Merge branch 'features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview' into...

[jalview.git] / src / jalview / ws / DasSequenceFeatureFetcher.java

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 0a61dff..c661e2c 100644 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -135,7 +135,7 @@ public class DasSequenceFeatureFetcher
           boolean useJDasMultiThread)
   {
     this.useJDASMultiThread = useJDasMultiThread;
-    this.selectedSources = new ArrayList<jalviewSourceI>();
+    this.selectedSources = new ArrayList<>();
     // filter both sequences and sources to eliminate duplicates
     for (jalviewSourceI src : selectedSources2)
     {
@@ -316,17 +316,17 @@ public class DasSequenceFeatureFetcher
     FeaturesClientMultipleSources fc = new FeaturesClientMultipleSources();
     fc.setConnProps(sourceRegistry.getSessionHandler());
     // Now sending requests one at a time to each server
-    ArrayList<jalviewSourceI> srcobj = new ArrayList<jalviewSourceI>();
-    ArrayList<String> src = new ArrayList<String>();
-    List<List<String>> ids = new ArrayList<List<String>>();
-    List<List<DBRefEntry>> idobj = new ArrayList<List<DBRefEntry>>();
-    List<Map<String, SequenceI>> sqset = new ArrayList<Map<String, SequenceI>>();
+    ArrayList<jalviewSourceI> srcobj = new ArrayList<>();
+    ArrayList<String> src = new ArrayList<>();
+    List<List<String>> ids = new ArrayList<>();
+    List<List<DBRefEntry>> idobj = new ArrayList<>();
+    List<Map<String, SequenceI>> sqset = new ArrayList<>();
     for (jalviewSourceI _sr : selectedSources)
     {
 
-      Map<String, SequenceI> slist = new HashMap<String, SequenceI>();
-      List<DBRefEntry> idob = new ArrayList<DBRefEntry>();
-      List<String> qset = new ArrayList<String>();
+      Map<String, SequenceI> slist = new HashMap<>();
+      List<DBRefEntry> idob = new ArrayList<>();
+      List<String> qset = new ArrayList<>();
 
       for (SequenceI seq : sequences)
       {
@@ -368,8 +368,8 @@ public class DasSequenceFeatureFetcher
         sqset.add(slist);
       }
     }
-    Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();
-    Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<String, Map<List<String>, DasGFFAdapter>>();
+    Map<String, Map<List<String>, Exception>> errors = new HashMap<>();
+    Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<>();
     if (!useJDASMultiThread)
     {
       Iterator<String> sources = src.iterator();
@@ -390,7 +390,7 @@ public class DasSequenceFeatureFetcher
             if (ers == null)
             {
               results.put(source,
-                      ers = new HashMap<List<String>, DasGFFAdapter>());
+                      ers = new HashMap<>());
             }
             ers.put(qid, dga);
           } catch (Exception ex)
@@ -399,7 +399,7 @@ public class DasSequenceFeatureFetcher
             if (ers == null)
             {
               errors.put(source,
-                      ers = new HashMap<List<String>, Exception>());
+                      ers = new HashMap<>());
             }
             ers.put(qid, ex);
           }
@@ -438,7 +438,7 @@ public class DasSequenceFeatureFetcher
           Map<List<String>, DasGFFAdapter> results,
           Map<List<String>, Exception> errors)
   {
-    Set<SequenceI> sequences = new HashSet<SequenceI>();
+    Set<SequenceI> sequences = new HashSet<>();
     String source = jvsource.getSourceURL();
     // process features
     DasGFFAdapter result = (results == null) ? null : results.get(ids);
@@ -622,7 +622,7 @@ public class DasSequenceFeatureFetcher
         if (seq == af.getViewport().getAlignment().getSequenceAt(index)
                 .getDatasetSequence())
         {
-          af.alignPanel.paintAlignment(true);
+          af.alignPanel.paintAlignment(true, true);
           index = end;
           break;
         }
@@ -647,8 +647,8 @@ public class DasSequenceFeatureFetcher
     // TODO: minimal list of DAS queries to make by querying with untyped ID if
     // distinct from any typed IDs
 
-    List<DBRefEntry> ids = new ArrayList<DBRefEntry>();
-    List<String> qstring = new ArrayList<String>();
+    List<DBRefEntry> ids = new ArrayList<>();
+    List<String> qstring = new ArrayList<>();
     boolean dasCoordSysFound = false;
 
     if (uprefs != null)