--- /dev/null
+package jalview.gui;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+
+import javax.swing.JDialog;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.event.ListSelectionEvent;
+
+import com.sun.tools.corba.se.idl.InvalidArgument;
+
+import net.miginfocom.swing.MigLayout;
+
+import jalview.jbgui.GRestInputParamEditDialog;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.rest.InputType;
+import jalview.ws.rest.RestServiceDescription;
+
+public class RestInputParamEditDialog extends GRestInputParamEditDialog
+ implements OptsParametersContainerI
+{
+ Hashtable<String, Class> typeclass = new Hashtable<String, Class>();
+
+ Hashtable<String, ArrayList<JPanel>> typeopts = new Hashtable<String, ArrayList<JPanel>>();
+
+ Hashtable<String,OptsAndParamsPage> opanps = new Hashtable<String, OptsAndParamsPage>();
+
+ private InputType getTypeFor(String name)
+ {
+ try
+ {
+ return (InputType) (typeclass.get(name).getConstructor()
+ .newInstance(null));
+ } catch (Throwable x)
+ {
+ System.err
+ .println("Unexpected exception when instantiating rest input type.");
+ x.printStackTrace();
+ }
+ return null;
+ }
+
+ int reply;
+ JalviewDialog frame = new JalviewDialog()
+ {
+
+ @Override
+ protected void raiseClosed()
+ {
+
+ }
+
+ @Override
+ protected void okPressed()
+ {
+ reply=JOptionPane.OK_OPTION;
+ }
+
+ @Override
+ protected void cancelPressed()
+ {
+ reply=JOptionPane.CANCEL_OPTION;
+
+ }
+ };
+ InputType old,current;
+ public RestInputParamEditDialog(
+ RestServiceEditorPane restServiceEditorPane,
+ RestServiceDescription currentservice, InputType toedit)
+ {
+ initFor(restServiceEditorPane, currentservice, toedit);
+ frame.waitForInput();
+ // TODO: warn user if they are about to overwrite an existing parameter because they have used the same name when editing a different parameter.
+ // TODO: make any press of the return key cause 'OK' to be pressed
+ }
+ private void initFor(RestServiceEditorPane restServiceEditorPane,
+ RestServiceDescription currentservice, InputType toedit)
+ {
+ okcancel.add(frame.cancel);
+ okcancel.add(frame.ok);
+ frame.initDialogFrame(dpane, true, true, "Edit parameter for service "+currentservice.getName(), 600,800);
+
+ initTypeLists();
+ reply=JOptionPane.CANCEL_OPTION;
+ old = toedit;
+ current = null;
+ if (old!=null) {
+ setStateFor(old);
+ }
+ updated = updated && reply==JOptionPane.OK_OPTION;
+ frame.validate();
+ }
+
+ public RestInputParamEditDialog(
+ RestServiceEditorPane restServiceEditorPane,
+ RestServiceDescription currentservice, String string)
+ {
+ initFor(restServiceEditorPane, currentservice,null);
+ tok.setText(string);
+ frame.waitForInput();
+ }
+
+ private void setStateFor(InputType current)
+ {
+ tok.setText(current.token);
+ OptsAndParamsPage opanp=opanps.get(current.getURLtokenPrefix());
+ for (OptionI ops:current.getOptions())
+ {
+ if (ops instanceof ParameterI)
+ {
+ opanp.setParameter((ParameterI) ops);
+ } else {
+ if (ops.getValue()!=null && ops.getValue().length()>0) {
+ opanp.selectOption(ops, ops.getValue());
+ }
+ }
+ }
+ typeList.setSelectedValue(current.getURLtokenPrefix(), true);
+ type_SelectionChangedActionPerformed(null);
+ }
+ private void updateCurrentType()
+ {
+ if (typeList.getSelectedValue()!=null) {
+ InputType newType = getTypeFor((String)typeList.getSelectedValue());
+ if (newType!=null) {
+ newType.token = tok.getText().trim();
+ try {
+ newType.configureFromArgumentI(opanps.get(newType.getURLtokenPrefix()).getCurrentSettings());
+ current=newType;
+ updated=true;
+ } catch (InvalidArgumentException ex) {
+ System.err.println("IMPLEMENTATION ERROR: Invalid argument for type : "+typeList.getSelectedValue()+"\n");
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ }
+ private void initTypeLists()
+ {
+ ArrayList<String> types=new ArrayList<String>();
+ // populate type list
+ for (Class type : RestServiceDescription.getInputTypes())
+ {
+
+ InputType jtype = null;
+ try
+ {
+ JPanel inopts = new JPanel(new MigLayout());
+ ArrayList<JPanel> opts = new ArrayList<JPanel>(), prms = new ArrayList<JPanel>();
+ jtype = (InputType) (type.getConstructor().newInstance(null));
+ typeclass.put(jtype.getURLtokenPrefix(), type);
+ // and populate parameters from this type
+ OptsAndParamsPage opanp = new OptsAndParamsPage(this,true);
+ opanps.put(jtype.getURLtokenPrefix(),opanp);
+ for (OptionI opt : jtype.getOptions())
+ {
+
+ if (opt instanceof ParameterI)
+ {
+ prms.add(opanp.addParameter((ParameterI) opt));
+ }
+ else
+ {
+ opts.add(opanp.addOption(opt));
+ }
+ }
+ // then tag the params at the end of the options.
