+++ /dev/null
-/**
- *
- */
-package org.vamsas.test.simpleclient.simpleapp;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Vector;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-
-import org.vamsas.test.simpleclient.ArchiveClient;
-import org.vamsas.test.simpleclient.ClientDoc;
-
-import uk.ac.vamsas.client.UserHandle;
-import uk.ac.vamsas.client.simpleclient.FileWatcher;
-import uk.ac.vamsas.client.simpleclient.VamsasArchive;
-import uk.ac.vamsas.client.simpleclient.VamsasFile;
-import uk.ac.vamsas.objects.core.Entry;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-
-/**
- * @author jimp
- *
- */
-public class VamsasClient extends ArchiveClient {
- org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasClient.class);
- /**
- * create a new vamsas client session from the archive at sessionPath.
- * @param sessionPath
- */
- public VamsasClient(File sessionPath) {
- super(System.getProperty("user.name"),System.getProperty("host.name"), "SimpleVamsasClientApp","0.1",
- sessionPath);
- }
- /**
- * Called by gui to read anything from the vamsas session into the apps datamodel
- * after it has started up.
- *
- */
- public void initial_update() {
- log.info("Jalview loading the Vamsas Session.");
- // load in the vamsas archive for the first time
- ClientDoc cdoc = this.getUpdateable();
- updateJalview(cdoc);
- // TODO: flush any new VorbaIds to the document : updateVamsasClient may actually generate new Vamsas Document data in the form of vamsas element ids - these should be written back to the document.
- //doUpdate(cdoc); // JBPNote: this should flush new VorbaIds but I've not tested it yet.
- cdoc.closeDoc();
- // then tell app to update its display based on the datamodel changes.
- }
- VamsasClientWatcher watcher=null;
- /**
- * Called by app when internal datamodel should exported (syncrhonised outwards) to vamsas document
- *
- */
- public void push_update() {
-
- watchForChange=false; // this makes any watch(long) loops return.
- // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped.
- try {
- Thread.sleep(WATCH_SLEEP);
- } catch (Exception e) {
-
- };
-
- ClientDoc cdoc = getUpdateable();
- updateVamsasDocument(cdoc);
- doUpdate(cdoc);
- cdoc.closeDoc();
- cdoc=null;
- watchForChange=true;
- startWatcher();
- }
- public void end_session() {
- watchForChange=false; // this makes any watch(long) loops return.
- // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped.
- try {
- Thread.sleep(WATCH_SLEEP);
- } catch (Exception e) {
-
- };
-
- // stop any update/watcher thread.
- log.info("VamsasClientApplication disconnecting from the Vamsas Session.");
- }
- public void updateJalview(ClientDoc cdoc) {
- ensureVamsasBindings();
- VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry());
- vds.updateToJalview();
- }
- private void ensureVamsasBindings() {
- if (jv2vobj==null) {
- jv2vobj = new IdentityHashMap();
- vobj2jv = new Hashtable();
- }
- }
- /**
- * App's object binding to VorbaIds
- */
- IdentityHashMap jv2vobj = null;
- Hashtable vobj2jv = null;
- /**
- * called with a vamsas document which will be updated with new data from the app
- * @param doc
- */
- public void updateVamsasDocument(ClientDoc doc) {
- ensureVamsasBindings();
- VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj, baseProvEntry());
- // wander through frames
- vds.storeVAMSAS(new Object()); // Object is the apps datamodel ;)
- }
- /**
- *
- * @return a base provenance entry used by the VamsasDatastore object to get attributes from. this isn't particularly elegant either.
- */
- private Entry baseProvEntry() {
- uk.ac.vamsas.objects.core.Entry pentry = new uk.ac.vamsas.objects.core.Entry();
- pentry.setUser(this.getProvenanceUser());
- pentry.setApp(this.getClientHandle().getClientName());
- pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
- pentry.setAction("created");
- return pentry;
- }
- protected class VamsasClientWatcher extends Thread implements Runnable {
- /* (non-Javadoc)
- * @see java.lang.Thread#run()
- */
- VamsasClient client=null;
- VamsasClientWatcher(VamsasClient client) {
- this.client = client;
- }
- boolean running=false;
- public void run() {
- running=true;
- while (client.watchForChange) {
- ClientDoc docio = client.watch(0);
- if (docio!=null) {
- // VamsasClient GUI bits should be disabled whilst an update is in progress so the user doesn't screw anything up.
