From 6d29534616acd0e2920eebaaeb98e22b2c7d79e8 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 8 Aug 2006 09:47:26 +0000 Subject: [PATCH] locally modified biojava-dasobert package is now org.biojava.dasobert --- .../biojava/dasobert/das2/Das2Capability.java | 45 ----- .../biojava/dasobert/das2/Das2CapabilityImpl.java | 109 ----------- src/jalview/biojava/dasobert/das2/Das2Source.java | 40 ---- .../biojava/dasobert/das2/Das2SourceImpl.java | 144 -------------- .../biojava/dasobert/das2/DasSourceConverter.java | 82 -------- .../dasobert/das2/io/DAS2SourceHandler.java | 181 ----------------- .../biojava/dasobert/das2/io/DasSourceReader.java | 32 --- .../dasobert/das2/io/DasSourceReaderImpl.java | 173 ---------------- .../biojava/dasobert/dasregistry/Das1Source.java | 206 -------------------- .../dasobert/dasregistry/Das2Validator.java | 43 ---- .../dasregistry/DasCoordSysComparator.java | 116 ----------- .../dasobert/dasregistry/DasCoordinateSystem.java | 159 --------------- .../biojava/dasobert/dasregistry/DasSource.java | 105 ---------- .../dasobert/dasregistry/DasSourceComparator.java | 140 ------------- .../biojava/dasobert/eventmodel/FeatureEvent.java | 72 ------- .../dasobert/eventmodel/FeatureListener.java | 49 ----- .../dasobert/eventmodel/ObjectListener.java | 47 ----- .../biojava/dasobert/eventmodel/SequenceEvent.java | 44 ----- .../dasobert/eventmodel/SequenceListener.java | 55 ------ 19 files changed, 1842 deletions(-) delete mode 100644 src/jalview/biojava/dasobert/das2/Das2Capability.java delete mode 100644 src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java delete mode 100644 src/jalview/biojava/dasobert/das2/Das2Source.java delete mode 100644 src/jalview/biojava/dasobert/das2/Das2SourceImpl.java delete mode 100644 src/jalview/biojava/dasobert/das2/DasSourceConverter.java delete mode 100755 src/jalview/biojava/dasobert/das2/io/DAS2SourceHandler.java delete mode 100644 src/jalview/biojava/dasobert/das2/io/DasSourceReader.java delete mode 100644 src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java delete mode 100644 src/jalview/biojava/dasobert/dasregistry/Das1Source.java delete mode 100755 src/jalview/biojava/dasobert/dasregistry/Das2Validator.java delete mode 100644 src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java delete mode 100644 src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java delete mode 100644 src/jalview/biojava/dasobert/dasregistry/DasSource.java delete mode 100644 src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java delete mode 100644 src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java delete mode 100644 src/jalview/biojava/dasobert/eventmodel/FeatureListener.java delete mode 100644 src/jalview/biojava/dasobert/eventmodel/ObjectListener.java delete mode 100644 src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java delete mode 100644 src/jalview/biojava/dasobert/eventmodel/SequenceListener.java diff --git a/src/jalview/biojava/dasobert/das2/Das2Capability.java b/src/jalview/biojava/dasobert/das2/Das2Capability.java deleted file mode 100644 index 5cff3f5..0000000 --- a/src/jalview/biojava/dasobert/das2/Das2Capability.java +++ /dev/null @@ -1,45 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Feb 9, 2006 - * - */ -package org.biojava.dasobert.das2; - -public interface Das2Capability { - - public boolean equals(Das2Capability other); - public int hashCode(); - - public void setCapability(String type); - public String getCapability(); - - public void setQueryUri(String id); - public String getQueryUri(); - - public void setFormats(String[] formats); - public String[] getFormats(); - - /** checks if this capability is actually of das1 style - * - * @return boolean true if the capability is in DAS1 style - */ - public boolean isDas1Style(); - -} diff --git a/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java b/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java deleted file mode 100644 index 507a2d3..0000000 --- a/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java +++ /dev/null @@ -1,109 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Feb 9, 2006 - * - */ -package org.biojava.dasobert.das2; - -public class Das2CapabilityImpl -implements Das2Capability{ - - String capability; - String[] formats; - String queryId; - - public static String DAS1_CAPABILITY_PREFIX = "das1:"; - - public Das2CapabilityImpl() { - super(); - capability = "undef"; - queryId = ""; - formats = new String[0]; - - } - - public boolean isDas1Style(){ - - if ( capability == null) - return false; - if ( capability.length() < DAS1_CAPABILITY_PREFIX.length()) - return false; - if ( capability.substring(0,DAS1_CAPABILITY_PREFIX.length()).equals(DAS1_CAPABILITY_PREFIX)) - return true; - return false; - - } - - public boolean equals(Das2Capability other){ - - boolean status = true; - - if (! capability.equals(other.getCapability())) - status = false; - if ( ! queryId.equals(other.getQueryUri())) - status = false; - - return status; - } - - public int hashCode(){ - int h = 7; - h = 31 * h + ( null == capability ? 