDoc()\r
{\r
DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
// conflicting update from document - we cannot map this feature anymore.\r
replaceJvObjMapping(feature, null);\r
Cache.log\r
- .warn("annotation ("+dsa.getVorbaId()+" bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");\r
- // - consider deleting the feature ?\r
+ .warn("annotation ("\r
+ + dsa.getVorbaId()\r
+ + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");\r
+ // - consider deleting the feature ?\r
dsSeq.deleteFeature(feature);\r
// doSync();\r
}\r
else\r
{\r
- // Sync the features to Jalview - easiest to delete and add the feature again\r
+ // Sync the features to Jalview - easiest to delete and add the feature\r
+ // again\r
jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);\r
dsSeq.deleteFeature(feature);\r
replaceJvObjMapping(feature, newsf);\r
dsSeq.addSequenceFeature(newsf);\r
- if (feature.otherDetails!=null) {\r
- // TODO later: leave this to finalise method ? \r
+ if (feature.otherDetails != null)\r
+ {\r
+ // TODO later: leave this to finalise method ?\r
feature.otherDetails.clear();\r
}\r
}\r
* TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class\r
* \r
* @param dsa\r
- * (typically DataSetAnnotations or\r
- * AlignmentSequenceAnnotation)\r
+ * (typically DataSetAnnotations or AlignmentSequenceAnnotation)\r
* @param feature\r
- * (the feature to be mapped from)\r
+ * (the feature to be mapped from)\r
* @return\r
*/\r
private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,\r
}\r
return dsa;\r
}\r
+\r
private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)\r
{\r
int[] se = getBounds(dseta);\r
{\r
Link[] links = dseta.getLink();\r
for (int i = 0; i < links.length; i++)\r
- { \r
+ {\r
// TODO: use URLLink parsing/validation here.\r
sf.addLink(links[i].getContent() + "|" + links[i].getHref());\r
}\r
}\r
- if (dseta.getScoreCount()>0)\r
+ if (dseta.getScoreCount() > 0)\r
{\r
Enumeration scr = dseta.enumerateScore();\r
while (scr.hasMoreElements())\r
if (score.getName().equals(sf.getType()))\r
{\r
sf.setScore(score.getContent());\r
- } else {\r
- sf.setValue(score.getName(), ""+score.getContent());\r
+ }\r
+ else\r
+ {\r
+ sf.setValue(score.getName(), "" + score.getContent());\r
}\r
}\r
}\r
{\r
Property p = (Property) props.nextElement();\r
Object val = null;\r
- if (Properties.isValid(p)) \r
+ if (Properties.isValid(p))\r
{\r
if (Properties.isString(p))\r
{\r
- val = p.getContent();\r
+ val = p.getContent();\r
}\r
if (Properties.isBoolean(p))\r
{\r
- try {\r
+ try\r
+ {\r
val = new Boolean(p.getContent());\r
- } catch (Exception e) {}\r
+ } catch (Exception e)\r
+ {\r
+ }\r
}\r
if (Properties.isFloat(p))\r
{\r
- try {\r
- val = new Float(p.getContent());\r
- \r
- } catch (Exception e)\r
- {\r
- }\r
+ try\r
+ {\r
+ val = new Float(p.getContent());\r
+\r
+ } catch (Exception e)\r
+ {\r
}\r
- if(Properties.isInteger(p))\r
+ }\r
+ if (Properties.isInteger(p))\r
{\r
- try {\r
- val = new Integer(p.getContent());\r
+ try\r
+ {\r
+ val = new Integer(p.getContent());\r
} catch (Exception e)\r
{\r
- } \r
+ }\r
}\r
- if (val!=null)\r
+ if (val != null)\r
{\r
sf.setValue(p.getName(), val);\r
}\r
git://source.jalview.org / jalview.git / blobdiff