status.colouring_chimera = Colouring Chimera
status.running_hmmbuild = Building Hidden Markov Model
status.running_hmmalign = Creating alignment with Hidden Markov Model
-status.running_hmmsearch = Searching for matching sequences
+status.running_search = Searching for matching sequences
label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
label.font_too_small = Font size is too small
label.error_loading_file_params = Error loading file {0}
label.free_text_search = Free Text Search
label.hmmalign = hmmalign
label.use_hmm = HMM profile to use
+label.use_sequence = Sequence to use
label.hmmbuild = hmmbuild
label.hmmsearch = hmmsearch
+label.jackhmmer = jackhmmer
label.installation = Installation
label.hmmer_location = HMMER Binaries Installation Location
label.cygwin_location = Cygwin Binaries Installation Location (Windows)
label.freq_uniprot = Use Uniprot background frequencies
label.hmmalign_options = hmmalign options
label.hmmsearch_options = hmmsearch options
+label.jackhmmer_options = jackhmmer options
label.executable_not_found = The ''{0}'' executable file was not found
warn.command_failed = {0} failed
label.invalid_folder = Invalid Folder
label.selected_group = Selected group
label.use_info_for_height = Use Information Content as Letter Height
action.search = Search
-||||||| merged common ancestors
-=======
label.backupfiles_confirm_delete = Confirm delete
label.backupfiles_confirm_delete_old_files = Delete the following older backup files? (see the Backups tab in Preferences for more options)
label.backupfiles_confirm_save_file = Confirm save file
{
return backgroundFrequencies;
}
+
}
import jalview.hmmer.HMMERPreset;
import jalview.hmmer.HMMSearch;
import jalview.hmmer.HmmerCommand;
+import jalview.hmmer.JackHMMER;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BackupFiles;
new Thread(new HMMSearch(this, args)).start();
alignPanel.repaint();
}
+
+ @Override
+ public void jackhmmer_actionPerformed(boolean withDefaults)
+ {
+
+ /*
+ * get default parameters, and (if requested) show
+ * dialog to allow modification
+ */
+
+ ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
+ List<ArgumentI> args = store.getServiceParameters();
+
+ if (!withDefaults)
+ {
+ WsParamSetI set = new HMMERPreset();
+ WsJobParameters params = new WsJobParameters(store, set, args);
+ if (params.showRunDialog())
+ {
+ args = params.getJobParams();
+ }
+ else
+ {
+ return; // user cancelled
+ }
+ }
+ new Thread(new JackHMMER(this, args)).start();
+ alignPanel.repaint();
+
+ }
/**
* Checks if the alignment has at least one hidden Markov model, if not shows
{
static final String HMMALIGN = "hmmalign";
- static final String ARG_TRIM = "--trim";
-
private final AlignmentI dataset;
/**
private static final String HMMSEARCH = "hmmsearch";
+ private static final String JACKHMMER = "jackhmmer";
+
private String name;
private List<WsParamSetI> presets = new ArrayList<>();
return new HMMERParamStore(HMMSEARCH, viewport);
}
+ public static HMMERParamStore forJackhmmer(AlignmentViewport viewport)
+ {
+ return new HMMERParamStore(JACKHMMER, viewport);
+ }
+
@Override
public List<WsParamSetI> getPresets()
{
case HMMBUILD:
getHMMBuildParams(args);
break;
+ case JACKHMMER:
+ getJackhmmerParams(args);
default:
}
}
/**
+ * Answers default parameters for jackhmmer, taking into account any configured
+ * as user preferences
+ *
+ * @param args
+ */
+ private void getJackhmmerParams(List<ArgumentI> args)
+ {
+
+ /*
+ * 'Parameters'
+ */
+ addChoiceOfSequence(args);
+
+ // addChoiceOfDatabase(args);
+
+ String thisAlignment = MessageManager
+ .getString(JackHMMER.THIS_ALIGNMENT_KEY);
+ String database = MessageManager.getString("label.database");
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString("action.search"), null,
+ Arrays.asList(thisAlignment, database), thisAlignment));
+ args.add(new FileParameter(database, "", false, "", ""));
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString(JackHMMER.REPORTING_CUTOFF_KEY), null,
+ Arrays.asList(JackHMMER.CUTOFF_NONE, JackHMMER.CUTOFF_EVALUE,
+ JackHMMER.CUTOFF_SCORE),
+ JackHMMER.CUTOFF_EVALUE));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(JackHMMER.SEQ_EVALUE_KEY),
+ MessageManager.getString("label.seq_e_value_desc"), false, 1D,
+ 1E-38, 10D));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(JackHMMER.DOM_EVALUE_KEY),
