X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fhmmer%2FHMMBuild.java;h=0c47c1dd8011fc05ef682d1f39fb113439eb94ac;hb=80238b0ded8d29f9f50399c51bc550bc1df9c426;hp=6de7029600d2a3d5a9d273ed4de94d97e7fdf86c;hpb=45ae91e9bc0b3a9046d2f587d7810f5d27c04890;p=jalview.git
diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 6de7029..0c47c1d 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -5,6 +5,7 @@ import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ResidueCount;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
@@ -105,14 +106,17 @@ public class HMMBuild extends HmmerCommand
{
foundArg = true;
String value = arg.getValue();
+
if (MessageManager.getString("label.alignment").equals(value))
{
- runBuildFor.add(alignment);
+ runBuildFor.add(viewport.getAlignmentView(false)
+ .getVisibleAlignment('-'));
}
else if (MessageManager.getString("label.groups_and_alignment")
.equals(value))
{
- runBuildFor.add(alignment);
+ runBuildFor.add(viewport.getAlignmentView(false)
+ .getVisibleAlignment('-'));
runBuildFor.addAll(viewport.getAlignment().getGroups());
}
else if (MessageManager.getString("label.groups").equals(value))
@@ -183,12 +187,18 @@ public class HMMBuild extends HmmerCommand
else
{
SequenceI[] sel = ((SequenceGroup) ac)
- .getSelectionAsNewSequences((AlignmentI) ac.getContext());
+ .getSelectionAsNewSequences((AlignmentI) ac.getContext());
for (SequenceI seq : sel)
{
- copy.add(seq);
+ if (seq != null)
+ {
+ copy.add(seq);
+ }
}
}
+ // TODO rather than copy alignment data we should anonymize in situ -
+ // export/File import could use anonymization hash to reinstate references
+ // at import level ?
SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
Hashtable sequencesHash = stashSequences(copyArray);
@@ -222,33 +232,6 @@ public class HMMBuild extends HmmerCommand
}
/**
- * A helper method that deletes any HMM consensus sequence from the given
- * collection, and from the parent alignment if ac
is a subgroup
- *
- * @param ac
- */
- void deleteHmmSequences(AnnotatedCollectionI ac)
- {
- List hmmSeqs = ac.getHmmSequences();
- for (SequenceI hmmSeq : hmmSeqs)
- {
- if (ac instanceof SequenceGroup)
- {
- ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
- AnnotatedCollectionI context = ac.getContext();
- if (context != null && context instanceof AlignmentI)
- {
- ((AlignmentI) context).deleteSequence(hmmSeq);
- }
- }
- else
- {
- ((AlignmentI) ac).deleteSequence(hmmSeq);
- }
- }
- }
-
- /**
* Constructs and executes the hmmbuild command as a separate process
*
* @param sequencesFile
@@ -326,8 +309,8 @@ public class HMMBuild extends HmmerCommand
args.add(ARG_DNA);
}
- args.add(getFilePath(hmmFile));
- args.add(getFilePath(sequencesFile));
+ args.add(getFilePath(hmmFile, true));
+ args.add(getFilePath(sequencesFile, true));
return runCommand(args);
}
@@ -355,6 +338,11 @@ public class HMMBuild extends HmmerCommand
new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
SequenceI hmmSeq = file.getHMM().getConsensusSequence();
+
+
+ ResidueCount counts = new ResidueCount(alignment.getSequences());
+ hmmSeq.getHMM().setBackgroundFrequencies(counts);
+
if (hmmSeq == null)
{
// hmmbuild failure not detected earlier