X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=95f6849883ea3b3eca9e7f124388286388317b4a;hb=1d534b200f4a912f02f869c9d860f462511ea46f;hp=e3134701f2cdea655cc9417bc054c81a6cabaf30;hpb=96f41aa46d3e568f8734834ab36fdc9ad8e54ac1;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index e313470..95f6849 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * 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 file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * 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
+ * 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;
 
@@ -144,11 +143,11 @@ public class VamsasAppDatastore
     {
       return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));
     }
-    // check if we're working with a string - then workaround 
+    // check if we're working with a string - then workaround
     // the use of IdentityHashTable because different strings
     // have different object IDs.
     if (jvobj instanceof String)
-    { 
+    {
       Object seqsetidobj = null;
       seqsetidobj = getVamsasObjectBinding().get(jvobj);
       if (seqsetidobj != null)
@@ -158,18 +157,19 @@ public class VamsasAppDatastore
           // what is expected. object returned by av.getSequenceSetId() -
           // reverse lookup to get the 'registered' instance of this string
           Vobject obj = getjv2vObj(seqsetidobj);
-          if (obj!=null && !(obj instanceof Alignment))
+          if (obj != null && !(obj instanceof Alignment))
           {
-            Cache.log.warn("IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
-                    + seqsetidobj + " to object " + obj);
+            Cache.log
+                    .warn("IMPLEMENTATION ERROR?: Unexpected mapping for unmapped jalview string object content:"
+                            + seqsetidobj + " to object " + obj);
           }
           return obj;
         }
         else
         {
           Cache.log.warn("Unexpected mapping for Jalview String Object ID "
-                  + seqsetidobj
-                  + " to another jalview dataset object " + seqsetidobj);
+                  + seqsetidobj + " to another jalview dataset object "
+                  + seqsetidobj);
         }
       }
     }
@@ -252,10 +252,11 @@ public class VamsasAppDatastore
    * put the alignment viewed by AlignViewport into cdoc.
    * 
    * @param av
-   *                alignViewport to be stored
+   *          alignViewport to be stored
    * @param aFtitle
-   *                title for alignment
-   * @return true if alignment associated with viewport was stored/synchronized to document
+   *          title for alignment
+   * @return true if alignment associated with viewport was stored/synchronized
+   *         to document
    */
   public boolean storeVAMSAS(AlignViewport av, String aFtitle)
   {
@@ -274,22 +275,25 @@ public class VamsasAppDatastore
         jal.setDataset(null);
         jds = jal.getDataset();
       }
-      
+
       // try and get alignment and association for sequence set id
 
