/*\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
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ * Andrew Waterhouse and Dominik Lindner.\r
+ * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ * \r
+ * The Vamsas Client 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
+ * GNU Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
package uk.ac.vamsas.test.simpleclient.simpleapp;\r
\r
-\r
-\r
import java.io.*;\r
import java.util.HashMap;\r
import java.util.HashSet;\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
+ org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory\r
+ .getLog(VamsasDatastore.class);\r
\r
+ Entry provEntry = null;\r
\r
org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(\r
new java.util.Date());\r
\r
public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,\r
IdentityHashMap jv2vobj, Entry provEntry) {\r
- this.cdoc = cdoc;\r
+ this.cdoc = cdoc;\r
this.vobj2jv = vobj2jv;\r
this.jv2vobj = jv2vobj;\r
this.provEntry = provEntry;\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 Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj) {\r
VorbaId id = vobj.getVorbaId();\r
- if (id == null)\r
- {\r
+ if (id == null) {\r
id = cdoc.registerObject(vobj);\r
- log\r
- .debug("Registering new object and returning null for getvObj2jv");\r
+ log.debug("Registering new object and returning null for getvObj2jv");\r
return null;\r
}\r
if (vobj2jv.containsKey(vobj.getVorbaId()))\r
\r
protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj) {\r
VorbaId id = vobj.getVorbaId();\r
- if (id == null)\r
- {\r
+ if (id == null) {\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
+ if (id == null || vobj.getVorbaId() == null)\r
+ log.error("Failed to get id for "\r
+ + (vobj.isRegisterable() ? "registerable" : "unregisterable")\r
+ + " 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
+ if (vobj2jv.containsKey(vobj.getVorbaId()) || jv2vobj.containsKey(jvobj)) {\r
+ log.error("Duplicate object binding! " + vobj + " id "\r
+ + vobj.getVorbaId().getId() + " to " + jvobj);\r
+ } else {\r
vobj2jv.put(vobj.getVorbaId(), jvobj);// JBPNote - better implementing a\r
// hybrid invertible hash.\r
jv2vobj.put(jvobj, vobj.getVorbaId());\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
+ if (dataset == null) {\r
root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.\r
dataset = new DataSet();\r
root.addDataSet(dataset);\r
}\r
\r
private Property newProperty(String name, String type, String content) {\r
- Property vProperty=new Property();\r
+ Property vProperty = new Property();\r
vProperty.setName(name);\r
- if (type!=null)\r
+ if (type != null)\r
vProperty.setType(type);\r
vProperty.setContent(content);\r
return vProperty;\r
/**\r
* get start<end range of segment, adjusting for inclusivity flag and\r
* polarity.\r
- * \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
+ * @param ensureDirection\r
+ * when true - always ensure start is less than end.\r
+ * @return int[] { start, end, direction} where direction==1 for range running\r
+ * from end to start.\r
*/\r
private int[] getSegRange(Seg visSeg, boolean ensureDirection) {\r
boolean incl = visSeg.getInclusive();\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
+ if (ensureDirection && pol == -1) {\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
+ 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
+ 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
+ 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
+ int jremain = 0;\r
+ if (appsdataset == null) {\r
log.debug("Initialising new dataset fields");\r
- newds=true;\r
- dsseqs=new Vector();\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
+ // etc for annotations, alignments, trees, etc.\r
}\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
+ * inclusive range within which all segments and positions lie. TODO: refactor\r
+ * to vamsas utils\r
+ * \r
* @param dseta\r
* @return int[] { start, end}\r
*/\r
private int[] getBounds(RangeType dseta) {\r
- if (dseta != null)\r
- {\r
+ if (dseta != null) {\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
+ if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)\r
+ throw new Error(\r
+ "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+ if (dseta.getSegCount() > 0) {\r
+ se = getSegRange(dseta.getSeg(0), true);\r
+ for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++) {\r
int nse[] = getSegRange(dseta.getSeg(s), true);\r
if (se[0] > nse[0])\r
se[0] = nse[0];\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
+ if (dseta.getPosCount() > 0) {\r
+ // could do a polarity for pos range too. and pass back indication of\r
+ // 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
+ for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) {\r
pos = dseta.getPos(p).getI();\r
if (se[0] > pos)\r
se[0] = pos;\r
}\r
return null;\r
}\r
+\r
/**\r
- * map from a rangeType's internal frame to the referenced object's coordinate frame.\r
+ * map from a rangeType's internal frame to the referenced object's coordinate\r
+ * frame.\r
+ * \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
+ Vector posList = new Vector();\r
+ if (dseta != null) {\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
+ if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)\r
+ throw new Error(\r
+ "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
+ if (dseta.getSegCount() > 0) {\r
+ for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++) {\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
+ 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(new Integer(p));\r
}\r
}\r
- } \r
- else if (dseta.getPosCount() > 0)\r
- {\r
+ } else if (dseta.getPosCount() > 0) {\r
int pos = dseta.getPos(0).getI();\r
\r
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
- {\r
+ for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) {\r
pos = dseta.getPos(p).getI();\r
posList.add(new Integer(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
+ 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
* \r
- * @return default initial provenance list for a VamsasDatastore created vamsas\r
- * object.\r
+ * @return default initial provenance list for a VamsasDatastore created\r
+ * vamsas object.\r
*/\r
Provenance dummyProvenance() {\r
return dummyProvenance(null);\r
git://source.jalview.org / vamsas.git / blobdiff