JAL-1628 drop getShowAnnotation accessor in favour of isShowAnnotation in AlignViewpo...

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 08fd306..c96b717 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -69,6 +69,8 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
@@ -1123,12 +1125,12 @@ public class Jalview2XML
       view.setFontSize(av.font.getSize());
       view.setFontStyle(av.font.getStyle());
       view.setRenderGaps(av.renderGaps);
-      view.setShowAnnotation(av.getShowAnnotation());
+      view.setShowAnnotation(av.isShowAnnotation());
       view.setShowBoxes(av.getShowBoxes());
       view.setShowColourText(av.getColourText());
       view.setShowFullId(av.getShowJVSuffix());
-      view.setRightAlignIds(av.rightAlignIds);
-      view.setShowSequenceFeatures(av.showSequenceFeatures);
+      view.setRightAlignIds(av.isRightAlignIds());
+      view.setShowSequenceFeatures(av.isShowSequenceFeatures());
       view.setShowText(av.getShowText());
       view.setShowUnconserved(av.getShowUnconserved());
       view.setWrapAlignment(av.getWrapAlignment());
@@ -1149,7 +1151,8 @@ public class Jalview2XML
       {
         jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
 
-        String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+        String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+                .getRenderOrder().toArray(new String[0]);
 
         Vector settingsAdded = new Vector();
         Object gstyle = null;
@@ -1158,7 +1161,7 @@ public class Jalview2XML
         {
           for (int ro = 0; ro < renderOrder.length; ro++)
           {
-            gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+            gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getFeatureStyle(renderOrder[ro]);
             Setting setting = new Setting();
             setting.setType(renderOrder[ro]);
@@ -1176,13 +1179,13 @@ public class Jalview2XML
             }
             else
             {
-              setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+              setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                       .getColour(renderOrder[ro]).getRGB());
             }
 
-            setting.setDisplay(av.getFeaturesDisplayed()
-                    .containsKey(renderOrder[ro]));
-            float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+            setting.setDisplay(av.getFeaturesDisplayed().isVisible(
+                    renderOrder[ro]));
+            float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                     .getOrder(renderOrder[ro]);
             if (rorder > -1)
             {
@@ -1194,8 +1197,8 @@ public class Jalview2XML
         }
 
         // Make sure we save none displayed feature settings
-        Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
-                .keySet().iterator();
+        Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+                .getFeatureColours().keySet().iterator();
         while (en.hasNext())
         {
           String key = en.next().toString();
@@ -1206,11 +1209,11 @@ public class Jalview2XML
 
           Setting setting = new Setting();
           setting.setType(key);
-          setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+          setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                   .getColour(key).getRGB());
 
           setting.setDisplay(false);
-          float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+          float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                   .getOrder(key);
           if (rorder > -1)
           {
@@ -1219,8 +1222,9 @@ public class Jalview2XML
           fs.addSetting(setting);
           settingsAdded.addElement(key);
         }
-        en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
-                .keySet().iterator();
+        // is groups actually supposed to be a map here ?
+        en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().getFeatureGroups()
+                .iterator();
         Vector groupsAdded = new Vector();
         while (en.hasNext())
         {
@@ -1231,8 +1235,8 @@ public class Jalview2XML
           }
           Group g = new Group();
           g.setName(grp);
-          g.setDisplay(((Boolean) ap.seqPanel.seqCanvas
-                  .getFeatureRenderer().featureGroups.get(grp))
+          g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
+                  .getFeatureRenderer().checkGroupVisibility(grp, false))
                   .booleanValue());
           fs.addGroup(g);
           groupsAdded.addElement(grp);
@@ -1429,6 +1433,7 @@ public class Jalview2XML
           an.addProperty(prop);
         }
       }
+
       AnnotationElement ae;
       if (aa[i].annotations != null)
       {
@@ -3474,7 +3479,7 @@ public class Jalview2XML
 
     af.viewport.setConservationSelected(view.getConservationSelected());
     af.viewport.setShowJVSuffix(view.getShowFullId());
-    af.viewport.rightAlignIds = view.getRightAlignIds();
+    af.viewport.setRightAlignIds(view.getRightAlignIds());
     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
             .getFontStyle(), view.getFontSize()));
     af.alignPanel.fontChanged();
@@ -3536,10 +3541,8 @@ public class Jalview2XML
 
     af.viewport.setColourAppliesToAllGroups(true);
 
-    if (view.getShowSequenceFeatures())
-    {
-      af.viewport.showSequenceFeatures = true;
-    }
+    af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
+
     if (view.hasCentreColumnLabels())
     {
       af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
@@ -3606,9 +3609,14 @@ public class Jalview2XML
     // recover featre settings
     if (jms.getFeatureSettings() != null)
     {
-      af.viewport.setFeaturesDisplayed(new Hashtable());
+      FeaturesDisplayed fdi;
+      af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
+      Hashtable featureGroups = new Hashtable();
+      Hashtable featureColours = new Hashtable();
+      Hashtable featureOrder = new Hashtable();
+
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
@@ -3635,41 +3643,42 @@ public class Jalview2XML
             gc.setColourByLabel(setting.getColourByLabel());
           }
           // and put in the feature colour table.
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
-                  setting.getType(), gc);
+          featureColours.put(setting.getType(), gc);
         }
         else
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
-                  setting.getType(),
+          featureColours.put(setting.getType(),
                   new java.awt.Color(setting.getColour()));
         }
         renderOrder[fs] = setting.getType();
         if (setting.hasOrder())
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
-                  setting.getType(), setting.getOrder());
+          featureOrder.put(setting.getType(), setting.getOrder());
         }
         else
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
-                  setting.getType(),
-                  fs / jms.getFeatureSettings().getSettingCount());
+          featureOrder.put(setting.getType(), new Float(fs
+                  / jms.getFeatureSettings().getSettingCount()));
         }
         if (setting.getDisplay())
         {
-          af.viewport.getFeaturesDisplayed().put(setting.getType(), new Integer(
-                  setting.getColour()));
+          fdi.setVisible(setting.getType());
         }
       }
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
-      Hashtable fgtable;
-      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+      Hashtable fgtable = new Hashtable();
       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);
         fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
       }
+      // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+      // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
+      // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder);
+      FeatureRendererSettings frs = new FeatureRendererSettings(
+              renderOrder, fgtable, featureColours, 1.0f, featureOrder);
+      af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+              .transferSettings(frs);
+
     }
 
     if (view.getHiddenColumnsCount() > 0)
@@ -4014,7 +4023,7 @@ 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);
     }
@@ -4531,5 +4540,4 @@ public class Jalview2XML
   {
     skipList = skipList2;
   }
-
 }