status.searching_for_pdb_structures = Searching for PDB Structures
status.opening_file_for = opening file for
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_hmmbuild = Building Hidden Markov Model
+status.running_hmmalign = Creating alignment with Hidden Markov Model
+status.running_hmmsearch = 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.hmmbuild_group = Build HMM from Selected Group
label.group_hmmbuild = Build HMM from Group
label.hmmsearch = hmmsearch
-label.change_hmmer_location = HMMER Binaries Installation Location
+label.hmmer_location = HMMER Binaries Installation Location
warn.null_hmm = Please ensure the alignment contains a hidden Markov model.
label.ignore_below_background_frequency = Ignore Below Background Frequency
label.information_description = Information content, measured in bits
-label.enter_location = Please enter the path of your HMMER binaries folder.
-label.invalid_hmmer_folder = The folder that you selected does not contain the necessary HMMER binaries.
warn.no_selected_hmm = Please select a hidden Markov model sequence.
label.select_hmm = Select HMM
warn.no_sequence_data = No sequence data found.
label.freq_uniprot = Use Uniprot Background Frequencies
label.hmmalign_label = hmmalign Options
label.hmmsearch_label = hmmsearch Options
-label.hmmbuild_not_found = The hmmbuild binary was not found.
-label.hmmalign_not_found = The hmmalign binary was not found.
-label.hmmsearch_not_found = The hmmsearch binary was not found.
-warn.hmmbuild_failed = hmmbuild was not found.
-warn.align_failed = hmmalign was not found.
+label.hmmbuild_not_found = The hmmbuild binary was not found
+label.hmmalign_not_found = The hmmalign binary was not found
+label.hmmsearch_not_found = The hmmsearch binary was not found
+warn.hmm_command_failed = hmm command not found
label.invalid_folder = Invalid Folder
label.folder_not_exists = HMMER binaries not found. \n Please enter the path to the HMMER binaries (if installed).
label.hmmer_installed = HMMER installed
-label.hmmer_no_sequences_found = No sequences found.
+label.hmmer_no_sequences_found = No sequences found
label.number_of_results = Number of Results to Return
label.auto_align_seqs = Automatically Align Fetched Sequences
label.use_accessions = Return Accessions
import jalview.hmmer.HMMERParamStore;
import jalview.hmmer.HMMERPreset;
import jalview.hmmer.HMMSearchThread;
+import jalview.hmmer.HmmerCommand;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.BioJsHTMLOutput;
}
});
buildColourMenu();
- buildHMMERMenu();
if (Desktop.desktop != null)
{
}
/**
- * Adds all menu items to the HMMER menu
- */
- private void buildHMMERMenu()
- {
- hmmerMenu.removeAll();
-
- hmmerMenu.add(hmmAlign);
- hmmerMenu.add(hmmBuild);
- hmmerMenu.add(hmmSearch);
- }
-
- /**
* Change the filename and format for the alignment, and enable the 'reload'
* button functionality.
