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

[jalview.git] / src / jalview / ws / jws1 / MsaWSThread.java

diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java
index a6ba751..89a370d 100644 (file)
--- a/src/jalview/ws/jws1/MsaWSThread.java
+++ b/src/jalview/ws/jws1/MsaWSThread.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.
  * 
@@ -20,16 +20,28 @@
  */
 package jalview.ws.jws1;
 
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
 import jalview.ws.WSClientI;
+
+import java.util.Hashtable;
+import java.util.Vector;
+
 import vamsas.objects.simple.MsaResult;
 
 class MsaWSThread extends JWS1Thread implements WSClientI
@@ -102,18 +114,17 @@ class MsaWSThread extends JWS1Thread implements WSClientI
       for (int i = 0, n = 0; i < seqs.length; i++)
       {
 
-        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+        String newname = SeqsetUtils.unique_name(i); // same
         // for
         // any
         // subjob
-        SeqNames.put(newname,
-                jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
+        SeqNames.put(newname, SeqsetUtils.SeqCharacterHash(seqs[i]));
         if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
         {
           seqarray[n] = new vamsas.objects.simple.Sequence();
           seqarray[n].setId(newname);
           seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
-                  : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                  : AlignSeq.extractGaps(Comparison.GapChars,
                           seqs[i].getSequenceAsString()));
         }
         else
@@ -122,7 +133,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
           if (seqs[i].getEnd() >= seqs[i].getStart())
           {
             empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
-                    .extractGaps(jalview.util.Comparison.GapChars,
+                    .extractGaps(Comparison.GapChars,
                             seqs[i].getSequenceAsString());
           }
           emptySeqs.add(new String[]
@@ -219,21 +230,21 @@ class MsaWSThread extends JWS1Thread implements WSClientI
             String[] es = (String[]) emptySeqs.get(i);
             if (es[1] == null)
             {
-              t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
+              t_alseqs[i + alseq_l] = new Sequence(es[0],
                       insbuff.toString(), 1, 0);
             }
             else
             {
               if (es[1].length() < nw)
               {
-                t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
+                t_alseqs[i + alseq_l] = new Sequence(
                         es[0],
                         es[1] + insbuff.substring(0, nw - es[1].length()),
                         1, 1 + es[1].length());
               }
               else
               {
-                t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
+                t_alseqs[i + alseq_l] = new Sequence(
                         es[0], es[1]);
               }
             }
@@ -242,9 +253,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI
         }
         AlignmentOrder msaorder = new AlignmentOrder(alseqs);
         // always recover the order - makes parseResult()'s life easier.
-        jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
+        AlignmentSorter.recoverOrder(alseqs);
         // account for any missing sequences
-        jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
+        SeqsetUtils.deuniquify(SeqNames, alseqs);
         return new Object[]
         { alseqs, msaorder };
       }
@@ -292,7 +303,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
    *          boolean
    */
   MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
-          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          WebserviceInfo wsinfo, AlignFrame alFrame,
           AlignmentView alview, String wsname, boolean subgaps,
           boolean presorder)
   {
@@ -317,7 +328,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
    *          Alignment
    */
   MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
-          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          WebserviceInfo wsinfo, AlignFrame alFrame,
           String wsname, String title, AlignmentView _msa, boolean subgaps,
           boolean presorder, Alignment seqset)
   {
@@ -493,16 +504,16 @@ class MsaWSThread extends JWS1Thread implements WSClientI
     }
   }
 
-  private jalview.datamodel.Sequence[] getVamsasAlignment(
+  private Sequence[] getVamsasAlignment(
           vamsas.objects.simple.Alignment valign)
   {
     // TODO: refactor to helper class for vamsas.objects.simple objects
     vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
-    jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
+    Sequence[] msa = new Sequence[seqs.length];
 
     for (int i = 0, j = seqs.length; i < j; i++)
     {
-      msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
+      msa[i] = new Sequence(seqs[i].getId(),
               seqs[i].getSeq());
     }
 
@@ -649,7 +660,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI
             while (j < l)
             {
               if (((AlignmentOrder) alorders.get(i))
-                      .equals(((AlignmentOrder) alorders.get(j))))
+                      .equals((alorders.get(j))))
               {
                 alorders.remove(j);
                 l--;