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Merge branch 'features/mchmmer' of https://source.jalview.org/git/jalview.git into...
[jalview.git]
/
src
/
jalview
/
hmmer
/
HMMSearch.java
diff --git
a/src/jalview/hmmer/HMMSearch.java
b/src/jalview/hmmer/HMMSearch.java
index
b4e7427
..
7413d14
100644
(file)
--- a/
src/jalview/hmmer/HMMSearch.java
+++ b/
src/jalview/hmmer/HMMSearch.java
@@
-1,5
+1,6
@@
package jalview.hmmer;
package jalview.hmmer;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@
-15,12
+16,14
@@
import jalview.util.FileUtils;
import jalview.util.MessageManager;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.simple.BooleanOption;
import jalview.util.MessageManager;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.Option;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import java.util.Scanner;
import java.util.List;
import java.util.Scanner;
@@
-28,6
+31,8
@@
import javax.swing.JOptionPane;
public class HMMSearch extends HmmerCommand
{
public class HMMSearch extends HmmerCommand
{
+ private static final String PARAMNAME_NO_OF_RESULTS = MessageManager.getString("label.number_of_results");
+
static final String HMMSEARCH = "hmmsearch";
boolean realign = false;
static final String HMMSEARCH = "hmmsearch";
boolean realign = false;
@@
-57,15
+62,15
@@
public class HMMSearch extends HmmerCommand
@Override
public void run()
{
@Override
public void run()
{
- HiddenMarkovModel hmm = af.getSelectedHMM();
+ HiddenMarkovModel hmm = getHmmProfile();
if (hmm == null)
{
if (hmm == null)
{
- JOptionPane.showMessageDialog(af,
- MessageManager.getString("warn.no_selected_hmm"));
+ // shouldn't happen if we got this far
+ Cache.log.error("Error: no hmm for hmmsearch");
return;
}
return;
}
- SequenceI hmmSeq = af.getSelectedHMMSequence();
+ SequenceI hmmSeq = hmm.getConsensusSequence();// af.getSelectedHMMSequence();
long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
msgId);
long msgId = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
msgId);
@@
-83,8
+88,8
@@
public class HMMSearch extends HmmerCommand
boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
if (!ran)
{
boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
if (!ran)
{
- JvOptionPane.showInternalMessageDialog(af,
- MessageManager.getString("warn.hmmsearch_failed"));
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "hmmsearch"));
return;
}
return;
}
@@
-197,15
+202,16
@@
public class HMMSearch extends HmmerCommand
{
/*
* no external database specified for search, so
{
/*
* no external database specified for search, so
- * export current alignment as 'database' to search
+ * export current alignment as 'database' to search,
+ * excluding any HMM consensus sequences it contains
*/
databaseFile = FileUtils.createTempFile("database", ".sto");
AlignmentI al = af.getViewport().getAlignment();
AlignmentI copy = new Alignment(al);
*/
databaseFile = FileUtils.createTempFile("database", ".sto");
AlignmentI al = af.getViewport().getAlignment();
AlignmentI copy = new Alignment(al);
- SequenceI hmms = copy.getHmmConsensus();
- if (hmms != null)
+ List<SequenceI> hmms = copy.getHmmSequences();
+ for (SequenceI hmmSeq : hmms)
{
{
- copy.deleteSequence(hmms);
+ copy.deleteSequence(hmmSeq);
}
exportStockholm(copy.getSequencesArray(), databaseFile, null);
// StockholmFile stoFile = new StockholmFile(copy);
}
exportStockholm(copy.getSequencesArray(), databaseFile, null);
// StockholmFile stoFile = new StockholmFile(copy);
@@
-253,10
+259,17
@@
public class HMMSearch extends HmmerCommand
hmmAndSeqs[0] = hmmSeq;
System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
hmmAndSeqs[0] = hmmSeq;
System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
- AlignmentI alignment = new Alignment(hmmAndSeqs);
- AlignFrame frame = new AlignFrame(alignment, 1, 1);
- frame.setSelectedHMMSequence(hmmSeq);
+ /*
+ * and align the search results to the HMM profile
+ */
+ AlignmentI al = new Alignment(hmmAndSeqs);
+ AlignFrame frame = new AlignFrame(al, 1, 1);
List<ArgumentI> alignArgs = new ArrayList<>();
List<ArgumentI> alignArgs = new ArrayList<>();
+ String defSeq = hmmSeq.getName();
+ List<String> options = Collections.singletonList(defSeq);
+ Option option = new Option(MessageManager.getString("label.use_hmm"),
+ "", true, defSeq, defSeq, options, null);
+ alignArgs.add(option);
if (trim)
{
alignArgs.add(new BooleanOption(
if (trim)
{
alignArgs.add(new BooleanOption(