X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=6293a1b39c67d134f02b2109f4d1bdbc8aef1c07;hb=5720f2cea034f014f366886b3cb9a170a909e988;hp=108bcb7b9db1e127d8e8ef117b5c03090d9e9541;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 108bcb7..6293a1b 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,30 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * 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/>.
+ * 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;
 
 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;
@@ -34,7 +33,7 @@ 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 jalview.util.MessageManager;
 
 import java.io.IOException;
 import java.util.Enumeration;
@@ -42,6 +41,7 @@ import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Vector;
 import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
@@ -51,14 +51,14 @@ 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
 {
@@ -224,8 +224,7 @@ public class VamsasAppDatastore
     {
       Cache.log.debug(
               "Warning? Overwriting existing vamsas id binding for "
-                      + vobj.getVorbaId(), new Exception(
-                      "Overwriting vamsas id binding."));
+                      + vobj.getVorbaId(), new Exception(MessageManager.getString("exception.overwriting_vamsas_id_binding")));
     }
     else if (jv2vobj.containsKey(jvobj)
             && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
@@ -312,8 +311,7 @@ public class VamsasAppDatastore
                 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.");
+                  throw new Error(MessageManager.getString("error.implementation_error_cannot_map_alignment_sequences"));
                   // This occurs because the dataset for the alignment we are
                   // trying to
                 }
@@ -424,8 +422,8 @@ public class VamsasAppDatastore
         {
           boolean modified = false;
           // check existing sequences in local and in document.
-          Vector docseqs = new Vector(alignment
-                  .getAlignmentSequenceAsReference());
+          Vector docseqs = new Vector(
+                  alignment.getAlignmentSequenceAsReference());
           for (int i = 0; i < jal.getHeight(); i++)
           {
             modified |= syncToAlignmentSequence(jal.getSequenceAt(i),
@@ -546,12 +544,8 @@ public class VamsasAppDatastore
             else
             {
               // first find the alignment sequence to associate this with.
-              SequenceI jvalsq = null;
-              Enumeration jval = av.getAlignment().getSequences()
-                      .elements();
-              while (jval.hasMoreElements())
+              for (SequenceI jvalsq : av.getAlignment().getSequences())
               {
-                jvalsq = (SequenceI) jval.nextElement();
                 // saveDatasetSequenceAnnotation(AlSeqMaps,(uk.ac.vamsas.objects.core.Sequence)
                 // sref, aa[i]);
                 if (jvalsq.getDatasetSequence() == aa[i].sequenceRef)
@@ -633,11 +627,9 @@ public class VamsasAppDatastore
                 if (aa[i].annotations[a].secondaryStructure != ' ')
                 {
                   Glyph ss = new Glyph();
-                  ss
-                          .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
-                  ss
-                          .setContent(String
-                                  .valueOf(aa[i].annotations[a].secondaryStructure));
+                  ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+                  ss.setContent(String
+                          .valueOf(aa[i].annotations[a].secondaryStructure));
                   ae.addGlyph(ss);
                 }
                 an.addAnnotationElement(ae);
@@ -657,10 +649,8 @@ 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
@@ -708,8 +698,8 @@ 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);
@@ -888,7 +878,7 @@ public class VamsasAppDatastore
    * creates/syncs the jvalsq from the alignment sequence
    */
   private boolean syncFromAlignmentSequence(AlignmentSequence valseq,
-          char valGapchar, char gapChar, Vector dsseqs)
+          char valGapchar, char gapChar, List<SequenceI> dsseqs)
 
   {
     boolean modal = false;
@@ -936,8 +926,8 @@ public class VamsasAppDatastore
     else
     {
       alseq = new jalview.datamodel.Sequence(valseq.getName(), valseq
-              .getSequence().replace(valGapchar, gapChar), (int) valseq
-              .getStart(), (int) valseq.getEnd());
+              .getSequence().replace(valGapchar, gapChar),
+              (int) valseq.getStart(), (int) valseq.getEnd());
 
       Vobject datsetseq = (Vobject) valseq.getRefid();
       if (datsetseq != null)
@@ -1037,8 +1027,7 @@ public class VamsasAppDatastore
       {
         // we only write an annotation where it really exists.
         Glyph ss = new Glyph();
-        ss
-                .setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
+        ss.setDict(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE);
         ss.setContent(String
                 .valueOf(alan.annotations[a].secondaryStructure));
         ae.addGlyph(ss);
@@ -1265,7 +1254,7 @@ 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)
@@ -1297,6 +1286,7 @@ public class VamsasAppDatastore
             jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
             {
 
+              @Override
               public String getFilename()
               {
 
@@ -1304,6 +1294,7 @@ public class VamsasAppDatastore
                 return "Jalview Vamsas Document Client Data";
               }
 
+              @Override
               public JarInputStream getJarInputStream() throws IOException
               {
                 jalview.bin.Cache.log
@@ -1343,6 +1334,7 @@ public class VamsasAppDatastore
           jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
           {
 
+            @Override
             public String getFilename()
             {
 
@@ -1350,6 +1342,7 @@ public class VamsasAppDatastore
               return "Jalview Vamsas Document User Data";
             }
 