       Alignment alignment = (Alignment) getjv2vObj(av.getSequenceSetId());
-      if (alignment!=null)
+      if (alignment != null)
       {
         dataset = (DataSet) alignment.getV_parent();
-      } else {
-      	// is the dataset already registered
-	dataset = (DataSet) getjv2vObj(jds);
       }
-      
+      else
+      {
+        // is the dataset already registered
+        dataset = (DataSet) getjv2vObj(jds);
+      }
+
       if (dataset == null)
       {
         // it might be that one of the dataset sequences does actually have a
-        // binding, so search for it indirectly. If it does, then the local jalview dataset
+        // binding, so search for it indirectly. If it does, then the local
+        // jalview dataset
         // must be merged with the existing vamsas dataset.
         jalview.datamodel.SequenceI[] jdatset = jds.getSequencesArray();
         for (int i = 0; i < jdatset.length; i++)
@@ -305,7 +309,8 @@ public class VamsasAppDatastore
               }
               else
               {
-                if (vbound.getV_parent()!=null && dataset != vbound.getV_parent())
+                if (vbound.getV_parent() != null
+                        && dataset != vbound.getV_parent())
                 {
                   throw new Error(
                           "IMPLEMENTATION ERROR: Cannot map an alignment of sequences from different datasets into a single alignment in the vamsas document.");
@@ -350,11 +355,14 @@ public class VamsasAppDatastore
         // referenced
         // sequences
         // to dataset.
-        Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(this, sq, dict, dataset);
+        Datasetsequence dssync = new jalview.io.vamsas.Datasetsequence(
+                this, sq, dict, dataset);
         sequence = (Sequence) dssync.getVobj();
-        if (dssync.getModified()) { 
-          dssmods.addElement(sequence); 
-        };
+        if (dssync.getModified())
+        {
+          dssmods.addElement(sequence);
+        }
+        ;
       }
       if (dssmods.size() > 0)
       {
@@ -488,16 +496,17 @@ public class VamsasAppDatastore
            * jalview.datamodel.SequenceFeature[] features = alseq
            * .getSequenceFeatures(); for (int f = 0; f < features.length; f++) {
            * if (features[f] != null) { AlignmentSequenceAnnotation valseqf = (
-           * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf ==
-           * null) {
+           * AlignmentSequenceAnnotation) getjv2vObj(features[i]); if (valseqf
+           * == null) {
            * 
            * valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
            * new AlignmentSequenceAnnotation(), features[i]);
            * valseqf.setGraph(false);
-           * valseqf.addProperty(newProperty("jalview:feature","boolean","true"));
-           * if (valseqf.getProvenance() == null) { valseqf.setProvenance(new
-           * Provenance()); } addProvenance(valseqf.getProvenance(), "created"); //
-           * JBPNote - // need to // update bindjvvobj(features[i], valseqf);
+           * valseqf.addProperty(newProperty("jalview:feature"
+           * ,"boolean","true")); if (valseqf.getProvenance() == null) {
+           * valseqf.setProvenance(new Provenance()); }
+           * addProvenance(valseqf.getProvenance(), "created"); // JBPNote - //
+           * need to // update bindjvvobj(features[i], valseqf);
            * valseq.addAlignmentSequenceAnnotation(valseqf); } } }
            */
         }
@@ -518,10 +527,11 @@ public class VamsasAppDatastore
           {
             continue;
           }
-          if (aa[i].groupRef!=null)
+          if (aa[i].groupRef != null)
           {
             // TODO: store any group associated annotation references
-            Cache.log.warn("Group associated sequence annotation is not stored in VAMSAS document.");
+            Cache.log
+                    .warn("Group associated sequence annotation is not stored in VAMSAS document.");
             continue;
           }
           if (aa[i].sequenceRef != null)
@@ -647,12 +657,15 @@ public class VamsasAppDatastore
                 an.setGroup(Integer.toString(aa[i].graphGroup));
                 if (aa[i].threshold != null && aa[i].threshold.displayed)
                 {
-                  an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE, ""
-                          + aa[i].threshold.value));
+                  an
+                          .addProperty(Properties.newProperty(THRESHOLD,
+                                  Properties.FLOATTYPE, ""
+                                          + aa[i].threshold.value));
                   if (aa[i].threshold.label != null)
                   {
-                    an.addProperty(Properties.newProperty(THRESHOLD + "Name", Properties.STRINGTYPE,
-                             "" + aa[i].threshold.label));
+                    an.addProperty(Properties.newProperty(THRESHOLD
+                            + "Name", Properties.STRINGTYPE, ""
+                            + aa[i].threshold.label));
                   }
                 }
               }
@@ -695,7 +708,8 @@ public class VamsasAppDatastore
           {
             TreePanel tp = (TreePanel) frames[t];
 
-            if (tp.getViewPort().getSequenceSetId().equals(av.getSequenceSetId()))
+            if (tp.getViewPort().getSequenceSetId().equals(
+                    av.getSequenceSetId()))
             {
               DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
                       jal, alignment);
@@ -716,10 +730,13 @@ public class VamsasAppDatastore
   }
 
