+++ /dev/null
-/**
- * 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 19.03.2004
- * @author Andreas Prlic
- *
- */
-package org.biojava.dasobert.das;
-
-
-import java.net.URL ;
-import java.io.InputStream ;
-import org.xml.sax.InputSource ;
-import org.xml.sax.XMLReader ;
-import javax.xml.parsers.* ;
-import org.xml.sax.* ;
-import java.util.ArrayList ;
-import java.util.List;
-import java.util.logging.* ;
-import java.net.HttpURLConnection ;
-import java.io.IOException;
-import java.net.ConnectException;
-import java.lang.reflect.Method;
-
-
-
-
-/**
- * A class to perform a DAS features request
- *
- * @author Andreas Prlic
- *
- */
-public class DAS_FeatureRetrieve {
-
- List features ;
- Logger logger ;
- int comeBackLater;
- URL url;
- /**
- * @param url the URL the features should be downloaded from
- *
- */
- public DAS_FeatureRetrieve(URL url) {
- super();
-
- logger = Logger.getLogger("org.biojava.spice");
- features = new ArrayList() ;
- comeBackLater = -1;
- this.url=url;
- reload();
- }
-
-
- /** contact the DAS-feature server again. Usually
- * it is not necessary to call this again, because the constructor already does, but
- * if comeBackLater > -1 this should be called again.
- *
- */
- public void reload(){
-
- try {
-
- InputStream dasInStream = null;
- try {
- dasInStream = open(url);
- } catch (Exception e ){
- comeBackLater = -1;
- logger.log(Level.FINE,"could not open connection to " + url,e);
- return ;
- }
-
-
- SAXParserFactory spfactory =
- SAXParserFactory.newInstance();
-
- spfactory.setValidating(false);
-
- SAXParser saxParser = null ;
-
- try{
- saxParser =
- spfactory.newSAXParser();
- } catch (ParserConfigurationException e) {
- e.printStackTrace();
- }
-
-
-
- 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);
-
- }
-
- DAS_Feature_Handler cont_handle = new DAS_Feature_Handler() ;
- cont_handle.setDASCommand(url.toString());
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource() ;
- insource.setByteStream(dasInStream);
-
- try {
- xmlreader.parse(insource);
- features = cont_handle.get_features();
- comeBackLater = cont_handle.getComBackLater();
- }
- catch ( Exception e){
- e.printStackTrace();
- logger.log(Level.FINE,"error while parsing response from "+ url);
- comeBackLater = -1;
- features = new ArrayList();
- }
- }
- catch (Exception ex) {
- ex.printStackTrace();
- comeBackLater = -1;
- }
- }
-
-
- /** open HttpURLConnection. Recommended way to open
- * HttpURLConnections, since this take care of setting timeouts
- * properly for java 1.4 and 1.5*/
- public static HttpURLConnection openHttpURLConnection(URL url)
- throws IOException, ConnectException {
- HttpURLConnection huc = null;
- huc = (HttpURLConnection) url.openConnection();
-
- String os_name = java.lang.System.getProperty("os.name");
- String os_version = java.lang.System.getProperty("os.version");
- String os_arch = java.lang.System.getProperty("os.arch");
- String VERSION = "1.0";
-
- String userAgent = "Jalview " + VERSION + "("+os_name+"; "+os_arch + " ; "+ os_version+")";
- //e.g. "Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.7.2) Gecko/20040803"
- huc.addRequestProperty("User-Agent", userAgent);
- //logger.finest("opening "+url);
-
-
- // use reflection to determine if get and set timeout methods for urlconnection are available
- // seems java 1.5 does not watch the System properties any longer...
- // and java 1.4 did not provide these...
- // for 1.4 see setSystemProperties
- int timeout = 15000;
- try {
- // try to use reflection to set timeout property
- Class urlconnectionClass = Class.forName("java.net.HttpURLConnection");
-
- Method setconnecttimeout = urlconnectionClass.getMethod (
- "setConnectTimeout", new Class [] {int.class}
- );
- setconnecttimeout.invoke(huc,new Object[] {new Integer(timeout)});
-
- Method setreadtimeout = urlconnectionClass.getMethod (
- "setReadTimeout", new Class[] {int.class}
- );
- setreadtimeout.invoke(huc,new Object[] {new Integer(timeout)});
- //System.out.println("successfully set java 1.5 timeout");
- } catch (Exception e) {
- //e.printStackTrace();
- // most likely it was a NoSuchMEthodException and we are running java 1.4.
