X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Forg%2Fvamsas%2Ftest%2Fsimpleclient%2Fsimpleapp%2FVamsasDatastore.java;fp=src%2Forg%2Fvamsas%2Ftest%2Fsimpleclient%2Fsimpleapp%2FVamsasDatastore.java;h=9114e8811eb2fd03fc98f1eaa26faaaaf0bbe8a5;hb=ef985efd6a509d94567170da164c57a65b3b11ee;hp=0000000000000000000000000000000000000000;hpb=6a22a06cc820ff240f5b37866b768fd7c0df16d7;p=vamsas.git

diff --git a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
new file mode 100644
index 0000000..9114e88
--- /dev/null
+++ b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
@@ -0,0 +1,333 @@
+/*
+ * VamsasClientSimpleApp - A framework for interoparable Sequence analysis
+ * Copyright (C) 2006 VAMSAS
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
+package org.vamsas.test.simpleclient.simpleapp;
+
+import org.vamsas.client.Vobject;
+import org.vamsas.client.VorbaId;
+import org.vamsas.objects.core.*;
+import org.vamsas.objects.utils.DocumentStuff;
+import org.vamsas.test.simpleclient.ClientDoc;
+
+
+import java.io.*;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+import java.util.jar.*;
+import org.exolab.castor.xml.*;
+import org.exolab.castor.mapping.Mapping;
+
+/*
+ * 
+ * static {
+ * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
+ * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
+ * 
+ */
+
+public class VamsasDatastore {
+  org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasDatastore.class);
+  Entry provEntry = null;
+
+
+  org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(
+      new java.util.Date());
+
+  ClientDoc cdoc;
+
+  Hashtable vobj2jv;
+
+  IdentityHashMap jv2vobj;
+
+  public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,
+      IdentityHashMap jv2vobj, Entry provEntry) {
+      this.cdoc = cdoc;
+    this.vobj2jv = vobj2jv;
+    this.jv2vobj = jv2vobj;
+    this.provEntry = provEntry;
+  }
+
+  /*
+   * public void storeJalview(String file, AlignFrame af) { try { // 1. Load the
+   * mapping information from the file Mapping map = new
+   * Mapping(getClass().getClassLoader()); java.net.URL url =
+   * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2.
+   * Unmarshal the data // Unmarshaller unmar = new Unmarshaller();
+   * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni =
+   * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data
+   * with the total price back and print the XML in the console Marshaller
+   * marshaller = new Marshaller( new FileWriter(file) );
+   * 
+   * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {
+   * e.printStackTrace(); } }
+   * 
+   * 
+   */
+  /**
+   * @return the Vobject bound to Jalview datamodel object
+   */
+  protected Vobject getjv2vObj(Object jvobj) {
+    if (jv2vobj.containsKey(jvobj))
+      return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
+    return null;
+  }
+
+  /**
+   * 
+   * @param vobj
+   * @return Jalview datamodel object bound to the vamsas document object
+   */
+  protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {
+    VorbaId id = vobj.getVorbaId();
+    if (id == null)
+    {
+      id = cdoc.registerObject(vobj);
+      log
+      .debug("Registering new object and returning null for getvObj2jv");
+      return null;
+    }
+    if (vobj2jv.containsKey(vobj.getVorbaId()))
+      return vobj2jv.get(vobj.getVorbaId());
+    return null;
+  }
+
+  protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {
+    VorbaId id = vobj.getVorbaId();
+    if (id == null)
+    {
+      id = cdoc.registerObject(vobj);
+      if (id==null || vobj.getVorbaId()==null)
+        log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);
+    }
+    if (vobj2jv.containsKey(vobj.getVorbaId()) || jv2vobj.containsKey(jvobj))
+    {
+      log.error("Duplicate object binding! "+vobj+" id " +vobj.getVorbaId().getId()+" to "+jvobj);
+    }
+    else
+    {
+      vobj2jv.put(vobj.getVorbaId(), jvobj);// JBPNote - better implementing a
+      // hybrid invertible hash.
+      jv2vobj.put(jvobj, vobj.getVorbaId());
+    }
+  }
+
+  /**
+   * put the alignment viewed by AlignViewport into cdoc.
+   * 
+   * @param av
+   */
+  public void storeVAMSAS(Object fromAppsDatamodel) {
+    boolean nw = false;
+    VAMSAS root = null; // will be resolved based on Dataset Parent.
+    DataSet dataset = (DataSet) getjv2vObj(fromAppsDatamodel);
+    if (dataset == null)
+    {
+      root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
+      dataset = new DataSet();
+      root.addDataSet(dataset);
+      bindjvvobj(fromAppsDatamodel, dataset);
+      dataset.setProvenance(dummyProvenance());
+      dataset.getProvenance().addEntry(provEntry);
+      nw = true;
+    } else {
+      root = (VAMSAS) dataset.getV_parent();
+    }
+    // etc...
+  }
+
+  private Property newProperty(String name, String type, String content) {
+    Property vProperty=new Property();
+    vProperty.setName(name);
+    if (type!=null)
+      vProperty.setType(type);
+    vProperty.setContent(content);
+    return vProperty;
+  }
+
+  /**
+   * get start<end range of segment, adjusting for inclusivity flag and
+   * polarity.
