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JAL-3899 Update usages of uniquify and deuniquify.
[jalview.git]
/
src
/
jalview
/
hmmer
/
HMMBuild.java
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;
package jalview.hmmer;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
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.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
/**
* A class that runs the hmmbuild command as a separate process.
/**
* 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()]);
// 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);
exportStockholm(copyArray, alignmentFile, ac);