X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=2c35547a69358651052cc9f4253172463d285c21;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=735f415206a55d692ab1c67532b4a21172b850c7;hpb=f1cf002d98f35e6d471ebf1af95b37c63cf86d1c;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 735f415..2c35547 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,19 +1,22 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * 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/>.
+ * 
+ * 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;
 
@@ -30,6 +33,9 @@ import jalview.io.vamsas.Datasetsequence;
 import jalview.io.vamsas.DatastoreItem;
 import jalview.io.vamsas.DatastoreRegistry;
 import jalview.io.vamsas.Rangetype;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.HashMap;
@@ -41,8 +47,30 @@ import java.util.Vector;
 import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
 
-import uk.ac.vamsas.client.*;
-import uk.ac.vamsas.objects.core.*;
+import uk.ac.vamsas.client.IClientAppdata;
+import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.client.Vobject;
+import uk.ac.vamsas.client.VorbaId;
+import uk.ac.vamsas.objects.core.Alignment;
+import uk.ac.vamsas.objects.core.AlignmentSequence;
+import uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation;
+import uk.ac.vamsas.objects.core.AnnotationElement;
+import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DataSetAnnotations;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Entry;
+import uk.ac.vamsas.objects.core.Glyph;
+import uk.ac.vamsas.objects.core.Local;
+import uk.ac.vamsas.objects.core.MapType;
+import uk.ac.vamsas.objects.core.Mapped;
+import uk.ac.vamsas.objects.core.Property;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.RangeAnnotation;
+import uk.ac.vamsas.objects.core.RangeType;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.core.VAMSAS;
 import uk.ac.vamsas.objects.utils.Properties;
 
 /*
@@ -122,7 +150,7 @@ public class VamsasAppDatastore
   private void buildSkipList()
   {
     skipList = new Hashtable();
-    AlignFrame[] al = Desktop.getAlignframes();
+    AlignFrame[] al = Desktop.getAlignFrames();
     for (int f = 0; al != null && f < al.length; f++)
     {
       skipList.put(al[f].getViewport().getSequenceSetId(), al[f]);
@@ -178,7 +206,7 @@ public class VamsasAppDatastore
   }
 
   /**
-   *
+   * 
    * @param vobj
    * @return Jalview datamodel object bound to the vamsas document object
    */
@@ -217,10 +245,12 @@ public class VamsasAppDatastore
     if (vobj2jv.containsKey(vobj.getVorbaId())
             && !((VorbaId) vobj2jv.get(vobj.getVorbaId())).equals(jvobj))
     {
-      Cache.log.debug(
-              "Warning? Overwriting existing vamsas id binding for "
-                      + vobj.getVorbaId(), new Exception(
-                      "Overwriting vamsas id binding."));
+      Cache.log
+              .debug("Warning? Overwriting existing vamsas id binding for "
+                      + vobj.getVorbaId(),
+                      new Exception(
+                              MessageManager
+                                      .getString("exception.overwriting_vamsas_id_binding")));
     }
     else if (jv2vobj.containsKey(jvobj)
             && !((VorbaId) jv2vobj.get(jvobj)).equals(vobj.getVorbaId()))
@@ -245,7 +275,7 @@ public class VamsasAppDatastore
 
   /**
    * put the alignment viewed by AlignViewport into cdoc.
-   *
+   * 
    * @param av
    *          alignViewport to be stored
    * @param aFtitle
@@ -308,7 +338,8 @@ public class VamsasAppDatastore
                         && 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.");
+                          MessageManager
+                                  .getString("error.implementation_error_cannot_map_alignment_sequences"));
                   // This occurs because the dataset for the alignment we are
                   // trying to
                 }
@@ -486,14 +517,14 @@ 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 +572,8 @@ 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)
@@ -719,17 +751,17 @@ 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.
    */
-  public boolean alignmentWillBeSkipped(AlignViewport av)
+  public boolean alignmentWillBeSkipped(AlignmentViewport av)
   {
     return (!av.getAlignment().isAligned());
   }
 
-  private void addToSkipList(AlignViewport av)
+  private void addToSkipList(AlignmentViewport av)
   {
     if (skipList == null)
     {
@@ -741,7 +773,7 @@ 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 +841,7 @@ 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)
@@ -1064,8 +1096,10 @@ public class VamsasAppDatastore
         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));
+        }
       }
       ((DataSet) sref.getV_parent()).addDataSetAnnotations(an);
       bindjvvobj(alan, an);
@@ -1158,7 +1192,7 @@ public class VamsasAppDatastore
 
   /**
    * set vamsas annotation object type from jalview annotation
-   *
+   * 
    * @param an
    * @param alan
    */
@@ -1206,7 +1240,7 @@ 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.
@@ -1228,12 +1262,11 @@ public class VamsasAppDatastore
       end = start;
       start = t;
     }
-    return new int[]
-    { start, end, pol < 0 ? 1 : 0 };
+    return new int[] { start, end, pol < 0 ? 1 : 0 };
   }
 
