Saves hidden seqs and DBRefs

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ca6e9f4..1060610 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -168,6 +168,14 @@ public class Jalview2XML
         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
 \r
         jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
+        jalview.datamodel.AlignmentI jalhidden = null;\r
+\r
+        if(av.hasHiddenRows)\r
+        {\r
+          jalhidden = jal;\r
+          jal = jal.getHiddenSequences().getFullAlignment();\r
+        }\r
+\r
 \r
         SequenceSet vamsasSet = new SequenceSet();\r
         Sequence vamsasSeq;\r
@@ -179,25 +187,57 @@ public class Jalview2XML
 \r
         //SAVE SEQUENCES\r
         int id = 0;\r
-\r
         for (int i = 0; i < jal.getHeight(); i++)\r
         {\r
             seqids.add(jal.getSequenceAt(i));\r
-\r
             vamsasSeq = new Sequence();\r
             vamsasSeq.setId(id + "");\r
             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
 \r
+            if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)\r
+            {\r
+              jalview.datamodel.DBRefEntry [] dbrefs =\r
+                  jal.getSequenceAt(i).getDatasetSequence().getDBRef();\r
+\r
+              for(int d=0; d<dbrefs.length; d++)\r
+              {\r
+                DBRef dbref = new DBRef();\r
+                dbref.setSource( dbrefs[d].getSource() );\r
+                dbref.setVersion( dbrefs[d].getVersion());\r
+                dbref.setAccessionId(dbrefs[d].getAccessionId());\r
+                vamsasSeq.addDBRef(dbref);\r
+              }\r
+            }\r
+\r
             jseq = new JSeq();\r
             jseq.setStart(jal.getSequenceAt(i).getStart());\r
             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
-\r
             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 \r
             jseq.setId(id);\r
 \r
+            if (av.hasHiddenRows)\r
+            {\r
+              jseq.setHidden(jalhidden.getHiddenSequences().isHidden(\r
+                  jal.getSequenceAt(i)));\r
+\r
+              if(jal.getSequenceAt(i).getHiddenSequences()!=null)\r
+              {\r
+                jalview.datamodel.SequenceI [] reps =\r
+                    jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);\r
+\r
+                for(int h=0; h<reps.length; h++)\r
+                {\r
+                  jseq.addHiddenSequences(\r
+                      jal.findIndex(reps[h])\r
+                      );\r
+                }\r
+              }\r
+            }\r
+\r
+\r
             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
             {\r
               jalview.datamodel.SequenceFeature[] sf\r
@@ -542,6 +582,27 @@ public class Jalview2XML
 \r
         }\r
 \r
+        if(av.hasHiddenColumns)\r
+        {\r
+          for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)\r
+          {\r
+            int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);\r
+            HiddenColumns hc = new HiddenColumns();\r
+            hc.setStart(region[0]);\r
+            hc.setEnd(region[1]);\r
+            view.addHiddenColumns(hc);\r
+          }\r
+        }\r
+\r
+        if(av.hasHiddenRows)\r
+        {\r
+        //  av.alignment.getHiddenSequences().get\r
+      //    HiddenSequences hs = new HiddenSequences();\r
+      //    hs.ad\r
+      //    view.addHiddenSequences();\r
+      //    av.showAllHiddenSeqs();.alignment.getHiddenSequences().\r
+        }\r
+\r
         jms.addViewport(view);\r
 \r
 \r
@@ -735,6 +796,7 @@ public class Jalview2XML
 \r
         //////////////////////////////////\r
         //LOAD SEQUENCES\r
+        Vector hiddenSeqs = null;\r
         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
         for (int i = 0; i < vamsasSeq.length; i++)\r
@@ -743,6 +805,12 @@ public class Jalview2XML
                     vamsasSeq[i].getSequence());\r
             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 \r
+            if(JSEQ[i].getHidden())\r
+            {\r
+              if(hiddenSeqs == null)\r
+                hiddenSeqs = new Vector();\r
+              hiddenSeqs.addElement(jseqs[i]);\r
+            }\r
             jseqs[i].setStart(JSEQ[i].getStart());\r
             jseqs[i].setEnd(JSEQ[i].getEnd());\r
             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
@@ -756,6 +824,7 @@ public class Jalview2XML
         al.setDataset(null);\r
         /////////////////////////////////\r
 \r
+\r
         for (int i = 0; i < vamsasSeq.length; i++)\r
         {\r
           if (JSEQ[i].getFeaturesCount() > 0)\r
@@ -784,9 +853,24 @@ public class Jalview2XML
             }\r
 \r
           }\r
+          if(vamsasSeq[i].getDBRefCount()>0)\r
+          {\r
+            for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)\r
+            {\r
+              jalview.datamodel.DBRefEntry entry =\r
+                  new jalview.datamodel.DBRefEntry(\r
+                      vamsasSeq[i].getDBRef(d).getSource(),\r
+                      vamsasSeq[i].getDBRef(d).getVersion(),\r
+                      vamsasSeq[i].getDBRef(d).getAccessionId()\r
+                      );\r
+              al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);\r
+            }\r
+\r
+          }\r
         }\r
 \r
 \r
+\r
          /////////////////////////////////\r
         //////////////////////////////////\r
         //LOAD ANNOTATIONS\r
@@ -932,7 +1016,29 @@ public class Jalview2XML
         Viewport[] views = jms.getViewport();\r
         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 \r
+\r
         AlignFrame af = new AlignFrame(al);\r
+\r
+        if(hiddenSeqs!=null)\r
+        {\r
+          for(int s=0; s<JSEQ.length; s++)\r
+          {\r
+            for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)\r
+            {\r
+              al.getSequenceAt(s).addHiddenSequence(\r
+                  al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )\r
+                  );\r
+            }\r
+          }\r
+\r
+          for(int s=0; s<hiddenSeqs.size(); s++)\r
+          {\r
+              af.viewport.hideSequence(\r
+                (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));\r
+          }\r
+        }\r
+\r
+\r
         if(hideConsensus || hideQuality || hideConservation)\r
         {\r
           int hSize = al.getAlignmentAnnotation().length;\r
@@ -1147,6 +1253,17 @@ public class Jalview2XML
          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
         }\r
 \r
+        if (view.getHiddenColumnsCount() > 0)\r
+        {\r
+          for (int c = 0; c < view.getHiddenColumnsCount(); c++)\r
+          {\r
+              af.viewport.hideColumns(\r
+                view.getHiddenColumns(c).getStart(),\r
+                view.getHiddenColumns(c).getEnd()+1\r
+                );\r
+          }\r
+        }\r
+\r
 \r
         Desktop.addInternalFrame(af, view.getTitle(),\r
              view.getWidth(), view.getHeight());\r