- }
- return huc;
- }
-
-
- private InputStream open(URL url)
- throws java.io.IOException, java.net.ConnectException
- {
- InputStream inStream = null;
-
-
- HttpURLConnection huc = openHttpURLConnection(url);
-
- inStream = huc.getInputStream();
-
- return inStream;
-
- }
-
- /** returns a List of Features
- * @return a List of Maps containing the features*/
- public List get_features() {
-
- return features;
- }
-
- /** returns the comeBackLater value - if a server returned suchh -
- *
- * @return comeBackLater in seconds, or -1 if not provided by server
- */
- public int getComeBackLater(){
-
- return comeBackLater;
-
- }
-
-
-}
+++ /dev/null
-/*
- * 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 19.03.2004
- * @author Andreas Prlic
- *
- */
-package org.biojava.dasobert.das;
-
-import org.xml.sax.helpers.DefaultHandler;
-import org.xml.sax.Attributes;
-
-import java.util.ArrayList ;
-import java.util.HashMap ;
-import java.util.List;
-
-/**
- * a class to parse the response of a DAS - Feature request
- * @author Andreas Prlic
- *
- */
-public class DAS_Feature_Handler extends DefaultHandler{
-
- /**
- *
- */
- List features ;
- boolean first_flag ;
- HashMap feature ;
- String featurefield ;
- String characterdata ;
- String dasCommand ;
-
- int comeBackLater ;
-
- int maxFeatures ;
-
- public DAS_Feature_Handler() {
- super();
-
- features= new ArrayList() ;
- first_flag = true ;
- featurefield = "" ;
- characterdata = "";
- dasCommand = "" ;
- comeBackLater = -1;
- maxFeatures = -1;
- }
-
- /** specifies a maximum number of features to be downloaded. if a
- server returns more, they will be ignored. default is to load
- all features
- @param max the maximium number of features to be downloaded
- */
-
- public void setMaxFeatures(int max) {
- maxFeatures = max;
- }
-
- public int getMaxFeatures() {
- return maxFeatures;
- }
-
- public void setDASCommand(String cmd) { dasCommand = cmd ;}
- public String getDASCommand() { return dasCommand; }
-
- public List get_features() {
- return features ;
- }
-
- public int getComBackLater(){
- return comeBackLater;
- }
-
- void start_feature(String uri, String name, String qName, Attributes atts) {
-
- if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
- characterdata = "";
- return;
- }
- feature = new HashMap() ;
- String id = atts.getValue("id");
- feature.put("id",id);
- feature.put("dassource",dasCommand);
- characterdata = "";
- }
-
- void add_featuredata(String uri, String name, String qName) {
- //System.out.println("featurefield "+featurefield+ " data "+characterdata);
- // NOTE can have multiple lines ..
