X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=14803df9e417c34951b9161faa8a05727c68328c;hb=cfea32f10dfe5cde2b5223d8a6c1c26280ac0185;hp=4b9c3481ae746f5e7fbac020b32a2d1936c3a469;hpb=3659ecfe7bb17dd25a0a6b5c94a7d9dab4525136;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 4b9c348..14803df 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -26,6 +26,7 @@ import static jalview.math.RotatableMatrix.Axis.Z;
 
 import java.awt.Color;
 import java.awt.Font;
+import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
@@ -89,6 +90,8 @@ 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 +151,7 @@ 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 +196,7 @@ 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;
@@ -1510,7 +1515,7 @@ public class Jalview2XML
                 ov.getCanvas().getResidueColour().getRGB());
         overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
         view.setOverview(overview);
-      }
+      } 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
         view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
@@ -1551,6 +1556,8 @@ public class Jalview2XML
 
       view.setConservationSelected(av.getConservationSelected());
       view.setPidSelected(av.getAbovePIDThreshold());
+      view.setCharHeight(av.getCharHeight());
+      view.setCharWidth(av.getCharWidth());
       final Font font = av.getFont();
       view.setFontName(font.getName());
       view.setFontSize(font.getSize());
@@ -2289,6 +2296,22 @@ 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 +3925,40 @@ 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));
@@ -4122,7 +4179,7 @@ public class Jalview2XML
       loadPCAViewers(jalviewModel, ap);
       loadPDBStructures(jprovider, jseqs, af, ap);
       loadRnaViewers(jprovider, jseqs, ap);
-      loadOverview(view, af);
+      loadOverview(view, jalviewModel.getVersion(), af);
     }
     // and finally return.
     return af;
@@ -4135,8 +4192,13 @@ public class Jalview2XML
    * @param view
    * @param af
    */
-  protected void loadOverview(Viewport view, AlignFrame af)
+  protected void loadOverview(Viewport view, String version, AlignFrame af)
   {
+    if (!isVersionStringLaterThan("2.11.3",
+            version) && view.getOverview()==null)
+    {
+      return;
+    }
     /*
      * first close any Overview that was opened automatically
      * (if so configured in Preferences) so that the view is
@@ -4676,7 +4738,7 @@ public class Jalview2XML
    *          - minimum version we are comparing against
    * @param version
    *          - version of data being processsed
-   * @return
+   * @return true if version is equal to or later than supported
    */
   public static boolean isVersionStringLaterThan(String supported,
           String version)
@@ -4823,7 +4885,12 @@ public class Jalview2XML
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
     viewport.setFont(new Font(view.getFontName(),
             safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
-            true);
+            (view.getCharWidth()!=null) ? false : true);
+    if (view.getCharWidth()!=null)
+    {
+      viewport.setCharWidth(view.getCharWidth());
+      viewport.setCharHeight(view.getCharHeight());
+    }
     ViewStyleI vs = viewport.getViewStyle();
     vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
     viewport.setViewStyle(vs);
@@ -5146,7 +5213,10 @@ public class Jalview2XML
               + annotationId);
       return null;
     }
-    if (matchedAnnotation.getThreshold() == null)
+    // belt-and-braces create a threshold line if the 
+    // colourscheme needs one but the matchedAnnotation doesn't have one
+    if (safeInt(viewAnnColour.getAboveThreshold()) != 0
+            && matchedAnnotation.getThreshold() == null)
     {
       matchedAnnotation.setThreshold(
               new GraphLine(safeFloat(viewAnnColour.getThreshold()),