-package uk.ac.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.Vector;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import uk.ac.vamsas.client.Vobject;
-import uk.ac.vamsas.client.VorbaIdFactory;
-import uk.ac.vamsas.client.VorbaXmlBinder;
-import uk.ac.vamsas.objects.core.VAMSAS;
-import uk.ac.vamsas.objects.core.VamsasDocument;
-import uk.ac.vamsas.objects.utils.AppDataReference;
-import uk.ac.vamsas.objects.utils.DocumentStuff;
-import uk.ac.vamsas.objects.utils.ProvenanceStuff;
-import uk.ac.vamsas.objects.utils.document.VersionEntries;
-
-/**
- * Base class for SimpleClient Vamsas Document Object Manipulation
- * holds static vamsasDocument from XML routines and
- * state objects for a particular unmarshalled Document instance.
- * @author jimp
- */
-
-
-public class SimpleDocBinding {
-
- protected VorbaIdFactory vorba;
- protected static Log log = LogFactory.getLog(SimpleDocBinding.class);
-
- /**
- * @return Returns the vorba.
- */
- public VorbaIdFactory getVorba() {
- return vorba;
- }
-
- /**
- * @param vorba The vorba to set.
- */
- public void setVorba(VorbaIdFactory vorba) {
- this.vorba = vorba;
- }
-
- /**
- * Uses VorbaXmlBinder to retrieve the VamsasDocument from the given stream
- */
- public VamsasDocument getVamsasDocument(VamsasArchiveReader oReader) throws IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- if (oReader!=null) {
- // check the factory
- if (vorba==null) {
- log.error("Invalid SimpleDocument construction - no VorbaIdFactory defined!");
- return null;
- }
-
- if (oReader.isValid()) {
- // Read vamsasDocument.xsd instance
- InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
- Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vdoc, vorba, new VamsasDocument());
- if (unmarsh==null)
- log.fatal("Couldn't unmarshall document!");
-
- Vobject vobjs = (Vobject) unmarsh[0];
- if (vobjs!=null) {
- VamsasDocument doc=(VamsasDocument) vobjs;
- if (doc!=null)
- return doc;
- }
- log.debug("Found no VamsasDocument object in properly formatted Vamsas Archive.");
- } else {
- // deprecated data handler (vamsas.xsd instance)
- InputStream vxmlis = oReader.getVamsasXmlStream();
- if (vxmlis!=null) { // Might be an old vamsas file.
- BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
- InputStreamReader vxml = new InputStreamReader(ixml);
- Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vxml, vorba, new VAMSAS());
-
- if (unmarsh==null)
- log.fatal("Couldn't unmarshall document!");
-
- VAMSAS root[]= new VAMSAS[] { null};
- root[0] = (VAMSAS) unmarsh[0];
-
- if (root[0]==null) {
- log.debug("Found no VAMSAS object in VamsasXML stream.");
- } else {
- log.debug("Making new VamsasDocument from VamsasXML stream.");
- VamsasDocument doc = DocumentStuff.newVamsasDocument(root,
- ProvenanceStuff.newProvenance(
- vorba.getUserHandle().getFullName(),
- "Vamsas Document constructed from vamsas.xml"), VersionEntries.ALPHA_VERSION);
- // VAMSAS: decide on 'system' operations provenance form
- // LATER: implement classes for translating Vorba properties into provenance user fields.
- // VAMSAS: decide on machine readable info embedding in provenance should be done
- root[0]=null;
- root=null;
- return doc;
- }
- }
- }
- }
- // otherwise - there was no valid original document to read.
- return null;
- }
-
- /**
- * Extract all jarEntries in an archive referenced by the vamsas document
- * LATER: a family of methods for finding extraneous jarEntries , and invalid appDataReferences
- * @param doc
- * @param oReader
- * @return array of the subset of JarEntry names that are referenced in doc
- */
- public Vector getReferencedEntries(VamsasDocument doc, VamsasArchiveReader oReader) {
- if (oReader==null)
- return null;
- if (doc==null) {
- try { doc = getVamsasDocument(oReader); }
- catch (Exception e) { log.warn("Failed to get document from "+oReader.jfileName); };
- }
- Vector docrefs = AppDataReference.getAppDataReferences(doc);
- if (docrefs==null)
- return null;
- Vector entries = oReader.getExtraEntries();
- if (entries!=null && entries.size()>0 && docrefs.size()>0) {
- int i=0, j=entries.size();
- do {
- if (!docrefs.contains(entries.get(i))) {
- entries.remove(i);
- j--;
- } else
- i++;
- } while (i<j);
- }
- return entries;
- }
-}
+/*\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 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
+package uk.ac.vamsas.client.simpleclient;\r
+\r
+import java.io.BufferedInputStream;\r
+import java.io.IOException;\r
+import java.io.InputStream;\r
+import java.io.InputStreamReader;\r
+import java.util.Vector;\r
+import org.apache.commons.logging.Log;\r
+import org.apache.commons.logging.LogFactory;\r
+\r
