/*\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, 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
* 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
}\r
\r
public DasSequenceFeatureFetcher(SequenceI[] oursequences,\r
- FeatureSettings fsettings, Vector selectedSources,\r
+ FeatureSettings fsettings, Vector ourselectedSources,\r
boolean checkDbrefs, boolean promptFetchDbrefs)\r
{\r
- this.selectedSources = new Vector(); \r
- Enumeration sources = selectedSources.elements();\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 (this.selectedSources.contains(src)) { selectedSources.addElement(src); };\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
+ for (int i = 0; i < oursequences.length; i++)\r
{\r
if (!sqs.contains(oursequences[i]))\r
{\r
}\r
}\r
sequences = new SequenceI[sqs.size()];\r
- for (int i=0; i<sequences.length; i++) {\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
sequences[i] = (SequenceI) sqs.elementAt(i);\r
}\r
if (fsettings != null)\r
af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
}\r
\r
-\r
if (selectedSources == null || selectedSources.size() == 0)\r
{\r
- try {\r
- DasSource[] sources = new jalview.gui.DasSourceBrowser().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
+ 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
- }\r
} catch (Exception ex)\r
{\r
- debug("Exception whilst setting default feature sources from registry and local preferences.",ex);\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
for (int i = 0; i < features.length; i++)\r
{\r
// standard DAS feature-> jalview sequence feature transformation\r
- SequenceFeature f = newSequenceFeature(features[i], source\r
- .getNickname());\r
+ SequenceFeature f = newSequenceFeature(features[i],\r
+ source.getNickname());\r
if (!parseSeqFeature(seq, f, features[i], source))\r
{\r
if (dbref.getMap() != null && f.getBegin() > 0\r
for (int i = 0; i < features.length; i++)\r
{\r
// standard DAS feature-> jalview sequence feature transformation\r
- SequenceFeature f = newSequenceFeature(features[i], source\r
- .getNickname());\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
* simple sequence feature.\r
* \r
* @param seq\r
- * the sequence to annotate\r
+ * the sequence to annotate\r
* @param f\r
- * the jalview sequence feature generated from the DAS feature\r
+ * the jalview sequence feature generated from the DAS feature\r
* @param map\r
- * the sequence feature attributes\r
+ * the sequence feature attributes\r
* @param source\r
- * the source that emitted the feature\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
+ while (seq.getDatasetSequence() != null)\r
{\r
seq = seq.getDatasetSequence();\r
}\r
if (type.equalsIgnoreCase("protein_name"))\r
{\r
// parse name onto the alignment sequence or the dataset sequence.\r
- if (seq.getDescription()==null || seq.getDescription().trim().length() == 0)\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 the moment just use the whole description string \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 || mseq.getDescription().trim().length() == 0)\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 the moment just use the whole description string \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
dbr.setAccessionId(st.nextToken());\r
}\r
seq.addDBRef(dbr);\r
- \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 URL pattern to the list of DB name associated links in the user's preferences ?\r
- // for the moment - just fix up the existing feature so it displays correctly.\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.setDescription();\r
f.setValue("linkonly", Boolean.TRUE);\r
- //f.setDescription("");\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
+ UrlLink urllink = new UrlLink(elm = (String) it.nextElement());\r
+ if (urllink.isValid())\r
+ {\r
urllink.setLabel(f.getDescription());\r
newlinks.addElement(urllink.toString());\r
- } else {\r
- // couldn't parse the link properly. Keep it anyway - just in case.\r
- debug("couldn't parse link string - "+elm);\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
{\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
* 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