/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
import jalview.bin.Cache;\r
import jalview.datamodel.*;\r
import jalview.gui.*;\r
+import jalview.util.UrlLink;\r
\r
/**\r
* DOCUMENT ME!\r
* Creates a new SequenceFeatureFetcher object. Uses default\r
* \r
* @param align\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
* @param ap\r
- * DOCUMENT ME!\r
+ * DOCUMENT ME!\r
*/\r
public DasSequenceFeatureFetcher(SequenceI[] sequences,\r
FeatureSettings fsettings, Vector selectedSources)\r
this(sequences, fsettings, selectedSources, true, true);\r
}\r
\r
- public DasSequenceFeatureFetcher(SequenceI[] sequences,\r
- FeatureSettings fsettings, Vector selectedSources,\r
+ public DasSequenceFeatureFetcher(SequenceI[] oursequences,\r
+ FeatureSettings fsettings, Vector ourselectedSources,\r
boolean checkDbrefs, boolean promptFetchDbrefs)\r
{\r
- this.selectedSources = selectedSources;\r
- this.sequences = sequences;\r
+ this.selectedSources = new Vector();\r
+ Enumeration sources = ourselectedSources.elements();\r
+ // filter both sequences and sources to eliminate duplicates\r
+ while (sources.hasMoreElements())\r
+ {\r
+ Object src = sources.nextElement();\r
+ if (!selectedSources.contains(src))\r
+ {\r
+ selectedSources.addElement(src);\r
+ }\r
+ ;\r
+ }\r
+ Vector sqs = new Vector();\r
+ for (int i = 0; i < oursequences.length; i++)\r
+ {\r
+ if (!sqs.contains(oursequences[i]))\r
+ {\r
+ sqs.addElement(oursequences[i]);\r
+ }\r
+ }\r
+ sequences = new SequenceI[sqs.size()];\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ sequences[i] = (SequenceI) sqs.elementAt(i);\r
+ }\r
if (fsettings != null)\r
{\r
this.fsettings = fsettings;\r
this.af = fsettings.af;\r
- af.getViewport().setShowSequenceFeatures(true);\r
+ af.setShowSeqFeatures(true);\r
}\r
int uniprotCount = 0;\r
for (int i = 0; i < selectedSources.size(); i++)\r
af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
}\r
\r
- DasSource[] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
-\r
if (selectedSources == null || selectedSources.size() == 0)\r
{\r
- String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",\r
- "uniprot");\r
- StringTokenizer st = new StringTokenizer(active, "\t");\r
- Vector selectedSources = new Vector();\r
- String token;\r
- while (st.hasMoreTokens())\r
+ try\r
{\r
- token = st.nextToken();\r
- for (int i = 0; i < sources.length; i++)\r
+ DasSource[] sources = new jalview.gui.DasSourceBrowser()\r
+ .getDASSource();\r
+\r
+ String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",\r
+ "uniprot");\r
+ StringTokenizer st = new StringTokenizer(active, "\t");\r
+ selectedSources = new Vector();\r
+ String token;\r
+ while (st.hasMoreTokens())\r
{\r
- if (sources[i].getNickname().equals(token))\r
+ token = st.nextToken();\r
+ for (int i = 0; i < sources.length; i++)\r
{\r
- selectedSources.addElement(sources[i]);\r
- break;\r
+ if (sources[i].getNickname().equals(token))\r
+ {\r
+ selectedSources.addElement(sources[i]);\r
+ break;\r
+ }\r
}\r
}\r
+ } catch (Exception ex)\r
+ {\r
+ debug("Exception whilst setting default feature sources from registry and local preferences.",\r
+ ex);\r
}\r
}\r
\r
private void setGuiFetchComplete()\r
{\r
\r
- if (af != null)\r
+ if (!cancelled && af != null)\r
{\r
+ // only update the progress bar if we've completed the fetch normally\r
af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
}\r
\r
{\r
for (int i = 0; i < features.length; i++)\r
{\r
- SequenceFeature f = newSequenceFeature(features[i], source\r
- .getNickname());\r
- if (dbref.getMap() != null && f.getBegin() > 0\r
