X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2Fsimpleclient%2FSimpleDocBinding.java;h=895bb0ffc596ff64182cd1bdc2c91681d4acebd2;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=68157060d11747ec74301c2a908b2a913102c521;hpb=a3440159d11615fae0dc30e124c3d906386c5d5f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java b/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
index 6815706..895bb0f 100644
--- a/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
+++ b/src/uk/ac/vamsas/client/simpleclient/SimpleDocBinding.java
@@ -1,139 +1,180 @@
-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;
-  }
-}
+/*
+ * 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 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.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;
+  }
+}