JAL-3899 Update usages of uniquify and deuniquify.

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index c2a6a9c..07a62c9 100644 (file)
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -22,6 +22,7 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.util.MessageManager;
 import jalview.util.ShiftList;
 
@@ -37,7 +38,7 @@ public class SeqCigar extends CigarSimple
 
   private SequenceI refseq = null;
 
-  private Hashtable seqProps;
+  private SequenceInfo seqProps;
 
   /**
    * Reference dataset sequence for the cigar string

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index d66ec33..dd85c74 100644 (file)
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -1,6 +1,7 @@
 package jalview.hmmer;
 
 import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
@@ -24,6 +25,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 import javax.swing.JInternalFrame;
 
@@ -80,7 +82,7 @@ public class HMMAlign extends HmmerCommand
     int job = 0;
     for (SequenceI[] seqs : subAlignments)
     {
-      Hashtable sequencesHash = stashSequences(seqs);
+      Map<String, SequenceInfo> sequencesHash = stashSequences(seqs);
       try
       {
         File modelFile = FileUtils.createTempFile("hmm", ".hmm");

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 0c47c1d..fa9cd92 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -1,5 +1,6 @@
 package jalview.hmmer;
 
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -22,6 +23,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 /**
  * A class that runs the hmmbuild command as a separate process.
@@ -201,7 +203,7 @@ public class HMMBuild extends HmmerCommand
       // at import level ?
 
       SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
-      Hashtable sequencesHash = stashSequences(copyArray);
+      Map<String, SequenceInfo> sequencesHash = stashSequences(copyArray);
 
       exportStockholm(copyArray, alignmentFile, ac);
 

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index 0240352..e241008 100644 (file)
--- a/src/jalview/hmmer/HmmerCommand.java
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -1,6 +1,7 @@
 package jalview.hmmer;
 
 import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -30,6 +31,7 @@ import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Base class for hmmbuild, hmmalign and hmmsearch
@@ -127,7 +129,7 @@ public abstract class HmmerCommand implements Runnable
    * 
    * @param seqs
    */
-  protected Hashtable stashSequences(SequenceI[] seqs)
+  protected Map<String, SequenceInfo> stashSequences(SequenceI[] seqs)
   {
     return SeqsetUtils.uniquify(seqs, true);
   }
@@ -135,12 +137,12 @@ public abstract class HmmerCommand implements Runnable
   /**
    * Restores the sequence data lost by uniquifying
    * 
-   * @param hashtable
+   * @param sequencesHash
    * @param seqs
    */
-  protected void recoverSequences(Hashtable hashtable, SequenceI[] seqs)
+  protected void recoverSequences(Map<String, SequenceInfo> sequencesHash, SequenceI[] seqs)
   {
-    SeqsetUtils.deuniquify(hashtable, seqs);
+    SeqsetUtils.deuniquify(sequencesHash, seqs);
   }
 
   /**

diff --git a/src/jalview/hmmer/Search.java b/src/jalview/hmmer/Search.java
index ceb79e5..6c3a71d 100644 (file)
--- a/src/jalview/hmmer/Search.java
+++ b/src/jalview/hmmer/Search.java
@@ -1,5 +1,6 @@
 package jalview.hmmer;
 
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -15,6 +16,7 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.Scanner;
 
 public abstract class Search extends HmmerCommand
@@ -34,7 +36,7 @@ public abstract class Search extends HmmerCommand
 
   boolean searchAlignment = true;
 
-  Hashtable sequencesHash;
+  Map<String, SequenceInfo> sequencesHash;
 
   public Search(AlignFrame alignFrame, List<ArgumentI> args)
   {

diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java
index 9f84c16..d4047d1 100644 (file)
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -20,6 +20,7 @@
  */
 package jalview.io.packed;
 
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.analysis.TreeModel;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentI;
@@ -76,7 +77,7 @@ public class JalviewDataset
   /**
    * @return the seqDetails
    */
-  public Hashtable getSeqDetails()
+  public Map<String, SequenceInfo> getSeqDetails()
   {
     return seqDetails;
   }
@@ -193,7 +194,7 @@ public class JalviewDataset
   /**
    * original identity of each sequence in results
    */
-  Hashtable seqDetails;
+  Map<String, SequenceInfo> seqDetails;
 
   public boolean relaxedIdMatching = false;
 
