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

[jalview.git] / src / jalview / ws / jws2 / MsaWSThread.java

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index d2c1b38..0ba4b11 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -21,6 +21,8 @@
 package jalview.ws.jws2;
 
 import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -33,6 +35,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.SplitFrame;
 import jalview.gui.WebserviceInfo;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
 import jalview.ws.JobStateSummary;
@@ -139,19 +142,18 @@ class MsaWSThread extends AWS2Thread 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)
         {
           // make new input sequence with or without gaps
           seq = new compbio.data.sequence.FastaSequence(newname,
                   (submitGaps) ? seqs[i].getSequenceAsString()
                           : AlignSeq.extractGaps(
-                                  jalview.util.Comparison.GapChars,
+                                  Comparison.GapChars,
                                   seqs[i].getSequenceAsString()));
           this.seqs.add(seq);
         }
@@ -161,7 +163,7 @@ class MsaWSThread extends AWS2Thread 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[]
@@ -293,9 +295,9 @@ class MsaWSThread extends AWS2Thread 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 };
       }
@@ -452,7 +454,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
    *          boolean
    */
   private MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
-          jalview.gui.AlignFrame alFrame, AlignmentView alview,
+          AlignFrame alFrame, AlignmentView alview,
           String wsname, boolean subgaps, boolean presorder)
   {
     super(alFrame, wsinfo, alview, wsname, wsUrl);
@@ -477,7 +479,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI
    */
   MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
           String wsUrl, WebserviceInfo wsinfo,
-          jalview.gui.AlignFrame alFrame, String wsname, String title,
+ AlignFrame alFrame,
+          String wsname, String title,
           AlignmentView _msa, boolean subgaps, boolean presorder,
           Alignment seqset)
   {