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JAL-3899 Update usages of uniquify and deuniquify.
[jalview.git]
/
src
/
jalview
/
hmmer
/
HMMAlign.java
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;
package jalview.hmmer;
import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
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.ArrayList;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map;
import javax.swing.JInternalFrame;
import javax.swing.JInternalFrame;
@@
-80,7
+82,7
@@
public class HMMAlign extends HmmerCommand
int job = 0;
for (SequenceI[] seqs : subAlignments)
{
int job = 0;
for (SequenceI[] seqs : subAlignments)
{
- Hashtable sequencesHash = stashSequences(seqs);
+ Map<String, SequenceInfo> sequencesHash = stashSequences(seqs);
try
{
File modelFile = FileUtils.createTempFile("hmm", ".hmm");
try
{
File modelFile = FileUtils.createTempFile("hmm", ".hmm");