+            @Override
             public JarInputStream getJarInputStream() throws IOException
             {
               jalview.bin.Cache.log
@@ -1448,7 +1441,8 @@ public class VamsasAppDatastore
           if (mappings != null && mappings.length > 0)
           {
             jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager().addMappings(mappings);
+                    .getStructureSelectionManager(Desktop.instance)
+                    .addMappings(mappings);
           }
         }
       }
@@ -1477,9 +1471,9 @@ public class VamsasAppDatastore
     Object vobject = jv2vobj.remove(oldjvobject);
     if (vobject == null)
     {
-      throw new Error(
-              "IMPLEMENTATION ERROR: old jalview object is not bound ! ("
-                      + oldjvobject + ")");
+      // NOTE: this happens if user deletes object in one session then updates
+      // from another client
+      throw new Error(MessageManager.formatMessage("error.implementation_error_old_jalview_object_not_bound", new String[]{oldjvobject.toString()}));
     }
     if (newjvobject != null)
     {
@@ -1512,8 +1506,7 @@ public class VamsasAppDatastore
       {
         // TODO raise GUI warning if user requests it.
         jalview.bin.Cache.log
-                .error(
-                        "Couldn't update jalview client application data. Giving up - local settings probably lost.",
+                .error("Couldn't update jalview client application data. Giving up - local settings probably lost.",
                         e);
       }
     }
@@ -1579,7 +1572,7 @@ public class VamsasAppDatastore
         // ///LOAD DATASET
         DataSet dataset = root.getDataSet(_ds);
         int i, iSize = dataset.getSequenceCount();
-        Vector dsseqs;
+        List<SequenceI> dsseqs;
         jalview.datamodel.Alignment jdataset = (jalview.datamodel.Alignment) getvObj2jv(dataset);
         int jremain = 0;
         if (jdataset == null)
@@ -1626,8 +1619,8 @@ public class VamsasAppDatastore
           SequenceI[] seqs = new SequenceI[dsseqs.size()];
           for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
           {
-            seqs[i] = (SequenceI) dsseqs.elementAt(i);
-            dsseqs.setElementAt(null, i);
+            seqs[i] = dsseqs.get(i);
+            dsseqs.set(i, null);
           }
           jdataset = new jalview.datamodel.Alignment(seqs);
           Cache.log.debug("New vamsas dataset imported into jalview.");
@@ -1720,8 +1713,7 @@ public class VamsasAppDatastore
               AlignmentSequence valseq = alignment.getAlignmentSequence(i);
               jalview.datamodel.Sequence alseq = (jalview.datamodel.Sequence) getvObj2jv(valseq);
               if (syncFromAlignmentSequence(valseq, valGapchar, gapChar,
-                      dsseqs)
-                      && alseq != null)
+                      dsseqs) && alseq != null)
               {
 
                 // updated to sequence from the document
@@ -1789,8 +1781,8 @@ public class VamsasAppDatastore
               SequenceI[] seqs = new SequenceI[dsseqs.size()];
               for (i = 0, iSize = dsseqs.size(); i < iSize; i++)
               {
-                seqs[i] = (SequenceI) dsseqs.elementAt(i);
-                dsseqs.setElementAt(null, i);
+                seqs[i] = dsseqs.get(i);
+                dsseqs.set(i, null);
               }
               jal = new jalview.datamodel.Alignment(seqs);
               Cache.log.debug("New vamsas alignment imported into jalview "
@@ -1867,8 +1859,10 @@ public class VamsasAppDatastore
                               .toString());
               av = alignFrame.getViewport();
               newAlignmentViews.addElement(av);
-              String title = alignment.getProvenance().getEntry(
-                      alignment.getProvenance().getEntryCount() - 1)
+              String title = alignment
+                      .getProvenance()
+                      .getEntry(
+                              alignment.getProvenance().getEntryCount() - 1)
                       .getAction();
               if (alignment.getPropertyCount() > 0)
               {
@@ -2059,16 +2053,14 @@ public class VamsasAppDatastore
             {
               if (glyphs[g]
                       .getDict()
-                      .equals(
-                              uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
+                      .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_SS_3STATE))
               {
                 ss = glyphs[g].getContent();
                 AeContent[HASSECSTR] = true;
               }
               else if (glyphs[g]
                       .getDict()
-                      .equals(
-                              uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
+                      .equals(uk.ac.vamsas.objects.utils.GlyphDictionary.PROTEIN_HD_HYDRO))
               {
                 Cache.log.debug("ignoring hydrophobicity glyph marker.");
                 AeContent[HASHPHOB] = true;
@@ -2107,14 +2099,14 @@ public class VamsasAppDatastore
           if (colour == null)
           {
             anot[row][pos] = new jalview.datamodel.Annotation(
-                    (dc != null) ? dc : "", desc, (ss != null) ? ss
-                            .charAt(0) : ' ', val);
+                    (dc != null) ? dc : "", desc,
+                    (ss != null) ? ss.charAt(0) : ' ', val);
           }
           else
           {
             anot[row][pos] = new jalview.datamodel.Annotation(
-                    (dc != null) ? dc : "", desc, (ss != null) ? ss
-                            .charAt(0) : ' ', val, colour);
+                    (dc != null) ? dc : "", desc,
+                    (ss != null) ? ss.charAt(0) : ' ', val, colour);
           }
         }
         else
@@ -2423,8 +2415,7 @@ public class VamsasAppDatastore
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+        throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -2482,8 +2473,7 @@ public class VamsasAppDatastore
       int[] se = null;
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
-        throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+          throw new Error(MessageManager.getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -2739,8 +2729,7 @@ public class VamsasAppDatastore
       }
     } catch (Exception e)
     {
-      throw new Exception("Couldn't store sequence mappings for " + title,
-              e);
+      throw new Exception(MessageManager.formatMessage("exception.couldnt_store_sequence_mappings", new String[]{title}),e);
     }
   }