From 383df9f8b9361eec5ea779a22ceecc90dc7e6960 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 25 Jul 2006 10:52:38 +0000 Subject: [PATCH] Renamed files not to conflict with BIOJAVA --- .../biojava/dasobert/das/DAS_FeatureRetrieve.java | 235 ++++++++++++++++++++ .../biojava/dasobert/das/DAS_Feature_Handler.java | 190 ++++++++++++++++ .../biojava/dasobert/das/FeatureThread.java | 180 +++++++++++++++ .../biojava/dasobert/das2/Das2Capability.java | 45 ++++ .../biojava/dasobert/das2/Das2CapabilityImpl.java | 109 +++++++++ src/jalview/biojava/dasobert/das2/Das2Source.java | 40 ++++ .../biojava/dasobert/das2/Das2SourceImpl.java | 144 ++++++++++++ .../biojava/dasobert/das2/DasSourceConverter.java | 82 +++++++ .../dasobert/das2/io/DAS2SourceHandler.java | 181 +++++++++++++++ .../biojava/dasobert/das2/io/DasSourceReader.java | 32 +++ .../dasobert/das2/io/DasSourceReaderImpl.java | 173 ++++++++++++++ .../biojava/dasobert/dasregistry/Das1Source.java | 206 +++++++++++++++++ .../dasobert/dasregistry/Das2Validator.java | 43 ++++ .../dasregistry/DasCoordSysComparator.java | 116 ++++++++++ .../dasobert/dasregistry/DasCoordinateSystem.java | 159 +++++++++++++ .../biojava/dasobert/dasregistry/DasSource.java | 105 +++++++++ .../dasobert/dasregistry/DasSourceComparator.java | 140 ++++++++++++ .../biojava/dasobert/eventmodel/FeatureEvent.java | 72 ++++++ .../dasobert/eventmodel/FeatureListener.java | 49 ++++ .../dasobert/eventmodel/ObjectListener.java | 47 ++++ .../biojava/dasobert/eventmodel/SequenceEvent.java | 44 ++++ .../dasobert/eventmodel/SequenceListener.java | 55 +++++ 22 files changed, 2447 insertions(+) create mode 100644 src/jalview/biojava/dasobert/das/DAS_FeatureRetrieve.java create mode 100644 src/jalview/biojava/dasobert/das/DAS_Feature_Handler.java create mode 100644 src/jalview/biojava/dasobert/das/FeatureThread.java create mode 100644 src/jalview/biojava/dasobert/das2/Das2Capability.java create mode 100644 src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java create mode 100644 src/jalview/biojava/dasobert/das2/Das2Source.java create mode 100644 src/jalview/biojava/dasobert/das2/Das2SourceImpl.java create mode 100644 src/jalview/biojava/dasobert/das2/DasSourceConverter.java create mode 100755 src/jalview/biojava/dasobert/das2/io/DAS2SourceHandler.java create mode 100644 src/jalview/biojava/dasobert/das2/io/DasSourceReader.java create mode 100644 src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java create mode 100644 src/jalview/biojava/dasobert/dasregistry/Das1Source.java create mode 100755 src/jalview/biojava/dasobert/dasregistry/Das2Validator.java create mode 100644 src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java create mode 100644 src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java create mode 100644 src/jalview/biojava/dasobert/dasregistry/DasSource.java create mode 100644 src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java create mode 100644 src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java create mode 100644 src/jalview/biojava/dasobert/eventmodel/FeatureListener.java create mode 100644 src/jalview/biojava/dasobert/eventmodel/ObjectListener.java create mode 100644 src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java create mode 100644 src/jalview/biojava/dasobert/eventmodel/SequenceListener.java diff --git a/src/jalview/biojava/dasobert/das/DAS_FeatureRetrieve.java b/src/jalview/biojava/dasobert/das/DAS_FeatureRetrieve.java new file mode 100644 index 0000000..cdfc493 --- /dev/null +++ b/src/jalview/biojava/dasobert/das/DAS_FeatureRetrieve.java @@ -0,0 +1,235 @@ +/** + * 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 jalview.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; + + } + + +} diff --git a/src/jalview/biojava/dasobert/das/DAS_Feature_Handler.java b/src/jalview/biojava/dasobert/das/DAS_Feature_Handler.java new file mode 100644 index 0000000..957d511 --- /dev/null +++ b/src/jalview/biojava/dasobert/das/DAS_Feature_Handler.java @@ -0,0 +1,190 @@ +/* + * 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 jalview.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]; + } + + } + +} diff --git a/src/jalview/biojava/dasobert/das/FeatureThread.java b/src/jalview/biojava/dasobert/das/FeatureThread.java new file mode 100644 index 0000000..5446789 --- /dev/null +++ b/src/jalview/biojava/dasobert/das/FeatureThread.java @@ -0,0 +1,180 @@ +/* + * 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 jalview.biojava.dasobert.das ; + +import java.util.*; +import java.net.*; +import java.util.logging.