0 : capability.hashCode()) ; - h = 31 * h + ( null == queryId ? 0 : queryId.hashCode()) ; - - return h; - } - - public String toString(){ - String txt ="capability " + capability + " queryId " + queryId; - return txt; - } - - public String getCapability() { - - return capability; - } - - public String[] getFormats() { - return formats; - } - - public String getQueryUri() { - return queryId; - } - - public void setCapability(String type) { - capability = type; - - } - - public void setFormats(String[] formats) { - - this.formats = formats; - } - - public void setQueryUri(String id) { - queryId = id; - - } - - - -} diff --git a/src/jalview/biojava/dasobert/das2/Das2Source.java b/src/jalview/biojava/dasobert/das2/Das2Source.java deleted file mode 100644 index c370de9..0000000 --- a/src/jalview/biojava/dasobert/das2/Das2Source.java +++ /dev/null @@ -1,40 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Feb 9, 2006 - * - */ -package org.biojava.dasobert.das2; - -import org.biojava.dasobert.dasregistry.DasSource; - -public interface Das2Source -extends DasSource { - - public Das2Capability[] getDas2Capabilities(); - public void setDas2Capabilities(Das2Capability[] capabilities); - - /** test if this is a DAS1 source represented as a DAS2 source - * if true - this source can be converted into a DAS1 source by using - * DasSourceConverter.toDas1(Das2Source); - * - * @return true if the DasSource has DAS1 capabilties - */ - public boolean hasDas1Capabilities(); -} diff --git a/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java b/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java deleted file mode 100644 index bb5325d..0000000 --- a/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java +++ /dev/null @@ -1,144 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Feb 9, 2006 - * - */ -package org.biojava.dasobert.das2; - -import org.biojava.dasobert.dasregistry.Das1Source; -import org.biojava.dasobert.dasregistry.DasSource; - -public class Das2SourceImpl -extends Das1Source -implements Das2Source - -{ - - Das2Capability[] capabilities; - - public Das2SourceImpl() { - super(); - - capabilities = new Das2Capability[0]; - } - - - /** compare if two DasSources are identical - * - */ - public boolean equals(DasSource other){ - - if ( this == other) - return true; - - if ( ( other == null) || (other.getClass() != this.getClass())) - return false; - - // to compare if two Das2Sources are identical we do the following: - // we check the capabilities - - Das2SourceImpl d2o = (Das2SourceImpl)other; - - if ( nickname.equals(d2o.getNickname())) - return true; - - Das2Capability[] othercaps = d2o.getDas2Capabilities(); - - if ( ! (capabilities.length == othercaps.length)) - return false; - - for ( int x=0;x - DasCoordinateSystem dcs = new DasCoordinateSystem(); - String id = atts.getValue("uri"); - dcs.setUniqueId(id); - - String source = atts.getValue("source"); - dcs.setCategory(source); - - String authority = atts.getValue("authority"); - dcs.setName(authority); - - String test_range = atts.getValue("test_range"); - dcs.setTestCode(test_range); - - try { - String taxidstr = atts.getValue("taxid"); - int taxid = Integer.parseInt(taxidstr); - dcs.setNCBITaxId(taxid); - } catch (Exception e){} - - String version = atts.getValue("version"); - if ( version != null) - dcs.setVersion(version); - - return dcs; - } - - public void startElement (String uri, String name, String qName, Attributes atts){ - //System.out.println("new element "+qName); - - if (qName.equals("SOURCE")) { - //System.out.println("new Source " + atts.getValue(uri)); - currentSource = new Das2SourceImpl(); - coordinates = new ArrayList(); - capabilities = new ArrayList(); - - startSource(uri,name, qName, atts); - - } else if ( qName.equals("MAINTAINER")){ - String email = atts.getValue("email"); - currentSource.setAdminemail(email); - } else if ( qName.equals("COORDINATES")){ - DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts); - coordinates.add(dcs); - - } else if ( qName.equals("CAPABILITY")){ - Das2Capability cap = getCapability(uri,name,qName,atts); - capabilities.add(cap); - } else if (qName.equals("PROPERTY")) { - addProperty(uri,name,qName,atts); - } - } - - private Das2Capability getCapability(String uri, String name, String qName, Attributes atts){ - // e.g - Das2Capability cap = new Das2CapabilityImpl(); - - String type = atts.getValue("type"); - cap.setCapability(type); - String query_uri = atts.getValue("query_uri"); - cap.setQueryUri(query_uri); - return cap; - - } - - private void addProperty(String uri, String name, String qName, Attributes atts){ - String pname = atts.getValue("name"); - String label = atts.getValue("value"); - if ( pname.equals(LABELPROPERTY) ) - labels.add(label); - } - - public void startDocument(){ - sources = new ArrayList(); - coordinates = new ArrayList(); - capabilities = new ArrayList(); - } - - public void endElement(String uri, String name, String qName) { - if ( qName.equals("SOURCE")) { - currentSource.setDas2Capabilities((Das2Capability[])capabilities.toArray(new Das2Capability[capabilities.size()])); - //System.out.println("got coordinates " + coordinates.size()); - currentSource.setCoordinateSystem((DasCoordinateSystem[])coordinates.toArray(new DasCoordinateSystem[coordinates.size()])); - - currentSource.setLabels((String[])labels.toArray(new String[labels.size()])); - labels.clear(); - - //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName); - //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId()); - sources.add(currentSource); - currentSource = new Das2SourceImpl(); - } - } - - public DasSource[] getSources(){ - //System.out.println("Das2SourceHandler: source size: " + sources.size()); - return (DasSource[])sources.toArray(new DasSource[sources.size()]); - } - - - -} diff --git a/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java b/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java deleted file mode 100644 index 8044fb7..0000000 --- a/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java +++ /dev/null @@ -1,32 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Feb 24, 2006 - * - */ -package org.biojava.dasobert.das2.io; - -import java.io.InputStream; - -import org.biojava.dasobert.dasregistry.DasSource; - -public interface DasSourceReader { - - public DasSource[] readDasSource(InputStream stream); -} diff --git a/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java b/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java deleted file mode 100644 index 3f0a07a..0000000 --- a/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java +++ /dev/null @@ -1,173 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Feb 24, 2006 - * - */ -package org.biojava.dasobert.das2.io; - -import java.io.InputStream; -import java.net.HttpURLConnection; -import java.net.URL; - - -import javax.xml.parsers.ParserConfigurationException; -import javax.xml.parsers.SAXParser; -import javax.xml.parsers.SAXParserFactory; - -//import org.biojava.dasobert.das.AlignmentThread; -import org.biojava.dasobert.das.DAS_FeatureRetrieve; -import org.biojava.dasobert.dasregistry.DasSource; -import org.xml.sax.InputSource; -import org.xml.sax.SAXException; -import org.xml.sax.SAXNotRecognizedException; -import org.xml.sax.XMLReader; - -public class DasSourceReaderImpl implements DasSourceReader { - - Exception loggedException; - - public DasSourceReaderImpl() { - super(); - loggedException = null; - - // open the stream to a server and then parse the result ... - } - - private InputStream open(URL url) - throws java.io.IOException, java.net.ConnectException - { - InputStream inStream = null; - - - HttpURLConnection huc = DAS_FeatureRetrieve.openHttpURLConnection(url); - - inStream = huc.getInputStream(); - - return inStream; - - } - - - public DasSource[] readDasSource(URL url){ - DasSource[] sources = new DasSource[0]; - - try { - InputStream stream = open(url); - - sources = readDasSource(stream); - } catch (Exception e){ - e.printStackTrace(); - loggedException = e; - } - return sources; - } - - /** read a DAS2 sources response and return a list of DAS sources. - * - */ - public DasSource[] readDasSource(InputStream stream) { - - DasSource[] sources = new DasSource[0]; - - try { - SAXParserFactory spfactory = - SAXParserFactory.newInstance(); - - spfactory.setValidating(false); - - SAXParser saxParser = null ; - - try{ - saxParser = - spfactory.newSAXParser(); - } catch (ParserConfigurationException e) { - e.printStackTrace(); - loggedException = e; - } - - String vali = System.getProperty("XMLVALIDATION"); - - boolean validation = false ; - if ( vali != null ) - if ( vali.equals("true") ) - validation = true ; - - - XMLReader xmlreader = saxParser.getXMLReader(); - - //XMLReader xmlreader = XMLReaderFactory.createXMLReader(); - try { - xmlreader.setFeature("http://xml.org/sax/features/validation", validation); - } catch (SAXException e) { - //logger.log(Level.FINE,"Cannot set validation " + validation); - } - - try { - xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation); - } catch (SAXNotRecognizedException e){ - e.printStackTrace(); - //logger.log(Level.FINE,"Cannot set load-external-dtd "+validation); - - } - - DAS2SourceHandler cont_handle = new DAS2SourceHandler() ; - - xmlreader.setContentHandler(cont_handle); - xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler()); - InputSource insource = new InputSource() ; - insource.setByteStream(stream); - - - xmlreader.parse(insource); - sources = cont_handle.getSources(); - - - - } catch (Exception e) { - e.printStackTrace(); - loggedException = e; - } - return sources; - } - - public Exception getLoggedException(){ - return loggedException; - } - - public static void main (String[] args){ - String url = "http://www.spice-3d.org/dasregistry/das2/sources/"; - DasSourceReaderImpl reader = new DasSourceReaderImpl(); - try { - URL u = new URL(url); - DasSource[] sources = reader.readDasSource(u); - for (int i=0; i< sources.length;i++){ - DasSource ds = sources[i]; - System.out.println(ds.toString()); - } - - } catch (Exception e){ - e.printStackTrace(); - } - - } - - - -} diff --git a/src/jalview/biojava/dasobert/dasregistry/Das1Source.java b/src/jalview/biojava/dasobert/dasregistry/Das1Source.java deleted file mode 100644 index de007d6..0000000 --- a/src/jalview/biojava/dasobert/dasregistry/Das1Source.java +++ /dev/null @@ -1,206 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on 15.04.2004 - * @author Andreas Prlic - * - */ -package org.biojava.dasobert.dasregistry; - -import java.util.Date ; -import java.io.IOException; -import java.io.PrintWriter; -import java.io.StringWriter; - - -//import org.biojava.dasobert.das2.io.DasSourceWriter; -//import org.biojava.dasobert.das2.io.DasSourceWriterImpl; -//import org.biojava.utils.xml.PrettyXMLWriter; - - -/** a simple Bean class to be returned via SOAP - * @author Andreas Prlic - */ - -public class Das1Source implements DasSource { - String url ; - protected String nickname ; - String adminemail ; - String description ; - DasCoordinateSystem[] coordinateSystem ; - String[] capabilities ; - String[] labels ; - String helperurl ; - Date registerDate ; - Date leaseDate ; - String id ; - boolean local; - - boolean alertAdmin; - - public static String EMPTY_ID = "UNK:-1" ; - - public Das1Source () { - id = EMPTY_ID; - url = ""; - adminemail = "" ; - description = "" ; - //String empty = "" ; - nickname = "" ; - coordinateSystem = new DasCoordinateSystem[0]; - //coordinateSystem[0] = new DasCoordinateSystem(); - capabilities = new String[0]; - labels = new String[0]; - //capabilities[0] = empty ; - registerDate = new Date() ; - leaseDate = new Date() ; - helperurl = ""; - local=true; - } - - - public boolean equals(DasSource other){ - System.out.println("Das1Source equals, comparing with other DasSource"); - if (! (other instanceof Das1Source)) - return false; - - Das1Source ods = (Das1Source) other; - - if ( ods.getUrl().equals(url)) - return true; - if ( ods.getNickname().equals(nickname)) - return true; - return false; - } - - public int hashCode() { - int h = 7; - - h = 31 * h + ( null == nickname ? 0 : nickname.hashCode()); - h = 31 * h + ( null == url ? 0 : url.hashCode()); - - return h; - } - - /** the DAS2 string representation of this DAS source - * - public String toString() { - - StringWriter writer = new StringWriter(); - - PrintWriter pw = new PrintWriter(writer); - PrettyXMLWriter xw = new PrettyXMLWriter(pw); - - DasSourceWriter dswriter = new DasSourceWriterImpl(); - try { - dswriter.writeDasSource(xw,this); - } catch (IOException e){ - e.printStackTrace(); - } - - return writer.toString(); - - } - */ - public void setLocal(boolean flag){ local = flag;} - public boolean isLocal(){return local;} - - public void setId(String i) { id = i; } - - /** get a the Id of the DasSource. The Id is a unique db - * identifier. The public DAS-Registry has Auto_Ids that look like - * DASSOURCE:12345; public look like XYZ:12345, where the XYZ - * prefix can be configured in the config file. - */ - public String getId() { return id;} - - public void setNickname(String name) { - nickname = name ; - } - public String getNickname(){ - return nickname; - } - public void setUrl(String u) { - char lastChar = u.charAt(u.length()-1); - if ( lastChar != '/') - u += "/"; - - url = u ; - } - - public void setAdminemail (String u) { - adminemail = u ; - } - - public void setDescription (String u) { - description = u; - } - - public void setCoordinateSystem (DasCoordinateSystem[] u){ - coordinateSystem=u ; - } - - public void setCapabilities (String[] u){ - capabilities = u ; - } - - public String getUrl(){return url;} - public String getAdminemail(){return adminemail;} - public String getDescription(){return description;} - public String[] getCapabilities(){return capabilities;} - public