package jalview.gui;
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.GridLayout;
+import java.awt.Rectangle;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ComponentEvent;
import java.awt.event.ComponentListener;
import java.awt.event.ContainerEvent;
import java.awt.event.ContainerListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.WindowEvent;
import java.util.EventObject;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Vector;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
+import javax.swing.JDialog;
import javax.swing.JFrame;
import javax.swing.JLabel;
+import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
+import javax.swing.JSlider;
import javax.swing.JTable;
import javax.swing.JTextArea;
+import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
+import javax.swing.SwingConstants;
import javax.swing.SwingUtilities;
import javax.swing.border.TitledBorder;
import javax.swing.event.CellEditorListener;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
import javax.swing.table.*;
import compbio.metadata.Argument;
import compbio.metadata.PresetManager;
import compbio.metadata.RunnerConfig;
import compbio.metadata.ValueConstrain;
+import compbio.metadata.WrongParameterException;
import compbio.metadata.ValueConstrain.Type;
import jalview.ws.jws2.Jws2Discoverer;
public class WsJobParameters extends JPanel
{
+ private static final int PARAM_WIDTH = 340, PARAM_HEIGHT = 120;
+
JPanel setDetails = new JPanel();
JPanel settingsPanel = new JPanel();
JPanel paramButtons = new JPanel();
+ JPanel paramPanel = new JPanel();
+ JLabel modified = new JLabel();
+ JButton startjob = new JButton();
+ JButton canceljob = new JButton();
+
JButton exportParams = new JButton();
JButton importParams = new JButton();
JTextArea setDescr = new JTextArea();
- JTable paramTable = new JTable();
-
JScrollPane paramPane = new JScrollPane();
+ // JList paramList = new JList();
+ JPanel paramList = new JPanel();
+
RunnerConfig serviceOptions;
List<Parameter> availableParameters;
public WsJobParameters(Jws2Instance service, Preset p)
{
- this(null, service, p);
+ this(null, service, p, null);
}
/**
* @param service
* @param p
*/
- public WsJobParameters(JFrame parent, Jws2Instance service, Preset p)
+ public WsJobParameters(JFrame parent, Jws2Instance service, Preset p,
+ List<Argument> jobArgset)
{
super();
jbInit();
- initTableUI();
+ argSetModified(false);
// populate parameter table
- initForService(service, p);
+ initForService(service, p, jobArgset);
// display in new JFrame attached to parent.
validate();
}
+ int response=-1;
+ JDialog frame=null;
+ public boolean showRunDialog() {
+
+ frame = new JDialog(
+ Desktop.instance, true);
+
+ frame.setTitle("Edit parameters for "+service.getActionText());
+ Rectangle deskr = Desktop.instance.getBounds();
+ frame.setBounds(new Rectangle((int) (deskr.getCenterX() - 240),
+ (int) (deskr.getCenterY() - 92), 380, 385));
+ frame.setContentPane(this);
+ frame.setVisible(true);
+
+ if (response>0)
+ {
+ return true;
+ }
+ return false;
+ }
+
private void jbInit()
{
+ modified.setText("Job Options Modified");
+ modified.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ modified.setForeground(Color.red);
+ modified.setHorizontalAlignment(SwingConstants.CENTER);
+
exportParams.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
exportParams.setText("Export");
exportParams.setToolTipText("Export parameters to a file");
editParam_actionPerformed(e);
}
});
+ startjob.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ startjob.setText("Start");
+ startjob.setToolTipText("Start Job");