* ; +import jalview.biojava.dasobert.eventmodel.FeatureListener; +import jalview.biojava.dasobert.eventmodel.FeatureEvent; +import jalview.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); + } + + } + + +} + diff --git a/src/jalview/biojava/dasobert/das2/Das2Capability.java b/src/jalview/biojava/dasobert/das2/Das2Capability.java new file mode 100644 index 0000000..12ad52b --- /dev/null +++ b/src/jalview/biojava/dasobert/das2/Das2Capability.java @@ -0,0 +1,45 @@ +/* + * 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 jalview.biojava.dasobert.das2; + +public interface Das2Capability { + + public boolean equals(Das2Capability other); + public int hashCode(); + + public void setCapability(String type); + public String getCapability(); + + public void setQueryUri(String id); + public String getQueryUri(); + + public void setFormats(String[] formats); + public String[] getFormats(); + + /** checks if this capability is actually of das1 style + * + * @return boolean true if the capability is in DAS1 style + */ + public boolean isDas1Style(); + +} diff --git a/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java b/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java new file mode 100644 index 0000000..a30b2fa --- /dev/null +++ b/src/jalview/biojava/dasobert/das2/Das2CapabilityImpl.java @@ -0,0 +1,109 @@ +/* + * 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 jalview.biojava.dasobert.das2; + +public class Das2CapabilityImpl +implements Das2Capability{ + + String capability; + String[] formats; + String queryId; + + public static String DAS1_CAPABILITY_PREFIX = "das1:"; + + public Das2CapabilityImpl() { + super(); + capability = "undef"; + queryId = ""; + formats = new String[0]; + + } + + public boolean isDas1Style(){ + + if ( capability == null) + return false; + if ( capability.length() < DAS1_CAPABILITY_PREFIX.length()) + return false; + if ( capability.substring(0,DAS1_CAPABILITY_PREFIX.length()).equals(DAS1_CAPABILITY_PREFIX)) + return true; + return false; + + } + + public boolean equals(Das2Capability other){ + + boolean status = true; + + if (! capability.equals(other.getCapability())) + status = false; + if ( ! queryId.equals(other.getQueryUri())) + status = false; + + return status; + } + + public int hashCode(){ + int h = 7; + h = 31 * h + ( null == capability ? 0 : capability.hashCode()) ; + h = 31 * h + ( null == queryId ? 0 : queryId.hashCode()) ; + + return h; + } + + public String toString(){ + String txt ="capability " + capability + " queryId " + queryId; + return txt; + } + + public String getCapability() { + + return capability; + } + + public String[] getFormats() { + return formats; + } + + public String getQueryUri() { + return queryId; + } + + public void setCapability(String type) { + capability = type; + + } + + public void setFormats(String[] formats) { + + this.formats = formats; + } + + public void setQueryUri(String id) { + queryId = id; + + } + + + +} diff --git a/src/jalview/biojava/dasobert/das2/Das2Source.java b/src/jalview/biojava/dasobert/das2/Das2Source.java new file mode 100644 index 0000000..882f0fd --- /dev/null +++ b/src/jalview/biojava/dasobert/das2/Das2Source.java @@ -0,0 +1,40 @@ +/* + * 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 jalview.biojava.dasobert.das2; + +import jalview.biojava.dasobert.dasregistry.DasSource; + +public interface Das2Source +extends DasSource { + + public Das2Capability[] getDas2Capabilities(); + public void setDas2Capabilities(Das2Capability[] capabilities); + + /** test if this is a DAS1 source represented as a DAS2 source + * if true - this source can be converted into a DAS1 source by using + * DasSourceConverter.toDas1(Das2Source); + * + * @return true if the DasSource has DAS1 capabilties + */ + public boolean hasDas1Capabilities(); +} diff --git a/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java b/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java new file mode 100644 index 0000000..5c49366 --- /dev/null +++ b/src/jalview/biojava/dasobert/das2/Das2SourceImpl.java @@ -0,0 +1,144 @@ +/* + * 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 jalview.biojava.dasobert.das2; + +import jalview.biojava.dasobert.dasregistry.Das1Source; +import jalview.biojava.dasobert.dasregistry.DasSource; + +public class Das2SourceImpl +extends Das1Source +implements Das2Source + +{ + + Das2Capability[] capabilities; + + public Das2SourceImpl() { + super(); + + capabilities = new Das2Capability[0]; + } + + + /** compare if two DasSources are identical + * + */ + public boolean equals(DasSource other){ + + if ( this == other) + return true; + + if ( ( other == null) || (other.getClass() != this.getClass())) + return