   /**
-   * very quick test to see if the viewport would be stored in the vamsas document.
-   * Reasons for not storing include the unaligned flag being false.
+   * very quick test to see if the viewport would be stored in the vamsas
+   * document. Reasons for not storing include the unaligned flag being false
+   * (for all sequences, including the hidden ones!)
+   * 
    * @param av
-   * @return true if alignment associated with this view will be stored in document.
+   * @return true if alignment associated with this view will be stored in
+   *         document.
    */
   public boolean alignmentWillBeSkipped(AlignViewport av)
   {
@@ -903,8 +920,9 @@ public class VamsasAppDatastore
         modal = true;
         alseq.setName(valseq.getName());
       }
-      if (alseq.getDescription()==null || (valseq.getDescription() != null && !alseq.getDescription()
-                      .equals(valseq.getDescription())))
+      if (alseq.getDescription() == null
+              || (valseq.getDescription() != null && !alseq
+                      .getDescription().equals(valseq.getDescription())))
       {
         alseq.setDescription(valseq.getDescription());
         modal = true;
@@ -920,19 +938,22 @@ public class VamsasAppDatastore
       alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq
               .getSequence().replace(valGapchar, gapChar), (int) valseq
               .getStart(), (int) valseq.getEnd());
-      
+
       Vobject datsetseq = (Vobject) valseq.getRefid();
       if (datsetseq != null)
       {
         alseq.setDatasetSequence((SequenceI) getvObj2jv(datsetseq)); // exceptions
-        if (valseq.getDescription()!=null)
+        if (valseq.getDescription() != null)
         {
           alseq.setDescription(valseq.getDescription());
-        } else {
+        }
+        else
+        {
           // inherit description line from dataset.
-          if (alseq.getDatasetSequence().getDescription()!=null)
+          if (alseq.getDatasetSequence().getDescription() != null)
           {
-            alseq.setDescription(alseq.getDatasetSequence().getDescription());
+            alseq.setDescription(alseq.getDatasetSequence()
+                    .getDescription());
           }
         }
         // if
@@ -1055,12 +1076,11 @@ public class VamsasAppDatastore
       // bits.
       if (alan.getThreshold() != null && alan.getThreshold().displayed)
       {
-        an.addProperty(Properties.newProperty(THRESHOLD, Properties.FLOATTYPE,
-                 ""
-                + alan.getThreshold().value));
+        an.addProperty(Properties.newProperty(THRESHOLD,
+                Properties.FLOATTYPE, "" + alan.getThreshold().value));
         if (alan.getThreshold().label != null)
-          an.addProperty(Properties.newProperty(THRESHOLD + "Name", Properties.STRINGTYPE, ""
-                  + alan.getThreshold().label));
+          an.addProperty(Properties.newProperty(THRESHOLD + "Name",
+                  Properties.STRINGTYPE, "" + alan.getThreshold().label));
       }
       ((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
       bindjvvobj(alan, an);
@@ -1186,24 +1206,25 @@ public class VamsasAppDatastore
     switch (alan.graph)
     {
     case AlignmentAnnotation.BAR_GRAPH:
-      an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION, Properties.BOOLEANTYPE, "true"));
+      an.addProperty(Properties.newProperty(DISCRETE_ANNOTATION,
+              Properties.BOOLEANTYPE, "true"));
       break;
     case AlignmentAnnotation.LINE_GRAPH:
-      an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION, Properties.BOOLEANTYPE, "true"));
+      an.addProperty(Properties.newProperty(CONTINUOUS_ANNOTATION,
+              Properties.BOOLEANTYPE, "true"));
       break;
     default:
       // don't add any kind of discrete or continous property info.
     }
   }
 
-
   /**
    * 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.
+   *          when true - always ensure start is less than end.
    * @return int[] { start, end, direction} where direction==1 for range running
    *         from end to start.
    */
@@ -1433,9 +1454,9 @@ public class VamsasAppDatastore
       }
       // ensure vamsas object binds to the stored views retrieved from
       // Jalview appdata
-      //jalview.structure.StructureSelectionManager
-      //       .getStructureSelectionManager()
-      //      .addStructureViewerListener(viewframe.alignPanel);
+      // jalview.structure.StructureSelectionManager
+      // .getStructureSelectionManager()
+      // .addStructureViewerListener(viewframe.alignPanel);
 