+ startjob.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ startjob_actionPerformed(e);
+ }
+ });
+ canceljob.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ canceljob.setText("Cancel");
+ canceljob.setToolTipText("Cancel Job");
+ canceljob.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ canceljob_actionPerformed(e);
+ }
+ });
setDetails.setBorder(new TitledBorder("Details"));
setDetails.setLayout(new GridLayout(2, 1));
setDescr.setColumns(40);
setDescr.setWrapStyleWord(true);
- setDescr.setPreferredSize(new Dimension(350, 100));
+ setDescr.setLineWrap(true);
+ setDescr.setPreferredSize(new Dimension(350, 90));
+ setDescr.setBackground(getBackground());
+ setDescr.setEditable(false);
setDetails.add(setName);
setDetails.add(setDescr);
- setDetails.setPreferredSize(new Dimension(360, 150));
+ setDetails.setPreferredSize(new Dimension(360, 100));
settingsPanel.setLayout(new BorderLayout());
jobOptions.setBorder(new TitledBorder("Options"));
jobParameters.setBorder(new TitledBorder("Parameters"));
jobParameters.setLayout(jparamLayout = new BorderLayout());
paramPane.setPreferredSize(new Dimension(360, 300));
+ paramPane.getVerticalScrollBar().setUnitIncrement(20);
+ // paramPanel.setPreferredSize(new Dimension(360, 300));
paramButtons.setLayout(new GridLayout(2, 3));
paramButtons.add(addParam);
paramButtons.add(editParam);
paramButtons.add(exportParams);
paramButtons.add(importParams);
paramButtons.add(resetParams);
+ paramPane.getViewport().setView(paramList);
jobParameters.add(paramPane, BorderLayout.NORTH);
- jobParameters.add(paramButtons, BorderLayout.SOUTH);
- settingsPanel.add(jobOptions, BorderLayout.NORTH);
+ //jobParameters.add(paramButtons, BorderLayout.SOUTH);
+ settingsPanel.add(modified, BorderLayout.NORTH);
+ settingsPanel.add(jobOptions, BorderLayout.CENTER);
settingsPanel.add(jobParameters, BorderLayout.SOUTH);
+
setLayout(new BorderLayout());
- setPreferredSize(new Dimension(400, 600));
- setSize(new Dimension(400, 600));
+ // setPreferredSize(new Dimension(400, 600));
+ // setSize(new Dimension(400, 600));
add(setDetails, BorderLayout.NORTH);
add(settingsPanel, BorderLayout.CENTER);
+ JPanel dialogpanel = new JPanel();
+ dialogpanel.add(startjob);
+ dialogpanel.add(canceljob);
+ add(dialogpanel, BorderLayout.SOUTH);
}
- /**
- * need to populate table and validate after calling this to set up table and
- * add it to pane
- */
- public void initTableUI()
+ protected void canceljob_actionPerformed(ActionEvent e)
{
- paramTable = new JTable();
- paramTable.getTableHeader()
- .setFont(new Font("Verdana", Font.PLAIN, 12));
- paramTable.setFont(new Font("Verdana", Font.PLAIN, 12));
-
- paramPane.getViewport().removeAll();
- paramPane.getViewport().add(paramTable);
- paramTable.setDefaultRenderer(Argument.class, new ArgumentRenderer());
- paramTable.setDefaultRenderer(Parameter.class, new ArgumentRenderer());
- paramTable.setDefaultRenderer(Option.class, new ArgumentRenderer());
- paramTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
- paramTable.addMouseListener(new MouseListener()
- {
-
- @Override
- public void mouseClicked(MouseEvent e)
- {
- if (e.getClickCount() > 1)
- {
- editParam_actionPerformed(null);
- }
- }
-
- @Override
- public void mouseEntered(MouseEvent e)
- {
- // tooltips
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void mouseExited(MouseEvent e)
- {
- // tooltips
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void mousePressed(MouseEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void mouseReleased(MouseEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- });