+ for (JPanel pnl : prms)
+ {
+ opts.add(pnl);
+ }
+ typeopts.put(jtype.getURLtokenPrefix(), opts);
+ types.add(jtype.getURLtokenPrefix());
+ } catch (Throwable x)
+ {
+ System.err
+ .println("Unexpected exception when instantiating rest input type.");
+ x.printStackTrace();
+ }
+ }
+ typeList.setListData(types.toArray());
+
+ }
+
+ @Override
+ protected void type_SelectionChangedActionPerformed(ListSelectionEvent e)
+ {
+ options.removeAll();
+ String typen = (String) typeList.getSelectedValue();
+ if (typeopts.get(typen) != null)
+ {
+ for (JPanel opt : typeopts.get(typen))
+ {
+ opt.setOpaque(true);
+ options.add(opt,"wrap");
+ }
+ options.invalidate();
+ optionsPanel.setVisible(true);
+ }
+ else
+ {
+ optionsPanel.setVisible(false);
+ }
+ dpane.revalidate();
+ updateCurrentType();
+ }
+
+ boolean updated=false;
+ public boolean wasUpdated()
+ {
+ return updated;
+ }
+
+ @Override
+ public void refreshParamLayout()
+ {
+ options.invalidate();
+ dpane.revalidate();
+ }
+
+ @Override
+ protected void tokChanged_actionPerformed()
+ {
+ if (tok.getText().trim().length()>0)
+ {
+ if (current!=null)
+ {
+ current.token = tok.getText().trim();
+ updated = true;
+ }
+ }
+ }
+ @Override
+ public void argSetModified(Object modifiedElement, boolean b)
+ {
+ updated = updated | b;
+ if (updated)
+ {
+ updateCurrentType();
+ }
+ }
+
+}
package jalview.gui;
-import jalview.bin.Cache;
import jalview.io.packed.DataProvider.JvDataType;
-import jalview.jbgui.*;
+import jalview.jbgui.GRestServiceEditorPane;
import jalview.ws.rest.InputType;
import jalview.ws.rest.RestServiceDescription;
-import java.awt.*;
+import java.awt.BorderLayout;
+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.WindowEvent;
-import java.awt.event.WindowListener;
-import java.awt.event.WindowStateListener;
-import java.util.ArrayList;
+import java.awt.event.MouseEvent;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.Vector;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import javax.swing.*;
-import javax.swing.event.CaretEvent;
+import javax.swing.JFrame;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-import javax.swing.text.GapContent;
-
-import org.apache.log4j.lf5.LogLevel;
public class RestServiceEditorPane extends GRestServiceEditorPane
{
// begin with initial text description box enabled.
