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

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

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index caf5b5e..bf96937 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,11 +20,24 @@
  */
 package jalview.ws;
 
+import jalview.analysis.CrossRef;
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.util.QuickSort;
+import jalview.ws.dbsources.EmblCdsSouce;
+import jalview.ws.dbsources.EmblSource;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.PfamFull;
+import jalview.ws.dbsources.PfamSeed;
+import jalview.ws.dbsources.RfamFull;
+import jalview.ws.dbsources.RfamSeed;
+import jalview.ws.dbsources.Uniprot;
+import jalview.ws.dbsources.UnprotName;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
@@ -55,18 +68,16 @@ public class SequenceFetcher extends ASequenceFetcher
 
   public SequenceFetcher(boolean addDas)
   {
-    addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
-    // alignment is
-    // 'default' for
-    // PFAM
-    addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
+    addDBRefSourceImpl(EmblSource.class);
+    addDBRefSourceImpl(EmblCdsSouce.class);
+    addDBRefSourceImpl(Uniprot.class);
+    addDBRefSourceImpl(UnprotName.class);
+    addDBRefSourceImpl(Pdb.class);
+    addDBRefSourceImpl(PfamFull.class);
+    addDBRefSourceImpl(PfamSeed.class);
+    // ensures Seed alignment is 'default' for PFAM
+    addDBRefSourceImpl(RfamFull.class);
+    addDBRefSourceImpl(RfamSeed.class);
     if (addDas)
     {
       registerDasSequenceSources();
@@ -96,7 +107,7 @@ public class SequenceFetcher extends ASequenceFetcher
         else
         {
           nm = dbs.getDbName();
-          if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+          if (getSourceProxy(srcs[i]) instanceof DasSequenceSource)
           {
             if (nm.startsWith("das:"))
             {
@@ -126,7 +137,7 @@ public class SequenceFetcher extends ASequenceFetcher
     {
       tosort[j] = tosort[j].toLowerCase();
     }
-    jalview.util.QuickSort.sort(tosort, sorted);
+    QuickSort.sort(tosort, sorted);
     // construct array with all sources listed
 
     srcs = new String[sorted.length + dassrc.size()];
@@ -143,7 +154,7 @@ public class SequenceFetcher extends ASequenceFetcher
     {
       tosort[j] = tosort[j].toLowerCase();
     }
-    jalview.util.QuickSort.sort(tosort, sorted);
+    QuickSort.sort(tosort, sorted);
     for (int j = sorted.length - 1; j >= 0; j--, i++)
     {
       srcs[i] = sorted[j];
@@ -163,7 +174,7 @@ public class SequenceFetcher extends ASequenceFetcher
       for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
       {
         String nm = dbs.getDbName();
-        if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+        if (getSourceProxy(srcs[i]) instanceof DasSequenceSource)
         {
           if (nm.startsWith("das:"))
           {
@@ -186,7 +197,7 @@ public class SequenceFetcher extends ASequenceFetcher
     {
       tosort[j] = ((String[]) sorted[j])[1];
     }
-    jalview.util.QuickSort.sort(tosort, sorted);
+    QuickSort.sort(tosort, sorted);
     int i = 0;
     // construct array with all sources listed
     srcs = new String[sorted.length + dassrc.size()];
@@ -203,7 +214,7 @@ public class SequenceFetcher extends ASequenceFetcher
     {
       tosort[j] = ((String[]) sorted[j])[1];
     }
-    jalview.util.QuickSort.sort(tosort, sorted);
+    QuickSort.sort(tosort, sorted);
     for (int j = sorted.length - 1; j >= 0; j--, i++)
     {
       srcs[i] = ((String[]) sorted[j])[0];
@@ -285,7 +296,9 @@ public class SequenceFetcher extends ASequenceFetcher
       String db = dbSources[dbsource];
       // skip me
       if (db.equals(DBRefSource.PDB))
+      {
         continue;
+      }
       for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
       {
         System.out.println("Source: " + sp.getDbName() + " (" + db
@@ -304,8 +317,8 @@ public class SequenceFetcher extends ASequenceFetcher
                     || sp.getDbSourceProperties().containsKey(
                             DBRefSource.CODINGSEQDB);
             // try and find products
-            String types[] = jalview.analysis.CrossRef
-                    .findSequenceXrefTypes(dna, al.getSequencesArray());
+            String types[] = CrossRef.findSequenceXrefTypes(dna,
+                    al.getSequencesArray());
             if (types != null)
             {
               System.out.println("Xref Types for: "
@@ -313,7 +326,7 @@ public class SequenceFetcher extends ASequenceFetcher
               for (int t = 0; t < types.length; t++)
               {
                 System.out.println("Type: " + types[t]);
-                SequenceI[] prod = jalview.analysis.CrossRef
+                SequenceI[] prod = CrossRef
                         .findXrefSequences(al.getSequencesArray(), dna,
                                 types[t]).getSequencesArray();
                 System.out.println("Found "
@@ -348,9 +361,13 @@ public class SequenceFetcher extends ASequenceFetcher
           System.out.println("ERROR:No alignment retrieved.");
           StringBuffer raw = sp.getRawRecords();
           if (raw != null)
+          {
             System.out.println(raw.toString());
+          }
           else
+          {
             System.out.println("ERROR:No Raw results.");
+          }
         }
         else
         {
@@ -395,7 +412,8 @@ public class SequenceFetcher extends ASequenceFetcher
           // have a bash at finding the products amongst all the retrieved
           // sequences.
           SequenceI[] seqs = al.getSequencesArray();
-          Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
+          Alignment prodal = CrossRef
+                  .findXrefSequences(
                   seqs, dna, null, ds);
           System.out.println("Found "
                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
@@ -434,8 +452,8 @@ public class SequenceFetcher extends ASequenceFetcher
   public void registerDasSequenceSources()
   {
     // TODO: define a context as a registry provider (either desktop,
-    // jalview.bin.cache, or something else).
-    for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()
+    // Cache, or something else).
+    for (jalviewSourceI source : Cache.getDasSourceRegistry()
             .getSources())
     {
       if (source.isSequenceSource())