- // paramTable.setDefaultEditor(Argument.class, new WsArgumentEditor(this));
+ response=0;
+ if (frame!=null) {
+ frame.setVisible(false);
+ }
}
- public class WsArgumentEditor implements TableCellEditor
+ protected void startjob_actionPerformed(ActionEvent e)
{
-
- int p;
-
- Argument arg;
-
- WsJobParameters wsparm;
-
- public WsArgumentEditor(WsJobParameters wsJobParameters)
- {
- wsparm = wsJobParameters;
- p = wsparm.paramTable.getSelectedRow();
- arg = (Argument) wsparm.paramTable.getValueAt(p, wsparm.paramTable
- .getSelectedColumn());
- /*
- * if (arg instanceof Option) { if
- * (JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- * "Remove option "+arg.getName(),
- * "Delete option ?",JOptionPane.YES_NO_OPTION,
- * JOptionPane.QUESTION_MESSAGE) == JOptionPane.YES_OPTION) {
- *
- * } }
- */
- }
-
- @Override
- public Component getTableCellEditorComponent(JTable table,
- Object value, boolean isSelected, int row, int column)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void addCellEditorListener(CellEditorListener l)
- {
- // TODO Auto-generated method stub
-
+ response=1;
+ if (frame!=null) {
+ frame.setVisible(false);
}
-
- @Override
- public void cancelCellEditing()
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Object getCellEditorValue()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public boolean isCellEditable(EventObject anEvent)
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public void removeCellEditorListener(CellEditorListener l)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public boolean shouldSelectCell(EventObject anEvent)
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public boolean stopCellEditing()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
}
protected void editParam_actionPerformed(ActionEvent e)
}
- void initForService(Jws2Instance service, Preset p)
+ Jws2Instance service;
+ void initForService(Jws2Instance service, Preset p,
+ List<Argument> jobArgset)
{
+ this.service=service;
serviceOptions = service.getRunnerConfig();
- updateTable(p);
+ updateTable(p, jobArgset);
}
@SuppressWarnings("unchecked")
- private void updateTable(Preset p)
+ private void updateTable(Preset p, List<Argument> jobArgset)
{
- WsParameterTableModel mdl = null;
- TableModel tmdl = paramTable.getModel();
- if (tmdl instanceof WsParameterTableModel)
- {
- mdl = (WsParameterTableModel) tmdl;
- }
- if (mdl == null)
- {
- paramTable.setModel(mdl = new WsParameterTableModel());
- }
availableParameters = new ArrayList<Parameter>();
List<Parameter> setargs = new ArrayList<Parameter>();
// populate table from default parameter set.
List<Argument> args = serviceOptions.getArguments();
-
+
// split to params and required arguments
{
for (Argument arg : args)
if (myarg instanceof Parameter)
{
Parameter parm = (Parameter) myarg;
- if (parm.isRequired())
+ if (true) // parm.isRequired())
{
- setargs.add(parm);
+ addParameter(parm);
}
else
{
}
}
}
+ args=null; // no more args to process.
}
-
if (p != null)
{
setDescr.setText(p.getDescription());
setName.setText(p.getName());
+ setDetails.setVisible(true);
// TODO - URL link
try
{
{
e.printStackTrace();
}
+ // TODO: check if args should be unselected prior to resetting using the preset
setargs.clear();
- // get setargs from current object
- if (args != null)
+ } else {
+ setDetails.setVisible(false);
+ }
+ if (jobArgset != null)
+ {
+ argSetModified(true);
+ args = jobArgset;
+ }
+ // get setargs from current object
+ if (args != null)
+ {
+ for (Argument arg : args)
{
- for (Argument arg : args)
+ if (arg instanceof Parameter)
{
- if (arg instanceof Parameter)
- {