@@ -211,7 +212,7 @@ public class JalviewDataset
    * @param parentAlignment
    */
   public JalviewDataset(AlignmentI aldataset,
-          Map<String, FeatureColourI> fc, Hashtable seqDets)
+          Map<String, FeatureColourI> fc, Map<String, SequenceInfo> seqDets)
   {
     // TODO not used - remove?
     this(aldataset, fc, seqDets, null);
@@ -233,7 +234,7 @@ public class JalviewDataset
    *          with.
    */
   public JalviewDataset(AlignmentI aldataset,
-          Map<String, FeatureColourI> fc, Hashtable seqDets,
+          Map<String, FeatureColourI> fc, Map<String, SequenceInfo> seqDets,
           AlignmentI parentAlignment)
   {
     this();

diff --git a/src/jalview/ws/AWsJob.java b/src/jalview/ws/AWsJob.java
index 4a9cb74..ed88ea9 100644 (file)
--- a/src/jalview/ws/AWsJob.java
+++ b/src/jalview/ws/AWsJob.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws;
 
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
@@ -156,7 +157,7 @@ public abstract class AWsJob
 
   protected List<ArgumentI> arguments = null;
 
-  protected Hashtable<String, Map> SeqNames = new Hashtable();
+  protected Hashtable<String, SequenceInfo> SeqNames = new Hashtable();
 
   public AWsJob()
   {

diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index 1c625fa..4af83f1 100644 (file)
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -21,6 +21,7 @@
 package jalview.ws.jws1;
 
 import jalview.analysis.AlignSeq;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SeqCigar;
@@ -34,6 +35,7 @@ import jalview.util.MessageManager;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.Hashtable;
+import java.util.Map;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
@@ -127,8 +129,8 @@ public class JPredClient extends WS1Client
         aln[i] = msf[i].getSeq('-');
       }
 
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
-              true);
+      Map<String, SequenceInfo> SequenceInfo = 
+          jalview.analysis.SeqsetUtils.uniquify(aln, true);
       if (viewonly)
       {
         // Remove hidden regions from sequence objects.
@@ -161,7 +163,7 @@ public class JPredClient extends WS1Client
               + (viewonly ? "visible " : "") + "sequence " + seq.getName()
               + " from " + title;
       String seqname = seq.getName();
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+      SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
               .SeqCharacterHash(seq);
       if (viewonly)
       {
@@ -249,8 +251,8 @@ public class JPredClient extends WS1Client
       aln[i] = new jalview.datamodel.Sequence(msf[i]);
     }
 
-    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
-            true);
+    Map<String, SequenceInfo> SequenceInfo = 
+        jalview.analysis.SeqsetUtils.uniquify(aln, true);
 
     Jpred server = locateWebService();
     if (server == null)
@@ -278,7 +280,7 @@ public class JPredClient extends WS1Client
     String altitle = "JPred prediction for sequence " + seq.getName()
             + " from " + title;
 
-    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+    SequenceInfo SequenceInfo = jalview.analysis.SeqsetUtils
             .SeqCharacterHash(seq);
 
     Jpred server = locateWebService();

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 23d9eb0..b7b8e5f 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -22,6 +22,7 @@ package jalview.ws.jws1;
 
 import jalview.analysis.AlignSeq;
 import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -47,6 +48,7 @@ import jalview.ws.WSClientI;
 
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 import vamsas.objects.simple.JpredResult;
 
@@ -66,7 +68,7 @@ class JPredThread extends JWS1Thread implements WSClientI
 
     vamsas.objects.simple.Msfalignment msa;
 
-    java.util.Hashtable SequenceInfo = null;
+    Object SequenceInfo = null;
 
     int msaIndex = 0; // the position of the original sequence in the array of
 
@@ -156,7 +158,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             {
               sqs[i] = al.getSequenceAt(i);
             }
-            if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
+            if (!SeqsetUtils.deuniquify((Map<String, SequenceInfo>)SequenceInfo, sqs))
             {
               throw (new Exception(MessageManager.getString(
                       "exception.couldnt_recover_sequence_properties_for_alignment")));
@@ -211,7 +213,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         }
 
         if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-                al.getSequenceAt(FirstSeq), SequenceInfo))
+                al.getSequenceAt(FirstSeq), (SequenceInfo)SequenceInfo))
         {
           throw (new Exception(MessageManager.getString(
                   "exception.couldnt_recover_sequence_props_for_jnet_query")));
@@ -332,7 +334,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
     }
 
-    public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
+    public JPredJob(Object SequenceInfo, SequenceI seq, int[] delMap)
     {
       super();
       this.predMap = delMap;
@@ -351,7 +353,7 @@ class JPredThread extends JWS1Thread implements WSClientI
       }
     }
 