   /**
-   *
+   * 
    * @param annotation
    * @return true if annotation is not to be stored in document
    */
@@ -1300,7 +1333,7 @@ public class VamsasAppDatastore
             };
             if (dojvsync)
             {
-              fromxml.LoadJalviewAlign(jprovider);
+              fromxml.loadJalviewAlign(jprovider);
             }
           } catch (Exception e)
           {
@@ -1348,7 +1381,7 @@ public class VamsasAppDatastore
           };
           if (dojvsync)
           {
-            fromxml.LoadJalviewAlign(jarstream);
+            fromxml.loadJalviewAlign(jarstream);
           }
         } catch (Exception e)
         {
@@ -1377,12 +1410,12 @@ public class VamsasAppDatastore
     // sync,
     // and if any contain more than one view, then remove the one generated by
     // document update.
-    AlignViewport views[], av = null;
+    AlignmentViewport views[], av = null;
     AlignFrame af = null;
     Iterator newviews = newAlignmentViews.iterator();
     while (newviews.hasNext())
     {
-      av = (AlignViewport) newviews.next();
+      av = (AlignmentViewport) newviews.next();
       af = Desktop.getAlignFrameFor(av);
       // TODO implement this : af.getNumberOfViews
       String seqsetidobj = av.getSequenceSetId();
@@ -1399,7 +1432,8 @@ public class VamsasAppDatastore
         // to the align frames.
         boolean gathered = false;
         String newviewid = null;
-        AlignedCodonFrame[] mappings = av.getAlignment().getCodonFrames();
+        List<AlignedCodonFrame> mappings = av.getAlignment()
+                .getCodonFrames();
         for (int i = 0; i < views.length; i++)
         {
           if (views[i] != av)
@@ -1434,10 +1468,11 @@ public class VamsasAppDatastore
         {
           // ensure sequence mappings from vamsas document view still
           // active
-          if (mappings != null && mappings.length > 0)
+          if (mappings != null)
           {
             jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager(Desktop.instance).addMappings(mappings);
+                    .getStructureSelectionManager(Desktop.instance)
+                    .registerMappings(mappings);
           }
         }
       }
@@ -1456,7 +1491,7 @@ public class VamsasAppDatastore
   /**
    * replaces oldjvobject with newjvobject in the Jalview Object <> VorbaID
    * binding tables
-   *
+   * 
    * @param oldjvobject
    * @param newjvobject
    *          (may be null)
@@ -1466,10 +1501,11 @@ 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 + ")");
+      // 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)
     {
@@ -1494,7 +1530,7 @@ public class VamsasAppDatastore
         jxml.setSkipList(skipList);
         if (dojvsync)
         {
-          jxml.SaveState(new JarOutputStream(cappdata
+          jxml.saveState(new JarOutputStream(cappdata
                   .getClientOutputStream()));
         }
 
@@ -1515,7 +1551,7 @@ public class VamsasAppDatastore
 
   /**
    * translate the Vobject keys to strings for use in Jalview2XML
-   *
+   * 
    * @param jv2vobj2
    * @return
    */
@@ -1533,7 +1569,7 @@ public class VamsasAppDatastore
 
   /**
    * translate the Vobject values to strings for use in Jalview2XML
-   *
+   * 
    * @param vobj2jv2
    * @return hashtable with string values
    */
@@ -1551,7 +1587,7 @@ public class VamsasAppDatastore
 
   /**
    * synchronize Jalview from the vamsas document
-   *
+   * 
    * @return number of new views from document
    */
   public int updateToJalview()
@@ -1678,7 +1714,7 @@ public class VamsasAppDatastore
             uk.ac.vamsas.objects.core.Alignment alignment = dataset
                     .getAlignment(al);
             // TODO check this handles multiple views properly
-            AlignViewport av = findViewport(alignment);
+            AlignmentViewport av = findViewport(alignment);
 
             jalview.datamodel.AlignmentI jal = null;
             if (av != null)
@@ -1778,7 +1814,7 @@ 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 "
@@ -1952,10 +1988,10 @@ public class VamsasAppDatastore
     return newAlignmentViews.size();
   }
 