- setargs.add((Parameter) arg);
- }
- else
+ setargs.add((Parameter) arg);
+ }
+ else
+ {
+ if (arg instanceof Option)
{
- if (arg instanceof Option)
- {
- selectOption((Option) arg, arg.getDefaultValue());
- }
+ selectOption((Option) arg, arg.getDefaultValue());
}
-
}
+
}
}
- mdl.setData(setargs);
- paramTable.setModel(mdl);
- // paramTable.validate();
- jobOptions.setLayout(new GridLayout(optSet.size() / 2 + 1, 2));
- jobOptions.validate();
+ // mdl.setData(setargs);
+ // jobOptions.setLayout(new GridLayout(optSet.size() / 2 + 1, 2));
+ jobOptions.setLayout(new GridLayout(optSet.size(), 1));
+ // paramPanel.setLayout(new GridLayout(paramSet.size(), 1));
+ // paramList.va
+ // paramPane.getViewport().validate();
+ paramList.setPreferredSize(new Dimension(350, paramSet.size()
+ * PARAM_HEIGHT));
+ paramList.setLayout(new GridLayout(paramSet.size(), 1));
+ paramList.validate();
+ paramPane.validate();
+ validate();
+ }
+
+ private void argSetModified(boolean b)
+ {
+
+ modified.setVisible(b);
+ if (isVisible())
+ {
+ validate();
+ }
+
+ }
+
+ private void addParameter(Parameter parm)
+ {
+ ParamBox pb = paramSet.get(parm.getName());
+ if (pb == null)
+ {
+ pb = new ParamBox(parm);
+ paramSet.put(parm.getName(), pb);
+ paramList.add(pb);
+ }
}
private void selectOption(Option opt, String string)
}
}
- Map<String, OptionBox> optSet = new Hashtable<String, OptionBox>();
+ Map<String, ParamBox> paramSet = new Hashtable<String, ParamBox>();
- public class OptionBox extends JPanel
+ public class ParamBox extends JPanel implements ChangeListener,
+ ActionListener
{
- JComboBox val = new JComboBox();
-
- JCheckBox enabled = new JCheckBox();
-
- public OptionBox(Option opt)
- {
- setLayout(new BorderLayout());
- enabled.setSelected(opt.isRequired());
- enabled.setFont(new Font("Verdana", Font.PLAIN, 11));
- enabled.setText(opt.getName());
- enabled.setToolTipText(opt.getDescription());
- add(enabled, BorderLayout.NORTH);
- if (opt.getPossibleValues().size() > 1)
- {
- setLayout(new GridLayout(1,2));
- for (Object str : opt.getPossibleValues())
+ JLabel name = new JLabel();
+
+ JTextArea string = new JTextArea();
+ JScrollPane descPanel = new JScrollPane();
+ JSlider slider = null;
+
+ JTextField valueField = null;
+
+ ValueConstrain validator = null;
+
+ boolean integ = false;
+ boolean choice=false;
+ public ParamBox(Parameter parm)
+ {
+ setLayout(new FlowLayout());
+ setBorder(new TitledBorder(parm.getName()));
+ setPreferredSize(new Dimension(PARAM_WIDTH, PARAM_HEIGHT));
+ string.setFont(new Font("Verdana", Font.PLAIN, 11));
+ string.setBackground(getBackground());
+ //string.setSize(new Dimension(PARAM_WIDTH, 80));
+ string.setEditable(false);
+ descPanel.setPreferredSize(new Dimension(PARAM_WIDTH, 70));
+ descPanel.getViewport().setView(string);
+ // string.setMinimumSize(new Dimension(140,80));
+ // string.setMaximumSize(new Dimension(280,80));
+ string.setWrapStyleWord(true);
+ string.setLineWrap(true);
+ string.setColumns(40);
+ string.setText(parm.getDescription());
+ descPanel.validate();
+ // name.setToolTipText(parm.getDescription());
+ add(descPanel); // , BorderLayout.NORTH);
+ validator = parm.getValidValue();
+ parameter=parm;
+ if (validator != null)
+ {
+ integ = validator.getType() == Type.Integer;
+ } else {
+ if (parameter.getPossibleValues()!=null)
{
- val.addItem((String) str);
+ choice=true;
}
- val.setSelectedItem((String) opt.getDefaultValue());
- add(val, BorderLayout.SOUTH);
}
- // TODO: add actionListeners for popup (to open further info),
- // and to update list of parameters if an option is enabled
- // that takes a value.