DasCoordinateSystem[] getCoordinateSystem(){return coordinateSystem;} - - public void setRegisterDate(Date d) { - registerDate = d; - } - public Date getRegisterDate() { - return registerDate ; - } - public void setLeaseDate(Date d) { - leaseDate =d ; - } - public Date getLeaseDate() { - return leaseDate ; - } - - public void setLabels(String[] ls) { - labels = ls ; - } - - public String[] getLabels() { - return labels; - } - - public void setHelperurl(String url) { - helperurl = url; - } - - public String getHelperurl() { - return helperurl; - } - - public void setAlertAdmin(boolean flag) { - alertAdmin = flag; - } - - public boolean getAlertAdmin() { - return alertAdmin; - } - -} diff --git a/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java b/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java deleted file mode 100755 index 48cb4f0..0000000 --- a/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java +++ /dev/null @@ -1,43 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Mar 20, 2006 - * - */ -package org.biojava.dasobert.dasregistry; - -import org.biojava.dasobert.das2.Das2Source; - -public class Das2Validator { - - public Das2Validator() { - super(); - - } - - public boolean validate(Das2Source ds){ - - // TODO this bit still needs to be implemented! - - return true; - } - - - -} diff --git a/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java b/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java deleted file mode 100644 index 621fbc8..0000000 --- a/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java +++ /dev/null @@ -1,116 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on 15.04.2004 - * @author Andreas Prlic - * - */ - - -package org.biojava.dasobert.dasregistry ; - -import java.util.Comparator ; -import java.util.Map ; -import java.util.HashMap ; - -import org.biojava.dasobert.dasregistry.DasCoordinateSystem; - -/** a comparator to sort DasSources - * @author Andreas Prlic - */ - - -public abstract class DasCoordSysComparator - implements Comparator -{ - - private final String name ; - private static final Map COMPS_BY_NAME; - - - public DasCoordSysComparator(String str) { - //System.out.println("new dasSourceComparator " + str); - name = str ; - } - - public static final Comparator BY_NAME = new DasCoordSysComparator("name") { - protected Comparable getField(DasCoordinateSystem ds) { - return ds.getName(); - } - }; - - public static final Comparator BY_ID = new DasCoordSysComparator("id") { - protected Comparable getField(DasCoordinateSystem ds) { - return ds.getUniqueId(); - } - }; - public static final Comparator BY_CATEGORY = new DasCoordSysComparator("category") { - protected Comparable getField(DasCoordinateSystem ds) { - return ds.getCategory(); - } - }; - public static final Comparator BY_ORGANISM = new DasCoordSysComparator("organism") { - protected Comparable getField(DasCoordinateSystem ds) { - return ds.getOrganismName(); - } - }; - public static final Comparator BY_TAXID = new DasCoordSysComparator("taxid") { - protected Comparable getField(DasCoordinateSystem ds) { - return ds.getNCBITaxId()+""; - } - }; - - - - static { - COMPS_BY_NAME = new HashMap(); - COMPS_BY_NAME.put(BY_ID.toString(), BY_ID); - COMPS_BY_NAME.put(BY_NAME.toString(), BY_NAME); - COMPS_BY_NAME.put(BY_CATEGORY.toString(), BY_CATEGORY); - COMPS_BY_NAME.put(BY_ORGANISM.toString(), BY_ORGANISM); - COMPS_BY_NAME.put(BY_TAXID.toString(), BY_TAXID); - } - - - - public static Comparator fromString(String name) { - if (COMPS_BY_NAME.containsKey(name)) { - return (Comparator) COMPS_BY_NAME.get(name); - } else { - throw new IllegalArgumentException("Can't compare by key " + name); - } - } - - protected abstract Comparable getField(DasCoordinateSystem ds); - - /** compare two DasCoordSys objects */ - public int compare( Object a, Object b) { - DasCoordinateSystem x = (DasCoordinateSystem) a ; - DasCoordinateSystem y = (DasCoordinateSystem) b ; - return getField(x).compareTo(getField(y)); - } - - public String toString() { - return name; - } - - -} - - diff --git a/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java b/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java deleted file mode 100644 index 8fc4ccb..0000000 --- a/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java +++ /dev/null @@ -1,159 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on 15.04.2004 - * @author Andreas Prlic - * - */ -package org.biojava.dasobert.dasregistry; - - -/** a Bean to be returned via SOAP. It takes care of the DAS - coordinate Systems - * @author Andreas Prlic - */ -public class DasCoordinateSystem { - - String name; - String category; - String organism_name; - int ncbi_tax_id ; - String uniqueId ; - String version; - String testCode; - - public