Difference between revisions of "DASworkshop200903"
From BioDAS
(→Day 3) |
(→Chromsome.java) |
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*/ | */ | ||
public class Chromosome { | public class Chromosome { | ||
| − | |||
private String id=""; | private String id=""; | ||
private int start=1; | private int start=1; | ||
private int end; | private int end; | ||
ArrayList features; | ArrayList features; | ||
| − | |||
public Chromosome(String id, int end){ | public Chromosome(String id, int end){ | ||
this.id=id; | this.id=id; | ||
this.end=end; | this.end=end; | ||
features =new ArrayList(); | features =new ArrayList(); | ||
| − | |||
} | } | ||
| − | |||
public void addFeature(GFFFeature feature){ | public void addFeature(GFFFeature feature){ | ||
this.features.add(feature); | this.features.add(feature); | ||
} | } | ||
| − | |||
public GFFFeature[] getFeatures(Segment seg){ | public GFFFeature[] getFeatures(Segment seg){ | ||
System.out.println("seg in chromosome="+seg); | System.out.println("seg in chromosome="+seg); | ||
| Line 217: | Line 212: | ||
//loop over arraylist of features and return a lis | //loop over arraylist of features and return a lis | ||
Iterator it=features.iterator(); | Iterator it=features.iterator(); | ||
| − | + | while(it.hasNext()){ | |
| − | |||
GFFFeature feature=(GFFFeature)it.next(); | GFFFeature feature=(GFFFeature)it.next(); | ||
int fStart=Integer.parseInt(feature.getStart()); | int fStart=Integer.parseInt(feature.getStart()); | ||
| Line 225: | Line 219: | ||
if((fStart>=start && fStart<=stop)||(fStop<=stop && fStop>=start)){ | if((fStart>=start && fStart<=stop)||(fStop<=stop && fStop>=start)){ | ||
featuresOnSegment.add(feature); | featuresOnSegment.add(feature); | ||
| − | |||
} | } | ||
} | } | ||
| Line 231: | Line 224: | ||
GFFFeature[featuresOnSegment.size()]); | GFFFeature[featuresOnSegment.size()]); | ||
//return new GFFFeature[0]; | //return new GFFFeature[0]; | ||
| − | |||
} | } | ||
| − | |||
| − | |||
} | } | ||
Revision as of 10:26, 9 March 2009
Contents
DAS workshop March 9th-11th 2009 Genome Campus, Hinxton
BioSapiens Network
Day 1
| Time | Title | Speaker | Resources |
|---|---|---|---|
| 8:45 - 9:30 | Minibus/Taxis to pick attendees up from hotels and bring to Campus | ||
| 9:30 - 10:00 | Coffee is served outside the training room | ||
| 10:00 - 10:10 | Welcome and Introduction to the Workshop | Jonathan Warren | |
| 10:10 - 11:10 | DAS - Technical Introduction | Andy Jenkinson | Powerpoint 2008 |
| 11:10 - 11:30 | The DAS Registration Service | Jonathan Warren | The Registry |
| 11:30 - 12:15 | Putting it all together | Rob Finn | |
| 12:15 - 13:15 | Lunch break | ||
| 13:15 - 15:10 | Hands On Tutorial - Setting up a DAS Server and creating a DAS Client. The room will be split into two groups: one for Java and one for Perl. | Jonathan Warren and Andy Jenkinson | Java server: Dazzle tutorial Java client: Dasobert tutorial |
| 15:10 - 15:30 | Coffee break | ||
| 15:30 - 16:30 | Hands On Tutorial - continued | ||
Day 2
| Time | ProjectName | Speaker | Presentation |
|---|---|---|---|
| 09:30 - 10:00 | Arrival - Tea, Coffee. | ||
| 10:00 | Opening talk | Tim Hubbard | |
| 10:20 | Collaborative Annotation tool (MaDAS) | Victor de la Torre | |
| 10:40 | Jalview / VAMSAS | Jim Procter / Geoff Barton | |
| 11:00 | Pfam | Rob Finn | |
| 11:20 | DASgenexp | Bernat Gel | |
| 11:40 | Dasty2 | Rafael Jimenez | |
| 12:00 | EMBOSS as an efficient DAS annotation source | Peter Rice, Mahmut Uludag | |
| 12:15-13:30 | Lunch break | ||
| 13:30 | Ensembl | James Smith | |
| 13:50 | Integration of info on gene expression and its temporal and spatial localization | Jose Ramon Macias | |
| 14:10 | DAS - writeback | Gustavo Salazar | |
| 14:30 | Interaction DAS | Hagen Blankenburg | |
| 14:50 | DAS for ENCODE data coordination | Felix Kokocinski | |
| 15:10-15:30 | coffee break | ||
| 15:30 | A web resource for selecting epitopes for antibodies | Niall Haslam | |
| 15:50 | DAS Searches | Andreas Prlic | |
| 16:10 | A karyotype DAS client | Rafael Jimenez | |
| 16:30 | DASher, a standalone Java client for DAS protein sequence features | David Messina | |
| 16:50 | Data Federation - BioMart & DAS | Syed Haider | |
| 17:10 | Trellis DAS2 framework- which includes the DAS1-->DAS2 proxy and alpha UCSC DAS2 server | Gregg Helt | |
| 17:30 | Discussion/talk about activity organisation of next day - preliminary groups and chairs of groups | ||
Day 3
Chromsome.java
package myplugins;
import java.util.ArrayList; import java.util.Iterator;
import org.biojava.servlets.dazzle.Segment; import org.biojava.servlets.dazzle.datasource.GFFFeature;
/**
* simple class for demo purposes that returns features from given
segments of a chromosome
* that has probably been specified in gff type format * @author jw12 * */
public class Chromosome {
private String id="";
private int start=1;
private int end;
ArrayList features;
public Chromosome(String id, int end){
this.id=id;
this.end=end;
features =new ArrayList();
}
public void addFeature(GFFFeature feature){
this.features.add(feature);
}
public GFFFeature[] getFeatures(Segment seg){
System.out.println("seg in chromosome="+seg);
ArrayList featuresOnSegment=new ArrayList();
int start=seg.getStart();
int stop =seg.getStop();
//loop over arraylist of features and return a lis
Iterator it=features.iterator();
while(it.hasNext()){
GFFFeature feature=(GFFFeature)it.next();
int fStart=Integer.parseInt(feature.getStart());
int fStop=Integer.parseInt(feature.getEnd());
//if between start and stop then include in returned list
if((fStart>=start && fStart<=stop)||(fStop<=stop && fStop>=start)){
featuresOnSegment.add(feature);
}
}
return (GFFFeature[]) featuresOnSegment.toArray(new
GFFFeature[featuresOnSegment.size()]);
//return new GFFFeature[0];
}
}