- }
- }
-
- private OptionBox addOption(Option opt)
- {
- OptionBox cb = optSet.get(opt.getName());
- if (cb == null)
- {
- cb = new OptionBox(opt);
- optSet.put(opt.getName(), cb);
- jobOptions.add(cb);
- }
- return cb;
- }
-
- class WsParameterTableModel extends AbstractTableModel
- {
- // arg list - vector for thread safety
- public Vector<Parameter> data = new Vector<Parameter>();
-
- private String[] colNames =
- { "Parameter", "Value" };
-
- @Override
- public int getColumnCount()
- {
- return 2;
- }
-
- @Override
- public int findColumn(String columnName)
- {
- // TODO Auto-generated method stub
- return super.findColumn(columnName);
+ updateControls(parm);
}
- public void setData(List<Parameter> setargs)
+ boolean adjusting = false;
+ Parameter parameter;
+ JComboBox choicebox;
+ public void updateControls(Parameter parm)
{
- if (setargs != null)
+ adjusting = true;
+ boolean init = valueField == null;
+ float fVal = 0f;
+ int iVal = 0;
+ if (init)
{
- data = new Vector<Parameter>(setargs);
-
+ if (choice)
+ {
+ choicebox = new JComboBox();
+ choicebox.addActionListener(this);
+ add(choicebox);
+ } else {
+ slider = new JSlider();
+ slider.addChangeListener(this);
+ valueField = new JTextField();
+ valueField.addActionListener(this);
+ valueField.setPreferredSize(new Dimension(80, 25));
+ JPanel container = new JPanel();
+ // container.setLayout(new FlowLayout());
+ add(slider);// , BorderLayout.SOUTH);
+ add(valueField);// ,BorderLayout.CENTER);
+ // add(container, BorderLayout.EAST);
+ // container.validate();
+
+ }}
+
+ if (parm != null)
+ {
+ if (choice) {
+ List vals = parm.getPossibleValues();
+ for (Object val: vals)
+ {
+ choicebox.addItem(val);
+ }
+ if (parm.getDefaultValue()!=null) {
+ choicebox.setSelectedItem(parm.getDefaultValue());
+ }
+ } else {
+ valueField.setText(parm.getDefaultValue());
+ }
}
- else
+ updateSliderFromValueField();
+ adjusting = false;
+ }
+ public Parameter getParameter() {
+ try {
+ if (choice)
+ {
+ parameter.setDefaultValue((String)choicebox.getSelectedItem());
+ }
+ else {
+ parameter.setDefaultValue(valueField.getText());
+ }
+ } catch (WrongParameterException e)
{
- data = new Vector<Parameter>();
+ e.printStackTrace();
+ return null;
}
+ return parameter;
}
-
- public List<Parameter> getData()
- {
- return new ArrayList<Parameter>(data);
- }
-
- @Override
- public int getRowCount()
- {
- return data.size();
- }
-
- @Override
- public Object getValueAt(int rowIndex, int columnIndex)
+ public Object updateSliderFromValueField()
{
- if (rowIndex >= 0 && rowIndex < data.size())
+ int iVal;
+ float fVal;
+ if (validator != null)
{
- Parameter prm = data.elementAt(rowIndex);
- switch (columnIndex)
+ if (integ)
{
- case 0:
- return prm.getName();
- case 1:
- Object exc = null;
- // the accessor name for the parameter value is possibly confusing
- String val = prm.getDefaultValue();
+ iVal = 0;
try
{
- if (prm.getValidValue().getType().equals(Type.Float))
- {
- exc = new Float(0);
- return Float.parseFloat(val);
- }
- if (prm.getValidValue().getType().equals(Type.Integer))
- {
- exc = new Integer(0);
- return Integer.parseInt(val);
- }
- } catch (NumberFormatException e)
+ valueField.setText(valueField.getText().trim());
+ iVal = Integer.valueOf(valueField.getText());
+ } catch (Exception e)
{
- return exc;
}
- // must be a string
- return val;
-
- default:
+ ;
+ if (validator.getMin() != null && validator.getMax() != null)
+ {
+ slider.getModel().setRangeProperties(iVal, 1,
+ validator.getMin().intValue(),
+ validator.getMax().intValue(), true);
+ }
+ else
+ {
+ slider.setVisible(false);
+ }
+ return new int[]
+ { iVal };
+ }
+ else
+ {
+ fVal = 0f;
+ try
+ {
+ fVal = Float.valueOf(valueField.getText());
+ } catch (Exception e)
+ {
+ }
+ ;
+ if (validator.getMin() != null && validator.getMax() != null)
+ {
+ slider.getModel().setRangeProperties((int) fVal * 1000, 1,
+ (int) validator.getMin().floatValue() * 1000,
+ (int) validator.getMax().floatValue() * 1000, true);
+ }
+ else
+ {
+ slider.setVisible(false);
+ }
+ return new float[]
+ { fVal };
}
}