- client.disableGui(true);
- log.debug("Updating VamsasClient app from changed vamsas document.");
- client.updateJalview(docio);
- log.debug("Finished updating from document change.");
- docio.closeDoc();
- docio=null;
- client.disableGui(false);
- }
- }
- running=false;
-
- }
-
- }
- /**
- * @param args
- */
- public static void main(String[] args) {
- // TODO Auto-generated method stub
-
- }
- /**
- * disable (if b is true) or enable (if b is true) the VamsasClient's vamsas session gui bits whilst a document change is being updated to the app.
- * @param b
- */
- public void disableGui(boolean b) {
- // in jalview, we turn off the VAMSAS Session menu : Desktop.instance.setVamsasUpdate(b);
- }
- /**
- * spawn a new thread to start the VamsasClientWatcher.
- *
- */
- public void startWatcher() {
- if (watcher==null)
- watcher=new VamsasClientWatcher(this);
- Thread thr = new Thread() {
- public void run() {
- watcher.start();
- }
- };
- thr.start();
- }
-
-}
+++ /dev/null
-/*\r
- * VamsasClientSimpleApp - A framework for interoparable Sequence analysis\r
- * Copyright (C) 2006 VAMSAS\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package org.vamsas.test.simpleclient.simpleapp;\r
-\r
-import org.vamsas.test.simpleclient.ClientDoc;\r
-\r
-\r
-import java.io.*;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
-import java.util.Hashtable;\r
-import java.util.IdentityHashMap;\r
-import java.util.Vector;\r
-import java.util.jar.*;\r
-import org.exolab.castor.xml.*;\r
-import org.exolab.castor.mapping.Mapping;\r
-\r
-import uk.ac.vamsas.client.Vobject;\r
-import uk.ac.vamsas.client.VorbaId;\r
-import uk.ac.vamsas.objects.core.*;\r
-import uk.ac.vamsas.objects.utils.DocumentStuff;\r
-\r
-/*\r
- * \r
- * static {\r
- * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(\r
- * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }\r
- * \r
- */\r
-\r
-public class VamsasDatastore {\r
- org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasDatastore.class);\r
- Entry provEntry = null;\r
-\r
-\r
- org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(\r
- new java.util.Date());\r
-\r
- ClientDoc cdoc;\r
-\r
- Hashtable vobj2jv;\r
-\r
- IdentityHashMap jv2vobj;\r
-\r
- public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,\r
- IdentityHashMap jv2vobj, Entry provEntry) {\r
- this.cdoc = cdoc;\r
- this.vobj2jv = vobj2jv;\r
- this.jv2vobj = jv2vobj;\r
- this.provEntry = provEntry;\r
- }\r
-\r
- /*\r
- * public void storeJalview(String file, AlignFrame af) { try { // 1. Load the\r
- * mapping information from the file Mapping map = new\r
- * Mapping(getClass().getClassLoader()); java.net.URL url =\r
- * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2.\r
- * Unmarshal the data // Unmarshaller unmar = new Unmarshaller();\r
- * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni =\r
- * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data\r
- * with the total price back and print the XML in the console Marshaller\r
- * marshaller = new Marshaller( new FileWriter(file) );\r
- * \r
- * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {\r
- * e.printStackTrace(); } }\r
- * \r
- * \r
- */\r
- /**\r
- * @return the Vobject bound to Jalview datamodel object\r
- */\r
- protected Vobject getjv2vObj(Object jvobj) {\r
- if (jv2vobj.containsKey(jvobj))\r
- return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));\r
- return null;\r
- }\r
-\r
- /**\r
- * \r
- * @param vobj\r
