JAL-1807 explicit imports (jalview.io.*)

[jalview.git] / src / jalview / io / StockholmFile.java

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 6490d28..3edcd75 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -31,7 +31,10 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.DBRefUtils;
 import jalview.util.Format;
+import jalview.util.MapList;
 import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
@@ -156,7 +159,7 @@ public class StockholmFile extends AlignFile
       for (int k = 0; k < rna.length(); k++)
       {
         ann[k] = new Annotation(annot[k], "",
-                jalview.schemes.ResidueProperties.getRNASecStrucState(
+                ResidueProperties.getRNASecStrucState(
                         annot[k]).charAt(0), 0f);
 
       }
@@ -309,7 +312,7 @@ public class StockholmFile extends AlignFile
             {
               String src = dbr.substring(0, dbr.indexOf(";"));
               String acn = dbr.substring(dbr.indexOf(";") + 1);
-              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
+              DBRefUtils.parseToDbRef(seqO, src, "0", acn);
             }
           }
 
@@ -738,14 +741,14 @@ public class StockholmFile extends AlignFile
       {
         // strip of last subdomain
         sdbac = sdbac.substring(0, sdbac.indexOf("."));
-        dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+        dbrf = DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
                 sdbac);
         if (dbrf != null)
         {
           dbrs.add(dbrf);
         }
       }
-      dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+      dbrf = DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
               dbr);
       if (dbr != null)
       {
@@ -760,7 +763,7 @@ public class StockholmFile extends AlignFile
       {
         // strip off last subdomain
         sdbac = sdbac.substring(0, sdbac.indexOf("."));
-        dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+        dbrf = DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
                 sdbac);
         if (dbrf != null)
         {
@@ -768,7 +771,7 @@ public class StockholmFile extends AlignFile
         }
       }
 
-      dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+      dbrf = DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
               dbr);
       if (dbrf != null)
       {
@@ -779,7 +782,7 @@ public class StockholmFile extends AlignFile
     {
       for (DBRefEntry d : dbrs)
       {
-        jalview.util.MapList mp = new jalview.util.MapList(new int[]
+        MapList mp = new MapList(new int[]
         { seqO.getStart(), seqO.getEnd() }, new int[]
         { st, en }, 1, 1);
         jalview.datamodel.Mapping mping = new Mapping(mp);
@@ -830,12 +833,12 @@ public class StockholmFile extends AlignFile
         {
           if (detectbrackets.search(pos))
           {
-            ann.secondaryStructure = jalview.schemes.ResidueProperties
+            ann.secondaryStructure = ResidueProperties
                     .getRNASecStrucState(pos).charAt(0);
           }
           else
           {
-            ann.secondaryStructure = jalview.schemes.ResidueProperties
+            ann.secondaryStructure = ResidueProperties
                     .getDssp3state(pos).charAt(0);
           }