+   *  
+   * @param visSeg
+   * @param ensureDirection when true - always ensure start is less than end.
+   * @return int[] { start, end, direction} where direction==1 for range running from end to start.
+   */
+  private int[] getSegRange(Seg visSeg, boolean ensureDirection) {
+    boolean incl = visSeg.getInclusive();
+    // adjust for inclusive flag.
+    int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of
+    // region.
+    int start = visSeg.getStart() + (incl ? 0 : pol);
+    int end = visSeg.getEnd() + (incl ? 0 : -pol);
+    if (ensureDirection && pol==-1)
+    {
+      // jalview doesn't deal with inverted ranges, yet.
+      int t = end;
+      end = start;
+      start = t;
+    }
+    return new int[] { start, end, pol<0 ? 1 : 0 };
+  }
+
+  public void updateToJalview() {
+    VAMSAS _roots[] = cdoc.getVamsasRoots();
+
+    for (int _root = 0; _root<_roots.length; _root++) {
+      VAMSAS root = _roots[_root];
+      boolean newds=false;
+      for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {
+        // ///////////////////////////////////
+        // ///LOAD DATASET
+        DataSet dataset = root.getDataSet(_ds);
+        int i, iSize = dataset.getSequenceCount();
+        Vector dsseqs;
+        Object appsdataset = (Object) getvObj2jv(dataset);
+        int jremain=0;
+        if (appsdataset==null) {
+          log.debug("Initialising new dataset fields");
+          newds=true;
+          dsseqs=new Vector();
+        } else {
+          log.debug("Update dataset from vamsas dataset.");
+        }
+        // etc for annotations, alignments, trees, etc. 
+      }
+    }
+  }
+  /**
+   * get real bounds of a RangeType's specification. start and end are an
+   * inclusive range within which all segments and positions lie.
+   * TODO: refactor to vamsas utils
+   * @param dseta
+   * @return int[] { start, end}
+   */
+  private int[] getBounds(RangeType dseta) {
+    if (dseta != null)
+    {
+      int[] se = null;
+      if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
+        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      if (dseta.getSegCount() > 0)
+      {
+        se = getSegRange(dseta.getSeg(0),true);
+        for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)
+        {
+          int nse[] = getSegRange(dseta.getSeg(s), true);
+          if (se[0] > nse[0])
+            se[0] = nse[0];
+          if (se[1] < nse[1])
+            se[1] = nse[1];
+        }
+      }
+      if (dseta.getPosCount() > 0)
+      {
+        // could do a polarity for pos range too. and pass back indication of discontinuities.
+        int pos = dseta.getPos(0).getI();
+        se = new int[] { pos, pos };
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
+        {
+          pos = dseta.getPos(p).getI();
+          if (se[0] > pos)
+            se[0] = pos;
+          if (se[1] < pos)
+            se[1] = pos;
+        }
+      }
+      return se;
+    }
+    return null;
+  }
+  /**
+   * map from a rangeType's internal frame to the referenced object's coordinate frame.
+   * @param dseta
+   * @return int [] { ref(pos)...} for all pos in rangeType's frame.
+   */
+  private int[] getMapping(RangeType dseta) {
+    Vector posList=new Vector();
+    if (dseta != null)
+    {
+      int[] se = null;
+      if (dseta.getSegCount()>0 && dseta.getPosCount()>0)
+        throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+      if (dseta.getSegCount() > 0)
+      {
+        for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)
+        {
+          se = getSegRange(dseta.getSeg(s), false);
+          int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);
+          for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {
+            posList.add(Integer.valueOf(p));
+          }
+        }
+      } 
+      else if (dseta.getPosCount() > 0)
+      {
+        int pos = dseta.getPos(0).getI();
+
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
+        {
+          pos = dseta.getPos(p).getI();
+          posList.add(Integer.valueOf(pos));
+        }
+      }
+    }
+    if (posList!=null && posList.size()>0) {
+      int[] range=new int[posList.size()];
+      for (int i=0; i<range.length; i++)
+        range[i] = ((Integer)posList.elementAt(i)).intValue();
+      posList.clear();
+      return range;
+    }
+    return null;
+  }
+  /**
+   * 
+   * @return default initial provenance list for a VamsasDatastore created vamsas
+   *         object.
+   */
+  Provenance dummyProvenance() {
+    return dummyProvenance(null);
+  }
+
+  Entry dummyPEntry(String action) {
+    Entry entry = new Entry();
+    entry.setApp(this.provEntry.getApp());
+    if (action != null)
+      entry.setAction(action);
+    else
+      entry.setAction("created.");
+    entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
+    entry.setUser(this.provEntry.getUser());
+    return entry;
+  }
+
+  Provenance dummyProvenance(String action) {
+    Provenance prov = new Provenance();
+    prov.addEntry(dummyPEntry(action));
+    return prov;
+  }
+
+  void addProvenance(Provenance p, String action) {
+    p.addEntry(dummyPEntry(action));
+  }
+
+}