X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=1f2cbb1708024243be75be38434d2a4cf228e8d0;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=562d5cbbd96b4dfdf04aaa92fb1051fe0270379e;hpb=b8446598292b2332e9919cd121981fa20aad43cc;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 562d5cb..1f2cbb1 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -253,6 +253,32 @@ public class Jalview2XML
                 features.setDescription(sf[index].getDescription());
                 features.setType(sf[index].getType());
                 features.setFeatureGroup(sf[index].getFeatureGroup());
+                features.setScore(sf[index].getScore());
+                if(sf[index].links!=null)
+                {
+                  for(int l=0; l<sf[index].links.size(); l++)
+                  {
+                    OtherData keyValue = new OtherData();
+                    keyValue.setKey("LINK_"+l);
+                    keyValue.setValue(sf[index].links.elementAt(l).toString());
+                    features.addOtherData(keyValue);
+                  }
+                }
+                if(sf[index].otherDetails!=null)
+                {
+                  String key;
+                  Enumeration keys = sf[index].otherDetails.keys();
+                  while(keys.hasMoreElements())
+                  {
+                    key = keys.nextElement().toString();
+                    OtherData keyValue = new OtherData();
+                    keyValue.setKey( key );
+                    keyValue.setValue(
+                        sf[index].otherDetails.get(key).toString());
+                    features.addOtherData(keyValue);
+                  }
+                }
+
                 jseq.addFeatures(features);
                 index ++;
               }
@@ -597,6 +623,8 @@ public class Jalview2XML
 
           String [] renderOrder =
               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+
+          Vector settingsAdded = new Vector();
           for(int ro=0; ro<renderOrder.length; ro++)
           {
             Setting setting = new Setting();
@@ -610,8 +638,30 @@ public class Jalview2XML
                 );
 
             fs.addSetting(setting);
+            settingsAdded.addElement(renderOrder[ro]);
+          }
+
+          //Make sure we save none displayed feature settings
+          Enumeration en =
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+          while(en.hasMoreElements())
+          {
+            String key = en.nextElement().toString();
+            if(settingsAdded.contains(key))
+              continue;
+
+            Setting setting = new Setting();
+            setting.setType(key);
+            setting.setColour(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+                );
 
+            setting.setDisplay(false);
+
+            fs.addSetting(setting);
+            settingsAdded.addElement(key);
           }
+
           jms.setFeatureSettings(fs);
 
         }
@@ -770,6 +820,9 @@ public class Jalview2XML
         }
         catch(java.net.UnknownHostException ex)
         {
+          if (Desktop.instance != null)
+            Desktop.instance.stopLoading();
+
           ex.printStackTrace();
           System.err.println("Couldn't locate Jalview XML file : " +
               ex + "\n");
@@ -781,6 +834,9 @@ public class Jalview2XML
         }
         catch (Exception ex)
         {
+          if (Desktop.instance != null)
+            Desktop.instance.stopLoading();
+
           //Is Version 1 Jar file?
           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 
@@ -901,6 +957,17 @@ public class Jalview2XML
                   features[f].getBegin(), features[f].getEnd(),
                   features[f].getFeatureGroup());
 
+              sf.setScore(features[f].getScore());
+              for(int od=0; od<features[f].getOtherDataCount(); od++)
+              {
+                OtherData keyValue = features[f].getOtherData(od);
+                if(keyValue.getKey().startsWith("LINK"))
+                  sf.addLink(keyValue.getValue());
+                else
+                  sf.setValue(keyValue.getKey(), keyValue.getValue());
+
+              }
+
               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
             }
           }
@@ -1164,16 +1231,11 @@ public class Jalview2XML
         af.viewport.setWrapAlignment(view.getWrapAlignment());
         af.wrapMenuItem.setSelected(view.getWrapAlignment());
 
-        if (view.getWrapAlignment())
-        {
-            af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-        }
-        else
-        {
-            af.annotationPanelMenuItem.setState(view.getShowAnnotation());
-            af.viewport.setShowAnnotation(view.getShowAnnotation());
-            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-        }
+        af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+
+        af.annotationPanelMenuItem.setState(view.getShowAnnotation());
+        af.viewport.setShowAnnotation(view.getShowAnnotation());
+        af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 
         af.viewport.setShowBoxes(view.getShowBoxes());
         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());