if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
{
final String setname = (String) setName.getSelectedItem();
- System.out.println("Item state changed for " + setname
- + " (handling ? " + !settingDialog + ")");
+ // System.out.println("Item state changed for " + setname
+ // + " (handling ? " + !settingDialog + ")");
if (settingDialog)
{
// ignore event
package jalview.hmmer;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
import jalview.gui.SplitFrame;
import jalview.io.DataSourceType;
import jalview.io.StockholmFile;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
import javax.swing.JInternalFrame;
-public class HMMAlignThread implements Runnable
+public class HMMAlignThread extends HmmerCommand implements Runnable
{
+ static final String HMMALIGN = "hmmalign";
- /**
+ /*
* feature settings from view that job was associated with
*/
protected FeatureRendererSettings featureSettings = null;
- /**
- * Object containing frequently used commands.
- */
- HMMERCommands cmds = new HMMERCommands();
-
- AlignFrame af;
-
AlignmentI alignment;
AlignmentI dataset;
long barID;
- Map<Integer, SequenceI> hmmSeqs;
-
File hmmTemp = null;
File outTemp = null;
barID = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
barID);
- cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
prepareAlignment();
SequenceI[][] subAlignments = msa.getVisibleContigs('-');
allOrders = new ArrayList<>();
int job = 0;
for (SequenceI[] seqs : subAlignments)
{
- cmds.uniquifySequences(seqs);
+ uniquifySequences(seqs);
try
{
createTemporaryFiles();
}
try
{
- cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
+ exportData(seqs, outTemp.getAbsoluteFile(), hmm,
hmmTemp.getAbsoluteFile(), null);
} catch (IOException e1)
{
displayResults(newFrame);
- af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
- barID);
+ af.setProgressBar("", barID);
}
}
/**
- * Executes the hmmalign command in the command line.
+ * Executes the hmmalign command in the command line
*
* @return
* @throws IOException
*/
private boolean runCommand() throws IOException, InterruptedException
{
- File file = new File(cmds.HMMERFOLDER + "/hmmalign");
- if (!file.canExecute())
- {
- file = new File(cmds.HMMERFOLDER + "/hmmalign.exe");
- {
- if (!file.canExecute())
- {
- return false;
- }
- }
+ String binaryPath = getCommandRoot(HMMALIGN);
+ if (binaryPath == null) {
+ return false;
}
- String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
+ String command = binaryPath + SPACE;
+ // todo parse version from ./hmmerbuild -h
String version = Cache.getProperty("HMMER_VERSION");
if (!"3.1b2".equals(version))
{
- command += cmds.ALLCOL;
+ // command += ALLCOL; // todo obsolete option?
}
if (args != null)
{
}
}
}
- command += " -o " + inputTemp.getAbsolutePath() + cmds.SPACE
- + hmmTemp.getAbsolutePath() + cmds.SPACE
+ command += " -o " + inputTemp.getAbsolutePath() + SPACE
+ + hmmTemp.getAbsolutePath() + SPACE
+ outTemp.getAbsolutePath();
- return cmds.runCommand(command);
+ return runCommand(command);
}
/**
DataSourceType.FILE);
SequenceI[] result = file.getSeqsAsArray();
AlignmentOrder msaorder = new AlignmentOrder(result);
- jalview.analysis.AlignmentSorter.recoverOrder(result);
- jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, result);
+ AlignmentSorter.recoverOrder(result);
+ SeqsetUtils.deuniquify(hash, result);
allOrders.add(msaorder);
allResults[index] = result;
hmmTemp.delete();
package jalview.hmmer;
-import jalview.bin.Cache;
+import jalview.analysis.SeqsetUtils;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.HMMFile;
import javax.swing.JOptionPane;
-public class HMMBuildThread implements Runnable
+public class HMMBuildThread extends HmmerCommand implements Runnable
{
- HMMERCommands cmds = new HMMERCommands();
-
- AlignFrame af;
-
AlignViewport viewport;
boolean multiJob = false;
af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