false; + + // to compare if two Das2Sources are identical we do the following: + // we check the capabilities + + Das2SourceImpl d2o = (Das2SourceImpl)other; + + if ( nickname.equals(d2o.getNickname())) + return true; + + Das2Capability[] othercaps = d2o.getDas2Capabilities(); + + if ( ! (capabilities.length == othercaps.length)) + return false; + + for ( int x=0;x + DasCoordinateSystem dcs = new DasCoordinateSystem(); + String id = atts.getValue("uri"); + dcs.setUniqueId(id); + + String source = atts.getValue("source"); + dcs.setCategory(source); + + String authority = atts.getValue("authority"); + dcs.setName(authority); + + String test_range = atts.getValue("test_range"); + dcs.setTestCode(test_range); + + try { + String taxidstr = atts.getValue("taxid"); + int taxid = Integer.parseInt(taxidstr); + dcs.setNCBITaxId(taxid); + } catch (Exception e){} + + String version = atts.getValue("version"); + if ( version != null) + dcs.setVersion(version); + + return dcs; + } + + public void startElement (String uri, String name, String qName, Attributes atts){ + //System.out.println("new element "+qName); + + if (qName.equals("SOURCE")) { + //System.out.println("new Source " + atts.getValue(uri)); + currentSource = new Das2SourceImpl(); + coordinates = new ArrayList(); + capabilities = new ArrayList(); + + startSource(uri,name, qName, atts); + + } else if ( qName.equals("MAINTAINER")){ + String email = atts.getValue("email"); + currentSource.setAdminemail(email); + } else if ( qName.equals("COORDINATES")){ + DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts); + coordinates.add(dcs); + + } else if ( qName.equals("CAPABILITY")){ + Das2Capability cap = getCapability(uri,name,qName,atts); + capabilities.add(cap); + } else if (qName.equals("PROPERTY")) { + addProperty(uri,name,qName,atts); + } + } + + private Das2Capability getCapability(String uri, String name, String qName, Attributes atts){ + // e.g + Das2Capability cap = new Das2CapabilityImpl(); + + String type = atts.getValue("type"); + cap.setCapability(type); + String query_uri = atts.getValue("query_uri"); + cap.setQueryUri(query_uri); + return cap; + + } + + private void addProperty(String uri, String name, String qName, Attributes atts){ + String pname = atts.getValue("name"); + String label = atts.getValue("value"); + if ( pname.equals(LABELPROPERTY) ) + labels.add(label); + } + + public void startDocument(){ + sources = new ArrayList(); + coordinates = new ArrayList(); + capabilities = new ArrayList(); + } + + public void endElement(String uri, String name, String qName) { + if ( qName.equals("SOURCE")) { + currentSource.setDas2Capabilities((Das2Capability[])capabilities.toArray(new Das2Capability[capabilities.size()])); + //System.out.println("got coordinates " + coordinates.size()); + currentSource.setCoordinateSystem((DasCoordinateSystem[])coordinates.toArray(new DasCoordinateSystem[coordinates.size()])); + + currentSource.setLabels((String[])labels.toArray(new String[labels.size()])); + labels.clear(); + + //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName); + //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId()); + sources.add(currentSource); + currentSource = new Das2SourceImpl(); + } + } + + public DasSource[] getSources(){ + //System.out.println("Das2SourceHandler: source size: " + sources.size()); + return (DasSource[])sources.toArray(new DasSource[sources.size()]); + } + + + +} diff --git a/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java b/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java new file mode 100644 index 0000000..547c968 --- /dev/null +++ b/src/jalview/biojava/dasobert/das2/io/DasSourceReader.java @@ -0,0 +1,32 @@ +/* + * 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 jalview.biojava.dasobert.das2.io; + +import java.io.InputStream; + +import jalview.biojava.dasobert.dasregistry.DasSource; + +public interface DasSourceReader { + + public DasSource[] readDasSource(InputStream stream); +} diff --git a/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java b/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java new file mode 100644 index 0000000..03b23ff --- /dev/null +++ b/src/jalview/biojava/dasobert/das2/io/DasSourceReaderImpl.java @@ -0,0 +1,173 @@ +/* + * 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 jalview.