+ MessageManager.getString("label.dom_e_value_desc"), false, 1D,
+ 1E-38, 10D));
+ args.add(new DoubleParameter(
+ MessageManager.getString(JackHMMER.SEQ_SCORE_KEY),
+ MessageManager.getString("label.seq_score_desc"), false, 0d, 0d,
+ 1000d));
+ args.add(new DoubleParameter(
+ MessageManager.getString(JackHMMER.DOM_SCORE_KEY),
+ MessageManager.getString("label.dom_score_desc"), false, 0d, 0d,
+ 1000d));
+ }
+
+ /**
* Constructs a choice parameter for database to search; always includes 'this
* alignment', and also includes any databases held under user preferences key
* "HMMSEARCH_DBS" as a comma-delimited list
}
/**
+ * Adds an argument representing the choice of sequence against which to perform
+ * jackhmmer
+ *
+ * @param args
+ */
+ protected void addChoiceOfSequence(List<ArgumentI> args)
+ {
+ List<SequenceI> sequences = viewport.getAlignment().getSequences();
+
+ List<String> options = new ArrayList<>();
+
+ for (SequenceI seq : sequences)
+ {
+ options.add(seq.getName());
+ }
+
+ String defseq = options.get(0);
+ ArgumentI arg = new StringParameter(
+ MessageManager.getString("label.use_sequence"), null, true,
+ defseq,
+ defseq, options, null);
+ args.add(arg);
+ }
+
+ /**
* Answers default parameters for hmmbuild, taking into account any configured
* as user preferences
*
{
static final String HMMSEARCH = "hmmsearch";
- /*
- * constants for i18n lookup of passed parameter names
- */
- static final String DATABASE_KEY = "label.database";
-
- static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
-
- static final String USE_ACCESSIONS_KEY = "label.use_accessions";
-
- static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
-
- static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
-
- static final String TRIM_TERMINI_KEY = "label.trim_termini";
-
- static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
-
- static final String CUTOFF_NONE = "None";
-
- static final String CUTOFF_SCORE = "Score";
-
- static final String CUTOFF_EVALUE = "E-Value";
-
- static final String SEQ_EVALUE_KEY = "label.seq_evalue";
-
- static final String DOM_EVALUE_KEY = "label.dom_evalue";
-
- static final String SEQ_SCORE_KEY = "label.seq_score";
-
- static final String DOM_SCORE_KEY = "label.dom_score";
-
boolean realign = false;
boolean trim = false;
SequenceI hmmSeq = hmm.getConsensusSequence();
long msgId = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+ af.setProgressBar(MessageManager.getString("status.running_search"),
msgId);
try
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.gui.Preferences;
+import jalview.io.FastaFile;
import jalview.io.HMMFile;
import jalview.io.StockholmFile;
import jalview.util.FileUtils;
import java.io.BufferedReader;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintWriter;
protected final List<ArgumentI> params;
+ /*
+ * constants for i18n lookup of passed parameter names
+ */
+ static final String DATABASE_KEY = "label.database";
+
+ static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
+
+ static final String USE_ACCESSIONS_KEY = "label.use_accessions";
+
+ static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
+
+ static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
+
+ static final String TRIM_TERMINI_KEY = "label.trim_termini";
+
+ static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
+
+ static final String CUTOFF_NONE = "None";
+
+ static final String CUTOFF_SCORE = "Score";
+
+ static final String CUTOFF_EVALUE = "E-Value";
+
+ static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+
+ static final String DOM_EVALUE_KEY = "label.dom_evalue";
+
+ static final String SEQ_SCORE_KEY = "label.seq_score";
+
+ static final String DOM_SCORE_KEY = "label.dom_score";
+
+ static final String ARG_TRIM = "--trim";
+
/**
* Constructor
*
writer.close();
}
+ public void exportFasta(SequenceI[] seqs, File toFile)
+ {
+ FastaFile file = new FastaFile();
+ String output = file.print(seqs, false);
+ PrintWriter writer;
+ try
+ {
+ writer = new PrintWriter(toFile);
+ writer.println(output);
+ writer.close();
+ } catch (FileNotFoundException e)
+ {
+ e.printStackTrace();
+ }
+
+ }
+
/**
* Answers the full path to the given hmmer executable, or null if file cannot
* be found or is not executable
}
}
+ // TODO is needed?