*
}
@Override
- public void hmmBuildSettings_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ public void hmmBuildSettings_actionPerformed()
{
if (!(alignmentIsSufficient(1)))
{
}
@Override
- public void hmmAlignSettings_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ public void hmmAlignSettings_actionPerformed()
{
if (!(checkForHMM() && alignmentIsSufficient(2)))
{
}
@Override
- public void hmmSearchSettings_actionPerformed(ActionEvent e)
+ public void hmmSearchSettings_actionPerformed()
{
if (!checkForHMM())
{
}
@Override
- public void hmmBuildRun_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ public void hmmBuildRun_actionPerformed()
{
if (!alignmentIsSufficient(1))
{
}
new Thread(new HMMBuildThread(this, null))
.start();
- alignPanel.repaint();
-
}
@Override
- public void hmmAlignRun_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ public void hmmAlignRun_actionPerformed()
{
if (!(checkForHMM() && alignmentIsSufficient(2)))
{
}
new Thread(new HMMAlignThread(this, true, null))
.start();
- alignPanel.repaint();
}
@Override
- public void hmmSearchRun_actionPerformed(ActionEvent e)
+ public void hmmSearchRun_actionPerformed()
{
if (!checkForHMM())
{
}
new Thread(new HMMSearchThread(this, true, null))
.start();
- alignPanel.repaint();
}
/**
}
@Override
- public void addDatabase_actionPerformed(ActionEvent e) throws IOException
+ public void addDatabase_actionPerformed() throws IOException
{
if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
{
.getProperty(Preferences.HMMSEARCH_DB_PATHS);
currentDbPaths += " " + path;
- String fileName = StringUtils.getLastToken(path, new String("/"));
+ String fileName = StringUtils.getLastToken(path, File.separator);
Scanner scanner = new Scanner(fileName).useDelimiter(".");
String name = scanner.next();
scanner.close();
/**
* Sets the status of the HMMER menu
- *
- * @param status
*/
- public void updateHMMERStatus(boolean status)
+ public void updateHMMERStatus()
{
- hmmerMenu.setEnabled(status);
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
}
/**
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenMarkovModel;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.hmmer.HMMBuildThread;
+import jalview.hmmer.HmmerCommand;
import jalview.io.FileFormatI;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import java.awt.Font;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
import java.awt.event.MouseEvent;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
-import java.util.Scanner;
import javax.help.HelpSetException;
import javax.swing.JColorChooser;
/*
* Set HMMER tab defaults
*/
- trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
- isHMMERInstalled
- .setSelected(Cache.getDefault("HMMER_INSTALLED", false));
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
if (Cache.getDefault("USE_UNIPROT", false))
{
- uniprot.setSelected(true);
+ hmmerBackgroundUniprot.setSelected(true);
}
else
{
- alignment.setSelected(true);
+ hmmerBackgroundAlignment.setSelected(true);
}
- numberOfSequencesToKeepField
+ hmmerSequenceCount
.setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
- installationLocation.setEnabled(isHMMERInstalled.isSelected());
- hmmerPath.setEnabled(isHMMERInstalled.isSelected());
hmmerPath.setText(Cache.getProperty(HMMER_PATH));
hmmerPath.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- validateHMMERPath();
+ validateHMMERPath(true);
+ }
+ });
+ hmmerPath.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ validateHMMERPath(true);
}
});
* Save HMMER settings
*/
Cache.applicationProperties.setProperty("TRIM_TERMINI",
- Boolean.toString(trimTermini.isSelected()));
+ Boolean.toString(hmmrTrimTermini.isSelected()));
Cache.applicationProperties.setProperty("USE_UNIPROT",
- Boolean.toString(uniprot.isSelected()));
+ Boolean.toString(hmmerBackgroundUniprot.isSelected()));
Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
- numberOfSequencesToKeepField.getText());
+ hmmerSequenceCount.getText());
Cache.applicationProperties.setProperty(HMMER_PATH,
hmmerPath.getText());
- boolean hmmerInstalled = isHMMERInstalled.isSelected();
- Cache.applicationProperties.setProperty("HMMER_INSTALLED",
- Boolean.toString(hmmerInstalled));
- boolean hmmerFunctioning = validateHMMERPath(false);
- Cache.applicationProperties.setProperty("HMMER_FUNCTIONING",
- Boolean.toString(hmmerFunctioning));
AlignFrame[] frames = Desktop.getAlignFrames();
- boolean hmmerStatus = hmmerFunctioning && hmmerInstalled ? true : false;
if (frames != null && frames.length > 0)
{
- for (AlignFrame frame : frames)
+ for (AlignFrame f : frames)
{
- frame.updateHMMERStatus(hmmerStatus);
+ f.updateHMMERStatus();
}
}
- trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
if (Cache.getDefault("USE_UNIPROT", false))
{
- uniprot.setSelected(true);
+ hmmerBackgroundUniprot.setSelected(true);
}
else
{
- alignment.setSelected(true);
+ hmmerBackgroundAlignment.setSelected(true);
}
- numberOfSequencesToKeepField
+ hmmerSequenceCount
.setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
hmmerPath.setText(Cache.getProperty(HMMER_PATH));
structureTab.requestFocusInWindow();
return false;
}
- if (isHMMERInstalled.isSelected())
- {
- if (!validateHMMER())
- {
- hmmerTab.requestFocusInWindow();
- return false;
- }
- }
return true;
}
}
- @Override
- protected boolean validateHMMER()
- {
- return validateHMMERPath();
-
- }
-
/**
* DOCUMENT ME!