- && f.getEnd() > 0)\r
+ // standard DAS feature-> jalview sequence feature transformation\r
+ SequenceFeature f = newSequenceFeature(features[i],\r
+ source.getNickname());\r
+ if (!parseSeqFeature(seq, f, features[i], source))\r
{\r
- debug("mapping from " + f.getBegin() + " - " + f.getEnd());\r
- SequenceFeature vf[] = null;\r
-\r
- try\r
- {\r
- vf = dbref.getMap().locateFeature(f);\r
- } catch (Exception ex)\r
+ if (dbref.getMap() != null && f.getBegin() > 0\r
+ && f.getEnd() > 0)\r
{\r
- Cache.log\r
- .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to help@jalview.org.");\r
- Cache.log.info("Mapping feature from " + f.getBegin()\r
- + " to " + f.getEnd() + " in dbref "\r
- + dbref.getAccessionId() + " in "\r
- + dbref.getSource());\r
- Cache.log.info("using das Source " + ds.getUrl());\r
- Cache.log.info("Exception", ex);\r
- }\r
+ debug("mapping from " + f.getBegin() + " - " + f.getEnd());\r
+ SequenceFeature vf[] = null;\r
\r
- if (vf != null)\r
- {\r
- for (int v = 0; v < vf.length; v++)\r
+ try\r
{\r
- debug("mapping to " + v + ": " + vf[v].getBegin() + " - "\r
- + vf[v].getEnd());\r
- seq.addSequenceFeature(vf[v]);\r
+ vf = dbref.getMap().locateFeature(f);\r
+ } catch (Exception ex)\r
+ {\r
+ Cache.log\r
+ .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");\r
+ Cache.log.info("Mapping feature from " + f.getBegin()\r
+ + " to " + f.getEnd() + " in dbref "\r
+ + dbref.getAccessionId() + " in "\r
+ + dbref.getSource());\r
+ Cache.log.info("using das Source " + ds.getUrl());\r
+ Cache.log.info("Exception", ex);\r
+ }\r
+\r
+ if (vf != null)\r
+ {\r
+ for (int v = 0; v < vf.length; v++)\r
+ {\r
+ debug("mapping to " + v + ": " + vf[v].getBegin()\r
+ + " - " + vf[v].getEnd());\r
+ seq.addSequenceFeature(vf[v]);\r
+ }\r
}\r
}\r
- }\r
- else\r
- {\r
- seq.addSequenceFeature(f);\r
+ else\r
+ {\r
+ seq.addSequenceFeature(f);\r
+ }\r
}\r
}\r
-\r
featuresAdded(seq);\r
}\r
else\r
{\r
for (int i = 0; i < features.length; i++)\r
{\r
- SequenceFeature f = newSequenceFeature(features[i], source\r
- .getNickname());\r
-\r
- seq.addSequenceFeature(f);\r
+ // standard DAS feature-> jalview sequence feature transformation\r
+ SequenceFeature f = newSequenceFeature(features[i],\r
+ source.getNickname());\r
+ if (!parseSeqFeature(seq, f, features[i], source))\r
+ {\r
+ // just add as a simple sequence feature\r
+ seq.addSequenceFeature(f);\r
+ }\r
}\r
\r
featuresAdded(seq);\r
}\r
\r
/**\r
+ * examine the given sequence feature to determine if it should actually be\r
+ * turned into sequence annotation or database cross references rather than a\r
+ * simple sequence feature.\r
+ * \r
+ * @param seq\r
+ * the sequence to annotate\r
+ * @param f\r
+ * the jalview sequence feature generated from the DAS feature\r
+ * @param map\r
+ * the sequence feature attributes\r
+ * @param source\r
+ * the source that emitted the feature\r
+ * @return true if feature was consumed as another kind of annotation.\r
+ */\r
+ protected boolean parseSeqFeature(SequenceI seq, SequenceFeature f,\r
+ Map map, Das1Source source)\r
+ {\r
+ SequenceI mseq = seq;\r
+ while (seq.getDatasetSequence() != null)\r
+ {\r
+ seq = seq.getDatasetSequence();\r
+ }\r
+ if (f.getType() != null)\r
+ {\r
+ String type = f.getType();\r
+ if (type.equalsIgnoreCase("protein_name"))\r
+ {\r
+ // parse name onto the alignment sequence or the dataset sequence.\r
+ if (seq.getDescription() == null\r
+ || seq.getDescription().trim().length() == 0)\r
+ {\r
+ // could look at the note series to pick out the first long name, for\r
+ // the moment just use the whole description string\r
