X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FDatasetsequence.java;h=297b85422ec5704d067b2c0fd0f27ed1578befb1;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=e57942b66780aa69eb7fed519fa5bf190fab1cbb;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index e57942b..297b854 100644
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -1,275 +1,278 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * This file is part of Jalview.
- * 
- * Jalview 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 3 of the License, or (at your option) any later version.
- * 
- * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
- */
-package jalview.io.vamsas;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.VamsasAppDatastore;
-import uk.ac.vamsas.objects.core.DataSet;
-import uk.ac.vamsas.objects.core.DbRef;
-import uk.ac.vamsas.objects.core.Sequence;
-
-/**
- * synchronize a vamsas dataset sequence with a jalview dataset sequence. This
- * class deals with all sequence features and database references associated
- * with the jalview sequence.
- * 
- * @author JimP
- * 
- */
-public class Datasetsequence extends DatastoreItem
-{
-  String dict;
-
-  private DataSet dataset;
-
-  // private AlignmentI jvdset;
-
-  public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
-          SequenceI sq, String dict, DataSet dataset)
-  {
-    super(vamsasAppDatastore, sq, uk.ac.vamsas.objects.core.Sequence.class);
-    this.dataset = dataset;
-    // this.jvdset = jvdset;
-    this.dict = dict;
-    doSync();
-  }
-
-  public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
-          Sequence vdseq)
-  {
-    super(vamsasAppDatastore, vdseq, SequenceI.class);
-    doJvUpdate();
-  }
-
-  public void addFromDocument()
-  {
-    Sequence vseq = (Sequence) vobj;
-    SequenceI dsseq = new jalview.datamodel.Sequence(vseq.getName(),
-            vseq.getSequence(), (int) vseq.getStart(), (int) vseq.getEnd());
-    dsseq.setDescription(vseq.getDescription());
-    bindjvvobj(dsseq, vseq);
-    dsseq.setVamsasId(vseq.getVorbaId().getId());
-    jvobj = dsseq;
-    modified = true;
-  }
-
-  public void updateFromDoc()
-  {
-    Sequence sq = (Sequence) vobj;
-    SequenceI sequence = (SequenceI) jvobj;
-    if (!sequence.getSequenceAsString().equals(sq.getSequence()))
-    {
-      log.warn("Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
-    }
-    else
-    {
-      // verify and update principal attributes.
-      if (sequence.getDescription() != null
-              && (sequence.getDescription() == null || !sequence
-                      .getDescription().equals(sq.getDescription())))
-      {
-        sequence.setDescription(sq.getDescription());
-        modified = true;
-      }
-      if (sequence.getSequence() == null
-              || !sequence.getSequenceAsString().equals(sq.getSequence()))
-      {
-        if (sequence.getStart() != sq.getStart()
-                || sequence.getEnd() != sq.getEnd())
-        {
-          // update modified sequence.
-          sequence.setSequence(sq.getSequence());
-          sequence.setStart((int) sq.getStart());
-          sequence.setEnd((int) sq.getEnd());
-          modified = true;
-        }
-      }
-      if (!sequence.getName().equals(sq.getName()))
-      {
-        sequence.setName(sq.getName());
-        modified = true;
-      }
-      modified |= updateJvDbRefs();
-      // updateJvFeatures();
-    }
-  }
-
-  /*
-   * private void updateJvFeatures() { Sequence vsq = (Sequence) vobj;
-   * 
-   * // add or update any new features/references on dataset sequence if
-   * (vsq.getgetSequenceFeatures() != null) { int sfSize =
-   * sq.getSequenceFeatures().length;
-   * 
-   * for (int sf = 0; sf < sfSize; sf++) { new
-   * jalview.io.vamsas.Sequencefeature(datastore,
-   * (jalview.datamodel.SequenceFeature) sq .getSequenceFeatures()[sf], dataset,
-   * (Sequence) vobj); } } }
-   */
-  private boolean updateSqFeatures()
-  {
-    boolean modified = false;
-    SequenceI sq = (SequenceI) jvobj;
-
