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

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

diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java
index 5d44ddd..f65bf03 100644 (file)
--- a/src/jalview/ws/jws1/SeqSearchWSThread.java
+++ b/src/jalview/ws/jws1/SeqSearchWSThread.java
@@ -20,17 +20,29 @@
  */
 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.SeqsetUtils;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
 import jalview.io.NewickFile;
+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;
 import vamsas.objects.simple.SeqSearchResult;
 
@@ -103,18 +115,17 @@ class SeqSearchWSThread 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
@@ -123,7 +134,7 @@ class SeqSearchWSThread 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[]
@@ -186,7 +197,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
          */
         // construct annotated alignment as it would be done by the jalview
         // applet
-        jalview.datamodel.Alignment al = new Alignment(alseqs);
+        Alignment al = new Alignment(alseqs);
         // al.setDataset(dataset);
         // make dataset
         String inFile = null;
@@ -195,8 +206,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           inFile = ((SeqSearchResult) result).getAnnotation();
           if (inFile != null && inFile.length() > 0)
           {
-            new jalview.io.AnnotationFile().readAnnotationFile(al, inFile,
-                    jalview.io.AppletFormatAdapter.PASTE);
+            new AnnotationFile().readAnnotationFile(al, inFile,
+                    AppletFormatAdapter.PASTE);
           }
         } catch (Exception e)
         {
@@ -211,8 +222,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           inFile = ((SeqSearchResult) result).getFeatures();
           if (inFile != null && inFile.length() > 0)
           {
-            jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(
-                    inFile, jalview.io.AppletFormatAdapter.PASTE);
+            FeaturesFile ff = new FeaturesFile(inFile,
+                    AppletFormatAdapter.PASTE);
             ff.parse(al, featureColours, false);
           }
         } catch (Exception e)
@@ -222,14 +233,13 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
           System.err.println(">>>EOF" + inFile + "\n<<<EOF\n");
           e.printStackTrace(System.err);
         }
-        jalview.io.NewickFile nf = null;
+        NewickFile nf = null;
         try
         {
           inFile = ((SeqSearchResult) result).getNewickTree();
           if (inFile != null && inFile.length() > 0)
           {
-            nf = new jalview.io.NewickFile(inFile,
-                    jalview.io.AppletFormatAdapter.PASTE);
+            nf = new NewickFile(inFile, AppletFormatAdapter.PASTE);
             if (!nf.isValid())
             {
               nf.close();
@@ -308,7 +318,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
    *          boolean
    */
   SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
-          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          WebserviceInfo wsinfo, AlignFrame alFrame,
           AlignmentView alview, String wsname, String db)
   {
     super(alFrame, wsinfo, alview, wsname, wsUrl);
@@ -331,7 +341,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
    *          Alignment
    */
   SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,
-          WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+          WebserviceInfo wsinfo, AlignFrame alFrame,
           String wsname, String title, AlignmentView _msa, String db,
           Alignment seqset)
   {
@@ -509,15 +519,15 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI
     }
   }
 
-  private jalview.datamodel.Sequence[] getVamsasAlignment(
+  private Sequence[] getVamsasAlignment(
           vamsas.objects.simple.Alignment valign)
   {
     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());
     }