+ seq.setDescription(f.getDescription());\r
+ }\r
+ if (mseq.getDescription() == null\r
+ || mseq.getDescription().trim().length() == 0)\r
+ {\r
+ // could look at the note series to pick out the first long name, for\r
+ // the moment just use the whole description string\r
+ mseq.setDescription(f.getDescription());\r
+ }\r
+ return true;\r
+ }\r
+ // check if source has biosapiens or other sequence ontology label\r
+ if (type.equalsIgnoreCase("DBXREF") || type.equalsIgnoreCase("DBREF"))\r
+ {\r
+ // try to parse the accession out\r
+\r
+ DBRefEntry dbr = new DBRefEntry();\r
+ dbr.setVersion(source.getNickname());\r
+ StringTokenizer st = new StringTokenizer(f.getDescription(), ":");\r
+ if (st.hasMoreTokens())\r
+ {\r
+ dbr.setSource(st.nextToken());\r
+ }\r
+ if (st.hasMoreTokens())\r
+ {\r
+ dbr.setAccessionId(st.nextToken());\r
+ }\r
+ seq.addDBRef(dbr);\r
+\r
+ if (f.links != null && f.links.size() > 0)\r
+ {\r
+ // feature is also appended to enable links to be seen.\r
+ // TODO: consider extending dbrefs to have their own links ?\r
+ // TODO: new feature: extract dbref links from DAS servers and add the\r
+ // URL pattern to the list of DB name associated links in the user's\r
+ // preferences ?\r
+ // for the moment - just fix up the existing feature so it displays\r
+ // correctly.\r
+ // f.setType(dbr.getSource());\r
+ // f.setDescription();\r
+ f.setValue("linkonly", Boolean.TRUE);\r
+ // f.setDescription("");\r
+ Vector newlinks = new Vector();\r
+ Enumeration it = f.links.elements();\r
+ while (it.hasMoreElements())\r
+ {\r
+ String elm;\r
+ UrlLink urllink = new UrlLink(elm = (String) it.nextElement());\r
+ if (urllink.isValid())\r
+ {\r
+ urllink.setLabel(f.getDescription());\r
+ newlinks.addElement(urllink.toString());\r
+ }\r
+ else\r
+ {\r
+ // couldn't parse the link properly. Keep it anyway - just in\r
+ // case.\r
+ debug("couldn't parse link string - " + elm);\r
+ newlinks.addElement(elm);\r
+ }\r
+ }\r
+ f.links = newlinks;\r
+ seq.addSequenceFeature(f);\r
+ }\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /**\r
* creates a jalview sequence feature from a das feature document\r
* \r
* @param dasfeature\r
}\r
try\r
{\r
- score = (float) Double.parseDouble(dasfeature.get("SCORE").toString());\r
+ Object scr = dasfeature.get("SCORE");\r
+ if (scr != null)\r
+ {\r
+ score = (float) Double.parseDouble(scr.toString());\r
+\r
+ }\r
} catch (Exception ex)\r
{\r
}\r
\r
- SequenceFeature f = new SequenceFeature((String) dasfeature\r
- .get("TYPE"), desc, start, end, score, nickname);\r
+ SequenceFeature f = new SequenceFeature(\r
+ (String) dasfeature.get("TYPE"), desc, start, end, score,\r
+ nickname);\r
\r
if (dasfeature.containsKey("LINK"))\r
{\r
// Do not put feature extent in link text for non-positional features\r
- if (f.begin==0 && f.end==0)\r
- { f.addLink(f.getType()+"|"\r
- + dasfeature.get("LINK"));\r
- } else {\r
+ if (f.begin == 0 && f.end == 0)\r
+ {\r
+ f.addLink(f.getType() + "|" + dasfeature.get("LINK"));\r
+ }\r
+ else\r
+ {\r
f.addLink(f.getType() + " " + f.begin + "_" + f.end + "|"\r
- + dasfeature.get("LINK"));\r
+ + dasfeature.get("LINK"));\r
}\r
}\r
\r
* query the given URL for DasSources.\r
* \r
* @param registryURL\r
- * return sources from registryURL\r
+ * return sources from registryURL\r
*/\r
public static DasSource[] getDASSources(String registryURL)\r
{\r
.size()]);\r
} catch (Exception ex)\r
{\r
+ System.err.println("Failed to contact DAS1 registry at "\r
+ + registryURL);\r
ex.printStackTrace();\r
return null;\r
}\r
git://source.jalview.org / jalview.git / blobdiff