Save features and pdbids

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 28840e7..bbe3389 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -192,6 +192,56 @@ public class Jalview2XML
 \r
             jseq.setId(id);\r
 \r
+            if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
+            {\r
+              Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements();\r
+              while(en.hasMoreElements())\r
+              {\r
+                Features features = new Features();\r
+                jalview.datamodel.SequenceFeature sf\r
+                   = (jalview.datamodel.SequenceFeature)en.nextElement();\r
+\r
+                features.setBegin(sf.getBegin());\r
+                features.setEnd(sf.getEnd());\r
+                features.setDescription(sf.getDescription());\r
+                features.setStatus(sf.getStatus());\r
+                features.setType(sf.getType());\r
+                jseq.addFeatures(features);\r
+              }\r
+            }\r
+\r
+            if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
+            {\r
+              Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
+              while(en.hasMoreElements())\r
+              {\r
+                Pdbids pdb = new Pdbids();\r
+                jalview.datamodel.PDBEntry entry\r
+                   = (jalview.datamodel.PDBEntry)en.nextElement();\r
+\r
+                pdb.setId(entry.getId());\r
+                pdb.setType(entry.getType());\r
+\r
+                if(entry.getProperty()!=null)\r
+                {\r
+                  PdbentryItem item = new PdbentryItem();\r
+                  Hashtable properties = entry.getProperty();\r
+                  Enumeration en2 = properties.keys();\r
+                  while(en2.hasMoreElements())\r
+                  {\r
+                    Property prop = new Property();\r
+                    String key = en2.nextElement().toString();\r
+                    prop.setName(key);\r
+                    prop.setValue( properties.get(key).toString() );\r
+                    item.addProperty(prop);\r
+                  }\r
+                  pdb.addPdbentryItem(item);\r
+                }\r
+\r
+                jseq.addPdbids(pdb);\r
+              }\r
+            }\r
+\r
             jms.addJSeq(jseq);\r
             vamsasSet.addSequence(vamsasSeq);\r
             id++;\r
@@ -346,6 +396,7 @@ public class Jalview2XML
             jms.setJGroup(groups);\r
         }\r
 \r
+\r
         ///////////SAVE VIEWPORT\r
         Viewport view = new Viewport();\r
         view.setTitle(af.getTitle());\r
@@ -570,7 +621,6 @@ public class Jalview2XML
         //LOAD SEQUENCES\r
         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
-\r
         for (int i = 0; i < vamsasSeq.length; i++)\r
         {\r
             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
@@ -582,9 +632,41 @@ public class Jalview2XML
             seqids.add(jseqs[i]);\r
         }\r
 \r
+        ///SequenceFeatures are added to the DatasetSequence,\r
+        // so we must create the dataset before loading features\r
         /////////////////////////////////\r
         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
+        al.setDataset(null);\r
+        /////////////////////////////////\r
+\r
+        for (int i = 0; i < vamsasSeq.length; i++)\r
+        {\r
+          if (JSEQ[i].getFeaturesCount() > 0)\r
+          {\r
+            Features[] features = JSEQ[i].getFeatures();\r
+            for (int f = 0; f < features.length; f++)\r
+            {\r
+              //features[f].getBegin()\r
+              jalview.datamodel.SequenceFeature sf\r
+                  = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
+                  features[f].getDescription(), features[f].getStatus(),\r
+                  features[f].getBegin(), features[f].getEnd());\r
+              al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
+            }\r
+          }\r
+          if (JSEQ[i].getPdbidsCount() > 0)\r
+          {\r
+            Pdbids[] ids = JSEQ[i].getPdbids();\r
+            for (int p = 0; p < ids.length; p++)\r
+            {\r
+              jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
+              entry.setId(ids[p].getId());\r
+              entry.setType(ids[p].getType());\r
+              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
+            }\r
 \r
+          }\r
+        }\r
         /////////////////////////////////\r
         //////////////////////////////////\r
         //LOAD ANNOTATIONS\r
@@ -763,11 +845,9 @@ public class Jalview2XML
 \r
         if (view.getShowSequenceFeatures())\r
         {\r
-            af.featureSettings.setEnabled(true);\r
-            af.viewport.showSequenceFeatures = true;\r
-            af.sequenceFeatures.setSelected(true);\r
-            new SequenceFeatureFetcher(al, af.alignPanel);\r
-            al.featuresAdded = true;\r
+           af.featureSettings.setEnabled(true);\r
+           af.viewport.showSequenceFeatures = true;\r
+           af.sequenceFeatures.setSelected(true);\r
         }\r
 \r
         Desktop.addInternalFrame(af, view.getTitle(),\r