JAL-3899 Update usages of uniquify and deuniquify.

[jalview.git] / src / jalview / hmmer / HmmerCommand.java

diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
index b311b76..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);
   }
 
   /**
@@ -154,14 +156,14 @@ public abstract class HmmerCommand implements Runnable
   public boolean runCommand(List<String> commands)
           throws IOException
   {
-    List<String> args = Platform.isWindows() ? wrapWithCygwin(commands)
+    List<String> args = Platform.isWindowsAndNotJS() ? wrapWithCygwin(commands)
             : commands;
 
     try
     {
       ProcessBuilder pb = new ProcessBuilder(args);
       pb.redirectErrorStream(true); // merge syserr to sysout
-      if (Platform.isWindows())
+      if (Platform.isWindowsAndNotJS())
       {
         String path = pb.environment().get("Path");
         path = jalview.bin.Cache.getProperty("CYGWIN_PATH") + ";" + path;
@@ -436,7 +438,7 @@ public abstract class HmmerCommand implements Runnable
   protected String getFilePath(File resultFile, boolean isInCygwin)
   {
     String path = resultFile.getAbsolutePath();
-    if (Platform.isWindows() && isInCygwin)
+    if (Platform.isWindowsAndNotJS() && isInCygwin)
     {
       // the first backslash escapes '\' for the regular expression argument
       path = path.replaceAll("\\" + File.separator, "/");