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

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

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 62566cf..f965572 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -21,7 +21,9 @@
 package jalview.ws.jws1;
 
 import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils;
 import jalview.bin.Cache;
+import jalview.commands.RemoveGapsCommand;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -32,6 +34,10 @@ import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.WebserviceInfo;
 import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.PileUpfile;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
@@ -42,6 +48,7 @@ import java.util.Hashtable;
 import java.util.List;
 
 import vamsas.objects.simple.JpredResult;
+import vamsas.objects.simple.Msfalignment;
 
 class JPredThread extends JWS1Thread implements WSClientI
 {
@@ -110,23 +117,22 @@ class JPredThread extends JWS1Thread implements WSClientI
 
       JpredResult result = (JpredResult) this.result;
 
-      jalview.bin.Cache.log.debug("Parsing output from JNet job.");
+      Cache.log.debug("Parsing output from JNet job.");
       // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
       // "File");
-      jalview.io.JPredFile prediction = new jalview.io.JPredFile(
-              result.getPredfile(), "Paste");
+      JPredFile prediction = new JPredFile(result.getPredfile(), "Paste");
       SequenceI[] preds = prediction.getSeqsAsArray();
-      jalview.bin.Cache.log.debug("Got prediction profile.");
+      Cache.log.debug("Got prediction profile.");
 
       if ((this.msa != null) && (result.getAligfile() != null))
       {
-        jalview.bin.Cache.log.debug("Getting associated alignment.");
+        Cache.log.debug("Getting associated alignment.");
         // we ignore the returned alignment if we only predicted on a single
         // sequence
-        String format = new jalview.io.IdentifyFile().Identify(
-                result.getAligfile(), "Paste");
+        String format = new IdentifyFile().Identify(result.getAligfile(),
+                "Paste");
 
-        if (jalview.io.FormatAdapter.isValidFormat(format))
+        if (FormatAdapter.isValidFormat(format))
         {
           SequenceI sqs[];
           if (predMap != null)
@@ -147,8 +153,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             {
               sqs[i] = al.getSequenceAt(i);
             }
-            if (!jalview.analysis.SeqsetUtils.deuniquify(
-                    SequenceInfo, sqs))
+            if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
             {
               throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_properties_for_alignment")));
             }
@@ -163,8 +168,8 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             al.setDataset(null);
           }
-          jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
-                  FirstSeq, false, predMap);
+          JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+                  false, predMap);
 
         }
         else
@@ -189,7 +194,8 @@ class JPredThread extends JWS1Thread implements WSClientI
           // ///
           // Uses RemoveGapsCommand
           // ///
-          new jalview.commands.RemoveGapsCommand(MessageManager.getString("label.remove_gaps"),
+          new RemoveGapsCommand(
+                  MessageManager.getString("label.remove_gaps"),
                   new SequenceI[]
                   { sqs[msaIndex] }, currentView);
 
@@ -197,7 +203,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
         }
 
-        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+        if (!SeqsetUtils.SeqCharacterUnhash(
                 al.getSequenceAt(FirstSeq), SequenceInfo))
         {
           throw (new Exception(MessageManager.getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
@@ -213,7 +219,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             al.setDataset(null);
           }
-          jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
+          JnetAnnotationMaker.add_annotation(prediction, al,
                   FirstSeq, true, predMap);
           SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
           alignToProfileSeq(al, profileseq);
@@ -348,8 +354,8 @@ class JPredThread extends JWS1Thread implements WSClientI
       {
         if (msf.length > 1)
         {
-          msa = new vamsas.objects.simple.Msfalignment();
-          jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
+          msa = new Msfalignment();
+          PileUpfile pileup = new PileUpfile();
           msa.setMsf(pileup.print(msf));
         }
       }
@@ -471,7 +477,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                 .println("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
                         + e.getMessage() + "\n");
 
-        jalview.bin.Cache.log.warn("Server Exception", e);
+        Cache.log.warn("Server Exception", e);
       }
       else
       {
@@ -479,7 +485,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         // JBPNote - this could be a popup informing the user of the problem.
         wsInfo.appendProgressText(j.getJobnum(), MessageManager.formatMessage("info.failed_to_submit_prediction", new String[]{e.getMessage(),wsInfo.getProgressText()}));
 
-        jalview.bin.Cache.log.debug(
+        Cache.log.debug(
                 "Failed Submission of job " + j.getJobnum(), e);
 
       }
@@ -557,9 +563,9 @@ class JPredThread extends JWS1Thread implements WSClientI
           msa = (j.msa != null) ? true : msa;
           try
           {
-            jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+            Cache.log.debug("Parsing output of job " + jn);
             jobres = j.getResultSet();
-            jalview.bin.Cache.log.debug("Finished parsing output.");
+            Cache.log.debug("Finished parsing output.");
             if (jobs.length == 1)
             {
               res = jobres;
@@ -571,7 +577,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             }
           } catch (Exception e)
           {
-            jalview.bin.Cache.log.error(
+            Cache.log.error(
                     "JNet Client: JPred Annotation Parse Error", e);
             wsInfo.setStatus(j.getJobnum(),
                     WebserviceInfo.STATE_STOPPED_ERROR);