barID);
}
- cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
List<SequenceGroup> groups = new ArrayList<>();
if (params != null)
if (af != null)
{
- af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
- barID);
+ af.setProgressBar("", barID);
}
}
array = alignment.getSequencesArray();
}
- cmds.setHmmSeqs(seqs);
-
if (array.length < 1)
{
if (af != null)
index++;
}
- cmds.uniquifySequences(newArr);
+ uniquifySequences(newArr);
if (forGroup)
{
- cmds.exportData(newArr, stoTemp, null, null, group);
+ exportData(newArr, stoTemp, null, null, group);
}
else
{
- cmds.exportData(newArr, stoTemp, null, null, alignment);
+ exportData(newArr, stoTemp, null, null, alignment);
}
- jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
+ SeqsetUtils.deuniquify(hash, array);
} catch (FileNotFoundException e)
{
*/
private boolean runCommand() throws IOException, InterruptedException
{
- File file = new File(cmds.HMMERFOLDER + "/hmmbuild");
- if (!file.canExecute())
+ String binaryPath = getCommandRoot(HMMBUILD);
+ if (binaryPath == null)
{
- file = new File(cmds.HMMERFOLDER + "/hmmbuild.exe");
- {
- if (!file.canExecute())
- {
- if (af != null)
- {
- JvOptionPane.showInternalMessageDialog(af,
- MessageManager.getString("warn.hmmbuild_failed"));
- }
- return false;
- }
- }
+ return false;
}
- String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.SPACE;
+ String command = binaryPath + SPACE;
String name = null;
if (params != null)
}
- command += "-n " + name.replace(' ', '_') + cmds.SPACE;
+ command += "-n " + name.replace(' ', '_') + SPACE;
if (!alignment.isNucleotide())
{
- command += cmds.FORCEAMINO; // TODO check for rna
+ command += FORCEAMINO; // TODO check for rna
}
else
{
- command += cmds.FORCEDNA;
+ command += FORCEDNA;
}
- command += hmmTemp.getAbsolutePath() + cmds.SPACE
- + stoTemp.getAbsolutePath() + cmds.SPACE;
- return cmds.runCommand(command);
+ command += hmmTemp.getAbsolutePath() + SPACE + stoTemp.getAbsolutePath()
+ + SPACE;
+ return runCommand(command);
}
/**
SequenceI[] seqs = file.getSeqsAsArray();
SequenceI seq = seqs[0];
seq.createDatasetSequence();
- HiddenMarkovModel hmm = file.getHMM();
if (group != null)
{
seq.insertCharAt(0, group.getStartRes(), '-');
{
args.add(new BooleanOption(
MessageManager.getString("label.trim_termini"),
- MessageManager.getString(
- "label.trim_termini = Trim Non-Matching Termini_desc"),
+ MessageManager.getString("label.trim_termini_desc"),
false, false, true, 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.JvOptionPane;
-import jalview.gui.Preferences;
import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StockholmFile;
import javax.swing.JOptionPane;
-public class HMMSearchThread implements Runnable
+public class HMMSearchThread extends HmmerCommand implements Runnable
{
- /**
+ static final String HMMSEARCH = "hmmsearch";
+
+ /*
* feature settings from view that job was associated with
*/
protected FeatureRendererSettings featureSettings = null;
- /**
- * Object containing frequently used commands.
- */
- HMMERCommands cmds = new HMMERCommands();
+ HiddenMarkovModel hmm;
- AlignFrame af;
+ boolean newFrame;
- HiddenMarkovModel hmm;
+ boolean realign = false;
- boolean newFrame, realign = false, trim = false;
+ boolean trim = false;
Integer numberOfSequences = null;
barID = System.currentTimeMillis();
af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
barID);
- cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
try
{
}
try
{
- cmds.exportData(null, null, hmm, hmmTemp.getAbsoluteFile(), null);
+ exportData(null, null, hmm, hmmTemp.getAbsoluteFile(), null);
} catch (IOException e1)
{
e1.printStackTrace();
e.printStackTrace();
}
- af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
- barID);
+ af.setProgressBar("", barID);
}
*/
private boolean runCommand() throws IOException, InterruptedException
{
- Boolean dbFound = false;
- String dbPath = "";