     }
 
@@ -1448,7 +1469,8 @@ public class VamsasAppDatastore
    * binding tables
    * 
    * @param oldjvobject
-   * @param newjvobject (may be null)
+   * @param newjvobject
+   *          (may be null)
    */
   private void replaceJvObjMapping(Object oldjvobject, Object newjvobject)
   {
@@ -1459,7 +1481,7 @@ public class VamsasAppDatastore
               "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
                       + oldjvobject + ")");
     }
-    if (newjvobject!=null)
+    if (newjvobject != null)
     {
       jv2vobj.put(newjvobject, vobject);
       vobj2jv.put(vobject, newjvobject);
@@ -1537,8 +1559,10 @@ public class VamsasAppDatastore
     }
     return mapped;
   }
+
   /**
    * synchronize Jalview from the vamsas document
+   * 
    * @return number of new views from document
    */
   public int updateToJalview()
@@ -1574,12 +1598,12 @@ public class VamsasAppDatastore
         // TODO: test sequence merging - we preserve existing non vamsas
         // sequences but add in any new vamsas ones, and don't yet update any
         // sequence attributes
-        for (i = 0; i < iSize
-        ; i++)
+        for (i = 0; i < iSize; i++)
         {
           Sequence vdseq = dataset.getSequence(i);
-          jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(this, vdseq);
-          
+          jalview.io.vamsas.Datasetsequence dssync = new Datasetsequence(
+                  this, vdseq);
+
           jalview.datamodel.SequenceI dsseq = (SequenceI) dssync.getJvobj();
           if (dssync.isAddfromdoc())
           {
@@ -1635,7 +1659,7 @@ public class VamsasAppDatastore
                 if (dseta.getAnnotationElementCount() == 0)
                 {
                   new jalview.io.vamsas.Sequencefeature(this, dseta, dsSeq);
-                  
+
                 }
                 else
                 {
@@ -1648,8 +1672,11 @@ public class VamsasAppDatastore
                           .warn("Ignoring dataset annotation with annotationElements. Not yet supported in jalview.");
                 }
               }
-            } else {
-              Cache.log.warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
+            }
+            else
+            {
+              Cache.log
+                      .warn("Ignoring multiply referenced dataset sequence annotation for binding to datsaet sequence features.");
             }
           }
         }
@@ -1672,7 +1699,7 @@ public class VamsasAppDatastore
               jal = (av.hasHiddenRows()) ? av.getAlignment()
                       .getHiddenSequences().getFullAlignment() : av
                       .getAlignment();
-            } 
+            }
             iSize = alignment.getAlignmentSequenceCount();
             boolean refreshal = false;
             Vector newasAnnots = new Vector();
@@ -1820,7 +1847,8 @@ public class VamsasAppDatastore
                 else
                 {
                   jan = getjAlignmentAnnotation(jal, an[j]);
-                  // TODO: ensure we add the alignment annotation before the automatic annotation rows
+                  // TODO: ensure we add the alignment annotation before the
+                  // automatic annotation rows
                   jal.addAnnotation(jan);
                   bindjvvobj(jan, an[j]);
                   refreshal = true;
@@ -2133,9 +2161,8 @@ public class VamsasAppDatastore
 
