X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=34c61d94f234a15f6011d5bdcd11f99adc327387;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=a2bf424957d83d3b137e22017f0152d049e33db4;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index a2bf424..34c61d9 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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
+ * 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
+ *  
+ * 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;
 
@@ -178,7 +179,7 @@ public class VamsasAppDatastore
   }
 
   /**
-   *
+   * 
    * @param vobj
    * @return Jalview datamodel object bound to the vamsas document object
    */
@@ -245,7 +246,7 @@ public class VamsasAppDatastore
 
   /**
    * put the alignment viewed by AlignViewport into cdoc.
-   *
+   * 
    * @param av
    *          alignViewport to be stored
    * @param aFtitle
@@ -486,14 +487,14 @@ public class VamsasAppDatastore
           /*
            * We do not put local Alignment Sequence Features into the vamsas
            * document yet.
-           *
-           *
+           * 
+           * 
            * 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) {
-           *
+           * 
            * valseqf = (AlignmentSequenceAnnotation) getDSAnnotationFromJalview(
            * new AlignmentSequenceAnnotation(), features[i]);
            * valseqf.setGraph(false);
@@ -541,7 +542,8 @@ public class VamsasAppDatastore
             else
             {
               // first find the alignment sequence to associate this with.
-              for (SequenceI jvalsq:av.getAlignment().getSequences()) {
+              for (SequenceI jvalsq : av.getAlignment().getSequences())
+              {
                 // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
                 // sref, aa[i]);
                 if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
@@ -719,7 +721,7 @@ 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
    * (for all sequences, including the hidden ones!)
-   *
+   * 
    * @param av
    * @return true if alignment associated with this view will be stored in
    *         document.
@@ -741,7 +743,7 @@ public class VamsasAppDatastore
   /**
    * remove docseqs from the given alignment marking provenance appropriately
    * and removing any references to the sequences.
-   *
+   * 
    * @param alignment
    * @param docseqs
    */
@@ -809,7 +811,7 @@ public class VamsasAppDatastore
    * vamsas alignment sequence for jvalsq and adds it to the alignment if
    * necessary. unbounddocseq is a duplicate of the vamsas alignment sequences
    * and these are removed after being processed w.r.t a bound jvalsq
-   *
+   * 
    */
   private boolean syncToAlignmentSequence(SequenceI jvalsq,
           Alignment alignment, Vector unbounddocseq)
@@ -1158,7 +1160,7 @@ public class VamsasAppDatastore
 
   /**
    * set vamsas annotation object type from jalview annotation
-   *
+   * 
    * @param an
    * @param alan
    */
@@ -1206,7 +1208,7 @@ public class VamsasAppDatastore
   /**
    * 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.
@@ -1233,7 +1235,7 @@ public class VamsasAppDatastore
   }
 
   /**
-   *
+   * 
    * @param annotation
    * @return true if annotation is not to be stored in document
    */
@@ -1437,7 +1439,8 @@ public class VamsasAppDatastore
           if (mappings != null && mappings.length > 0)
           {
             jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance).addMappings(mappings);
+                    .getStructureSelectionManager(Desktop.instance)
+                    .addMappings(mappings);
           }
         }
       }
@@ -1456,7 +1459,7 @@ public class VamsasAppDatastore
   /**
    * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
    * binding tables
-   *
+   * 
    * @param oldjvobject
    * @param newjvobject
    *          (may be null)
@@ -1466,6 +1469,8 @@ public class VamsasAppDatastore
     Object vobject = jv2vobj.remove(oldjvobject);
     if (vobject == null)
     {
+      // NOTE: this happens if user deletes object in one session then updates
+      // from another client
       throw new Error(
               "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
                       + oldjvobject + ")");
@@ -1514,7 +1519,7 @@ public class VamsasAppDatastore
 
   /**
    * translate the Vobject keys to strings for use in Jalview2XML
-   *
+   * 
    * @param jv2vobj2
    * @return
    */
@@ -1532,7 +1537,7 @@ public class VamsasAppDatastore
 
   /**
    * translate the Vobject values to strings for use in Jalview2XML
-   *
+   * 
    * @param vobj2jv2
    * @return hashtable with string values
    */
@@ -1550,7 +1555,7 @@ public class VamsasAppDatastore
 
   /**
    * synchronize Jalview from the vamsas document
-   *
+   * 
    * @return number of new views from document
    */
   public int updateToJalview()
@@ -1777,7 +1782,7 @@ public class VamsasAppDatastore
               for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
               {
                 seqs[i] = dsseqs.get(i);
-                dsseqs.set(i,null);
+                dsseqs.set(i, null);
               }
               jal = new jalview.datamodel.Alignment(seqs);
               Cache.log.debug("New vamsas alignment imported into jalview "
@@ -1981,7 +1986,7 @@ public class VamsasAppDatastore
    * jalview.datamodel.Annotation[] rows Two annotation rows are made if there
    * are distinct annotation for both at 'pos' and 'after pos' at any particular
    * site.
-   *
+   * 
    * @param annotation
    * @return { boolean[static int constants ], int[ae.length] - map to annotated
    *         object frame, jalview.datamodel.Annotation[],
@@ -2399,7 +2404,7 @@ public class VamsasAppDatastore
    * get real bounds of a RangeType's specification. start and end are an
    * inclusive range within which all segments and positions lie. TODO: refactor
    * to vamsas utils
-   *
+   * 
    * @param dseta
    * @return int[] { start, end}
    */
@@ -2457,7 +2462,7 @@ public class VamsasAppDatastore
   /**
    * map from a rangeType's internal frame to the referenced object's coordinate
    * frame.
-   *
+   * 
    * @param dseta
    * @return int [] { ref(pos)...} for all pos in rangeType's frame.
    */
@@ -2509,7 +2514,7 @@ 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
@@ -2534,7 +2539,7 @@ public class VamsasAppDatastore
 
   /**
    * initialise a range type object from a set of start/end inclusive intervals
-   *
+   * 
    * @param mrt
    * @param range
    */
@@ -2551,7 +2556,7 @@ public class VamsasAppDatastore
 
   /**
    * initialise a MapType object from a MapList object.
-   *
+   * 
    * @param maprange
    * @param ml
    * @param setUnits
@@ -2576,12 +2581,12 @@ public class VamsasAppDatastore
    * App and Action here. Provenance prov = new Provenance();
    * org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( new
    * java.util.Date()); Entry provEntry;
-   *
+   * 
    * 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();
-   *
+   * 
    * date = new org.exolab.castor.types.Date(entries[i].getDate()); }
    * provEntry.setDate(date); provEntry.setUser(entries[i].getUser());
    * provEntry.setAction(entries[i].getAction()); prov.addEntry(provEntry); } }
@@ -2589,7 +2594,7 @@ public class VamsasAppDatastore
    * provEntry.setUser(System.getProperty("user.name")); // TODO: ext string
    * provEntry.setApp("JVAPP"); // TODO: ext string provEntry.setAction(action);
    * prov.addEntry(provEntry); }
-   *
+   * 
    * return prov; }
    */
   jalview.datamodel.Provenance getJalviewProvenance(Provenance prov)
@@ -2607,7 +2612,7 @@ public class VamsasAppDatastore
   }
 
   /**
-   *
+   * 
    * @return default initial provenance list for a Jalview created vamsas
    *         object.
    */