DasCoordinateSystem () { - uniqueId = ""; - name = ""; - category =""; - organism_name = ""; - ncbi_tax_id = 0; - version = ""; - testCode = ""; - } - - public boolean equals(DasCoordinateSystem other){ - boolean match = true; - System.out.println("comparing " + this.toString() + " to " + other.toString()); - // URI has piority - if ( (! uniqueId.equals("")) && ( uniqueId.equals( other.getUniqueId()))) - return true; - - if ( ncbi_tax_id != other.getNCBITaxId()) { - System.out.println("mismatch in ncbi tax id " + ncbi_tax_id + " != " + other.getNCBITaxId()); - match = false; - } - if ( ! version.equals(other.getVersion() )){ - System.out.println("mismatch in version"); - match = false; - } - if ( ! category.equals(other.getCategory()) ) { - System.out.println("mismatch in category"); - match = false; - } - if ( ! name.equals(other.getName())) { - System.out.println("mismatch in name"); - match = false; - } - System.out.println(" match: " + match); - - return match; - } - - public Object clone() { - DasCoordinateSystem d = new DasCoordinateSystem(); - d.setTestCode(testCode); - d.setCategory(category); - d.setName(name); - d.setNCBITaxId(ncbi_tax_id); - d.setUniqueId(getUniqueId()); - d.setOrganismName(getOrganismName()); - d.setVersion(getVersion()); - return d; - } - - public String getTestCode() { - return testCode; - } - - - - public void setTestCode(String testCode) { - if ( testCode == null) - testCode = ""; - this.testCode = testCode; - } - - - - public void setUniqueId(String id) { uniqueId = id ; } - public String getUniqueId() { return uniqueId; } - - public void setName(String n) { name = n; } - public String getName() { return name; } - - public void setCategory(String c) { category = c;} - public String getCategory() { return category;} - - public void setOrganismName(String t) { organism_name =t;} - public String getOrganismName() { return organism_name;} - - public void setNCBITaxId(int id) { ncbi_tax_id = id;} - public int getNCBITaxId(){ return ncbi_tax_id ;} - - - - - public String getVersion() { - return version; - } - - public void setVersion(String version) { - if ( version == null) - version = ""; - this.version = version; - } - - public String toString() { - String nam = name; - if ( ! version.equals("")) - nam += "_" + version; - - if ( organism_name.equals("") ) - return nam+","+category ; - else - return nam+","+category+"," + organism_name ; - } - - public static DasCoordinateSystem fromString(String rawString) { - String[] spl = rawString.split(","); - DasCoordinateSystem dcs = new DasCoordinateSystem(); - if ( spl.length == 2 ) { - dcs.setName(spl[0]); - dcs.setCategory(spl[1]); - } - if ( spl.length == 3 ) { - dcs.setName(spl[0]); - dcs.setCategory(spl[1]); - dcs.setOrganismName(spl[2]); - } - return dcs; - } - - -} diff --git a/src/jalview/biojava/dasobert/dasregistry/DasSource.java b/src/jalview/biojava/dasobert/dasregistry/DasSource.java deleted file mode 100644 index 6dd49e5..0000000 --- a/src/jalview/biojava/dasobert/dasregistry/DasSource.java +++ /dev/null @@ -1,105 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Feb 8, 2006 - * - */ -package org.biojava.dasobert.dasregistry; - -import java.util.Date; - -public interface DasSource { - - public void setLocal(boolean flag); - - public boolean isLocal(); - - /** compare if two das sources are equal - * - * @param ds - * @return returns true if two DAS sources are equivalent - */ - public boolean equals(DasSource ds); - - /** classes that implement equals, should also implement hashKey - * - * @return the hash code of a das source - */ - public int hashCode(); - - - public void setId(String i); - - /** get a the Id of the DasSource. The Id is a unique db - * identifier. The public DAS-Registry has Auto_Ids that look like - * DASSOURCE:12345; public look like XYZ:12345, where the XYZ - * prefix can be configured in the config file. - * @return String the ID of a Das Source - */ - public String getId(); - - public void setNickname(String name); - - public String getNickname(); - - public void setUrl(String u); - - public void setAdminemail(String u); - - public void setDescription(String u); - - public void setCoordinateSystem(DasCoordinateSystem[] u); - - public void setCapabilities(String[] u); - - public String getUrl(); - - public String getAdminemail(); - - public String getDescription(); - - public String[] getCapabilities(); - - public DasCoordinateSystem[] getCoordinateSystem(); - - public void setRegisterDate(Date d); - - public Date getRegisterDate(); - - public void setLeaseDate(Date d); - - public Date getLeaseDate(); - - public void setLabels(String[] ls); - - public String[] getLabels(); - - public void setHelperurl(String url); - - public String