-    // add or update any new features/references on dataset sequence
-    if (sq.getSequenceFeatures() != null)
-    {
-      int sfSize = sq.getSequenceFeatures().length;
-
-      for (int sf = 0; sf < sfSize; sf++)
-      {
-        modified |= new jalview.io.vamsas.Sequencefeature(datastore,
-                (jalview.datamodel.SequenceFeature) sq
-                        .getSequenceFeatures()[sf], dataset,
-                (Sequence) vobj).docWasUpdated();
-      }
-    }
-    return modified;
-  }
-
-  public void addToDocument()
-  {
-    SequenceI sq = (SequenceI) jvobj;
-    Sequence sequence = new Sequence();
-    bindjvvobj(sq, sequence);
-    sq.setVamsasId(sequence.getVorbaId().getId());
-    sequence.setSequence(sq.getSequenceAsString());
-    sequence.setDictionary(dict);
-    sequence.setName(sq.getName());
-    sequence.setStart(sq.getStart());
-    sequence.setEnd(sq.getEnd());
-    sequence.setDescription(sq.getDescription());
-    dataset.addSequence(sequence);
-    vobj = sequence;
-    updateSqFeatures();
-    updateDbRefs();// sq,(Sequence) vobj, dataset);
-  }
-
-  /**
-   * sync database references from jv to document
-   * 
-   * @return true if document was modified
-   */
-  private boolean updateDbRefs()
-  {
-    boolean modifiedthedoc = false;
-    SequenceI sq = (SequenceI) jvobj;
-
-    if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
-    {
-      // only sync database references for dataset sequences
-      DBRefEntry[] entries = sq.getDBRef();
-      // jalview.datamodel.DBRefEntry dbentry;
-      for (int db = 0; db < entries.length; db++)
-      {
-        modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
-        // dbentry =
-                entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
-
-      }
-
-    }
-    return modifiedthedoc;
-  }
-
-  /**
-   * sync database references from document to jv sequence
-   * 
-   * @return true if local sequence refs were modified
-   */
-  private boolean updateJvDbRefs()
-  {
-    boolean modifiedtheseq = false;
-    SequenceI sq = (SequenceI) jvobj;
-    Sequence vsq = (Sequence) vobj;
-    if (vsq.getDbRefCount() > 0)
-    {
-      // only sync database references for dataset sequences
-      DbRef[] entries = vsq.getDbRef();
-      // DbRef dbentry;
-      for (int db = 0; db < entries.length; db++)
-      {
-        modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
-        // dbentry =
-                entries[db], vsq, sq).jvWasUpdated();
-      }
-    }
-    return modifiedtheseq;
-  }
-
-  public void conflict()
-  {
-    log.warn("Conflict in dataset sequence update to document. Overwriting document");
-    // TODO: could try to import from document data to jalview first. and then
-    updateToDoc();
-  }
-
-  boolean modified = false;
-
-  public void updateToDoc()
-  {
-    SequenceI sq = (SequenceI) jvobj;
-    Sequence sequence = (Sequence) vobj;
-    // verify and update principal attributes.
-    if (sequence.getDescription() != null
-            && (sequence.getDescription() == null || !sequence
-                    .getDescription().equals(sq.getDescription())))
-    {
-      sequence.setDescription(sq.getDescription());
-      modified = true;
-    }
-    if (sequence.getSequence() == null
-            || !sequence.getSequence().equals(sq.getSequenceAsString()))
-    {
-      if (sequence.getStart() != sq.getStart()
-              || sequence.getEnd() != sq.getEnd())
-      {
-        // update modified sequence.
-        sequence.setSequence(sq.getSequenceAsString());
-        sequence.setStart(sq.getStart());
-        sequence.setEnd(sq.getEnd());
-        modified = true;
-      }
-    }
-    if (!dict.equals(sequence.getDictionary()))
-    {
-      sequence.setDictionary(dict);
-      modified = true;
-    }
-    if (!sequence.getName().equals(sq.getName()))
-    {
-      sequence.setName(sq.getName());
-      modified = true;
-    }
-    modified |= updateDbRefs();
-    modified |= updateSqFeatures();
-  }
-
-  /**
-   * (probably could just do vobj.isModified(), but..)