-    public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
+    public JPredJob(Object SequenceInfo, SequenceI[] msf, int[] delMap)
     {
       this(SequenceInfo, msf[0], delMap);
       if (sequence != null)
@@ -387,7 +389,7 @@ class JPredThread extends JWS1Thread implements WSClientI
   }
 
   JPredThread(WebserviceInfo wsinfo, String altitle,
-          ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
+          ext.vamsas.Jpred server, String wsurl, SequenceInfo SequenceInfo,
           SequenceI seq, int[] delMap, AlignmentView alview,
           AlignFrame alframe)
   {
@@ -406,9 +408,9 @@ class JPredThread extends JWS1Thread implements WSClientI
   }
 
   JPredThread(WebserviceInfo wsinfo, String altitle,
-          ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
-          int[] delMap, AlignmentView alview, AlignFrame alframe,
-          String wsurl)
+          ext.vamsas.Jpred server, Map<String, SequenceInfo> SequenceInfo,
+          SequenceI[] msf, int[] delMap, AlignmentView alview, 
+          AlignFrame alframe, String wsurl)
   {
     this(wsinfo, altitle, server, wsurl, alview, alframe);
     JPredJob job = new JPredJob(SequenceInfo, msf, delMap);

diff --git a/src/jalview/ws/jws2/JPredThread.java b/src/jalview/ws/jws2/JPredThread.java
index 67f44fa..f4ad8b2 100644 (file)
--- a/src/jalview/ws/jws2/JPredThread.java
+++ b/src/jalview/ws/jws2/JPredThread.java
@@ -4,8 +4,10 @@ import static java.lang.String.format;
 
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 import jalview.analysis.SeqsetUtils;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.bin.Cache;
 import jalview.commands.RemoveGapsCommand;
 import jalview.datamodel.Alignment;
@@ -34,13 +36,13 @@ public class JPredThread extends AWSThread implements WSClientI
 
   private static class JPredJob extends WsJob
   {
-    private final Hashtable<?, ?> sequenceInfo;
+    private final Object sequenceInfo;
     private final List<SequenceI> msf;
     private final int[] delMap;
     private AlignmentI alignment = null;
     private HiddenColumns hiddenCols = null;
 
-    private JPredJob(Hashtable<?, ?> sequenceInfo, SequenceI[] msf, int[] delMap)
+    private JPredJob(Object sequenceInfo, SequenceI[] msf, int[] delMap)
     {
       this.sequenceInfo = sequenceInfo;
       this.msf = List.of(msf);
@@ -68,12 +70,12 @@ public class JPredThread extends AWSThread implements WSClientI
 
   private JPredServiceI server;
   private String title;
-  private Hashtable<?, ?> sequenceInfo;
+  private Object sequenceInfo;
   private SequenceI[] msf;
   private int[] delMap;
 
   public JPredThread(WebserviceInfo wsInfo, String title,
-      JPredServiceI server, Hashtable<?, ?> sequenceInfo,
+      JPredServiceI server, Object sequenceInfo,
       SequenceI[] msf, int[] delMap, AlignmentView view, AlignFrame frame,
       String wsURL)
   {
@@ -261,7 +263,7 @@ public class JPredThread extends AWSThread implements WSClientI
         {
           seqs[i] = alignment.getSequenceAt(i);
         }
-        if (!SeqsetUtils.deuniquify(sequenceInfo, seqs))
+        if (!SeqsetUtils.deuniquify((Map<String, SequenceInfo>)sequenceInfo, seqs))
         {
           throw (new Exception(MessageManager.getString(
                   "exception.couldnt_recover_sequence_properties_for_alignment")));
@@ -293,7 +295,7 @@ public class JPredThread extends AWSThread implements WSClientI
         profileSeq.setSequence(seqs[msaIndex].getSequenceAsString());
       }
       if (!SeqsetUtils.SeqCharacterUnhash(
-              alignment.getSequenceAt(firstSeq), sequenceInfo))
+              alignment.getSequenceAt(firstSeq), (SequenceInfo)sequenceInfo))
       {
         throw new Exception(MessageManager.getString(
                 "exception.couldnt_recover_sequence_props_for_jnet_query"));

diff --git a/src/jalview/ws/rest/RestJob.java b/src/jalview/ws/rest/RestJob.java
index 824af90..67f11c2 100644 (file)
--- a/src/jalview/ws/rest/RestJob.java
+++ b/src/jalview/ws/rest/RestJob.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.rest;
 
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
@@ -52,7 +53,7 @@ public class RestJob extends AWsJob
 
   boolean gotresult;
 
-  Hashtable squniq;
+  Map<String, SequenceInfo> squniq;
 
   /**
    * dataset associated with this input data.