getHelperurl(); - - // TestCode is now part of the coordinate system! - //public void setTestCode(String code); - //public String getTestCode(); - - public void setAlertAdmin(boolean flag); - - public boolean getAlertAdmin(); - -} diff --git a/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java b/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java deleted file mode 100644 index ddbad1a..0000000 --- a/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java +++ /dev/null @@ -1,140 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on 15.04.2004 - * @author Andreas Prlic - * - */ - - -package org.biojava.dasobert.dasregistry ; - -import java.util.Comparator ; -import java.util.Map ; -import java.util.HashMap ; - - -/** a comparator to sort DasSources - * @author Andreas Prlic, Thomas Down - */ - - -public abstract class DasSourceComparator - implements Comparator -{ - - private final String name ; - private static final Map COMPS_BY_NAME; - - - public DasSourceComparator(String str) { - //System.out.println("new dasSourceComparator " + str); - name = str ; - } - - public static final Comparator BY_ID = new DasSourceComparator("id") { - protected Comparable getField(DasSource ds) { - return ds.getId(); - } - }; - - public static final Comparator BY_NICKNAME = new DasSourceComparator("nickname") { - protected Comparable getField(DasSource ds) { - return ds.getNickname(); - } - }; - public static final Comparator BY_REGISTER_DATE = new DasSourceComparator("registerdate") { - protected Comparable getField(DasSource ds) { - return ds.getRegisterDate(); - } - }; - public static final Comparator BY_LEASE_DATE = new DasSourceComparator("leasedate") { - protected Comparable getField(DasSource ds) { - return ds.getLeaseDate(); - } - }; - public static final Comparator BY_URL = new DasSourceComparator("url") { - protected Comparable getField(DasSource ds) { - return ds.getUrl(); - } - }; - public static final Comparator BY_ADMIN_EMAIL = new DasSourceComparator("adminemail") { - protected Comparable getField(DasSource ds) { - return ds.getAdminemail(); - } - }; - public static final Comparator BY_DESCRIPTION = new DasSourceComparator("description") { - protected Comparable getField(DasSource ds) { - return ds.getDescription(); - } - }; - public static final Comparator BY_CAPABILITIES = new DasSourceComparator("capabilities") { - protected Comparable getField(DasSource ds) { - String[] caps = ds.getCapabilities(); - return caps.length == 0 ? "" : caps[0]; - } - }; - public static final Comparator BY_COORDINATE_SYSTEM = new DasSourceComparator("coordinateSystem") { - protected Comparable getField(DasSource ds) { - DasCoordinateSystem[] dcss = ds.getCoordinateSystem(); - return dcss.length == 0 ? "" : dcss[0].toString(); - } - }; - - static { - COMPS_BY_NAME = new HashMap(); - COMPS_BY_NAME.put(BY_ID.toString(), BY_ID); - COMPS_BY_NAME.put(BY_NICKNAME.toString(), BY_NICKNAME); - COMPS_BY_NAME.put(BY_REGISTER_DATE.toString(), BY_REGISTER_DATE); - COMPS_BY_NAME.put(BY_LEASE_DATE.toString(), BY_LEASE_DATE); - COMPS_BY_NAME.put(BY_URL.toString(), BY_URL); - COMPS_BY_NAME.put(BY_ADMIN_EMAIL.toString(), BY_ADMIN_EMAIL); - COMPS_BY_NAME.put(BY_DESCRIPTION.toString(), BY_DESCRIPTION); - COMPS_BY_NAME.put(BY_CAPABILITIES.toString(), BY_CAPABILITIES); - COMPS_BY_NAME.put(BY_COORDINATE_SYSTEM.toString(), BY_COORDINATE_SYSTEM); - } - - - - public static Comparator fromString(String name) { - if (COMPS_BY_NAME.containsKey(name)) { - return (Comparator) COMPS_BY_NAME.get(name); - } else { - throw new IllegalArgumentException("Can't compare by key " + name); - } - } - - protected abstract Comparable getField(DasSource ds); - - /** compare two DasSource objects */ - public int compare( Object a, Object b) { - - DasSource x = (DasSource) a ; - DasSource y = (DasSource) b ; - return getField(x).compareTo(getField(y)); - } - - public String toString() { - return name; - } - - -} - - diff --git a/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java b/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java deleted file mode 100644 index 63b5da4..0000000 --- a/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java +++ /dev/null @@ -1,72 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Oct 28, 2005 - * - */ -package org.biojava.dasobert.eventmodel; - -import java.util.Map; - -import org.biojava.dasobert.dasregistry.Das1Source; -public class FeatureEvent { - - Map[] features; - Das1Source dasSource; - int comeBackLater; - - public FeatureEvent(Map[] features,Das1Source dasSource) { - super(); - this.features =features; - this.dasSource = dasSource; - comeBackLater = -1; - } - - public int getComeBackLater(){ - return comeBackLater; - } - - public void setComeBackLater(int comeBackLater){ - this.comeBackLater = comeBackLater; - } - - - /** get the features that have been found. - * - * do something like - * Map[] features = event.getFeatures(); - * 