   /**
    * @param jal
-   *                the jalview alignment to which the annotation will be
-   *                attached (ideally - freshly updated from corresponding
-   *                vamsas alignment)
+   *          the jalview alignment to which the annotation will be attached
+   *          (ideally - freshly updated from corresponding vamsas alignment)
    * @param annotation
    * @return unbound jalview alignment annotation object.
    */
@@ -2236,11 +2263,12 @@ public class VamsasAppDatastore
       // way its 'odd' - there is already an existing TODO about removing this
       // flag as being redundant
       /*
-       * if
-       * ((annotation.getClass().equals(uk.ac.vamsas.objects.core.AlignmentAnnotation.class) &&
-       * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph()) ||
-       * (hasSequenceRef=true &&
-       * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)annotation).getGraph())) {
+       * if((annotation.getClass().equals(uk.ac.vamsas.objects.core.
+       * AlignmentAnnotation.class) &&
+       * ((uk.ac.vamsas.objects.core.AlignmentAnnotation)annotation).getGraph())
+       * || (hasSequenceRef=true &&
+       * ((uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
+       * )annotation).getGraph())) {
        */
       if (has[HASVALS])
       {
@@ -2380,7 +2408,6 @@ public class VamsasAppDatastore
     return null;
   }
 
-
   /**
    * get real bounds of a RangeType's specification. start and end are an
    * inclusive range within which all segments and positions lie. TODO: refactor
@@ -2497,12 +2524,10 @@ public class VamsasAppDatastore
   /**
    * 
    * @param maprange
-   *                where the from range is the local mapped range, and the to
-   *                range is the 'mapped' range in the MapRangeType
-   * @param default
-   *                unit for local
-   * @param default
-   *                unit for mapped
+   *          where the from range is the local mapped range, and the to range
+   *          is the 'mapped' range in the MapRangeType
+   * @param default unit for local
+   * @param default unit for mapped
    * @return MapList
    */
   private jalview.util.MapList parsemapType(MapType maprange, int localu,
@@ -2567,8 +2592,8 @@ public class VamsasAppDatastore
    * 
    * if (jprov != null) { entries = jprov.getEntries(); for (int i = 0; i <
    * entries.length; i++) { provEntry = new Entry(); try { date = new
-   * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex) {
-   * ex.printStackTrace();
+   * org.exolab.castor.types.Date(entries[i].getDate()); } catch (Exception ex)
+   * { ex.printStackTrace();
    * 
    * date = new org.exolab.castor.types.Date(entries[i].getDate()); }
    * provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
@@ -2670,11 +2695,13 @@ public class VamsasAppDatastore
         Cache.log.warn("Creating new dataset for an alignment.");
         jal.setDataset(null);
       }
-      dataset = (DataSet) ((Alignment) getjv2vObj(viewport.getSequenceSetId())).getV_parent(); //   jal.getDataset());
-      if (dataset==null)
+      dataset = (DataSet) ((Alignment) getjv2vObj(viewport
+              .getSequenceSetId())).getV_parent(); // jal.getDataset());
+      if (dataset == null)
       {
         dataset = (DataSet) getjv2vObj(jal.getDataset());
-        Cache.log.error("Can't find the correct dataset for the alignment in this view. Creating new one.");
+        Cache.log
+                .error("Can't find the correct dataset for the alignment in this view. Creating new one.");
 
       }
       // Store any sequence mappings.
@@ -2685,7 +2712,8 @@ public class VamsasAppDatastore
                 .getCodonFrames();
         for (int cf = 0; cf < cframes.length; cf++)
         {
-          if (cframes[cf].getdnaSeqs()!=null && cframes[cf].getdnaSeqs().length > 0)
+          if (cframes[cf].getdnaSeqs() != null
+                  && cframes[cf].getdnaSeqs().length > 0)
           {
             jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
             jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
@@ -2733,19 +2761,22 @@ public class VamsasAppDatastore
   }
 
   /**
-   * @param skipList the skipList to set
+   * @param skipList
+   *          the skipList to set
    */
   public void setSkipList(Hashtable skipList)
   {
     this.skipList = skipList;
   }
+
   /**
    * registry for datastoreItems
    */
   DatastoreRegistry dsReg = new DatastoreRegistry();
+
   public DatastoreRegistry getDatastoreRegisty()
   {
-    if (dsReg==null)
+    if (dsReg == null)
     {
       dsReg = new DatastoreRegistry();
     }