*/
}
/**
- * Returns true if hmmer path contains the necessary valid executables, else
- * show an error dialog (if showing dialog).
+ * Returns true if hmmer path is to a folder that contains an executable
+ * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning
+ * dialog)
*/
- private boolean validateHMMERPath(boolean showDialog)
+ @Override
+ protected boolean validateHMMERPath(boolean showWarning)
{
- int missing = 0;
- String message = "";
String folder = hmmerPath.getText().trim();
- if (folder.length() > 0)
- {
- File f = new File(folder);
- if (!f.exists())
- {
- if (showDialog)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.folder_not_exists"),
- MessageManager.getString("label.invalid_folder"),
- JvOptionPane.ERROR_MESSAGE);
- }
- return false;
- }
- AlignmentI alignment = new Alignment(
- new SequenceI[]
- { new Sequence("test", "WLWL", 0, 3) });
- if (canExecute(folder + "/hmmbuild"))
- {
- validateHMMBuild(alignment);
- }
- else
- {
- message += MessageManager.getString("label.hmmbuild_not_found")
- + "\n";
- missing++;
- }
-
-
- if (canExecute(folder + "/hmmalign"))
- {
-
- }
- else
- {
- message += MessageManager.getString("label.hmmalign_not_found")
- + "\n";
- missing++;
- }
-
- if (canExecute(folder + "/hmmsearch"))
- {
-
- }
- else
- {
- message += MessageManager.getString("label.hmmsearch_not_found")
- + "\n";
- missing++;
- }
- }
-
- if (missing > 0)
- {
- if (missing < 3)
- {
- if (showDialog)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
- MessageManager.getString("label.invalid_folder"),
- JvOptionPane.ERROR_MESSAGE);
- }
- return false;
- }
- else
- {
- if (showDialog)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.no_binaries"),
- MessageManager.getString("label.invalid_folder"),
- JvOptionPane.ERROR_MESSAGE);
- }
-
- return false;
- }
- }
-
- return true;
+ if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null)
+ {
+ return true;
+ }
+ if (showWarning && folder.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.hmmbuild_not_found"),
+ MessageManager.getString("label.invalid_folder"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return false;
}
/**
}
/**
- * Runs hmmbuild to check if it is working. While doing this it parses the
- * version of HMMER.
- *
- * @param frame
- * @return
- */
- public boolean validateHMMBuild(AlignmentI alignment)
- {
- HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
- hmmbuild.hmmbuildWaitTillComplete();
- SequenceI hmmSeq = alignment.getSequenceAt(0);
- HiddenMarkovModel hmm;
- if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
- {
- hmm = hmmSeq.getHMM();
-
- if (hmm.getNumberOfSymbols() < 1)
- {
- return false;
- }
- }
- else
- {
- return false;
- }
-
- String header = hmm.getFileHeader();
- if (header == null)
- {
- return false;
- }
- else
- {
- Scanner scanner = new Scanner(header);
- scanner.next();
- String string = scanner.next();
- String version = string.substring(1);
- Cache.setProperty("HMMER_VERSION", version);
- scanner.close();
-
- }
- return true;
- }
-
-
- private boolean validateHMMERPath()
- {
- return validateHMMERPath(true);
- }
-
- /**
* If Chimera is selected, check it can be found on default or user-specified
* path, if not show a warning/help dialog.
