Merge branch 'develop' into features/JAL-1956_featureStyles

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 9a9c7b3..3a16bb8 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -165,7 +165,7 @@ public class Jalview2XML
    */
   Map<String, SequenceI> seqRefIds = null;
 
-  Vector frefedSequence = null;
+  Vector<Object[]> frefedSequence = null;
 
   boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
 
@@ -260,7 +260,7 @@ public class Jalview2XML
       int r = 0, rSize = frefedSequence.size();
       while (r < rSize)
       {
-        Object[] ref = (Object[]) frefedSequence.elementAt(r);
+        Object[] ref = frefedSequence.elementAt(r);
         if (ref != null)
         {
           String sref = (String) ref[0];
@@ -763,10 +763,11 @@ public class Jalview2XML
           if (sf[index].otherDetails != null)
           {
             String key;
-            Enumeration keys = sf[index].otherDetails.keys();
-            while (keys.hasMoreElements())
+            Iterator<String> keys = sf[index].otherDetails.keySet()
+                    .iterator();
+            while (keys.hasNext())
             {
-              key = keys.nextElement().toString();
+              key = keys.next();
               OtherData keyValue = new OtherData();
               keyValue.setKey(key);
               keyValue.setValue(sf[index].otherDetails.get(key).toString());
@@ -881,7 +882,7 @@ public class Jalview2XML
     // SAVE MAPPINGS
     if (jal.getCodonFrames() != null)
     {
-      Set<AlignedCodonFrame> jac = jal.getCodonFrames();
+      List<AlignedCodonFrame> jac = jal.getCodonFrames();
       for (AlignedCodonFrame acf : jac)
       {
         AlcodonFrame alc = new AlcodonFrame();
@@ -1198,41 +1199,41 @@ public class Jalview2XML
         Vector<String> settingsAdded = new Vector<String>();
         if (renderOrder != null)
         {
-          for (int ro = 0; ro < renderOrder.length; ro++)
+          for (String featureType : renderOrder)
           {
-            FeatureColourI gstyle = ap.getSeqPanel().seqCanvas
+            FeatureColourI fcol = ap.getSeqPanel().seqCanvas
                     .getFeatureRenderer()
-                    .getFeatureStyle(renderOrder[ro]);
+                    .getFeatureStyle(featureType);
             Setting setting = new Setting();
-            setting.setType(renderOrder[ro]);
-            if (!gstyle.isSimpleColour())
+            setting.setType(featureType);
+            if (!fcol.isSimpleColour())
             {
-              setting.setColour(gstyle.getMaxColour().getRGB());
-              setting.setMincolour(gstyle.getMinColour().getRGB());
-              setting.setMin(gstyle.getMin());
-              setting.setMax(gstyle.getMax());
-              setting.setColourByLabel(gstyle.isColourByLabel());
-              setting.setAutoScale(gstyle.isAutoScaled());
-              setting.setThreshold(gstyle.getThreshold());
+              setting.setColour(fcol.getMaxColour().getRGB());
+              setting.setMincolour(fcol.getMinColour().getRGB());
+              setting.setMin(fcol.getMin());
+              setting.setMax(fcol.getMax());
+              setting.setColourByLabel(fcol.isColourByLabel());
+              setting.setAutoScale(fcol.isAutoScaled());
+              setting.setThreshold(fcol.getThreshold());
               // -1 = No threshold, 0 = Below, 1 = Above
-              setting.setThreshstate(gstyle.isAboveThreshold() ? 1
-                      : (gstyle.isBelowThreshold() ? 0 : -1));
+              setting.setThreshstate(fcol.isAboveThreshold() ? 1
+                      : (fcol.isBelowThreshold() ? 0 : -1));
             }
             else
             {
-              setting.setColour(gstyle.getColour().getRGB());
+              setting.setColour(fcol.getColour().getRGB());
             }
 
             setting.setDisplay(av.getFeaturesDisplayed().isVisible(
-                    renderOrder[ro]));
+                    featureType));
             float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                    .getOrder(renderOrder[ro]);
+                    .getOrder(featureType);
             if (rorder > -1)
             {
               setting.setOrder(rorder);
             }
             fs.addSetting(setting);
-            settingsAdded.addElement(renderOrder[ro]);
+            settingsAdded.addElement(featureType);
           }
         }
 
@@ -1243,7 +1244,7 @@ public class Jalview2XML
         Vector<String> groupsAdded = new Vector<String>();
         while (en.hasNext())
         {
-          String grp = en.next().toString();
+          String grp = en.next();
           if (groupsAdded.contains(grp))
           {
             continue;
@@ -2227,7 +2228,7 @@ public class Jalview2XML
     }
     if (frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<Object[]>();
     }
 
     AlignFrame af = null, _af = null;
@@ -2823,7 +2824,7 @@ public class Jalview2XML
             {
               mapping = addMapping(maps[m].getMapping());
             }
-            if (dnaseq != null)
+            if (dnaseq != null && mapping.getTo() != null)
             {
               cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
             }