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 jalview.biojava.dasobert.das.AlignmentThread; +import jalview.biojava.dasobert.das.DAS_FeatureRetrieve; +import jalview.biojava.dasobert.dasregistry.DasSource; +import org.xml.sax.InputSource; +import org.xml.sax.SAXException; +import org.xml.sax.SAXNotRecognizedException; +import org.xml.sax.XMLReader; + +public class DasSourceReaderImpl implements DasSourceReader { + + Exception loggedException; + + public DasSourceReaderImpl() { + super(); + loggedException = null; + + // open the stream to a server and then parse the result ... + } + + private InputStream open(URL url) + throws java.io.IOException, java.net.ConnectException + { + InputStream inStream = null; + + + HttpURLConnection huc = DAS_FeatureRetrieve.openHttpURLConnection(url); + + inStream = huc.getInputStream(); + + return inStream; + + } + + + public DasSource[] readDasSource(URL url){ + DasSource[] sources = new DasSource[0]; + + try { + InputStream stream = open(url); + + sources = readDasSource(stream); + } catch (Exception e){ + e.printStackTrace(); + loggedException = e; + } + return sources; + } + + /** read a DAS2 sources response and return a list of DAS sources. + * + */ + public DasSource[] readDasSource(InputStream stream) { + + DasSource[] sources = new DasSource[0]; + + try { + SAXParserFactory spfactory = + SAXParserFactory.newInstance(); + + spfactory.setValidating(false); + + SAXParser saxParser = null ; + + try{ + saxParser = + spfactory.newSAXParser(); + } catch (ParserConfigurationException e) { + e.printStackTrace(); + loggedException = e; + } + + String vali = System.getProperty("XMLVALIDATION"); + + boolean validation = false ; + if ( vali != null ) + if ( vali.equals("true") ) + validation = true ; + + + XMLReader xmlreader = saxParser.getXMLReader(); + + //XMLReader xmlreader = XMLReaderFactory.createXMLReader(); + try { + xmlreader.setFeature("http://xml.org/sax/features/validation", validation); + } catch (SAXException e) { + //logger.log(Level.FINE,"Cannot set validation " + validation); + } + + try { + xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validation); + } catch (SAXNotRecognizedException e){ + e.printStackTrace(); + //logger.log(Level.FINE,"Cannot set load-external-dtd "+validation); + + } + + DAS2SourceHandler cont_handle = new DAS2SourceHandler() ; + + xmlreader.setContentHandler(cont_handle); + xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler()); + InputSource insource = new InputSource() ; + insource.setByteStream(stream); + + + xmlreader.parse(insource); + sources = cont_handle.getSources(); + + + + } catch (Exception e) { + e.printStackTrace(); + loggedException = e; + } + return sources; + } + + public Exception getLoggedException(){ + return loggedException; + } + + public static void main (String[] args){ + String url = "http://www.spice-3d.org/dasregistry/das2/sources/"; + DasSourceReaderImpl reader = new DasSourceReaderImpl(); + try { + URL u = new URL(url); + DasSource[] sources = reader.readDasSource(u); + for (int i=0; i< sources.length;i++){ + DasSource ds = sources[i]; + System.out.println(ds.toString()); + } + + } catch (Exception e){ + e.printStackTrace(); + } + + } + + + +} diff --git a/src/jalview/biojava/dasobert/dasregistry/Das1Source.java b/src/jalview/biojava/dasobert/dasregistry/Das1Source.java new file mode 100644 index 0000000..4a54353 --- /dev/null +++ b/src/jalview/biojava/dasobert/dasregistry/Das1Source.java @@ -0,0 +1,206 @@ +/* + * 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 jalview.biojava.dasobert.dasregistry; + +import java.util.Date ; +import java.io.IOException; +import java.io.PrintWriter; +import java.io.StringWriter; + + +//import jalview.biojava.dasobert.das2.io.DasSourceWriter; +//import jalview.biojava.dasobert.das2.io.DasSourceWriterImpl; +//import jalview.biojava.utils.xml.PrettyXMLWriter; + + +/** a simple Bean class to be returned via SOAP + * @author Andreas Prlic + */ + +public class Das1Source implements DasSource { + String url ; + protected String nickname ; + String adminemail ; + String description ; + DasCoordinateSystem[] coordinateSystem ; + String[] capabilities ; + String[] labels ; + String helperurl ; + Date registerDate ; + Date leaseDate ; + String id ; + boolean local; + + boolean alertAdmin; + + public static String EMPTY_ID = "UNK:-1" ; + + public Das1Source () { + id = EMPTY_ID; + url = ""; + adminemail = "" ; + description = "" ; + //String empty = "" ; + nickname = "" ; + coordinateSystem = new DasCoordinateSystem[0]; + //coordinateSystem[0] = new DasCoordinateSystem(); + capabilities = new String[0]; + labels = new String[0]; + //capabilities[0] = empty ; + registerDate = new Date() ; + leaseDate = new Date() ; + helperurl = ""; + local=true; + } + + + public boolean equals(DasSource other){ + System.out.println("Das1Source equals, comparing with other DasSource"); + if (! (other instanceof Das1Source)) + return false; + + Das1Source ods = (Das1Source) other; + + if ( ods.getUrl().equals(url)) + return true; + if ( ods.getNickname().equals(nickname)) + return true; + return false; + } + + public int hashCode() { + int h = 7; + + h = 31 * h + ( null == nickname ? 