*/
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
+import jalview.hmmer.HmmerCommand;
import jalview.io.FileFormatException;
import jalview.io.FileFormats;
import jalview.util.MessageManager;
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
hmmerMenu.setText(MessageManager.getString("action.hmmer"));
- String status = Cache.getProperty("HMMER_FUNCTIONING");
- if ("false".equals(status) || status == null)
- {
- hmmerMenu.setEnabled(false);
- }
- else
- {
- hmmerMenu.setEnabled(true);
- }
+ hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
hmmerMenu.addActionListener(new ActionListener()
{
@Override
hmmerMenu_actionPerformed(e);
}
});
+ hmmerMenu.add(hmmBuild);
+ hmmerMenu.add(hmmAlign);
+ hmmerMenu.add(hmmSearch);
+
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
"label.action_with_default_settings", "hmmbuild"));
hmmBuildRun.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- try
- {
- hmmBuildRun_actionPerformed(e);
- } catch (IOException | InterruptedException e1)
- {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
+ hmmBuildRun_actionPerformed();
}
-
});
hmmBuildSettings.setText(
MessageManager.getString("label.edit_settings_and_run"));
hmmBuildSettings.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- try
- {
- hmmBuildSettings_actionPerformed(e);
- } catch (IOException | InterruptedException e1)
- {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
+ hmmBuildSettings_actionPerformed();
}
-
});
hmmAlignRun.setText(MessageManager.formatMessage(
"label.action_with_default_settings", "hmmalign"));
hmmAlignRun.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- try
- {
- hmmAlignRun_actionPerformed(e);
- } catch (IOException | InterruptedException e1)
- {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
+ hmmAlignRun_actionPerformed();
}
-
});
hmmAlignSettings.setText(
MessageManager.getString("label.edit_settings_and_run"));
hmmAlignSettings.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- try
- {
- hmmAlignSettings_actionPerformed(e);
- } catch (IOException | InterruptedException e1)
- {
- // TODO Auto-generated catch block
- e1.printStackTrace();
- }
+ hmmAlignSettings_actionPerformed();
}
-
});
hmmSearchRun.setText(MessageManager.formatMessage(
"label.action_with_default_settings", "hmmsearch"));
hmmSearchRun.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- hmmSearchRun_actionPerformed(e);
+ hmmSearchRun_actionPerformed();
}
-
});
addDatabase.setText(MessageManager.getString("label.add_database"));
addDatabase.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
try
{
- addDatabase_actionPerformed(e);
+ addDatabase_actionPerformed();
} catch (IOException e1)
{
- // TODO Auto-generated catch block
e1.printStackTrace();
}
}
-
});
hmmSearchSettings.setText(
MessageManager.getString("label.edit_settings_and_run"));
hmmSearchSettings.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- hmmSearchSettings_actionPerformed(e);
+ hmmSearchSettings_actionPerformed();
}
-
});
selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
{
}
- protected void hmmBuildRun_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ protected void hmmBuildRun_actionPerformed()
{
}
- protected void hmmSearchRun_actionPerformed(ActionEvent e)
+ protected void hmmSearchRun_actionPerformed()
{
}
- protected void addDatabase_actionPerformed(ActionEvent e)
+ protected void addDatabase_actionPerformed()
throws FileFormatException, IOException
{
}
- protected void hmmAlignRun_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ protected void hmmAlignRun_actionPerformed()
{
}
- protected void hmmBuildSettings_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ protected void hmmBuildSettings_actionPerformed()
{
}
- protected void hmmSearchSettings_actionPerformed(ActionEvent e)
+ protected void hmmSearchSettings_actionPerformed()
{
}
- protected void hmmAlignSettings_actionPerformed(ActionEvent e)
- throws IOException, InterruptedException
+ protected void hmmAlignSettings_actionPerformed()
{
}
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
*/
protected JPanel hmmerTab = new JPanel();
- protected JCheckBox trimTermini = new JCheckBox();
+ protected JCheckBox hmmrTrimTermini = new JCheckBox();
- protected ButtonGroup backgroundFreqSource = new ButtonGroup();
+ protected AbstractButton hmmerBackgroundUniprot = new JCheckBox();
- protected AbstractButton uniprot = new JCheckBox();
+ protected AbstractButton hmmerBackgroundAlignment = new JCheckBox();
- protected AbstractButton alignment = new JCheckBox();
-
- protected JLabel sequencesToKeep = new JLabel();
-
- protected JTextField numberOfSequencesToKeepField = new JTextField();
-
- protected JLabel installationLocation = new JLabel();
-
- protected JCheckBox isHMMERInstalled = new JCheckBox();
+ protected JTextField hmmerSequenceCount = new JTextField();
protected JTextField hmmerPath = new JTextField();
- protected JLabel hmmsearch = new JLabel();
-
- protected JLabel hmmalign = new JLabel();
-
/*
* DAS Settings tab
*/
/*
* Handler to validate a tab before leaving it - currently only for
- * Structure.
