JAL-845 code/refactoring/tests related to linking DNA and protein

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d003cb0..d3a7e2c 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -22,12 +22,12 @@ package jalview.gui;
 
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
+import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.schemabinding.version2.AlcodMap;
-import jalview.schemabinding.version2.Alcodon;
 import jalview.schemabinding.version2.AlcodonFrame;
 import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
@@ -402,8 +402,7 @@ public class Jalview2XML
 
           for (ap = 0; ap < apSize; ap++)
           {
-            AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
-                    .elementAt(ap);
+            AlignmentPanel apanel = af.alignPanels.get(ap);
             String fileName = apSize == 1 ? shortName : ap + shortName;
             if (!fileName.endsWith(".xml"))
             {
@@ -458,8 +457,8 @@ public class Jalview2XML
       Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
       for (ap = 0; ap < apSize; ap++)
       {
-        AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
-                .elementAt(ap);
+        AlignmentPanel apanel = af.alignPanels
+                .get(ap);
         String jfileName = apSize == 1 ? fileName : fileName + ap;
         if (!jfileName.endsWith(".xml"))
         {
@@ -862,31 +861,18 @@ public class Jalview2XML
       jal = av.getAlignment();
     }
     // SAVE MAPPINGS
-    if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
+    Set<AlignedCodonFrame> jac = jal.getCodonFrames();
+    if (jac != null)
     {
-      jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
-      for (int i = 0; i < jac.length; i++)
+      for (AlignedCodonFrame acf : jac)
       {
         AlcodonFrame alc = new AlcodonFrame();
         vamsasSet.addAlcodonFrame(alc);
-        for (int p = 0; p < jac[i].aaWidth; p++)
+        if (acf.getProtMappings() != null
+                && acf.getProtMappings().length > 0)
         {
-          Alcodon cmap = new Alcodon();
-          if (jac[i].codons[p] != null)
-          {
-            // Null codons indicate a gapped column in the translated peptide
-            // alignment.
-            cmap.setPos1(jac[i].codons[p][0]);
-            cmap.setPos2(jac[i].codons[p][1]);
-            cmap.setPos3(jac[i].codons[p][2]);
-          }
-          alc.addAlcodon(cmap);
-        }
-        if (jac[i].getProtMappings() != null
-                && jac[i].getProtMappings().length > 0)
-        {
-          SequenceI[] dnas = jac[i].getdnaSeqs();
-          jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
+          SequenceI[] dnas = acf.getdnaSeqs();
+          jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
           for (int m = 0; m < pmaps.length; m++)
           {
             AlcodMap alcmap = new AlcodMap();
@@ -1253,8 +1239,8 @@ public class Jalview2XML
           for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
                   .size(); c++)
           {
-            int[] region = (int[]) av.getColumnSelection()
-                    .getHiddenColumns().elementAt(c);
+            int[] region = av.getColumnSelection().getHiddenColumns()
+                    .get(c);
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -2397,28 +2383,7 @@ public class Jalview2XML
       AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
       for (int i = 0; i < alc.length; i++)
       {
-        jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
-                alc[i].getAlcodonCount());
-        if (alc[i].getAlcodonCount() > 0)
-        {
-          Alcodon[] alcods = alc[i].getAlcodon();
-          for (int p = 0; p < cf.codons.length; p++)
-          {
-            if (alcods[p].hasPos1() && alcods[p].hasPos2()
-                    && alcods[p].hasPos3())
-            {
-              // translated codons require three valid positions
-              cf.codons[p] = new int[3];
-              cf.codons[p][0] = (int) alcods[p].getPos1();
-              cf.codons[p][1] = (int) alcods[p].getPos2();
-              cf.codons[p][2] = (int) alcods[p].getPos3();
-            }
-            else
-            {
-              cf.codons[p] = null;
-            }
-          }
-        }
+        AlignedCodonFrame cf = new AlignedCodonFrame();
         if (alc[i].getAlcodMapCount() > 0)
         {
           AlcodMap[] maps = alc[i].getAlcodMap();
@@ -3421,8 +3386,8 @@ public class Jalview2XML
       if (av != null)
       {
         // propagate shared settings to this new view
-        af.viewport.historyList = av.historyList;
-        af.viewport.redoList = av.redoList;
+        af.viewport.setHistoryList(av.getHistoryList());
+        af.viewport.setRedoList(av.getRedoList());
       }
       else
       {
@@ -4014,7 +3979,7 @@ public class Jalview2XML
       addDatasetRef(vamsasSet.getDatasetId(), ds);
     }
     // set the dataset for the newly imported alignment.
-    if (al.getDataset() == null)
+    if (al.getDataset() == null && !ignoreUnrefed)
     {
       al.setDataset(ds);
     }