0 : nickname.hashCode()); + h = 31 * h + ( null == url ? 0 : url.hashCode()); + + return h; + } + + /** the DAS2 string representation of this DAS source + * + public String toString() { + + StringWriter writer = new StringWriter(); + + PrintWriter pw = new PrintWriter(writer); + PrettyXMLWriter xw = new PrettyXMLWriter(pw); + + DasSourceWriter dswriter = new DasSourceWriterImpl(); + try { + dswriter.writeDasSource(xw,this); + } catch (IOException e){ + e.printStackTrace(); + } + + return writer.toString(); + + } + */ + public void setLocal(boolean flag){ local = flag;} + public boolean isLocal(){return local;} + + public void setId(String i) { id = i; } + + /** get a the Id of the DasSource. The Id is a unique db + * identifier. The public DAS-Registry has Auto_Ids that look like + * DASSOURCE:12345; public look like XYZ:12345, where the XYZ + * prefix can be configured in the config file. + */ + public String getId() { return id;} + + public void setNickname(String name) { + nickname = name ; + } + public String getNickname(){ + return nickname; + } + public void setUrl(String u) { + char lastChar = u.charAt(u.length()-1); + if ( lastChar != '/') + u += "/"; + + url = u ; + } + + public void setAdminemail (String u) { + adminemail = u ; + } + + public void setDescription (String u) { + description = u; + } + + public void setCoordinateSystem (DasCoordinateSystem[] u){ + coordinateSystem=u ; + } + + public void setCapabilities (String[] u){ + capabilities = u ; + } + + public String getUrl(){return url;} + public String getAdminemail(){return adminemail;} + public String getDescription(){return description;} + public String[] getCapabilities(){return capabilities;} + public DasCoordinateSystem[] getCoordinateSystem(){return coordinateSystem;} + + public void setRegisterDate(Date d) { + registerDate = d; + } + public Date getRegisterDate() { + return registerDate ; + } + public void setLeaseDate(Date d) { + leaseDate =d ; + } + public Date getLeaseDate() { + return leaseDate ; + } + + public void setLabels(String[] ls) { + labels = ls ; + } + + public String[] getLabels() { + return labels; + } + + public void setHelperurl(String url) { + helperurl = url; + } + + public String getHelperurl() { + return helperurl; + } + + public void setAlertAdmin(boolean flag) { + alertAdmin = flag; + } + + public boolean getAlertAdmin() { + return alertAdmin; + } + +} diff --git a/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java b/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java new file mode 100755 index 0000000..2a9e8d0 --- /dev/null +++ b/src/jalview/biojava/dasobert/dasregistry/Das2Validator.java @@ -0,0 +1,43 @@ +/* + * 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 jalview.biojava.dasobert.dasregistry; + +import jalview.biojava.dasobert.das2.Das2Source; + +public class Das2Validator { + + public Das2Validator() { + super(); + + } + + public boolean validate(Das2Source ds){ + + // TODO this bit still needs to be implemented! + + return true; + } + + + +} diff --git a/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java b/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java new file mode 100644 index 0000000..ce9ddc5 --- /dev/null +++ b/src/jalview/biojava/dasobert/dasregistry/DasCoordSysComparator.java @@ -0,0 +1,116 @@ +/* + * 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 jalview.biojava.dasobert.dasregistry ; + +import java.util.Comparator ; +import java.util.Map ; +import java.util.HashMap ; + +import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem; + +/** a comparator to sort DasSources + * @author Andreas Prlic + */ + + +public abstract class DasCoordSysComparator + implements Comparator +{ + + private final String name ; + private static final Map COMPS_BY_NAME; + + + public DasCoordSysComparator(String str) { + //System.out.println("new dasSourceComparator " + str); + name = str ; + } + + public static final Comparator BY_NAME = new DasCoordSysComparator("name") { + protected Comparable getField(DasCoordinateSystem ds) { + return ds.getName(); + } + }; + + public static final Comparator BY_ID = new DasCoordSysComparator("id") { + protected Comparable getField(DasCoordinateSystem ds) { + return ds.getUniqueId(); + } + }; + public static final Comparator BY_CATEGORY = new DasCoordSysComparator("category") { + protected