+ /**
+ * Exports a sequence to the specified file
+ *
+ * @param hmm
+ * @param hmmFile
+ * @throws IOException
+ */
+ public void exportSequence(SequenceI seq, File seqFile) throws IOException
+ {
+ if (seq != null)
+ {
+ FastaFile file = new FastaFile();
+ PrintWriter writer = new PrintWriter(seqFile);
+ writer.print(file.print(new SequenceI[] { seq }, false));
+ writer.close();
+ }
+ }
+
/**
* Answers the HMM profile for the profile sequence the user selected (default
* is just the first HMM sequence in the alignment)
}
/**
+ * Answers the HMM profile for the profile sequence the user selected (default
+ * is just the first HMM sequence in the alignment)
+ *
+ * @return
+ */
+ protected SequenceI getSequence()
+ {
+ String alignToParamName = MessageManager
+ .getString("label.use_sequence");
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+ if (name.equals(alignToParamName))
+ {
+ String seqName = arg.getValue();
+ SequenceI seq = alignment.findName(seqName);
+ return seq;
+ }
+ }
+ return null;
+ }
+
+ /**
* Answers an absolute path to the given file, in a format suitable for
* processing by a hmmer command. On a Windows platform, the native Windows file
* path is converted to Cygwin format, by replacing '\'with '/' and drive letter
--- /dev/null
+package jalview.hmmer;
+
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StockholmFile;
+import jalview.util.FileUtils;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+import javax.swing.JOptionPane;
+
+public class JackHMMER extends HmmerCommand
+{
+ static final String JACKHMMER = "jackhmmer";
+
+ boolean realign = false;
+
+ boolean trim = false;
+
+ int seqsToReturn = Integer.MAX_VALUE;
+
+ SequenceI[] seqs;
+
+ private String databaseName;
+
+ /**
+ * Constructor for the JackhmmerThread
+ *
+ * @param af
+ */
+ public JackHMMER(AlignFrame af, List<ArgumentI> args)
+ {
+ super(af, args);
+ }
+
+ /**
+ * Runs the JackhmmerThread: the data on the alignment or group is exported,
+ * then the command is executed in the command line and then the data is
+ * imported and displayed in a new frame. Call this method directly to execute
+ * synchronously, or via start() in a new Thread for asynchronously.
+ */
+ @Override
+ public void run()
+ {
+ SequenceI seq = getSequence();
+ if (seq == null)
+ {
+ // shouldn't happen if we got this far
+ Cache.log.error("Error: no sequence for jackhmmer");
+ return;
+ }
+
+ long msgId = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.running_search"),
+ msgId);
+
+ try
+ {
+ File seqFile = FileUtils.createTempFile("seq", ".fa");
+ File hitsAlignmentFile = FileUtils.createTempFile("hitAlignment",
+ ".sto");
+ File searchOutputFile = FileUtils.createTempFile("searchOutput",
+ ".txt");
+
+ exportSequence(seq, seqFile.getAbsoluteFile());
+
+ boolean ran = runCommand(searchOutputFile, hitsAlignmentFile,
+ seqFile);
+ if (!ran)
+ {
+ JvOptionPane.showInternalMessageDialog(af, MessageManager
+ .formatMessage("warn.command_failed", "jackhmmer"));
+ return;
+ }
+
+ importData(hitsAlignmentFile, seqFile, searchOutputFile);
+ // TODO make realignment of search results a step at this level
+ // and make it conditional on this.realign
+ } catch (IOException | InterruptedException e)
+ {
+ e.printStackTrace();
+ } finally
+ {
+ af.setProgressBar("", msgId);
+ }
+ }
+
+ /**
+ * Executes an jackhmmer search with the given sequence as input. The database
+ * to be searched is a local file as specified by the 'Database' parameter, or
+ * the current alignment (written to file) if none is specified.