- * @return Jalview datamodel object bound to the vamsas document object\r
- */\r
- protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj) {\r
- VorbaId id = vobj.getVorbaId();\r
- if (id == null)\r
- {\r
- id = cdoc.registerObject(vobj);\r
- log\r
- .debug("Registering new object and returning null for getvObj2jv");\r
- return null;\r
- }\r
- if (vobj2jv.containsKey(vobj.getVorbaId()))\r
- return vobj2jv.get(vobj.getVorbaId());\r
- return null;\r
- }\r
-\r
- protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj) {\r
- VorbaId id = vobj.getVorbaId();\r
- if (id == null)\r
- {\r
- id = cdoc.registerObject(vobj);\r
- if (id==null || vobj.getVorbaId()==null)\r
- log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);\r
- }\r
- if (vobj2jv.containsKey(vobj.getVorbaId()) || jv2vobj.containsKey(jvobj))\r
- {\r
- log.error("Duplicate object binding! "+vobj+" id " +vobj.getVorbaId().getId()+" to "+jvobj);\r
- }\r
- else\r
- {\r
- vobj2jv.put(vobj.getVorbaId(), jvobj);// JBPNote - better implementing a\r
- // hybrid invertible hash.\r
- jv2vobj.put(jvobj, vobj.getVorbaId());\r
- }\r
- }\r
-\r
- /**\r
- * put the alignment viewed by AlignViewport into cdoc.\r
- * \r
- * @param av\r
- */\r
- public void storeVAMSAS(Object fromAppsDatamodel) {\r
- boolean nw = false;\r
- VAMSAS root = null; // will be resolved based on Dataset Parent.\r
- DataSet dataset = (DataSet) getjv2vObj(fromAppsDatamodel);\r
- if (dataset == null)\r
- {\r
- root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.\r
- dataset = new DataSet();\r
- root.addDataSet(dataset);\r
- bindjvvobj(fromAppsDatamodel, dataset);\r
- dataset.setProvenance(dummyProvenance());\r
- dataset.getProvenance().addEntry(provEntry);\r
- nw = true;\r
- } else {\r
- root = (VAMSAS) dataset.getV_parent();\r
- }\r
- // etc...\r
- }\r
-\r
- private Property newProperty(String name, String type, String content) {\r
- Property vProperty=new Property();\r
- vProperty.setName(name);\r
- if (type!=null)\r
- vProperty.setType(type);\r
- vProperty.setContent(content);\r
- return vProperty;\r
- }\r
-\r
- /**\r
- * get start<end range of segment, adjusting for inclusivity flag and\r
- * polarity.\r
- * \r
- * @param visSeg\r
- * @param ensureDirection when true - always ensure start is less than end.\r
- * @return int[] { start, end, direction} where direction==1 for range running from end to start.\r
- */\r
- private int[] getSegRange(Seg visSeg, boolean ensureDirection) {\r
- boolean incl = visSeg.getInclusive();\r
- // adjust for inclusive flag.\r
- int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of\r
- // region.\r
- int start = visSeg.getStart() + (incl ? 0 : pol);\r
- int end = visSeg.getEnd() + (incl ? 0 : -pol);\r
- if (ensureDirection && pol==-1)\r
- {\r
- // jalview doesn't deal with inverted ranges, yet.\r
- int t = end;\r
- end = start;\r
- start = t;\r
- }\r
- return new int[] { start, end, pol<0 ? 1 : 0 };\r
- }\r
-\r
- public void updateToJalview() {\r
- VAMSAS _roots[] = cdoc.getVamsasRoots();\r
-\r
- for (int _root = 0; _root<_roots.length; _root++) {\r
- VAMSAS root = _roots[_root];\r
- boolean newds=false;\r
- for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {\r
- // ///////////////////////////////////\r
- // ///LOAD DATASET\r
- DataSet dataset = root.getDataSet(_ds);\r
- int i, iSize = dataset.getSequenceCount();\r
- Vector dsseqs;\r
- Object appsdataset = (Object) getvObj2jv(dataset);\r
- int jremain=0;\r
- if (appsdataset==null) {\r
- log.debug("Initialising new dataset fields");\r