Comparable getField(DasCoordinateSystem ds) { + return ds.getCategory(); + } + }; + public static final Comparator BY_ORGANISM = new DasCoordSysComparator("organism") { + protected Comparable getField(DasCoordinateSystem ds) { + return ds.getOrganismName(); + } + }; + public static final Comparator BY_TAXID = new DasCoordSysComparator("taxid") { + protected Comparable getField(DasCoordinateSystem ds) { + return ds.getNCBITaxId()+""; + } + }; + + + + static { + COMPS_BY_NAME = new HashMap(); + COMPS_BY_NAME.put(BY_ID.toString(), BY_ID); + COMPS_BY_NAME.put(BY_NAME.toString(), BY_NAME); + COMPS_BY_NAME.put(BY_CATEGORY.toString(), BY_CATEGORY); + COMPS_BY_NAME.put(BY_ORGANISM.toString(), BY_ORGANISM); + COMPS_BY_NAME.put(BY_TAXID.toString(), BY_TAXID); + } + + + + public static Comparator fromString(String name) { + if (COMPS_BY_NAME.containsKey(name)) { + return (Comparator) COMPS_BY_NAME.get(name); + } else { + throw new IllegalArgumentException("Can't compare by key " + name); + } + } + + protected abstract Comparable getField(DasCoordinateSystem ds); + + /** compare two DasCoordSys objects */ + public int compare( Object a, Object b) { + DasCoordinateSystem x = (DasCoordinateSystem) a ; + DasCoordinateSystem y = (DasCoordinateSystem) b ; + return getField(x).compareTo(getField(y)); + } + + public String toString() { + return name; + } + + +} + + diff --git a/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java b/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java new file mode 100644 index 0000000..58fa023 --- /dev/null +++ b/src/jalview/biojava/dasobert/dasregistry/DasCoordinateSystem.java @@ -0,0 +1,159 @@ +/* + * 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 jalview.biojava.dasobert.dasregistry; + + +/** a Bean to be returned via SOAP. It takes care of the DAS - coordinate Systems + * @author Andreas Prlic + */ +public class DasCoordinateSystem { + + String name; + String category; + String organism_name; + int ncbi_tax_id ; + String uniqueId ; + String version; + String testCode; + + public DasCoordinateSystem () { + uniqueId = ""; + name = ""; + category =""; + organism_name = ""; + ncbi_tax_id = 0; + version = ""; + testCode = ""; + } + + public boolean equals(DasCoordinateSystem other){ + boolean match = true; + System.out.println("comparing " + this.toString() + " to " + other.toString()); + // URI has piority + if ( (! uniqueId.equals("")) && ( uniqueId.equals( other.getUniqueId()))) + return true; + + if ( ncbi_tax_id != other.getNCBITaxId()) { + System.out.println("mismatch in ncbi tax id " + ncbi_tax_id + " != " + other.getNCBITaxId()); + match = false; + } + if ( ! version.equals(other.getVersion() )){ + System.out.println("mismatch in version"); + match = false; + } + if ( ! category.equals(other.getCategory()) ) { + System.out.println("mismatch in category"); + match = false; + } + if ( ! name.equals(other.getName())) { + System.out.println("mismatch in name"); + match = false; + } + System.out.println(" match: " + match); + + return match; + } + + public Object clone() { + DasCoordinateSystem d = new DasCoordinateSystem(); + d.setTestCode(testCode); + d.setCategory(category); + d.setName(name); + d.setNCBITaxId(ncbi_tax_id); + d.setUniqueId(getUniqueId()); + d.setOrganismName(getOrganismName()); + d.setVersion(getVersion()); + return d; + } + + public String getTestCode() { + return testCode; + } + + + + public void setTestCode(String testCode) { + if ( testCode == null) + testCode = ""; + this.testCode = testCode; + } + + + + public void setUniqueId(String id) { uniqueId = id ; } + public String getUniqueId() { return uniqueId; } + + public void setName(String n) { name = n; } + public String getName() { return name; } + + public void setCategory(String c) { category = c;} + public String getCategory() { return category;} + + public void setOrganismName(String t) { organism_name =t;} + public String getOrganismName() { return organism_name;} + + public void setNCBITaxId(int id) { ncbi_tax_id = id;} + public int getNCBITaxId(){ return ncbi_tax_id ;} + + + + + public String getVersion() { + return version; + } + + public void setVersion(String version) { + if ( version == null) + version = ""; + this.version = version; + } + + public String toString() { + String nam = name; + if ( ! version.equals("")) + nam += "_" + version; + + if ( organism_name.equals("") ) + return nam+","+category ; + else + return nam+","+category+"," + organism_name ; + } + + public static DasCoordinateSystem fromString(String rawString) { + String[] spl = rawString.split(","); + DasCoordinateSystem dcs = new DasCoordinateSystem(); + if ( spl.length == 2 ) { + dcs.setName(spl[0]); + dcs.setCategory(spl[1]); + } + if ( spl.length == 3 ) { + dcs.setName(spl[0]); + dcs.setCategory(spl[1]); + dcs.setOrganismName(spl[2]); + } + return dcs; + } + + +} diff --git a/src/jalview/biojava/dasobert/dasregistry/DasSource.java b/src/jalview/biojava/dasobert/dasregistry/DasSource.java new file mode 100644 index 0000000..a6e0096 --- /dev/null +++ b/src/jalview/biojava/dasobert/dasregistry/DasSource.java @@ -0,0 +1,105 @@ +/* + * 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 jalview.