+ *
+ * @param searchOutputFile
+ * @param hitsAlignmentFile
+ * @param seqFile
+ *
+ * @return
+ * @throws IOException
+ */
+ private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,
+ File seqFile) throws IOException
+ {
+ String command = getCommandPath(JACKHMMER);
+ if (command == null)
+ {
+ return false;
+ }
+
+ List<String> args = new ArrayList<>();
+ args.add(command);
+ buildArguments(args, searchOutputFile, hitsAlignmentFile, seqFile);
+
+ return runCommand(args);
+ }
+
+ /**
+ * Appends command line arguments to the given list, to specify input and output
+ * files for the search, and any additional options that may have been passed
+ * from the parameters dialog
+ *
+ * @param args
+ * @param searchOutputFile
+ * @param hitsAlignmentFile
+ * @param seqFile
+ * @throws IOException
+ */
+ protected void buildArguments(List<String> args, File searchOutputFile,
+ File hitsAlignmentFile, File seqFile) throws IOException
+ {
+ args.add("-o");
+ args.add(getFilePath(searchOutputFile, true));
+ args.add("-A");
+ args.add(getFilePath(hitsAlignmentFile, true));
+
+ boolean dbFound = false;
+ String dbPath = "";
+ File databaseFile = null;
+
+ boolean useEvalueCutoff = false;
+ boolean useScoreCutoff = false;
+ String seqEvalueCutoff = null;
+ String domEvalueCutoff = null;
+ String seqScoreCutoff = null;
+ String domScoreCutoff = null;
+ databaseName = "Alignment";
+ boolean searchAlignment = false;
+
+ if (params != null)
+ {
+ for (ArgumentI arg : params)
+ {
+ String name = arg.getName();
+
+ if (MessageManager.getString("action.search").equals(name))
+ {
+ searchAlignment = arg.getValue().equals(
+ MessageManager.getString(JackHMMER.THIS_ALIGNMENT_KEY));
+ }
+ else if (MessageManager.getString(DATABASE_KEY).equals(name))
+ {
+ dbPath = arg.getValue();
+ int pos = dbPath.lastIndexOf(File.separator);
+ databaseName = dbPath.substring(pos + 1);
+ databaseFile = new File(dbPath);
+ }
+ else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
+ .equals(name))
+ {
+ if (CUTOFF_EVALUE.equals(arg.getValue()))
+ {
+ useEvalueCutoff = true;
+ }
+ else if (CUTOFF_SCORE.equals(arg.getValue()))
+ {
+ useScoreCutoff = true;
+ }
+ }
+ else if (MessageManager.getString(SEQ_EVALUE_KEY).equals(name))
+ {
+ seqEvalueCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(SEQ_SCORE_KEY).equals(name))
+ {
+ seqScoreCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(DOM_EVALUE_KEY).equals(name))
+ {
+ domEvalueCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(DOM_SCORE_KEY).equals(name))
+ {
+ domScoreCutoff = arg.getValue();
+ }
+ else if (MessageManager.getString(DATABASE_KEY).equals(name))
+ {
+ dbFound = true;
+ dbPath = arg.getValue();
+ if (!MessageManager.getString(THIS_ALIGNMENT_KEY).equals(dbPath))
+ {
+ int pos = dbPath.lastIndexOf(File.separator);
+ databaseName = dbPath.substring(pos + 1);
+ databaseFile = new File(dbPath);
+ }
+ }
+ }
+ }
+
+ if (useEvalueCutoff)
+ {
+ args.add("-E");
+ args.add(seqEvalueCutoff);
+ args.add("--domE");
+ args.add(domEvalueCutoff);
+ }
+ else if (useScoreCutoff)
+ {
+ args.add("-T");
+ args.add(seqScoreCutoff);
+ args.add("--domT");
+ args.add(domScoreCutoff);
+ }
+
+ // if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
+ // .equals(dbPath))
+ if (searchAlignment)
+ {
+ /*
+ * no external database specified for search, so
+ * export current alignment as 'database' to search
+ */
+ databaseFile = FileUtils.createTempFile("database", ".fa");
+ AlignmentI al = af.getViewport().getAlignment();
+ exportFasta(al.getSequencesArray(), databaseFile);
+ }
+
+ args.add(getFilePath(seqFile, true));
+ args.add(getFilePath(databaseFile, true));
+ }
+
+ /**
+ * Imports the data from the temporary file to which the output of jackhmmer was
+ * directed.