-   * 
-   * @return true if document's dataset sequence was modified
-   */
-  public boolean getModified()
-  {
-    return modified;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io.vamsas;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Sequence;
+
+/**
+ * synchronize a vamsas dataset sequence with a jalview dataset sequence. This
+ * class deals with all sequence features and database references associated
+ * with the jalview sequence.
+ * 
+ * @author JimP
+ * 
+ */
+public class Datasetsequence extends DatastoreItem
+{
+  String dict;
+
+  private DataSet dataset;
+
+  // private AlignmentI jvdset;
+
+  public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
+          SequenceI sq, String dict, DataSet dataset)
+  {
+    super(vamsasAppDatastore, sq, uk.ac.vamsas.objects.core.Sequence.class);
+    this.dataset = dataset;
+    // this.jvdset = jvdset;
+    this.dict = dict;
+    doSync();
+  }
+
+  public Datasetsequence(VamsasAppDatastore vamsasAppDatastore,
+          Sequence vdseq)
+  {
+    super(vamsasAppDatastore, vdseq, SequenceI.class);
+    doJvUpdate();
+  }
+
+  public void addFromDocument()
+  {
+    Sequence vseq = (Sequence) vobj;
+    SequenceI dsseq = new jalview.datamodel.Sequence(vseq.getName(),
+            vseq.getSequence(), (int) vseq.getStart(), (int) vseq.getEnd());
+    dsseq.setDescription(vseq.getDescription());
+    bindjvvobj(dsseq, vseq);
+    dsseq.setVamsasId(vseq.getVorbaId().getId());
+    jvobj = dsseq;
+    modified = true;
+  }
+
+  public void updateFromDoc()
+  {
+    Sequence sq = (Sequence) vobj;
+    SequenceI sequence = (SequenceI) jvobj;
+    if (!sequence.getSequenceAsString().equals(sq.getSequence()))
+    {
+      log.warn("Potential Client Error ! - mismatch of dataset sequence: and jalview internal dataset sequence.");
+    }
+    else
+    {
+      // verify and update principal attributes.
+      if (sequence.getDescription() != null
+              && (sequence.getDescription() == null || !sequence
+                      .getDescription().equals(sq.getDescription())))
+      {
+        sequence.setDescription(sq.getDescription());
+        modified = true;
+      }
+      if (sequence.getSequence() == null
+              || !sequence.getSequenceAsString().equals(sq.getSequence()))
+      {
+        if (sequence.getStart() != sq.getStart()
+                || sequence.getEnd() != sq.getEnd())
+        {
+          // update modified sequence.
+          sequence.setSequence(sq.getSequence());
+          sequence.setStart((int) sq.getStart());
+          sequence.setEnd((int) sq.getEnd());
+          modified = true;
+        }
+      }
+      if (!sequence.getName().equals(sq.getName()))
+      {
+        sequence.setName(sq.getName());
+        modified = true;
+      }
+      modified |= updateJvDbRefs();
+      // updateJvFeatures();
+    }
+  }
+
+  /*
+   * private void updateJvFeatures() { Sequence vsq = (Sequence) vobj;
+   * 
+   * // add or update any new features/references on dataset sequence if
+   * (vsq.getgetSequenceFeatures() != null) { int sfSize =
+   * sq.getSequenceFeatures().length;
+   * 
+   * for (int sf = 0; sf < sfSize; sf++) { new
+   * jalview.io.vamsas.Sequencefeature(datastore,
+   * (jalview.datamodel.SequenceFeature) sq .getSequenceFeatures()[sf], dataset,
+   * (Sequence) vobj); } } }
+   */
+  private boolean updateSqFeatures()
+  {
+    boolean modified = false;
+    SequenceI sq = (SequenceI) jvobj;
+
+    // add or update any new features/references on dataset sequence
+    if (sq.getSequenceFeatures() != null)
+    {
+      int sfSize = sq.getSequenceFeatures().length;
+
+      for (int sf = 0; sf < sfSize; sf++)
+      {
+        modified |= new jalview.io.vamsas.Sequencefeature(datastore,
+                (jalview.datamodel.SequenceFeature) sq