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(); + +} \ No newline at end of file diff --git a/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java b/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java new file mode 100644 index 0000000..fb6b249 --- /dev/null +++ b/src/jalview/biojava/dasobert/dasregistry/DasSourceComparator.java @@ -0,0 +1,140 @@ +/* + * 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 jalview.biojava.dasobert.dasregistry ; + +import java.util.Comparator ; +import java.util.Map ; +import java.util.HashMap ; + + +/** a comparator to sort DasSources + * @author Andreas Prlic, Thomas Down + */ + + +public abstract class DasSourceComparator + implements Comparator +{ + + private final String name ; + private static final Map COMPS_BY_NAME; + + + public DasSourceComparator(String str) { + //System.out.println("new dasSourceComparator " + str); + name = str ; + } + + public static final Comparator BY_ID = new DasSourceComparator("id") { + protected Comparable getField(DasSource ds) { + return ds.getId(); + } + }; + + public static final Comparator BY_NICKNAME = new DasSourceComparator("nickname") { + protected Comparable getField(DasSource ds) { + return ds.getNickname(); + } + }; + public static final Comparator BY_REGISTER_DATE = new DasSourceComparator("registerdate") { + protected Comparable getField(DasSource ds) { + return ds.getRegisterDate(); + } + }; + public static final Comparator BY_LEASE_DATE = new DasSourceComparator("leasedate") { + protected Comparable getField(DasSource ds) { + return ds.getLeaseDate(); + } + }; + public static final Comparator BY_URL = new DasSourceComparator("url") { + protected Comparable getField(DasSource ds) { + return ds.getUrl(); + } + }; + public static final Comparator BY_ADMIN_EMAIL = new DasSourceComparator("adminemail") { + protected Comparable getField(DasSource ds) { + return ds.getAdminemail(); + } + }; + public static final Comparator BY_DESCRIPTION = new DasSourceComparator("description") { + protected Comparable getField(DasSource ds) { + return ds.getDescription(); + } + }; + public static final Comparator BY_CAPABILITIES = new DasSourceComparator("capabilities") { + protected Comparable getField(DasSource ds) { + String[] caps = ds.getCapabilities(); + return caps.length == 0 ? "" : caps[0]; + } + }; + public static final Comparator BY_COORDINATE_SYSTEM = new DasSourceComparator("coordinateSystem") { + protected Comparable getField(DasSource ds) { + DasCoordinateSystem[] dcss = ds.getCoordinateSystem(); + return dcss.length == 0 ? "" : dcss[0].toString(); + } + }; + + static { + COMPS_BY_NAME = new HashMap(); + COMPS_BY_NAME.put(BY_ID.toString(), BY_ID); + COMPS_BY_NAME.put(BY_NICKNAME.toString(), BY_NICKNAME); + COMPS_BY_NAME.put(BY_REGISTER_DATE.toString(), BY_REGISTER_DATE); + COMPS_BY_NAME.put(BY_LEASE_DATE.toString(), BY_LEASE_DATE); + COMPS_BY_NAME.put(BY_URL.toString(), BY_URL); + COMPS_BY_NAME.put(BY_ADMIN_EMAIL.toString(), BY_ADMIN_EMAIL); + COMPS_BY_NAME.put(BY_DESCRIPTION.toString(), BY_DESCRIPTION); + COMPS_BY_NAME.put(BY_CAPABILITIES.toString(), BY_CAPABILITIES); + COMPS_BY_NAME.put(BY_COORDINATE_SYSTEM.toString(), BY_COORDINATE_SYSTEM); + } + + + + public static Comparator fromString(String name) { + if (COMPS_BY_NAME.containsKey(name)) { + return (Comparator) COMPS_BY_NAME.get(name); + } else { + throw new IllegalArgumentException("Can't compare by key " + name); + } + } + + protected abstract Comparable getField(DasSource ds); + + /** compare two DasSource objects */ + public int compare( Object a, Object b) { + + DasSource x = (DasSource) a ; + DasSource y = (DasSource) b ; + return getField(x).compareTo(getField(y)); + } + + public String toString() { + return name; + } + + +} + + diff --git a/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java b/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java new file mode 100644 index 0000000..0df2358 --- /dev/null +++ b/src/jalview/biojava/dasobert/eventmodel/FeatureEvent.java @@ -0,0 +1,72 @@ +/* + * 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 jalview.biojava.dasobert.eventmodel; + +import java.util.Map; + +import jalview.biojava.dasobert.dasregistry.Das1Source; +public class FeatureEvent { + + Map[] features; + Das1Source dasSource; + int comeBackLater; + + public FeatureEvent(Map[] features,Das1Source dasSource) { + super(); + this.features =features; + this.dasSource = dasSource; + comeBackLater = -1; + } + + public int getComeBackLater(){ + return comeBackLater; + } + + public void setComeBackLater(int comeBackLater){ + this.comeBackLater = comeBackLater; + } + + + /** get the features that have been found. + * + * do something like + * Map[] features = event.getFeatures(); + * 