-
- if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
- return;
- }
-
-
- String data = (String)feature.get(featurefield);
- if (data != null){
- characterdata = data + " " + characterdata;
- }
-
- feature.put(featurefield,characterdata);
- featurefield = "";
- characterdata = "";
- }
-
- private void addLink(String uri, String name, String qName, Attributes atts) {
- String href = atts.getValue("href");
- feature.put("LINK",href);
- characterdata="";
- featurefield = "LINK-TEXT";
-
- }
-
- public void startElement (String uri, String name, String qName, Attributes atts){
- //System.out.println("new element "+qName);
-
- if (qName.equals("FEATURE"))
- start_feature(uri, name, qName, atts);
- else if ( qName.equals("LINK"))
- addLink(uri,name,qName, atts);
- else if ( qName.equals("METHOD") ||
- qName.equals("TYPE") ||
- qName.equals("START") ||
- qName.equals("END") ||
- qName.equals("NOTE") ||
- qName.equals("SCORE")
- ){
- characterdata ="";
- featurefield = qName ;
- }
-
- }
-
- public void startDocument() {
- }
-
- public void endDocument () {
- }
- public void endElement(String uri, String name, String qName) {
-
- if ( qName.equals("METHOD") ||
- qName.equals("TYPE") ||
- qName.equals("START") ||
- qName.equals("END") ||
- qName.equals("NOTE") ||
- qName.equals("LINK") ||
- qName.equals("SCORE")
- ) {
- add_featuredata(uri,name,qName);
- }
- else if ( qName.equals("FEATURE")) {
-
- if ( maxFeatures > 0 ) {
- if ( features.size() < maxFeatures ) {
- features.add(feature);
- }
- } else {
- // no restriction
- features.add(feature);
- }
- }
- }
-
- public void characters (char ch[], int start, int length){
-
- for (int i = start; i < start + length; i++) {
-
- characterdata += ch[i];
- }
-
- }
-
-}
+++ /dev/null
-/*
- * 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 21.09.2004
- * @author Andreas Prlic
- *
- */
-
-package org.biojava.dasobert.das ;
-
-import java.util.*;
-import java.net.*;
-import java.util.logging.* ;
-import org.biojava.dasobert.eventmodel.FeatureListener;
-import org.biojava.dasobert.eventmodel.FeatureEvent;
-import org.biojava.dasobert.dasregistry.Das1Source;
-
-/** a thread that connects to a DAS - Feature service and gets the features
- *
- * @author Andreas Prlic
- */
-
-
-
-public class FeatureThread
- implements Runnable
-{
-
- /** number of times the client tries to reconnect to the server if a "come back later" is returned.
- * the server should provide a reasonable estimation how long it will take him to create results.
- * if this number of requests is still not successfull, give up.
- */
- public static int MAX_COME_BACK_ITERATIONS = 5;
-
- public static int MAX_NR_FEATURES = 300;
-
- static Logger logger = Logger.getLogger("org.biojava.spice");
-
- Das1Source dasSource;
- String ac ;
- List featureListeners;
- Thread thread;
-
- public FeatureThread (String accessionCode, Das1Source dasSource) {
- this.dasSource = dasSource;
- this.ac = accessionCode;
- featureListeners = new ArrayList();
- }
-
- public void addFeatureListener(FeatureListener li) {
- featureListeners.add(li);
- }
-
- public void clearFeatureListeners() {
- featureListeners.clear();
- }
-
- public synchronized void stop(){
- thread = null;
- notify();
- }
-
-
-
-
- public void run() {
- Thread me = Thread.currentThread();
- while ( thread == me) {
- String url = dasSource.getUrl();
- String queryString = url + "features?segment="+ ac ;
- URL cmd = null ;
- try {
- cmd = new URL(queryString);
- } catch (MalformedURLException e ) {
- logger.warning("got MalformedURL from das source " +dasSource);
- e.printStackTrace();
-
- }
-
- logger.info("requesting features from " + cmd);
- DAS_FeatureRetrieve ftmp = new DAS_FeatureRetrieve(cmd);
-
-
- int comeBackLater = ftmp.getComeBackLater();
- int securityCounter = 0;
- while ( (thread == me) && ( comeBackLater > 0 )) {
- securityCounter++;
- if ( securityCounter >= MAX_COME_BACK_ITERATIONS){