- newds=true;\r
- dsseqs=new Vector();\r
- } else {\r
- log.debug("Update dataset from vamsas dataset.");\r
- }\r
- // etc for annotations, alignments, trees, etc. \r
- }\r
- }\r
- }\r
- /**\r
- * get real bounds of a RangeType's specification. start and end are an\r
- * inclusive range within which all segments and positions lie.\r
- * TODO: refactor to vamsas utils\r
- * @param dseta\r
- * @return int[] { start, end}\r
- */\r
- private int[] getBounds(RangeType dseta) {\r
- if (dseta != null)\r
- {\r
- int[] se = null;\r
- if (dseta.getSegCount()>0 && dseta.getPosCount()>0)\r
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
- if (dseta.getSegCount() > 0)\r
- {\r
- se = getSegRange(dseta.getSeg(0),true);\r
- for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)\r
- {\r
- int nse[] = getSegRange(dseta.getSeg(s), true);\r
- if (se[0] > nse[0])\r
- se[0] = nse[0];\r
- if (se[1] < nse[1])\r
- se[1] = nse[1];\r
- }\r
- }\r
- if (dseta.getPosCount() > 0)\r
- {\r
- // could do a polarity for pos range too. and pass back indication of discontinuities.\r
- int pos = dseta.getPos(0).getI();\r
- se = new int[] { pos, pos };\r
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
- {\r
- pos = dseta.getPos(p).getI();\r
- if (se[0] > pos)\r
- se[0] = pos;\r
- if (se[1] < pos)\r
- se[1] = pos;\r
- }\r
- }\r
- return se;\r
- }\r
- return null;\r
- }\r
- /**\r
- * map from a rangeType's internal frame to the referenced object's coordinate frame.\r
- * @param dseta\r
- * @return int [] { ref(pos)...} for all pos in rangeType's frame.\r
- */\r
- private int[] getMapping(RangeType dseta) {\r
- Vector posList=new Vector();\r
- if (dseta != null)\r
- {\r
- int[] se = null;\r
- if (dseta.getSegCount()>0 && dseta.getPosCount()>0)\r
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
- if (dseta.getSegCount() > 0)\r
- {\r
- for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)\r
- {\r
- se = getSegRange(dseta.getSeg(s), false);\r
- int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);\r
- for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {\r
- posList.add(Integer.valueOf(p));\r
- }\r
- }\r
- } \r
- else if (dseta.getPosCount() > 0)\r
- {\r
- int pos = dseta.getPos(0).getI();\r
-\r
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
- {\r
- pos = dseta.getPos(p).getI();\r
- posList.add(Integer.valueOf(pos));\r
- }\r
- }\r
- }\r
- if (posList!=null && posList.size()>0) {\r
- int[] range=new int[posList.size()];\r
- for (int i=0; i<range.length; i++)\r
- range[i] = ((Integer)posList.elementAt(i)).intValue();\r
- posList.clear();\r
- return range;\r
- }\r
- return null;\r
- }\r
- /**\r
- * \r
- * @return default initial provenance list for a VamsasDatastore created vamsas\r
- * object.\r
- */\r
- Provenance dummyProvenance() {\r
- return dummyProvenance(null);\r
- }\r
-\r
- Entry dummyPEntry(String action) {\r
- Entry entry = new Entry();\r
- entry.setApp(this.provEntry.getApp());\r
- if (action != null)\r
- entry.setAction(action);\r
- else\r
- entry.setAction("created.");\r
- entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));\r
- entry.setUser(this.provEntry.getUser());\r
- return entry;\r
- }\r
-\r
- Provenance dummyProvenance(String action) {\r
- Provenance prov = new Provenance();\r
- prov.addEntry(dummyPEntry(action));\r
- return prov;\r
- }\r
-\r
- void addProvenance(Provenance p, String action) {\r
- p.addEntry(dummyPEntry(action));\r
- }\r
-\r
-}\r
git://source.jalview.org / vamsas.git / commitdiff