+                        .getSequenceFeatures()[sf], dataset,
+                (Sequence) vobj).docWasUpdated();
+      }
+    }
+    return modified;
+  }
+
+  public void addToDocument()
+  {
+    SequenceI sq = (SequenceI) jvobj;
+    Sequence sequence = new Sequence();
+    bindjvvobj(sq, sequence);
+    sq.setVamsasId(sequence.getVorbaId().getId());
+    sequence.setSequence(sq.getSequenceAsString());
+    sequence.setDictionary(dict);
+    sequence.setName(sq.getName());
+    sequence.setStart(sq.getStart());
+    sequence.setEnd(sq.getEnd());
+    sequence.setDescription(sq.getDescription());
+    dataset.addSequence(sequence);
+    vobj = sequence;
+    updateSqFeatures();
+    updateDbRefs();// sq,(Sequence) vobj, dataset);
+  }
+
+  /**
+   * sync database references from jv to document
+   * 
+   * @return true if document was modified
+   */
+  private boolean updateDbRefs()
+  {
+    boolean modifiedthedoc = false;
+    SequenceI sq = (SequenceI) jvobj;
+
+    if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
+    {
+      // only sync database references for dataset sequences
+      DBRefEntry[] entries = sq.getDBRef();
+      // jalview.datamodel.DBRefEntry dbentry;
+      for (int db = 0; db < entries.length; db++)
+      {
+        modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
+        // dbentry =
+                entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
+
+      }
+
+    }
+    return modifiedthedoc;
+  }
+
+  /**
+   * sync database references from document to jv sequence
+   * 
+   * @return true if local sequence refs were modified
+   */
+  private boolean updateJvDbRefs()
+  {
+    boolean modifiedtheseq = false;
+    SequenceI sq = (SequenceI) jvobj;
+    Sequence vsq = (Sequence) vobj;
+    if (vsq.getDbRefCount() > 0)
+    {
+      // only sync database references for dataset sequences
+      DbRef[] entries = vsq.getDbRef();
+      // DbRef dbentry;
+      for (int db = 0; db < entries.length; db++)
+      {
+        modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
+        // dbentry =
+                entries[db], vsq, sq).jvWasUpdated();
+      }
+    }
+    return modifiedtheseq;
+  }
+
+  public void conflict()
+  {
+    log.warn("Conflict in dataset sequence update to document. Overwriting document");
+    // TODO: could try to import from document data to jalview first. and then
+    updateToDoc();
+  }
+
+  boolean modified = false;
+
+  public void updateToDoc()
+  {
+    SequenceI sq = (SequenceI) jvobj;
+    Sequence sequence = (Sequence) vobj;
+    // verify and update principal attributes.
+    if (sequence.getDescription() != null
+            && (sequence.getDescription() == null || !sequence
+                    .getDescription().equals(sq.getDescription())))
+    {
+      sequence.setDescription(sq.getDescription());
+      modified = true;
+    }
+    if (sequence.getSequence() == null
+            || !sequence.getSequence().equals(sq.getSequenceAsString()))
+    {
+      if (sequence.getStart() != sq.getStart()
+              || sequence.getEnd() != sq.getEnd())
+      {
+        // update modified sequence.
+        sequence.setSequence(sq.getSequenceAsString());
+        sequence.setStart(sq.getStart());
+        sequence.setEnd(sq.getEnd());
+        modified = true;
+      }
+    }
+    if (!dict.equals(sequence.getDictionary()))
+    {
+      sequence.setDictionary(dict);
+      modified = true;
+    }
+    if (!sequence.getName().equals(sq.getName()))
+    {
+      sequence.setName(sq.getName());
+      modified = true;
+    }
+    modified |= updateDbRefs();
+    modified |= updateSqFeatures();
+  }
+
+  /**
+   * (probably could just do vobj.isModified(), but..)
+   * 
+   * @return true if document's dataset sequence was modified
+   */
+  public boolean getModified()
+  {
+    return modified;
+  }
+
+}