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 be89829..d3a7e2c 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -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"))
         {
@@ -862,18 +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);
-        if (jac[i].getProtMappings() != null
-                && jac[i].getProtMappings().length > 0)
+        if (acf.getProtMappings() != null
+                && acf.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();
@@ -1240,8 +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]);