- File file = new File(cmds.HMMERFOLDER + "/hmmsearch");
- if (!file.canExecute())
+ String binaryPath = getCommandRoot(HMMSEARCH);
+ if (binaryPath == null)
{
- file = new File(cmds.HMMERFOLDER + "/hmmsearch.exe");
- {
- if (!file.canExecute())
- {
- return false;
- }
- }
+ return false;
}
- String command = cmds.HMMERFOLDER + "/hmmsearch -o "
+ String command = binaryPath + " -o "
+ inputTableTemp.getAbsolutePath() + " -A "
- + inputAlignmentTemp.getAbsolutePath() + cmds.SPACE;
+ + inputAlignmentTemp.getAbsolutePath() + SPACE;
+
+ boolean dbFound = false;
+ String dbPath = "";
if (params != null)
{
for (ArgumentI arg : params)
}
break;
case "Sequence E-value Cutoff":
- command += "--incE " + arg.getValue() + cmds.SPACE;
+ command += "--incE " + arg.getValue() + SPACE;
break;
case "Sequence Score Threshold":
- command += "-incT " + arg.getValue() + cmds.SPACE;
+ command += "-incT " + arg.getValue() + SPACE;
break;
case "Domain E-value Threshold":
- command += "--incdomE " + arg.getValue() + cmds.SPACE;
+ command += "--incdomE " + arg.getValue() + SPACE;
break;
case "Domain Score Threshold":
- command += "--incdomT " + arg.getValue() + cmds.SPACE;
+ command += "--incdomT " + arg.getValue() + SPACE;
break;
case "Trim Non-Matching Termini":
trim = true;
}
}
- if (dbFound == false || MessageManager.getString("label.this_alignment")
+ if (!dbFound || MessageManager.getString("label.this_alignment")
.equals(dbPath))
{
AlignmentI alignment = af.getViewport().getAlignment();
writer.close();
}
- command += hmmTemp.getAbsolutePath() + cmds.SPACE
+ command += hmmTemp.getAbsolutePath() + SPACE
+ databaseFile.getAbsolutePath();
- return cmds.runCommand(command);
+ return runCommand(command);
}
/**
{
BufferedReader br = new BufferedReader(
new FileReader(inputAlignmentTemp));
- if (br.readLine() == null)
+ try
{
- JOptionPane.showMessageDialog(af,
- MessageManager.getString("label.no_sequences_found"));
- return;
- }
- StockholmFile file = new StockholmFile(new FileParse(
- inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
- seqs = file.getSeqsAsArray();
+ 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();
+ readTable();
- SequenceI[] hmmAndSeqs;
- if (numberOfSequences != null && numberOfSequences < seqs.length)
- {
- hmmAndSeqs = new SequenceI[numberOfSequences + 1];
- }
- else
- {
- hmmAndSeqs = new SequenceI[seqs.length + 1];
- }
- hmmAndSeqs[0] = hmmSeq;
+ SequenceI[] hmmAndSeqs;
+ if (numberOfSequences != null && numberOfSequences < seqs.length)
+ {
+ hmmAndSeqs = new SequenceI[numberOfSequences + 1];
+ }
+ else
+ {
+ hmmAndSeqs = new SequenceI[seqs.length + 1];
+ }
+ hmmAndSeqs[0] = hmmSeq;
- if (numberOfSequences != null && seqs.length > numberOfSequences)
- {
- System.arraycopy(seqs, 0, hmmAndSeqs, 1, numberOfSequences);
- }
- else
- {
- System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqs.length);
- }
+ if (numberOfSequences != null && seqs.length > numberOfSequences)
+ {
+ System.arraycopy(seqs, 0, hmmAndSeqs, 1, numberOfSequences);
+ }
+ else
+ {
+ System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqs.length);
+ }
- AlignmentI alignment = new Alignment(hmmAndSeqs);
- AlignFrame frame = new AlignFrame(alignment, 1, 1);
- frame.setSelectedHMMSequence(hmmSeq);
- List<ArgumentI> alignArgs = new ArrayList<>();
- if (trim)
+ AlignmentI alignment = new Alignment(hmmAndSeqs);
+ AlignFrame frame = new AlignFrame(alignment, 1, 1);
+ frame.setSelectedHMMSequence(hmmSeq);
+ List<ArgumentI> alignArgs = new ArrayList<>();
+ if (trim)
+ {
+ alignArgs.add(new BooleanOption(
+ MessageManager.getString("label.trim_termini"),
+ MessageManager.getString("label.trim_termini_desc"), true,
+ true, true, null));
+ }
+ HMMAlignThread hmmalign = new HMMAlignThread(frame, true, alignArgs);
+ hmmalign.hmmalignWaitTillComplete();
+ frame = null;
+ hmmTemp.delete();
+ inputAlignmentTemp.delete();
+ inputTableTemp.delete();