+ */
+ private void importData(File inputAlignmentTemp, File seqTemp,
+ File searchOutputFile) throws IOException, InterruptedException
+ {
+ BufferedReader br = new BufferedReader(
+ new FileReader(inputAlignmentTemp));
+ try
+ {
+ if (br.readLine() == null)
+ {
+ JOptionPane.showMessageDialog(af,
+ MessageManager.getString("label.no_sequences_found"));
+ return;
+ }
+ StockholmFile file = new StockholmFile(new FileParse(
+ inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
+ seqs = file.getSeqsAsArray();
+
+ readTable(searchOutputFile);
+
+ int seqCount = Math.min(seqs.length, seqsToReturn);
+
+ AlignmentI al = new Alignment(seqs);
+
+ AlignFrame alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ String ttl = "jackhmmer search of " + databaseName + " using "
+ + seqs[0].getName();
+ Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ seqTemp.delete();
+ inputAlignmentTemp.delete();
+ searchOutputFile.delete();
+ } finally
+ {
+ if (br != null)
+ {
+ br.close();
+ }
+ }
+ }
+
+ /**
+ * Reads in the scores table output by jackhmmer and adds annotation to
+ * sequences for E-value and bit score
+ *
+ * @param inputTableTemp
+ * @throws IOException
+ */
+ void readTable(File inputTableTemp) throws IOException
+ {
+ BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
+ String line = "";
+ while (!line.startsWith("Query:"))
+ {
+ line = br.readLine();
+ }
+ while (!line.contains("-------"))
+ {
+ line = br.readLine();
+ }
+ line = br.readLine();
+
+ int index = 0;
+ while (!" ------ inclusion threshold ------".equals(line)
+ && !"".equals(line))
+ {
+ SequenceI seq = seqs[index];
+ AlignmentAnnotation pp = null;
+ if (seq.getAlignmentAnnotations("", "Posterior Probability")
+ .size() != 0)
+ {
+ pp = seq.getAlignmentAnnotations("", "Posterior Probability")
+ .get(0);
+ }
+ Scanner scanner = new Scanner(line);
+ String str = scanner.next();
+ str = scanner.next();
+ addScoreAnnotation(str, seq, "jackhmmer E-value",
+ "Full sequence E-value", pp);
+ str = scanner.next();
+ addScoreAnnotation(str, seq, "jackhmmer Score",
+ "Full sequence bit score", pp);
+ seq.removeAlignmentAnnotation(pp);
+ scanner.close();
+ line = br.readLine();
+ index++;
+ }
+
+ br.close();
+ }
+
+ /**
+ * A helper method that adds one score-only (non-positional) annotation to a
+ * sequence
+ *
+ * @param value
+ * @param seq
+ * @param label
+ * @param description
+ */
+ protected void addScoreAnnotation(String value, SequenceI seq,
+ String label, String description)
+ {
+ addScoreAnnotation(value, seq, label, description, null);
+ }
+
+ /**
+ * A helper method that adds one score-only (non-positional) annotation to a
+ * sequence
+ *
+ * @param value
+ * @param seq
+ * @param label
+ * @param description
+ * @param pp
+ * existing posterior probability annotation - values
+ * copied to new annotation row
+ */
+ protected void addScoreAnnotation(String value, SequenceI seq,
+ String label, String description, AlignmentAnnotation pp)
+ {
+ try
+ {
+ AlignmentAnnotation annot = null;
+ if (pp == null)
+ {
+ annot = new AlignmentAnnotation(label, description, null);
+ }
+ else
+ {
+ annot = new AlignmentAnnotation(pp);
+ annot.label = label;
+ annot.description = description;