-  public AlignViewport findViewport(Alignment alignment)
+  public AlignmentViewport findViewport(Alignment alignment)
   {
-    AlignViewport av = null;
-    AlignViewport[] avs = Desktop
+    AlignmentViewport av = null;
+    AlignmentViewport[] avs = Desktop
             .getViewports((String) getvObj2jv(alignment));
     if (avs != null)
     {
@@ -1982,7 +2018,7 @@ 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[],
@@ -1998,8 +2034,7 @@ public class VamsasAppDatastore
     // may not quite cope with this (without binding an array of annotations to
     // a vamsas alignment annotation)
     // summary flags saying what we found over the set of annotation rows.
-    boolean[] AeContent = new boolean[]
-    { false, false, false, false, false };
+    boolean[] AeContent = new boolean[] { false, false, false, false, false };
     int[] rangeMap = getMapping(annotation);
     jalview.datamodel.Annotation[][] anot = new jalview.datamodel.Annotation[][]
     { new jalview.datamodel.Annotation[rangeMap.length],
@@ -2134,15 +2169,13 @@ public class VamsasAppDatastore
           anot[1][i].description = anot[1][i].description + " (after)";
         }
       }
-      return new Object[]
-      { AeContent, rangeMap, anot[0], anot[1] };
+      return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
     }
     else
     {
       // no annotations to parse. Just return an empty annotationElement[]
       // array.
-      return new Object[]
-      { AeContent, rangeMap, anot[0], anot[1] };
+      return new Object[] { AeContent, rangeMap, anot[0], anot[1] };
     }
     // return null;
   }
@@ -2203,6 +2236,7 @@ public class VamsasAppDatastore
             Cache.log.warn("Failed to parse threshold property");
           }
           if (val != null)
+          {
             if (gl == null)
             {
               gl = new GraphLine(val.floatValue(), "", java.awt.Color.black);
@@ -2211,11 +2245,14 @@ public class VamsasAppDatastore
             {
               gl.value = val.floatValue();
             }
+          }
         }
         else if (props[p].getName().equalsIgnoreCase(THRESHOLD + "Name"))
         {
           if (gl == null)
+          {
             gl = new GraphLine(0, "", java.awt.Color.black);
+          }
           gl.label = props[p].getContent();
         }
       }
@@ -2400,7 +2437,7 @@ 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}
    */
@@ -2412,7 +2449,8 @@ public class VamsasAppDatastore
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
         throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+                MessageManager
+                        .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -2435,8 +2473,7 @@ public class VamsasAppDatastore
         // could do a polarity for pos range too. and pass back indication of
         // discontinuities.
         int pos = dseta.getPos(0).getI();
-        se = new int[]
-        { pos, pos };
+        se = new int[] { pos, pos };
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
@@ -2458,7 +2495,7 @@ 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.
    */
@@ -2471,7 +2508,8 @@ public class VamsasAppDatastore
       if (dseta.getSegCount() > 0 && dseta.getPosCount() > 0)
       {
         throw new Error(
-                "Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");
+                MessageManager
+                        .getString("error.invalid_vamsas_rangetype_cannot_resolve_lists"));
       }
       if (dseta.getSegCount() > 0)
       {
@@ -2510,7 +2548,7 @@ 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
@@ -2535,24 +2573,24 @@ public class VamsasAppDatastore
 
   /**
    * initialise a range type object from a set of start/end inclusive intervals
-   *
+   * 
    * @param mrt
-   * @param range
+   * @param ranges
    */
-  private void initRangeType(RangeType mrt, int[] range)
+  private void initRangeType(RangeType mrt, List<int[]> ranges)
   {
-    for (int i = 0; i < range.length; i += 2)
+    for (int[] range : ranges)
     {
       Seg vSeg = new Seg();
-      vSeg.setStart(range[i]);
-      vSeg.setEnd(range[i + 1]);
+      vSeg.setStart(range[0]);
+      vSeg.setEnd(range[1]);
       mrt.addSeg(vSeg);
     }
   }
 
   /**
    * initialise a MapType object from a MapList object.
-   *
+   * 
    * @param maprange
    * @param ml
    * @param setUnits
@@ -2577,12 +2615,12 @@ 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); } }
@@ -2590,7 +2628,7 @@ 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)
@@ -2608,7 +2646,7 @@ public class VamsasAppDatastore
   }
 
   /**
-   *
+   * 
    * @return default initial provenance list for a Jalview created vamsas
    *         object.
    */
@@ -2668,10 +2706,10 @@ public class VamsasAppDatastore
     return vobj2jv;
   }
 
-  public void storeSequenceMappings(AlignViewport viewport, String title)
+  public void storeSequenceMappings(AlignmentViewport viewport, String title)
           throws Exception
   {
-    AlignViewport av = viewport;
+    AlignmentViewport av = viewport;
     try
     {
       jalview.datamodel.AlignmentI jal = av.getAlignment();
@@ -2693,18 +2731,15 @@ public class VamsasAppDatastore
 
       }
       // Store any sequence mappings.
-      if (av.getAlignment().getCodonFrames() != null
-              && av.getAlignment().getCodonFrames().length > 0)
+      List<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
+      if (cframes != null)
       {
-        jalview.datamodel.AlignedCodonFrame[] cframes = av.getAlignment()
-                .getCodonFrames();
-        for (int cf = 0; cf < cframes.length; cf++)
+        for (AlignedCodonFrame acf : cframes)
         {
-          if (cframes[cf].getdnaSeqs() != null
-                  && cframes[cf].getdnaSeqs().length > 0)
+          if (acf.getdnaSeqs() != null && acf.getdnaSeqs().length > 0)
           {
-            jalview.datamodel.SequenceI[] dmps = cframes[cf].getdnaSeqs();
-            jalview.datamodel.Mapping[] mps = cframes[cf].getProtMappings();
+            jalview.datamodel.SequenceI[] dmps = acf.getdnaSeqs();
+            jalview.datamodel.Mapping[] mps = acf.getProtMappings();
             for (int smp = 0; smp < mps.length; smp++)
             {
               uk.ac.vamsas.objects.core.SequenceType mfrom = (SequenceType) getjv2vObj(dmps[smp]);
@@ -2727,8 +2762,9 @@ 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);
     }
   }