+import uk.ac.vamsas.client.Vobject;\r
+import uk.ac.vamsas.client.VorbaIdFactory;\r
+import uk.ac.vamsas.client.VorbaXmlBinder;\r
+import uk.ac.vamsas.objects.core.VAMSAS;\r
+import uk.ac.vamsas.objects.core.VamsasDocument;\r
+import uk.ac.vamsas.objects.utils.AppDataReference;\r
+import uk.ac.vamsas.objects.utils.DocumentStuff;\r
+import uk.ac.vamsas.objects.utils.ProvenanceStuff;\r
+import uk.ac.vamsas.objects.utils.document.VersionEntries;\r
+\r
+/**\r
+ * Base class for SimpleClient Vamsas Document Object Manipulation holds static\r
+ * vamsasDocument from XML routines and state objects for a particular\r
+ * unmarshalled Document instance.\r
+ * \r
+ * @author jimp\r
+ */\r
+\r
+public class SimpleDocBinding {\r
+\r
+ protected VorbaIdFactory vorba;\r
+\r
+ protected static Log log = LogFactory.getLog(SimpleDocBinding.class);\r
+\r
+ /**\r
+ * @return Returns the vorba.\r
+ */\r
+ public VorbaIdFactory getVorba() {\r
+ return vorba;\r
+ }\r
+\r
+ /**\r
+ * @param vorba\r
+ * The vorba to set.\r
+ */\r
+ public void setVorba(VorbaIdFactory vorba) {\r
+ this.vorba = vorba;\r
+ }\r
+\r
+ /**\r
+ * Uses VorbaXmlBinder to retrieve the VamsasDocument from the given stream\r
+ */\r
+ public VamsasDocument getVamsasDocument(VamsasArchiveReader oReader)\r
+ throws IOException, org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException {\r
+ if (oReader != null) {\r
+ // check the factory\r
+ if (vorba == null) {\r
+ log\r
+ .error("Invalid SimpleDocument construction - no VorbaIdFactory defined!");\r
+ return null;\r
+ }\r
+\r
+ if (oReader.isValid()) {\r
+ // Read vamsasDocument.xsd instance\r
+ InputStreamReader vdoc = new InputStreamReader(oReader\r
+ .getVamsasDocumentStream());\r
+ Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vdoc, vorba,\r
+ new VamsasDocument());\r
+ if (unmarsh == null)\r
+ log.fatal("Couldn't unmarshall document!");\r
+\r
+ Vobject vobjs = (Vobject) unmarsh[0];\r
+ if (vobjs != null) {\r
+ VamsasDocument doc = (VamsasDocument) vobjs;\r
+ if (doc != null)\r
+ return doc;\r
+ }\r
+ log\r
+ .debug("Found no VamsasDocument object in properly formatted Vamsas Archive.");\r
+ } else {\r
+ // deprecated data handler (vamsas.xsd instance)\r
+ InputStream vxmlis = oReader.getVamsasXmlStream();\r
+ if (vxmlis != null) { // Might be an old vamsas file.\r
+ BufferedInputStream ixml = new BufferedInputStream(oReader\r
+ .getVamsasXmlStream());\r
+ InputStreamReader vxml = new InputStreamReader(ixml);\r
+ Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vxml, vorba,\r
+ new VAMSAS());\r
+\r
+ if (unmarsh == null)\r
+ log.fatal("Couldn't unmarshall document!");\r
+\r
+ VAMSAS root[] = new VAMSAS[] { null };\r
+ root[0] = (VAMSAS) unmarsh[0];\r
+\r
+ if (root[0] == null) {\r
+ log.debug("Found no VAMSAS object in VamsasXML stream.");\r
+ } else {\r
+ log.debug("Making new VamsasDocument from VamsasXML stream.");\r
+ VamsasDocument doc = DocumentStuff.newVamsasDocument(root,\r
+ ProvenanceStuff.newProvenance(vorba.getUserHandle()\r
+ .getFullName(),\r
+ "Vamsas Document constructed from vamsas.xml"),\r
+ VersionEntries.ALPHA_VERSION);\r
+ // VAMSAS: decide on 'system' operations provenance form\r
+ // LATER: implement classes for translating Vorba properties into\r
+ // provenance user fields.\r
+ // VAMSAS: decide on machine readable info embedding in provenance\r
+ // should be done\r
+ root[0] = null;\r
+ root = null;\r
+ return doc;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ // otherwise - there was no valid original document to read.\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Extract all jarEntries in an archive referenced by the vamsas document\r
+ * LATER: a family of methods for finding extraneous jarEntries , and invalid\r
+ * appDataReferences\r
+ * \r
+ * @param doc\r
+ * @param oReader\r
+ * @return array of the subset of JarEntry names that are referenced in doc\r
+ */\r
+ public Vector getReferencedEntries(VamsasDocument doc,\r
+ VamsasArchiveReader oReader) {\r
+ if (oReader == null)\r
+ return null;\r
+ if (doc == null) {\r
+ try {\r
+ doc = getVamsasDocument(oReader);\r
+ } catch (Exception e) {\r
+ log.warn("Failed to get document from " + oReader.jfileName);\r
+ }\r
+ ;\r
+ }\r
+ Vector docrefs = AppDataReference.getAppDataReferences(doc);\r
+ if (docrefs == null)\r
+ return null;\r
+ Vector entries = oReader.getExtraEntries();\r
+ if (entries != null && entries.size() > 0 && docrefs.size() > 0) {\r
+ int i = 0, j = entries.size();\r
+ do {\r
+ if (!docrefs.contains(entries.get(i))) {\r
+ entries.remove(i);\r
+ j--;\r
+ } else\r
+ i++;\r
+ } while (i < j);\r
+ }\r
+ return entries;\r
+ }\r
+}\r
git://source.jalview.org / vamsas.git / blobdiff