+ } finally
{
- alignArgs.add(new BooleanOption(
- MessageManager.getString("label.trim_termini"),
- MessageManager.getString("label.trim_termini_desc"), true,
- true, true, null));
+ if (br != null)
+ {
+ br.close();
+ }
}
- HMMAlignThread hmmalign = new HMMAlignThread(frame, true, alignArgs);
- hmmalign.hmmalignWaitTillComplete();
- frame = null;
- hmmTemp.delete();
- inputAlignmentTemp.delete();
- inputTableTemp.delete();
}
/**
}
- public void readTable() throws IOException
+ void readTable() throws IOException
{
BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
String line = "";
{
Scanner scanner = new Scanner(line);
- String str = scanner.next();
- Annotation[] annots = new Annotation[seqs[index].getLength()];
- for (Annotation an : annots)
+ String str = scanner.next(); // full sequence eValue score
+ float eValue = Float.parseFloat(str);
+ int seqLength = seqs[index].getLength();
+ Annotation[] annots = new Annotation[seqLength];
+ for (int j = 0; j < seqLength; j++)
{
- an = new Annotation(Float.parseFloat(str));
+ annots[j] = new Annotation(eValue);
}
AlignmentAnnotation annot = new AlignmentAnnotation("E-value",
"Score", annots);
package jalview.hmmer;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.gui.Preferences;
import jalview.io.HMMFile;
import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.File;
import java.util.List;
/**
- * Contains multiple commands and methods frequently used to run hmmbuild,
- * hmmalign and hmmsearch
+ * Base class for hmmbuild, hmmalign and hmmsearch
*
* @author TZVanaalten
*
*/
-public class HMMERCommands
+public class HmmerCommand
{
- // Path of hmmer binaries directory
- String HMMERFOLDER = "/Documents/";
+ public static final String HMMBUILD = "hmmbuild";
- public String JALVIEWDIRECTORY = System.getProperty("user.dir") + "/";
-
- public final String HMMALIGN = "/hmmalign ";
-
- public final String HMMBUILD = "/hmmbuild ";
-
- public final String HMMSEARCH = "/hmmsearch ";
+ public String JALVIEWDIRECTORY = System.getProperty("user.dir")
+ + File.separator;
public String OUTPUTALIGNMENT;
List<SequenceI> hmmSeqs;
+ protected AlignFrame af;
+
+ public static boolean isHmmerAvailable()
+ {
+ File exec = getExecutable(HMMBUILD, Cache.getProperty(Preferences.HMMER_PATH));
+ return exec != null;
+ }
+
/**
* Uniquifies the sequences when exporting and stores their details in a
* hashtable.
if (seqs != null)
{
AlignmentI newAl = new Alignment(seqs);
- if (stoLocation != null)
+ if (stoLocation != null && al != null)
{
for (AlignmentAnnotation annot : al.getAlignmentAnnotation())
{
{
this.hmmSeqs = hmmSeqs;
}
+
+ /**
+ * Answers the full path to the given hmmer executable, or null if file cannot
+ * be found or is not executable
+ *
+ * @param cmd
+ * command short name e.g. hmmalign
+ * @return
+ */
+ protected String getCommandRoot(String cmd)
+ {
+ String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
+ File file = getExecutable(cmd, binariesFolder);
+ if (file == null && af != null)
+ {
+ JvOptionPane.showInternalMessageDialog(af,
+ MessageManager.getString("warn.hmm_command_failed"));
+ }
+
+ return file == null ? null : file.getAbsolutePath();
+ }
+
+ /**
+ * Answers the executable file for the given hmmer command, or null if not
+ * found or not executable. The path to the executable is the command name
+ * prefixed by the hmmer binaries folder path, optionally with .exe appended.
+ *
+ * @param cmd
+ * hmmer command short name, for example hmmbuild
+ * @param binaryPath
+ * parent folder containing hmmer executables
+ * @return
+ */
+ public static File getExecutable(String cmd, String binaryPath)
+ {
+ File file = new File(binaryPath, cmd);
+ if (!file.canExecute())
+ {
+ file = new File(binaryPath, cmd + ".exe");
+ {
+ if (!file.canExecute())
+ {
+ file = null;
+ }
+ }
+ }
+ return file;
+ }
}
git://source.jalview.org / jalview.git / commitdiff