/Users/BSoares/uod-development/git/develop/jalview/src/jalview/gui/AlignFrame.java:978: warning: [deprecation] addJalviewPropertyChangeListener(String,PropertyChangeListener) in Desktop has been deprecated Desktop.getInstance().addJalviewPropertyChangeListener("services", ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/gui/AlignFrame.java:993: warning: [deprecation] removeJalviewPropertyChangeListener(String,PropertyChangeListener) in Desktop has been deprecated Desktop.getInstance().removeJalviewPropertyChangeListener( ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java:298: warning: [synchronization] attempt to synchronize on an instance of a value-based class synchronized (firing) ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/bin/GetMemory.java:61: warning: [deprecation] getTotalPhysicalMemorySize() in OperatingSystemMXBean has been deprecated return osb.getTotalPhysicalMemorySize(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/InputType.java:138: warning: [deprecation] StringBody(String) in StringBody has been deprecated return new StringBody( ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/InputType.java:143: warning: [deprecation] StringBody(String,String,Charset) in StringBody has been deprecated return new StringBody( ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/RestJobThread.java:226: warning: [deprecation] MultipartEntity in org.apache.http.entity.mime has been deprecated MultipartEntity postentity = new MultipartEntity( ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/RestJobThread.java:226: warning: [deprecation] MultipartEntity in org.apache.http.entity.mime has been deprecated MultipartEntity postentity = new MultipartEntity( ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/RestJobThread.java:250: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated DefaultHttpClient httpclient = new DefaultHttpClient(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/RestJobThread.java:250: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated DefaultHttpClient httpclient = new DefaultHttpClient(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/HttpResultSet.java:154: warning: [deprecation] MultipartEntity in org.apache.http.entity.mime has been deprecated if (!(en instanceof MultipartEntity)) ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/HttpResultSet.java:211: warning: [deprecation] consumeContent() in HttpEntity has been deprecated en.consumeContent(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/ebi/hmmerClient.java:97: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated DefaultHttpClient httpCl = new DefaultHttpClient(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/ebi/hmmerClient.java:97: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated DefaultHttpClient httpCl = new DefaultHttpClient(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/ebi/hmmerClient.java:143: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated DefaultHttpClient httpCl = new DefaultHttpClient(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/ebi/hmmerClient.java:143: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated DefaultHttpClient httpCl = new DefaultHttpClient(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/dbsources/GeneDbSource.java:34: warning: [deprecation] EmblXmlSource in jalview.ws.dbsources has been deprecated public class GeneDbSource extends EmblXmlSource ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:74: warning: [deprecation] HttpParams in org.apache.http.params has been deprecated HttpParams params = new BasicHttpParams(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:74: warning: [deprecation] BasicHttpParams in org.apache.http.params has been deprecated HttpParams params = new BasicHttpParams(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:75: warning: [deprecation] CoreProtocolPNames in org.apache.http.params has been deprecated params.setParameter(CoreProtocolPNames.PROTOCOL_VERSION, ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:79: warning: [deprecation] HttpConnectionParams in org.apache.http.params has been deprecated HttpConnectionParams.setConnectionTimeout(params, ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:84: warning: [deprecation] HttpConnectionParams in org.apache.http.params has been deprecated HttpConnectionParams.setSoTimeout(params, readTimeoutMs); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:86: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated HttpClient httpclient = new DefaultHttpClient(params); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:109: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated HttpClient httpclient = new DefaultHttpClient(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:111: warning: [deprecation] MultipartEntity in org.apache.http.entity.mime has been deprecated MultipartEntity mpe = new MultipartEntity( ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:111: warning: [deprecation] MultipartEntity in org.apache.http.entity.mime has been deprecated MultipartEntity mpe = new MultipartEntity( ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:115: warning: [deprecation] StringBody(String) in StringBody has been deprecated mpe.addPart(nvp.getName(), new StringBody(nvp.getValue())); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:118: warning: [deprecation] FileBody(File,String) in FileBody has been deprecated FileBody fb = new FileBody(file, ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:143: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated HttpClient httpclient = new DefaultHttpClient(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:145: warning: [deprecation] MultipartEntity in org.apache.http.entity.mime has been deprecated MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.STRICT); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:145: warning: [deprecation] MultipartEntity in org.apache.http.entity.mime has been deprecated MultipartEntity mpe = new MultipartEntity(HttpMultipartMode.STRICT); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:148: warning: [deprecation] StringBody(String) in StringBody has been deprecated mpe.addPart(nvp.getName(), new StringBody(nvp.getValue())); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:152: warning: [deprecation] InputStreamBody(InputStream,String,String) in InputStreamBody has been deprecated ? new InputStreamBody(is, fname, mtype) ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:187: warning: [deprecation] HttpParams in org.apache.http.params has been deprecated HttpParams params = new BasicHttpParams(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:187: warning: [deprecation] BasicHttpParams in org.apache.http.params has been deprecated HttpParams params = new BasicHttpParams(); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:188: warning: [deprecation] CoreProtocolPNames in org.apache.http.params has been deprecated params.setParameter(CoreProtocolPNames.PROTOCOL_VERSION, ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:192: warning: [deprecation] HttpConnectionParams in org.apache.http.params has been deprecated HttpConnectionParams.setConnectionTimeout(params, ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:197: warning: [deprecation] HttpConnectionParams in org.apache.http.params has been deprecated HttpConnectionParams.setSoTimeout(params, readTimeoutMs); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/HttpClientUtils.java:214: warning: [deprecation] DefaultHttpClient in org.apache.http.impl.client has been deprecated HttpClient httpclient = new DefaultHttpClient(params); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/params/AnnotationFile.java:74: warning: [deprecation] StringBody(String) in StringBody has been deprecated return new StringBody(new jalview.io.AnnotationFile() ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/params/AnnotationFile.java:85: warning: [deprecation] StringBody(String) in StringBody has been deprecated return new StringBody(new jalview.io.AnnotationFile() ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/params/SeqIdVector.java:73: warning: [deprecation] StringBody(String) in StringBody has been deprecated return new StringBody(idvector.toString()); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/params/JobConstant.java:68: warning: [deprecation] StringBody(String) in StringBody has been deprecated return new StringBody(value); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/params/Alignment.java:88: warning: [deprecation] FileBody(File,String) in FileBody has been deprecated return new FileBody(fa, "text/plain"); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/params/Alignment.java:99: warning: [deprecation] StringBody(String) in StringBody has been deprecated return new StringBody( ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/params/SeqGroupIndexVector.java:195: warning: [deprecation] StringBody(String) in StringBody has been deprecated return new StringBody(idvector.toString()); ^ /Users/BSoares/uod-development/git/develop/jalview/src/jalview/ws/rest/params/SeqVector.java:70: warning: [deprecation] StringBody(String) in StringBody has been deprecated return new StringBody(idvector.toString()); ^ Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 47 warnings