X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=735f415206a55d692ab1c67532b4a21172b850c7;hb=9c00e25bfdf274009a471eba895f39e2fac4c0ac;hp=93460e3ad983afe15b3dffd864c7fa9d33260c98;hpb=d6509fcf3a8cc90616e18cb22cec97f85c722bb8;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 93460e3..735f415 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,18 +1,18 @@
 /*
  * 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
- * 
+ *
  * 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/>.
  */
 package jalview.io;
@@ -20,11 +20,7 @@ package jalview.io;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
@@ -34,8 +30,6 @@ import jalview.io.vamsas.Datasetsequence;
 import jalview.io.vamsas.DatastoreItem;
 import jalview.io.vamsas.DatastoreRegistry;
 import jalview.io.vamsas.Rangetype;
-import jalview.util.UrlLink;
-
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.HashMap;
@@ -52,14 +46,14 @@ import uk.ac.vamsas.objects.core.*;
 import uk.ac.vamsas.objects.utils.Properties;
 
 /*
- * 
+ *
  * static {
  * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(
  * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
- * 
+ *
  */
 /*
- * TODO: check/verify consistency for vamsas sync with group associated alignment annotation  
+ * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
  */
 public class VamsasAppDatastore
 {
@@ -184,7 +178,7 @@ public class VamsasAppDatastore
   }
 
   /**
-   * 
+   *
    * @param vobj
    * @return Jalview datamodel object bound to the vamsas document object
    */
@@ -251,7 +245,7 @@ public class VamsasAppDatastore
 
   /**
    * put the alignment viewed by AlignViewport into cdoc.
-   * 
+   *
    * @param av
    *          alignViewport to be stored
    * @param aFtitle
@@ -492,14 +486,14 @@ 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);
@@ -725,7 +719,7 @@ 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.
@@ -747,7 +741,7 @@ public class VamsasAppDatastore
   /**
    * remove docseqs from the given alignment marking provenance appropriately
    * and removing any references to the sequences.
-   * 
+   *
    * @param alignment
    * @param docseqs
    */
@@ -815,7 +809,7 @@ 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)
@@ -1164,7 +1158,7 @@ public class VamsasAppDatastore
 
   /**
    * set vamsas annotation object type from jalview annotation
-   * 
+   *
    * @param an
    * @param alan
    */
@@ -1212,7 +1206,7 @@ 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.
@@ -1239,7 +1233,7 @@ public class VamsasAppDatastore
   }
 
   /**
-   * 
+   *
    * @param annotation
    * @return true if annotation is not to be stored in document
    */
@@ -1256,7 +1250,7 @@ public class VamsasAppDatastore
   /**
    * list of alignment views created when updating Jalview from document.
    */
-  private Vector newAlignmentViews = new Vector();
+  private final Vector newAlignmentViews = new Vector();
 
   /**
    * update local jalview view settings from the stored appdata (if any)
@@ -1288,6 +1282,7 @@ public class VamsasAppDatastore
             jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
             {
 
+              @Override
               public String getFilename()
               {
 
@@ -1295,6 +1290,7 @@ public class VamsasAppDatastore
                 return "Jalview Vamsas Document Client Data";
               }
 
+              @Override
               public JarInputStream getJarInputStream() throws IOException
               {
                 jalview.bin.Cache.log
@@ -1334,6 +1330,7 @@ public class VamsasAppDatastore
           jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
           {
 
+            @Override
             public String getFilename()
             {
 
@@ -1341,6 +1338,7 @@ public class VamsasAppDatastore
               return "Jalview Vamsas Document User Data";
             }
 
+            @Override
             public JarInputStream getJarInputStream() throws IOException
             {
               jalview.bin.Cache.log
@@ -1458,7 +1456,7 @@ public class VamsasAppDatastore
   /**
    * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
    * binding tables
-   * 
+   *
    * @param oldjvobject
    * @param newjvobject
    *          (may be null)
@@ -1468,6 +1466,7 @@ 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 + ")");
@@ -1516,7 +1515,7 @@ public class VamsasAppDatastore
 
   /**
    * translate the Vobject keys to strings for use in Jalview2XML
-   * 
+   *
    * @param jv2vobj2
    * @return
    */
@@ -1534,7 +1533,7 @@ public class VamsasAppDatastore
 
   /**
    * translate the Vobject values to strings for use in Jalview2XML
-   * 
+   *
    * @param vobj2jv2
    * @return hashtable with string values
    */
@@ -1552,7 +1551,7 @@ public class VamsasAppDatastore
 
   /**
    * synchronize Jalview from the vamsas document
-   * 
+   *
    * @return number of new views from document
    */
   public int updateToJalview()
@@ -1983,7 +1982,7 @@ 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[],
@@ -2401,7 +2400,7 @@ 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}
    */
@@ -2459,7 +2458,7 @@ 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.
    */
@@ -2511,7 +2510,7 @@ 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
@@ -2536,7 +2535,7 @@ public class VamsasAppDatastore
 
   /**
    * initialise a range type object from a set of start/end inclusive intervals
-   * 
+   *
    * @param mrt
    * @param range
    */
@@ -2553,7 +2552,7 @@ public class VamsasAppDatastore
 
   /**
    * initialise a MapType object from a MapList object.
-   * 
+   *
    * @param maprange
    * @param ml
    * @param setUnits
@@ -2578,12 +2577,12 @@ 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); } }
@@ -2591,7 +2590,7 @@ 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)
@@ -2609,7 +2608,7 @@ public class VamsasAppDatastore
   }
 
   /**
-   * 
+   *
    * @return default initial provenance list for a Jalview created vamsas
    *         object.
    */