JAL-3858 persist PAE matrix (only so far) as serialised floats in element on dataset...

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 8d2efe0..2b1b687 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -89,6 +89,8 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactMatrix;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
 import jalview.datamodel.GraphLine;
@@ -148,6 +150,7 @@ import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -192,6 +195,7 @@ import jalview.xml.binding.jalview.JalviewUserColours.Colour;
 import jalview.xml.binding.jalview.MapListType.MapListFrom;
 import jalview.xml.binding.jalview.MapListType.MapListTo;
 import jalview.xml.binding.jalview.Mapping;
+import jalview.xml.binding.jalview.MatrixType;
 import jalview.xml.binding.jalview.NoValueColour;
 import jalview.xml.binding.jalview.ObjectFactory;
 import jalview.xml.binding.jalview.PcaDataType;
@@ -2289,6 +2293,22 @@ public class Jalview2XML
           line.setColour(annotation.getThreshold().colour.getRGB());
           an.setThresholdLine(line);
         }
+        if (annotation.graph==AlignmentAnnotation.CONTACT_MAP)
+        {
+          if (annotation.sequenceRef.getContactMaps()!=null)
+          {
+            ContactMatrixI cm = annotation.sequenceRef.getContactMatrixFor(annotation);
+            if (cm!=null)
+            {
+              MatrixType xmlmat = new MatrixType();
+              xmlmat.setType(cm.getType());
+              xmlmat.setRows(BigInteger.valueOf(cm.getWidth()));
+              xmlmat.setCols(BigInteger.valueOf(cm.getHeight()));
+              xmlmat.setValue(ContactMatrix.contactToFloatString(cm));
+              an.getContactmatrix().add(xmlmat);
+            }
+          }
+        }
       }
       else
       {
@@ -3902,6 +3922,40 @@ public class Jalview2XML
             jaa.setProperty(prop.getName(), prop.getValue());
           }
         }
+        if (jaa.graph == AlignmentAnnotation.CONTACT_MAP)
+        {
+          if (annotation.getContactmatrix() != null
+                  && annotation.getContactmatrix().size() > 0)
+          {
+            for (MatrixType xmlmat : annotation.getContactmatrix())
+            {
+              if (PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType()))
+              {
+                if (!xmlmat.getRows().equals(xmlmat.getCols()))
+                {
+                  Console.error("Can't handle non square PAE Matrices");
+                }
+                else
+                {
+                  float[][] elements = ContactMatrix
+                          .fromFloatStringToContacts(xmlmat.getValue(),
+                                  xmlmat.getCols().intValue(),
+                                  xmlmat.getRows().intValue());
+
+                  PAEContactMatrix newpae = new PAEContactMatrix(
+                          jaa.sequenceRef, elements);
+                  jaa.sequenceRef.addContactListFor(jaa, newpae);
+                }
+              }
+              else
+              {
+                Console.error("Ignoring CONTACT_MAP annotation with type "
+                        + xmlmat.getType());
+              }
+            }
+          }
+        }
+
         if (jaa.autoCalculated)
         {
           autoAlan.add(new JvAnnotRow(i, jaa));