+ * Structure
*/
tabbedPane.addChangeListener(new ChangeListener()
{
return;
}
}
- else if (lastTab == hmmerTab
- && tabbedPane.getSelectedComponent() != hmmerTab
- && isHMMERInstalled.isSelected())
- {
- if (!validateHMMER())
- {
- tabbedPane.setSelectedComponent(hmmerTab);
- }
- return;
- }
lastTab = tabbedPane.getSelectedComponent();
}
}
/**
- * Initialises the hmmer tabbed panel.
+ * Initialises the hmmer tabbed panel
*
* @return
*/
{
hmmerTab.setLayout(null);
- hmmalign.setFont(LABEL_FONT);
- hmmalign.setText(MessageManager.getString("label.hmmalign_label"));
- hmmalign.setBounds(new Rectangle(22, 10, 200, 23));
-
- trimTermini.setFont(LABEL_FONT);
- trimTermini.setText(MessageManager.getString("label.trim_termini"));
- trimTermini.setBounds(new Rectangle(22, 30, 200, 23));
-
- hmmsearch.setFont(LABEL_FONT);
- hmmsearch.setText(MessageManager.getString("label.hmmsearch_label"));
- hmmsearch.setBounds(new Rectangle(250, 10, 200, 23));
-
- sequencesToKeep.setFont(LABEL_FONT);
- sequencesToKeep
- .setText(MessageManager.getString("label.no_of_sequences"));
- sequencesToKeep.setBounds(new Rectangle(250, 30, 125, 23));
- numberOfSequencesToKeepField.setBounds(new Rectangle(375, 30, 40, 23));
-
- isHMMERInstalled.setFont(LABEL_FONT);
- isHMMERInstalled.setText(
- MessageManager.getString("label.hmmer_installed"));
- isHMMERInstalled.setBounds(new Rectangle(22, 180, 200, 23));
- isHMMERInstalled.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- boolean status = isHMMERInstalled.isSelected();
- installationLocation.setEnabled(status);
- hmmerPath.setEnabled(status);
- }
- });
+ JLabel installationLocation = new JLabel(
+ MessageManager.getString("label.hmmer_location"));
installationLocation.setFont(LABEL_FONT);
- installationLocation.setText(
- MessageManager.getString("label.change_hmmer_location"));
- installationLocation.setBounds(new Rectangle(22, 200, 200, 23));
- hmmerPath.setBounds(new Rectangle(22, 220, 200, 23));
+ installationLocation.setBounds(new Rectangle(22, 10, 250, 23));
+ hmmerPath.setBounds(new Rectangle(22, 30, 300, 23));
hmmerPath.addMouseListener(new MouseAdapter()
{
@Override
}
});
- backgroundFreqSource.add(uniprot);
- backgroundFreqSource.add(alignment);
- backgroundFreqSource.setSelected(uniprot.getModel(), true);
+ JLabel hmmalign = new JLabel(
+ MessageManager.getString("label.hmmalign_label"));
+ hmmalign.setFont(LABEL_FONT);
+ hmmalign.setBounds(new Rectangle(22, 50, 200, 23));
- uniprot.setText(MessageManager.getString("label.freq_uniprot"));
- uniprot.setFont(LABEL_FONT);
- uniprot.setBounds(new Rectangle(22, 260, 255, 23));
+ hmmrTrimTermini.setFont(LABEL_FONT);
+ hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+ hmmrTrimTermini.setBounds(new Rectangle(22, 70, 200, 23));
- alignment.setText(MessageManager.getString("label.freq_alignment"));
- alignment.setFont(LABEL_FONT);
- alignment.setBounds(new Rectangle(22, 280, 255, 23));
+ JLabel hmmsearch = new JLabel(
+ MessageManager.getString("label.hmmsearch_label"));
+ hmmsearch.setFont(LABEL_FONT);
+ hmmsearch.setBounds(new Rectangle(22, 90, 200, 23));
- hmmerTab.add(uniprot);
- hmmerTab.add(alignment);
+ JLabel sequencesToKeep = new JLabel(
+ MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setFont(LABEL_FONT);
+ sequencesToKeep.setBounds(new Rectangle(22, 110, 125, 23));
+ hmmerSequenceCount.setBounds(new Rectangle(150, 110, 40, 23));
+
+ ButtonGroup backgroundFreqSource = new ButtonGroup();
+ backgroundFreqSource.add(hmmerBackgroundUniprot);
+ backgroundFreqSource.add(hmmerBackgroundAlignment);
+ backgroundFreqSource.setSelected(hmmerBackgroundUniprot.getModel(), true);
+
+ hmmerBackgroundUniprot.setText(MessageManager.getString("label.freq_uniprot"));
+ hmmerBackgroundUniprot.setFont(LABEL_FONT);
+ hmmerBackgroundUniprot.setBounds(new Rectangle(22, 130, 255, 23));
+
+ hmmerBackgroundAlignment.setText(MessageManager.getString("label.freq_alignment"));
+ hmmerBackgroundAlignment.setFont(LABEL_FONT);
+ hmmerBackgroundAlignment.setBounds(new Rectangle(22, 150, 300, 23));
+
+ hmmerTab.add(hmmerBackgroundUniprot);
+ hmmerTab.add(hmmerBackgroundAlignment);
hmmerTab.add(hmmalign);
hmmerTab.add(hmmsearch);
hmmerTab.add(installationLocation);
hmmerTab.add(hmmerPath);
- hmmerTab.add(trimTermini);
+ hmmerTab.add(hmmrTrimTermini);
hmmerTab.add(sequencesToKeep);
hmmerTab.add(sequencesToKeep);
- hmmerTab.add(numberOfSequencesToKeepField);
- hmmerTab.add(isHMMERInstalled);
+ hmmerTab.add(hmmerSequenceCount);
return hmmerTab;
}
return choice;
}
- /**
- * Validate the structure tab preferences; if invalid, set focus on this tab.
- *
- * @param e
- */
- protected boolean validateStructure(FocusEvent e)
- {
- if (!validateStructure())
- {
- e.getComponent().requestFocusInWindow();
- return false;
- }
- return true;
- }
-
- /**
- * Validate the hmmer tab preferences; if invalid, set focus on this tab.
- *
- * @param e
- */
- protected boolean validateHMMER(FocusEvent e)
- {
- if (!validateHMMER())
- {
- e.getComponent().requestFocusInWindow();
- return false;
- }
- return true;
- }
-
protected boolean validateStructure()
{
return false;
}
- protected boolean validateHMMER()
+ protected boolean validateHMMERPath(boolean showWarning)
{
return false;
}
git://source.jalview.org / jalview.git / commitdiff