--- /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