JAL-4134 column grouping model and methods moved to their own object held by by Conta...

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 333c62b..a2ded9f 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -96,6 +96,7 @@ import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.GroupSet;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Point;
 import jalview.datamodel.RnaViewerModel;
@@ -2323,8 +2324,7 @@ public class Jalview2XML
               {
                 for (BitSet gp: cm.getGroups())
                 {
-                  BigInteger val = new BigInteger(gp.toByteArray());
-                  xmlmat.getGroups().add(val.toString());
+                  xmlmat.getGroups().add(stringifyBitset(gp));
                 }
               }
               if (cm.hasTree())
@@ -2478,6 +2478,38 @@ public class Jalview2XML
 
   }
 
+  private String stringifyBitset(BitSet gp) {
+    StringBuilder sb = new StringBuilder();
+    for (long val:gp.toLongArray())
+    {
+      if (sb.length()>0) {
+        sb.append(",");
+      }
+      sb.append(val);
+    }
+    return sb.toString();
+  }
+  private BitSet deStringifyBitset(String stringified) {
+    if ("".equals(stringified) || stringified==null)
+    {
+      return new BitSet();
+    }
+    String[] longvals = stringified.split(",");
+    long[] newlongvals = new long[longvals.length];
+    for (int lv=0;lv<longvals.length;lv++)
+    {
+      try {
+      newlongvals[lv]=Long.valueOf(longvals[lv]);
+      } catch (Exception x)
+      {
+        errorMessage+="Couldn't destringify bitset from: '"+stringified+"'";
+        newlongvals[lv]=0;
+      }
+    }
+    return BitSet.valueOf(newlongvals);
+
+    
+  }
   private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
   {
     AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
@@ -4030,20 +4062,12 @@ public class Jalview2XML
 
                     mapping = new jalview.util.MapList(fr, fto, m.getMapFromUnit().intValue(),m.getMapToUnit().intValue());
                   }
-                  PAEContactMatrix newpae = new PAEContactMatrix(
-                          jaa.sequenceRef, mapping, elements);
                   List<BitSet> newgroups=new ArrayList<BitSet>();
                   if (xmlmat.getGroups().size()>0)
                   {
                     for (String sgroup:xmlmat.getGroups())
                     {
-                      try {
-                        BigInteger group = new BigInteger(sgroup);
-                        newgroups.add(BitSet.valueOf(group.toByteArray()));
-                      } catch (NumberFormatException nfe)
-                      {
-                        Console.error("Problem parsing groups for a contact matrix (\""+sgroup+"\"",nfe);
-                      }
+                      newgroups.add(deStringifyBitset(sgroup));
                     }
                   }
                   String nwk=xmlmat.getNewick().size()>0 ? xmlmat.getNewick().get(0):null;
@@ -4055,7 +4079,10 @@ public class Jalview2XML
                   
                   String treeMethod = xmlmat.getTreeMethod();
                   double thresh = xmlmat.getCutHeight()!=null ? xmlmat.getCutHeight() : 0;
-                  newpae.restoreGroups(newgroups, treeMethod, nwk, thresh);
+                  GroupSet grpset = new GroupSet();
+                  grpset.restoreGroups(newgroups, treeMethod, nwk, thresh);
+                  PAEContactMatrix newpae = new PAEContactMatrix(
+                          jaa.sequenceRef, mapping, elements,grpset);
                   jaa.sequenceRef.addContactListFor(jaa, newpae);
                 }
               }