-     * for (int i = 0 ; i< features;i++) {
-     *      Map f = features[i];
-     *      String type = (String) f.get("TYPE") ;
-     *      System.out.println(type);
-     * }
-     *
- * @return a Map containng the features - */ - public Map[] getFeatures(){ - return features; - } - - public Das1Source getDasSource(){ - return dasSource; - } - -} - diff --git a/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java b/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java deleted file mode 100644 index 299a6bf..0000000 --- a/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java +++ /dev/null @@ -1,49 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Oct 28, 2005 - * - */ -package org.biojava.dasobert.eventmodel; - -//import org.biojava.spice.multipanel.eventmodel.FeatureEvent; - -/** a feature listener that returns the raw features as returned by a DAS source. - * - */ -public interface FeatureListener { - - /** new features have been returned from the Annotation server - * - * @param e - */ - public void newFeatures(FeatureEvent e); - - /** the server says that he is busy and we should try again in x seconds - * - * @param e - */ - public void comeBackLater(FeatureEvent e); - -} - - - - - diff --git a/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java b/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java deleted file mode 100644 index 640b413..0000000 --- a/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java +++ /dev/null @@ -1,47 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Nov 1, 2005 - * - */ -package org.biojava.dasobert.eventmodel; - -/** an interface for the listeners of new PDB code requested / new Uniprot code requested - * - * @author Andreas Prlic - * - */ -public interface ObjectListener { - - /** a new object has been requested - * - * @param accessionCode - */ - public void newObjectRequested(String accessionCode); - - /** no object with that accessionCode has been found - * - * @param accessionCode - */ - public void noObjectFound(String accessionCode); - - - // public void exceptionOccured(Exception e); - -} diff --git a/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java b/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java deleted file mode 100644 index 7798da1..0000000 --- a/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java +++ /dev/null @@ -1,44 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Nov 20, 2005 - * - */ -package org.biojava.dasobert.eventmodel; - - -public class SequenceEvent { - - String sequence; - String accessionCode; - public SequenceEvent(String accessionCode, String seq) { - super(); - sequence = seq; - this.accessionCode = accessionCode; - } - - public String getAccessionCode(){ - return accessionCode; - } - - public String getSequence(){ - return sequence; - } - -} diff --git a/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java b/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java deleted file mode 100644 index 37779bd..0000000 --- a/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java +++ /dev/null @@ -1,55 +0,0 @@ -/* - * BioJava development code - * - * This code may be freely distributed and modified under the - * terms of the GNU Lesser General Public Licence. This should - * be distributed with the code. If you do not have a copy, - * see: - * - * http://www.gnu.org/copyleft/lesser.html - * - * Copyright for this code is held jointly by the individual - * authors. These should be listed in @author doc comments. - * - * For more information on the BioJava project and its aims, - * or to join the biojava-l mailing list, visit the home page - * at: - * - * http://www.biojava.org/ - * - * Created on Jun 10, 2005 - * - */ -package org.biojava.dasobert.eventmodel; - -/** An interface fore events related to selections of sequence - * position, sequence range and locking of the selection. - * - * @author Andreas Prlic - * - */ -public interface SequenceListener -extends ObjectListener{ - - /* select a certain sequence position */ - public void selectedSeqPosition(int position); - - /** select a certain range of a sequence - * @param start the start - * @param end the end of the range - * */ - public void selectedSeqRange(int start, int end); - - /** the current selecetion is locked and can not be changed - * @param flag true if selection should be locked - * */ - public void selectionLocked(boolean flag); - - public void newSequence(SequenceEvent e); - - /** clear what has been selected - * - * - */ - public void clearSelection(); -} -- 1.7.10.2