+     * for (int i = 0 ; i< features;i++) {
+     *      Map f = features[i];
+     *      String type = (String) f.get("TYPE") ;
+     *      System.out.println(type);
+     * }
+     *
+ * @return a Map containng the features + */ + public Map[] getFeatures(){ + return features; + } + + public Das1Source getDasSource(){ + return dasSource; + } + +} + diff --git a/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java b/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java new file mode 100644 index 0000000..fb58345 --- /dev/null +++ b/src/jalview/biojava/dasobert/eventmodel/FeatureListener.java @@ -0,0 +1,49 @@ +/* + * 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 jalview.biojava.dasobert.eventmodel; + +//import jalview.biojava.spice.multipanel.eventmodel.FeatureEvent; + +/** a feature listener that returns the raw features as returned by a DAS source. + * + */ +public interface FeatureListener { + + /** new features have been returned from the Annotation server + * + * @param e + */ + public void newFeatures(FeatureEvent e); + + /** the server says that he is busy and we should try again in x seconds + * + * @param e + */ + public void comeBackLater(FeatureEvent e); + +} + + + + + diff --git a/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java b/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java new file mode 100644 index 0000000..497d382 --- /dev/null +++ b/src/jalview/biojava/dasobert/eventmodel/ObjectListener.java @@ -0,0 +1,47 @@ +/* + * 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 jalview.biojava.dasobert.eventmodel; + +/** an interface for the listeners of new PDB code requested / new Uniprot code requested + * + * @author Andreas Prlic + * + */ +public interface ObjectListener { + + /** a new object has been requested + * + * @param accessionCode + */ + public void newObjectRequested(String accessionCode); + + /** no object with that accessionCode has been found + * + * @param accessionCode + */ + public void noObjectFound(String accessionCode); + + + // public void exceptionOccured(Exception e); + +} diff --git a/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java b/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java new file mode 100644 index 0000000..14038c9 --- /dev/null +++ b/src/jalview/biojava/dasobert/eventmodel/SequenceEvent.java @@ -0,0 +1,44 @@ +/* + * 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 jalview.biojava.dasobert.eventmodel; + + +public class SequenceEvent { + + String sequence; + String accessionCode; + public SequenceEvent(String accessionCode, String seq) { + super(); + sequence = seq; + this.accessionCode = accessionCode; + } + + public String getAccessionCode(){ + return accessionCode; + } + + public String getSequence(){ + return sequence; + } + +} diff --git a/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java b/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java new file mode 100644 index 0000000..0f6d724 --- /dev/null +++ b/src/jalview/biojava/dasobert/eventmodel/SequenceListener.java @@ -0,0 +1,55 @@ +/* + * 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 jalview.biojava.dasobert.eventmodel; + +/** An interface fore events related to selections of sequence + * position, sequence range and locking of the selection. + * + * @author Andreas Prlic + * + */ +public interface SequenceListener +extends ObjectListener{ + + /* select a certain sequence position */ + public void selectedSeqPosition(int position); + + /** select a certain range of a sequence + * @param start the start + * @param end the end of the range + * */ + public void selectedSeqRange(int start, int end); + + /** the current selecetion is locked and can not be changed + * @param flag true if selection should be locked + * */ + public void selectionLocked(boolean flag); + + public void newSequence(SequenceEvent e); + + /** clear what has been selected + * + * + */ + public void clearSelection(); +} -- 1.7.10.2