X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FVamsasAppDatastore.java;h=fb6465cb93baacac99bd34d2306381e82d7049d4;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=95f6849883ea3b3eca9e7f124388286388317b4a;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 95f6849..fb6465c 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
  * 
@@ -424,8 +424,8 @@ 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),
@@ -633,11 +633,9 @@ 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 +655,8 @@ 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 +704,8 @@ 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);
@@ -936,8 +932,8 @@ 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 +1033,7 @@ 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);
@@ -1448,7 +1443,7 @@ public class VamsasAppDatastore
           if (mappings != null && mappings.length > 0)
           {
             jalview.structure.StructureSelectionManager
-                    .getStructureSelectionManager().addMappings(mappings);
+                    .getStructureSelectionManager(Desktop.instance).addMappings(mappings);
           }
         }
       }
@@ -1512,8 +1507,7 @@ 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);
       }
     }
@@ -1720,8 +1714,7 @@ 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
@@ -1867,8 +1860,10 @@ 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 +2054,14 @@ 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 +2100,14 @@ 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