- return null;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.table.AbstractTableModel#getColumnClass(int)
- */
- @Override
- public Class<?> getColumnClass(int columnIndex)
- {
- switch (columnIndex)
+ else
{
- case 0:
- return String.class;
- case 1:
- return Parameter.class;
+ if (!choice) {
+ slider.setVisible(false);
+ return new String[]
+ { valueField.getText().trim() };
+ }
+ else {
+ return new String[] { (String) choicebox.getSelectedItem()};
+ }
}
- return super.getColumnClass(columnIndex);
+
}
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.table.AbstractTableModel#getColumnName(int)
- */
@Override
- public String getColumnName(int column)
+ public void stateChanged(ChangeEvent e)
{
- return colNames[column];
+ if (!adjusting)
+ {
+ valueField.setText(""
+ + ((integ) ? ("" + (int) slider.getValue())
+ : ("" + (float) (slider.getValue() / 1000f))));
+ }
}
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.table.AbstractTableModel#isCellEditable(int, int)
- */
@Override
- public boolean isCellEditable(int rowIndex, int columnIndex)
+ public void actionPerformed(ActionEvent e)
{
- if (columnIndex == 1)
+ if (choice)
{
- return true;
+ } else if (!adjusting)
+ {
+ updateSliderFromValueField();
}
- return false;
+ argSetModified(true);
}
+
}
- class ArgumentRenderer implements TableCellRenderer
+ Map<String, OptionBox> optSet = new Hashtable<String, OptionBox>();
+
+ public class OptionBox extends JPanel implements ActionListener
{
+ JComboBox val = new JComboBox();
- @Override
- public Component getTableCellRendererComponent(JTable table,
- Object value, boolean isSelected, boolean hasFocus, int row,
- int column)
+ JCheckBox enabled = new JCheckBox();
+ Option option;
+ public OptionBox(Option opt)
{
- if (value instanceof Option)
+ option = opt;
+ setLayout(new BorderLayout());
+ enabled.setSelected(opt.isRequired());
+ enabled.setFont(new Font("Verdana", Font.PLAIN, 11));
+ enabled.setText(opt.getName());
+ enabled.setToolTipText(opt.getDescription());
+ add(enabled, BorderLayout.NORTH);
+ if (opt.getPossibleValues().size() > 1)
{
- JCheckBox cb = new JCheckBox();
- cb.setSelected(true);
- return cb;
+ setLayout(new GridLayout(1, 2));
+ for (Object str : opt.getPossibleValues())
+ {
+ val.addItem((String) str);
+ }
+ val.setSelectedItem((String) opt.getDefaultValue());
+ val.addActionListener(this);
+ add(val, BorderLayout.SOUTH);
}
- if (value instanceof Boolean)
+ // TODO: add actionListeners for popup (to open further info),
+ // and to update list of parameters if an option is enabled
+ // that takes a value.
+ }
+ public Option getOptionIfEnabled() {
+ if (!enabled.isSelected())
{
- JCheckBox cb = new JCheckBox();
- cb.setSelected(((Boolean) value).booleanValue());
- return cb;
+ return null;
}
- if (value instanceof String)
+ try {
+ if (val.getSelectedItem()!=null)
+ {
+ option.setDefaultValue((String) val.getSelectedItem());
+ }
+ } catch (WrongParameterException e)
{
- JLabel lbl = new JLabel();
- lbl.setFont(new Font("Verdana", Font.PLAIN, 11));
- lbl.setText((String) value);
- return lbl;
- }
- if (value instanceof Parameter)
- {
- String val = ((Parameter) value).getDefaultValue();
- ValueConstrain constr = ((Parameter) value).getValidValue();
- JLabel lbl = new JLabel();
- lbl.setFont(new Font("Verdana", Font.PLAIN, 11));
- lbl.setText(val);
- return lbl;
- /*
- * type dependent return value if
- * (constr.getType().equals(Type.Integer))
- *
- * { lbl.setText(val); } if (constr.getType().equals(Type.Float)) { }
- * return lbl;
- */
+ e.printStackTrace();
+ return null;
}
- return null;
+ return option;
+ }
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ argSetModified(true);
+ enabled.setSelected(true);
}
}
+ private OptionBox addOption(Option opt)
+ {
+ OptionBox cb = optSet.get(opt.getName());
+ if (cb == null)
+ {
+ cb = new OptionBox(opt);
+ optSet.put(opt.getName(), cb);
+ jobOptions.add(cb);
+ }
+ return cb;
+ }
+
/**
* testing method - grab a service and parameter set and show the window
*
}
if (lastserv != null)
{
+ List<Preset> prl = null;
Preset pr = null;
if (++p < args.length)
{
if (pr == null)
{
// just grab the last preset.
