JAL-2349 store/restore mappable contact matrix in project and fix up interactive...

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ddf2afd..333c62b 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -152,6 +152,7 @@ import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.ws.datamodel.MappableContactMatrixI;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.dm.AAConSettings;
@@ -194,6 +195,7 @@ import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
 import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
 import jalview.xml.binding.jalview.JalviewUserColours;
 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.MapListType;
 import jalview.xml.binding.jalview.MapListType.MapListFrom;
 import jalview.xml.binding.jalview.MapListType.MapListTo;
 import jalview.xml.binding.jalview.Mapping;
@@ -2337,6 +2339,38 @@ public class Jalview2XML
               }
               
               // set/get properties
+              if (cm instanceof MappableContactMatrixI)
+              {
+                jalview.util.MapList mlst = ((MappableContactMatrixI) cm)
+                        .getMapFor(annotation.sequenceRef);
+                if (mlst != null)
+                {
+                  MapListType mp = new MapListType();
+                  List<int[]> r = mlst.getFromRanges();
+                  for (int[] range : r)
+                  {
+                    MapListFrom mfrom = new MapListFrom();
+                    mfrom.setStart(range[0]);
+                    mfrom.setEnd(range[1]);
+                    // mp.addMapListFrom(mfrom);
+                    mp.getMapListFrom().add(mfrom);
+                  }
+                  r = mlst.getToRanges();
+                  for (int[] range : r)
+                  {
+                    MapListTo mto = new MapListTo();
+                    mto.setStart(range[0]);
+                    mto.setEnd(range[1]);
+                    // mp.addMapListTo(mto);
+                    mp.getMapListTo().add(mto);
+                  }
+                  mp.setMapFromUnit(
+                          BigInteger.valueOf(mlst.getFromRatio()));
+                  mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
+                  xmlmat.setMapping(mp);
+                }
+              }
+              // and add to model
               an.getContactmatrix().add(xmlmat);
             }
           }
@@ -2664,7 +2698,7 @@ public class Jalview2XML
     }
     return vamsasSeq;
   }
-
+  
   private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
           SequenceI parentseq, SequenceI jds, boolean recurse)
   {
@@ -3972,9 +4006,32 @@ public class Jalview2XML
                           .fromFloatStringToContacts(xmlmat.getElements(),
                                   xmlmat.getCols().intValue(),
                                   xmlmat.getRows().intValue());
+                  jalview.util.MapList mapping = null;
+                  if (xmlmat.getMapping()!=null)
+                  {
+                    MapListType m = xmlmat.getMapping();
+                    // Mapping m = dr.getMapping();
+                    int fr[] = new int[m.getMapListFrom().size() * 2];
+                    Iterator<MapListFrom> from = m.getMapListFrom().iterator();// enumerateMapListFrom();
+                    for (int _i = 0; from.hasNext(); _i += 2)
+                    {
+                      MapListFrom mf = from.next();
+                      fr[_i] = mf.getStart();
+                      fr[_i + 1] = mf.getEnd();
+                    }
+                    int fto[] = new int[m.getMapListTo().size() * 2];
+                    Iterator<MapListTo> to = m.getMapListTo().iterator();// enumerateMapListTo();
+                    for (int _i = 0; to.hasNext(); _i += 2)
+                    {
+                      MapListTo mf = to.next();
+                      fto[_i] = mf.getStart();
+                      fto[_i + 1] = mf.getEnd();
+                    }
 
+                    mapping = new jalview.util.MapList(fr, fto, m.getMapFromUnit().intValue(),m.getMapToUnit().intValue());
+                  }
                   PAEContactMatrix newpae = new PAEContactMatrix(
-                          jaa.sequenceRef, elements);
+                          jaa.sequenceRef, mapping, elements);
                   List<BitSet> newgroups=new ArrayList<BitSet>();
                   if (xmlmat.getGroups().size()>0)
                   {