- comeBackLater = -1;
- break;
-
- }
- notifyComeBackLater(comeBackLater);
- // server is still calculating - asks us to come back later
- try {
- wait (comeBackLater);
- } catch (InterruptedException e){
- comeBackLater = -1;
- break;
- }
-
- ftmp.reload();
- comeBackLater = ftmp.getComeBackLater();
- }
-
- if ( ! (thread == me ) ) {
- break;
- }
-
- List features = ftmp.get_features();
-
- // a fallback mechanism to prevent DAS sources from bringing down spice
- if ( features.size() > MAX_NR_FEATURES){
- logger.warning("DAS source returned more than " + MAX_NR_FEATURES + "features. " +
- " throwing away excess features at " +cmd);
- features = features.subList(0,MAX_NR_FEATURES);
- }
-
-
- // notify FeatureListeners
- Map[] feats = (Map[])features.toArray(new Map[features.size()]);
- notifyFeatureListeners(feats);
-
- break;
-
-
- }
- thread = null;
-
- }
-
- public void start() {
- thread = new Thread(this);
- thread.start();
- }
-
- private void notifyFeatureListeners(Map[] feats){
- logger.finest("FeatureThread found " + feats.length + " features");
- FeatureEvent fevent = new FeatureEvent(feats,dasSource);
- Iterator fiter = featureListeners.iterator();
- while (fiter.hasNext()){
- FeatureListener fi = (FeatureListener)fiter.next();
- fi.newFeatures(fevent);
- }
- }
-
- /** the Annotation server requested to be queried again in a while
- *
- * @param comeBackLater
- */
- private void notifyComeBackLater(int comeBackLater){
- FeatureEvent event = new FeatureEvent(new HashMap[0],dasSource);
- event.setComeBackLater(comeBackLater);
- Iterator fiter = featureListeners.iterator();
- while (fiter.hasNext()){
- FeatureListener fi = (FeatureListener)fiter.next();
- fi.comeBackLater(event);
- }
-
- }
-
-
-}
-
+++ /dev/null
-/*
- * 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();
-
-}
+++ /dev/null
-/*
- * 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;
-
- }
-
-
-
-}
+++ /dev/null
-/*
- * 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();
-}
+++ /dev/null
-/*
- * 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<capabilities.length;x++){
- Das2Capability tmpcap = capabilities[x];
- boolean foundCap = false;
- for (int y=0; y< othercaps.length;y++){
- Das2Capability tmpcapo = othercaps[y];
- if ( tmpcap.equals(tmpcapo))
- foundCap = true;
- }
- if ( ! foundCap)
- return false;
- }
-
-
- //TODO?
- // should we add a check for coordinate systems?
- // but we already check for the endpoints, that should be enough...
-
- return true;
-
- }
-
- public int hashCode(){
- int h = 7 ;
-
- h = 31 * h + (null == nickname ? 0 : nickname.hashCode());
-
- for ( int x=0;x<capabilities.length;x++){
- Das2Capability cap = capabilities[x];
- h = 31 * h + cap.hashCode();
- }
-
- return h;
- }
-
-
- public boolean hasDas1Capabilities(){
-
- // test if any of the capabilities is a das1 capabilitiy
-
- for (int i = 0 ; i < capabilities.length; i++) {
- Das2Capability cap = capabilities[i];
- if ( cap.isDas1Style())
- return true;
- }
- return false;
-
-
- }
-
- public String[] getCapabilities() {
- //todo mark as not needed / not appropriate ...
- return super.getCapabilities();
- }
-
-
-
- public void setCapabilities(String[] u) {
- // TODO Auto-generated method stub
- super.setCapabilities(u);
- }
-
-
-
- public Das2Capability[] getDas2Capabilities() {
- // TODO Auto-generated method stub
- return capabilities;
- }
-
- public void setDas2Capabilities(Das2Capability[] capabilities) {
- // TODO Auto-generated method stub
- this.capabilities = capabilities;
-
- }
-
-
-
-
-}
+++ /dev/null
-/*
- * 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 23, 2006
- *
- */
-package org.biojava.dasobert.das2;
-
-//import org.biojava.bio.program.das.dasalignment.DASException;
-import org.biojava.dasobert.dasregistry.Das1Source;
-
-public class DasSourceConverter {
-
- public DasSourceConverter() {
- super();
-
- }
-
-
- /** convert a das2 source to a das 1 source.