- List<Preset> prl = prman.getPresets();
- pr = prl.get(prl.size() - 1);
+ prl = prman.getPresets();
}
}
}
+ Iterator<Preset> en = (prl == null) ? null : prl.iterator();
while (true)
{
+ if (en != null)
+ {
+ if (!en.hasNext())
+ {
+ en = prl.iterator();
+ }
+ pr = en.next();
+ }
WsJobParameters pgui = new WsJobParameters(lastserv, pr);
JFrame jf = new JFrame("Parameters for " + lastserv.getActionText());
JPanel cont = new JPanel();
- cont.setSize(new Dimension(600, 800));
+ jf.setPreferredSize(new Dimension(600, 800));
cont.add(pgui);
jf.add(cont);
final Thread thr = Thread.currentThread();
}
}
}
+
+ public List<Argument> getJobParams()
+ {
+ List<Argument> argSet = new ArrayList<Argument>();
+ // recover options and parameters from GUI
+ for (OptionBox opts: optSet.values())
+ {
+ Option opt = opts.getOptionIfEnabled();
+ if (opt!=null)
+ {
+ argSet.add(opt);
+ }
+ }
+ for (ParamBox parambox: paramSet.values())
+ {
+ Parameter parm = parambox.getParameter();
+ if (parm!=null)
+ {
+ argSet.add(parm);
+ }
+ }
+
+ return argSet;
+ }
}
* server is a WSDL2Java generated stub for an archetypal MsaWSI service.
*/
MsaWS server;
+
AlignFrame alignFrame;
+
private Preset preset;
- private List<Argument> paramset;
+ private List<Argument> paramset;
public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
{
- this(sh, null, null, altitle, msa, submitGaps, preserveOrder, seqdataset, _alignFrame);
+ this(sh, null, null, false, altitle, msa, submitGaps, preserveOrder,
+ seqdataset, _alignFrame);
// TODO Auto-generated constructor stub
}
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset, String altitle,
- jalview.datamodel.AlignmentView msa, boolean submitGaps,
- boolean preserveOrder, Alignment seqdataset,
+ public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
+ String altitle, jalview.datamodel.AlignmentView msa,
+ boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
{
- this(sh, preset, null, altitle, msa, submitGaps, preserveOrder, seqdataset, _alignFrame);
+ this(sh, preset, null, false, altitle, msa, submitGaps, preserveOrder,
+ seqdataset, _alignFrame);
// TODO Auto-generated constructor stub
}
+
/**
* Creates a new MsaWSClient object that uses a service given by an externally
* retrieved ServiceHandle
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset, List<Argument> arguments, String altitle,
+ public MsaWSClient(Jws2Discoverer.Jws2Instance sh, Preset preset,
+ List<Argument> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
- AlignFrame _alignFrame) {
+ AlignFrame _alignFrame)
+ {
super();
alignFrame = _alignFrame;
if (!(sh.service instanceof MsaWS))
server = sh.service;
this.preset = preset;
this.paramset = arguments;
+ if (editParams)
+ {
+ WsJobParameters jobParams = new WsJobParameters(sh, preset);
+ if (!jobParams.showRunDialog())
+ {
+ return;
+ }
+ preset = null;
+ paramset = jobParams.getJobParams();
+ }
+
if ((wsInfo = setWebService(sh, false)) == null)
{
JOptionPane.showMessageDialog(Desktop.desktop,
private void startMsaWSClient(String altitle, AlignmentView msa,
boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
{
- //if (!locateWebService())
- // {
- // return;
- // }
+ // if (!locateWebService())
+ // {
+ // return;
+ // }
wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")
+ " of " + altitle + "\nJob details\n");
+ "alignment of " + altitle;
}
- MsaWSThread msathread = new MsaWSThread(server, preset, paramset, WsURL, wsInfo,
- alignFrame, WebServiceName, jobtitle, msa, submitGaps,
- preserveOrder, seqdataset);
+ MsaWSThread msathread = new MsaWSThread(server, preset, paramset,
+ WsURL, wsInfo, alignFrame, WebServiceName, jobtitle, msa,
+ submitGaps, preserveOrder, seqdataset);
