X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Ftest%2Fsimpleclient%2Fsimpleapp%2FVamsasDatastore.java;h=c14598c37ddc4acb7bff69bf5ad4937128b1b90c;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=7d74186891c90fc8de015d81bf12a9e463dae4e1;hpb=3b92275c26c14a678519f1d7d2ffaa477eb76cdb;p=vamsas.git

diff --git a/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java b/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
index 7d74186..c14598c 100644
--- a/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
+++ b/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java
@@ -1,26 +1,26 @@
 /*
- * 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,
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client 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
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package uk.ac.vamsas.test.simpleclient.simpleapp;
 
-
-
 import java.io.*;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -46,9 +46,10 @@ import uk.ac.vamsas.test.simpleclient.ClientDoc;
  */
 
 public class VamsasDatastore {
-  org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasDatastore.class);
-  Entry provEntry = null;
+  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());
@@ -61,7 +62,7 @@ public class VamsasDatastore {
 
   public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,
       IdentityHashMap jv2vobj, Entry provEntry) {
-      this.cdoc = cdoc;
+    this.cdoc = cdoc;
     this.vobj2jv = vobj2jv;
     this.jv2vobj = jv2vobj;
     this.provEntry = provEntry;
@@ -80,8 +81,6 @@ public class VamsasDatastore {
    * 
    * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {
    * e.printStackTrace(); } }
-   * 
-   * 
    */
   /**
    * @return the Vobject bound to Jalview datamodel object
@@ -99,11 +98,9 @@ public class VamsasDatastore {
    */
   protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj) {
     VorbaId id = vobj.getVorbaId();
-    if (id == null)
-    {
+    if (id == null) {
       id = cdoc.registerObject(vobj);
-      log
-      .debug("Registering new object and returning null for getvObj2jv");
+      log.debug("Registering new object and returning null for getvObj2jv");
       return null;
     }
     if (vobj2jv.containsKey(vobj.getVorbaId()))
@@ -113,18 +110,17 @@ public class VamsasDatastore {
 
   protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj) {
     VorbaId id = vobj.getVorbaId();
-    if (id == null)
-    {
+    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 (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
-    {
+    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());
@@ -140,8 +136,7 @@ public class VamsasDatastore {
     boolean nw = false;
     VAMSAS root = null; // will be resolved based on Dataset Parent.
     DataSet dataset = (DataSet) getjv2vObj(fromAppsDatamodel);
-    if (dataset == null)
-    {
+    if (dataset == null) {
       root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.
       dataset = new DataSet();
       root.addDataSet(dataset);
@@ -156,9 +151,9 @@ public class VamsasDatastore {
   }
 
   private Property newProperty(String name, String type, String content) {
-    Property vProperty=new Property();
+    Property vProperty = new Property();
     vProperty.setName(name);
-    if (type!=null)
+    if (type != null)
       vProperty.setType(type);
     vProperty.setContent(content);
     return vProperty;
@@ -167,10 +162,12 @@ public class VamsasDatastore {
   /**
    * 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.
+   * @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();
@@ -179,59 +176,58 @@ public class VamsasDatastore {
     // region.
     int start = visSeg.getStart() + (incl ? 0 : pol);
     int end = visSeg.getEnd() + (incl ? 0 : -pol);
-    if (ensureDirection && pol==-1)
-    {
+    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 };
+    return new int[] { start, end, pol < 0 ? 1 : 0 };
   }
 
   public void updateToJalview() {
     VAMSAS _roots[] = cdoc.getVamsasRoots();
 
-    for (int _root = 0; _root<_roots.length; _root++) {
+    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++) {
+      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) {
+        int jremain = 0;
+        if (appsdataset == null) {
           log.debug("Initialising new dataset fields");
-          newds=true;
-          dsseqs=new Vector();
+          newds = true;
+          dsseqs = new Vector();
         } else {
           log.debug("Update dataset from vamsas dataset.");
         }
-        // etc for annotations, alignments, trees, etc. 
+        // 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
+   * 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)
-    {
+    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++)
-        {
+      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];
@@ -239,13 +235,12 @@ public class VamsasDatastore {
             se[1] = nse[1];
         }
       }
-      if (dseta.getPosCount() > 0)
-      {
-        // could do a polarity for pos range too. and pass back indication of discontinuities.
+      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++)
-        {
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) {
           pos = dseta.getPos(p).getI();
           if (se[0] > pos)
             se[0] = pos;
@@ -257,53 +252,52 @@ public class VamsasDatastore {
     }
     return null;
   }
+
   /**
-   * map from a rangeType's internal frame to the referenced object's coordinate frame.
+   * 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)
-    {
+    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++)
-        {
+      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));
+          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(new Integer(p));
           }
         }
-      } 
-      else if (dseta.getPosCount() > 0)
-      {
+      } else if (dseta.getPosCount() > 0) {
         int pos = dseta.getPos(0).getI();
 
-        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
-        {
+        for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) {
           pos = dseta.getPos(p).getI();
-          posList.add(Integer.valueOf(pos));
+          posList.add(new Integer(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();
+    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.
+   * @return default initial provenance list for a VamsasDatastore created
+   *         vamsas object.
    */
   Provenance dummyProvenance() {
     return dummyProvenance(null);
@@ -316,7 +310,7 @@ public class VamsasDatastore {
       entry.setAction(action);
     else
       entry.setAction("created.");
-    entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));
+    entry.setDate(new java.util.Date());
     entry.setUser(this.provEntry.getUser());
     return entry;
   }