+ }
+ annot.setCalcId(JACKHMMER);
+ double eValue = Double.parseDouble(value);
+ annot.setScore(eValue);
+ annot.setSequenceRef(seq);
+ seq.addAlignmentAnnotation(annot);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("Error parsing " + label + " from " + value);
+ }
+ }
+
+}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Enumeration;
-import java.util.HashMap;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import java.util.Map.Entry;
import java.util.Vector;
import com.stevesoft.pat.Regex;
if (alAnot != null)
{
Annotation[] ann;
+
for (int j = 0; j < alAnot.length; j++)
{
-
- String key = type2id(alAnot[j].label);
- boolean isrna = alAnot[j].isValidStruc();
-
- if (isrna)
- {
- // hardwire to secondary structure if there is RNA secondary
- // structure on the annotation
- key = "SS";
- }
- if (key == null)
+ if (alAnot[j].annotations != null)
{
+ String key = type2id(alAnot[j].label);
+ boolean isrna = alAnot[j].isValidStruc();
- continue;
- }
+ if (isrna)
+ {
+ // hardwire to secondary structure if there is RNA secondary
+ // structure on the annotation
+ key = "SS";
+ }
+ if (key == null)
+ {
- // out.append("#=GR ");
- out.append(new Format("%-" + maxid + "s").form(
- "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
- ann = alAnot[j].annotations;
- String seq = "";
- for (int k = 0; k < ann.length; k++)
- {
- seq += outputCharacter(key, k, isrna, ann, s[i]);
+ continue;
+ }
+
+ // out.append("#=GR ");
+ out.append(new Format("%-" + maxid + "s").form(
+ "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
+ ann = alAnot[j].annotations;
+ String seq = "";
+ for (int k = 0; k < ann.length; k++)
+ {
+ seq += outputCharacter(key, k, isrna, ann, s[i]);
+ }
+ out.append(seq);
+ out.append(newline);
}
- out.append(seq);
- out.append(newline);
}
+
}
out.append(new Format("%-" + maxid + "s")
// hmmSearch.add(addDatabase);
/*
+ * jackhmmer
+ */
+ JMenu jackhmmer = new JMenu(
+ MessageManager.getString("label.jackhmmer"));
+ JMenuItem jackhmmerSettings = new JMenuItem(
+ MessageManager.getString("label.edit_settings_and_run"));
+ jackhmmerSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jackhmmer_actionPerformed(false);
+ }
+ });
+ JMenuItem jackhmmerRun = new JMenuItem(MessageManager.formatMessage(
+ "label.action_with_default_settings", "jackhmmer"));
+ jackhmmerRun.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jackhmmer_actionPerformed(true);
+ }
+
+ });
+ /*
+ JMenuItem addDatabase = new JMenuItem(
+ MessageManager.getString("label.add_database"));
+ addDatabase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ addDatabase_actionPerformed();
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ */
+ jackhmmer.add(jackhmmerRun);
+ jackhmmer.add(jackhmmerSettings);
+ // hmmSearch.add(addDatabase);
+
+ /*
* top level menu
*/
hmmerMenu.setText(MessageManager.getString("action.hmmer"));
hmmerMenu.add(hmmBuild);
hmmerMenu.add(hmmAlign);
hmmerMenu.add(hmmSearch);
+ hmmerMenu.add(jackhmmer);
}
{
}
+ protected void jackhmmer_actionPerformed(boolean b)
+ {
+ }
+
protected void addDatabase_actionPerformed()
throws FileFormatException, IOException
{
git://source.jalview.org / jalview.git / commitdiff