- * This only will work if is passes the Das2Source.isDas1Source() test
- * i.e. this is really a das1 server there
- *
- * @param das2source a DAS2Source to be converted
- * @return a Das1Source
- * @throws DASException
- */
- public static Das1Source toDas1Source (Das2Source das2source) throws Exception{
- if ( ! das2source.hasDas1Capabilities())
- throw new Exception("this das source does not have das1 capabilitites");
-
- Das1Source ds = new Das1Source();
- ds.setAdminemail(das2source.getAdminemail());
- ds.setDescription(das2source.getDescription());
- ds.setHelperurl(das2source.getHelperurl());
- ds.setRegisterDate(das2source.getRegisterDate());
- ds.setLeaseDate(das2source.getLeaseDate());
- ds.setLabels(das2source.getLabels());
- ds.setCoordinateSystem(das2source.getCoordinateSystem());
- ds.setNickname(das2source.getNickname());
- ds.setId(das2source.getId());
- ds.setLabels(das2source.getLabels());
-
- // convert the capabilitites to das1 capabiltities and get the url
- Das2Capability[] caps = das2source.getDas2Capabilities();
- String[] das1capabilitites = new String[caps.length];
- int DASPREFIXLENGTH = Das2CapabilityImpl.DAS1_CAPABILITY_PREFIX.length();
-
- for ( int i = 0 ; i< caps.length;i++){
- Das2Capability cap = caps[i];
-
- String c = cap.getCapability();
-
- das1capabilitites[i] = c.substring(DASPREFIXLENGTH,c.length());
-
- String query_uri = cap.getQueryUri();
-
- String url = query_uri.substring(0,(query_uri.length() - c.length() + DASPREFIXLENGTH));
- ds.setUrl(url);
- }
- ds.setCapabilities(das1capabilitites);
-
- return ds ;
- }
-
-}
+++ /dev/null
-/*
- * 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 15, 2006
- *
- */
-package org.biojava.dasobert.das2.io;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.biojava.dasobert.das2.Das2Capability;
-import org.biojava.dasobert.das2.Das2CapabilityImpl;
-import org.biojava.dasobert.das2.Das2Source;
-import org.biojava.dasobert.das2.Das2SourceImpl;
-import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
-import org.biojava.dasobert.dasregistry.DasSource;
-import org.xml.sax.Attributes;
-import org.xml.sax.helpers.DefaultHandler;
-
-/** a parser for the DAS2 sources response
- *
- * @author Andreas Prlic
- * @since 6:53:45 PM
- * @version %I% %G%
- */
-public class DAS2SourceHandler extends DefaultHandler{
-
- List sources;
- Das2Source currentSource;
- List coordinates;
- List capabilities;
- List labels;
-
- public static final String LABELPROPERTY = "label";
-
- public DAS2SourceHandler() {
- super();
-
- sources = new ArrayList();
- currentSource = new Das2SourceImpl();
- coordinates = new ArrayList();
- capabilities = new ArrayList();
- labels = new ArrayList();
- }
-
- private void startSource (String uri, String name, String qName, Attributes atts){
-
- String id = atts.getValue("uri");
- String title = atts.getValue("title");
- String doc_ref = atts.getValue("doc_href");
- String description = atts.getValue("description");
-
-
- currentSource.setId(id);
- currentSource.setNickname(title);
- currentSource.setHelperurl(doc_ref);
- currentSource.setDescription(description);
-
- }
-
- private DasCoordinateSystem getCoordinateSystem(String uri, String name, String qname, Attributes atts){
- // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
- // source="Protein Sequence" authority="UniProt" test_range="P06213" />
- 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 <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
- 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()]);
- }
-
-
-
-}
+++ /dev/null
-/*
- * 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);
-}
+++ /dev/null
-/*
- * 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();
- }
-
- }
-
-
-
-}
+++ /dev/null
-/*
- * 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;
- }
-
-}
+++ /dev/null
-/*
- * 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;
- }
-
-
-
-}
+++ /dev/null
-/*
- * 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;
- }
-
-
-}
-
-
+++ /dev/null
-/*
- * 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;
- }
-
-
-}
+++ /dev/null
-/*
- * 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();
-
-}
+++ /dev/null
-/*
- * 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;
- }
-
-
-}
-
-
+++ /dev/null
-/*
- * 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();
- * <pre>
- * for (int i = 0 ; i< features;i++) {
- * Map f = features[i];
- * String type = (String) f.get("TYPE") ;
- * System.out.println(type);
- * }
- * </pre>
- * @return a Map containng the features
- */
- public Map[] getFeatures(){
- return features;
- }
-
- public Das1Source getDasSource(){
- return dasSource;
- }
-
-}
-
+++ /dev/null
-/*
- * 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);
-
-}
-
-
-
-
-
+++ /dev/null
-/*
- * 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);
-
-}
+++ /dev/null
-/*
- * 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;
- }
-
-}
+++ /dev/null
-/*
- * 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();
-}
git://source.jalview.org / jalview.git / commitdiff