wsInfo.setthisService(msathread);
msathread.start();
}
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
- public void attachWSMenuEntry(JMenu msawsmenu,
+ public void attachWSMenuEntry(JMenu rmsawsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{
setWebService(service, true); // headless
- JMenuItem method = new JMenuItem(WebServiceName);
- method.setToolTipText(WsURL);
- method.addActionListener(new ActionListener()
+ boolean finished = true, submitGaps = false;
+ JMenu msawsmenu = rmsawsmenu;
+ String calcName = WebServiceName + " ";
+ if (canSubmitGaps())
{
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, alignFrame.getTitle(),
- msa, false, true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ msawsmenu = new JMenu(WebServiceName);
+ rmsawsmenu.add(msawsmenu);
+ calcName = "";
+ }
+ do
+ {
+ if (submitGaps == true)
+ {
+ msawsmenu = new JMenu("profile " + WebServiceName);
+ rmsawsmenu.add(msawsmenu);
}
+ final boolean withGaps = submitGaps;
+ JMenuItem method = new JMenuItem(calcName + "Defaults");
+ method.setToolTipText(WsURL);
- });
- msawsmenu.add(method);
- if (canSubmitGaps())
- {
- // We know that ClustalWS can accept partial alignments for refinement.
- final JMenuItem methodR = new JMenuItem(WebServiceName
- + " (With Gaps)");
- methodR.setToolTipText(WsURL);
- methodR.addActionListener(new ActionListener()
+ method.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, alignFrame.getTitle(),
- msa, true, true, alignFrame.getViewport().getAlignment()
+ new MsaWSClient(service, alignFrame.getTitle(), msa, withGaps,
+ true, alignFrame.getViewport().getAlignment()
.getDataset(), alignFrame);
}
-
});
- msawsmenu.add(methodR);
+ msawsmenu.add(method);
+ method = new JMenuItem(calcName + " Edit Parameters...");
+ method.setToolTipText(WsURL);
- }
- PresetManager presets = service.getPresets();
- if (presets!=null && presets.getPresets().size()>0)
- {
- JMenu presetlist = new JMenu("Presets for "+WebServiceName+"(Without gaps)");
-
- for (final Preset preset : (List<Preset>) presets.getPresets())
+ method.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ new MsaWSClient(service, null, null, true, alignFrame.getTitle(),
+ msa, withGaps, true, alignFrame.getViewport()
+ .getAlignment().getDataset(), alignFrame);
+
+ }
+ });
+ msawsmenu.add(method);
+ PresetManager presets = service.getPresets();
+ if (presets != null && presets.getPresets().size() > 0)
{
- final JMenuItem methodR = new JMenuItem(preset.getName());
- methodR.setToolTipText(preset.getDescription());
- methodR.addActionListener(new ActionListener()
+ JMenu presetlist = new JMenu(calcName + "Presets");
+
+ for (final Preset preset : (List<Preset>) presets.getPresets())
{
- public void actionPerformed(ActionEvent e)
+ final JMenuItem methodR = new JMenuItem(preset.getName());
+ methodR.setToolTipText(preset.getDescription());
+ methodR.addActionListener(new ActionListener()
{
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- new MsaWSClient(service, preset, alignFrame.getTitle(),
- msa, false, true, alignFrame.getViewport().getAlignment()
- .getDataset(), alignFrame);
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentView msa = alignFrame.gatherSequencesForAlignment();
+ new MsaWSClient(service, preset, alignFrame.getTitle(), msa,
+ false, true, alignFrame.getViewport().getAlignment()
+ .getDataset(), alignFrame);
- }
+ }
- });
- presetlist.add(methodR);
+ });
+ presetlist.add(methodR);
+ }
+ msawsmenu.add(presetlist);
}
- msawsmenu.add(presetlist);
- }
-
+ if (!submitGaps && canSubmitGaps())
+ {
+ submitGaps = true;
+ finished = false;
+ }
+ else
+ {
+ finished = true;
+ }
+ } while (!finished);
}
-
}
git://source.jalview.org / jalview.git / commitdiff