urldesc.addKeyListener(new KeyListener()
{
- long lastWait;
- boolean doUpdate;
- Thread updater=null;
@Override
public void keyTyped(KeyEvent e)
{
@Override
public void keyPressed(KeyEvent e)
{
- // TODO Auto-generated method stub
}
});
}
});
+ currentservice = new RestServiceDescription("Analysis", "service description", "service name", "http://localhost/", "", null, false, false, '-');
+ initGuiWith(currentservice);
+ refreshCutnPaste(false);
+ updateButtons();
}
public RestServiceEditorPane(RestServiceDescription toedit)
{
- this();
+ super();
oldservice = toedit;
- currentservice = new RestServiceDescription(toedit);
+ if (oldservice!=null)
+ { currentservice = new RestServiceDescription(toedit);
+ } else {
+ currentservice = new RestServiceDescription("Analysis", "service description", "service name", "http://localhost/", "", null, false, false, '-');
+ }
initGuiWith(currentservice);
refreshCutnPaste(false);
updateButtons();
*/
public void updateButtons()
{
- cancelButton.setEnabled(oldservice != null);
+ cancelButton.setEnabled(true);
okButton.setEnabled(currentservice != null && currentservice.isValid());
}
*/
private void initGuiWith(RestServiceDescription currentservice)
{
+ _iparam.clear();
+ _rparam.clear();
+ action.removeAllItems();
+ action.addItem("Alignment");
+ action.addItem("Analysis");
+ gapChar.removeAllItems();
+ gapChar.addItem(".");
+ gapChar.addItem(" ");
+ gapChar.addItem("-");
+ if (currentservice==null)
+ {
+ name.setText("");
+ descr.setText("");
+ url.setText("");
+ urlsuff.setText("");
+ action.setSelectedItem("Analysis");
+ gapChar.setSelectedItem("-");
+ } else {
name.setText(currentservice.getName());
descr.setText(currentservice.getDescription());
url.setText(currentservice.getPostUrl());
urlsuff.setText(currentservice.getUrlSuffix());
- _iparam.clear();
- _rparam.clear();
for (Map.Entry<String, InputType> inparam : currentservice
.getInputParams().entrySet())
{
+ inparam.getValue().getURLtokenPrefix() + ":"
+ inparam.getValue().getURLEncodedParameter().toString());
}
+
for (JvDataType oparam : currentservice.getResultDataTypes())
{
- _rparam.add((oparam.name()));
+ _rparam.add(oparam.name());
}
iprms.setListData(_iparam);
rdata.setListData(_rparam);
- action.removeAllItems();
- action.addItem("Alignment");
- action.addItem("Analysis");
- // action.addItem("Analysis");
action.setSelectedItem(currentservice.getAction());
+
+ gapChar.setSelectedItem(""+currentservice.getGapCharacter());
+ }
revalidate();
}
+ private String getSelectedInputToken()
+ {
+ if (iprms.getSelectedIndex()>-1)
+ {
+ String toktoedit = (String) iprms.getSelectedValue();
+ toktoedit=toktoedit.substring(0, toktoedit.indexOf(" "));
+ return toktoedit;
+ }
+ return null;
+ }
+ @Override
+ protected void iprmListSelection_doubleClicked()
+ {
+ String toktoedit = getSelectedInputToken();
+ if (toktoedit!=null)
+ {
+ InputType toedit = currentservice.getInputParams().get(toktoedit);
+ String oldParam=toktoedit;
+ RestInputParamEditDialog dialog=new RestInputParamEditDialog(this, currentservice, toedit);
+ if (dialog.wasUpdated()) {
+ currentservice.getInputParams().remove(oldParam);
+ currentservice.getInputParams().put(dialog.current.token, dialog.current);
+ initGuiWith(currentservice);
+ }
+
+ }
+ }
+ @Override
+ protected void iprmsAdd_actionPerformed(ActionEvent e)
+ {
+ RestInputParamEditDialog dialog=new RestInputParamEditDialog(this, currentservice, "param"+(1+currentservice.getInputParams().size()));
+ if (dialog.wasUpdated()) {
+ currentservice.getInputParams().put(dialog.current.token, dialog.current);
+ initGuiWith(currentservice);
+ }
+
+ }
+ @Override
+ protected void iprmsRem_actionPerformed(ActionEvent e)
+ {
+ String toktoedit = getSelectedInputToken();
+ if (toktoedit!=null)
+ {
+ currentservice.getInputParams().remove(toktoedit);
+ initGuiWith(currentservice);
+
+ }
+ }
+ @Override
+ protected void rdata_rightClicked(MouseEvent mouse)
+ {
+ final int rdatasel = rdata.getSelectedIndex();
+ if (rdatasel>-1)
+ {
+ JPopupMenu popup = new JPopupMenu("Select return type");
+ for (final JvDataType type:JvDataType.values()) {
+ popup.add(new JMenuItem(type.name())).addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ currentservice.getResultDataTypes().set(rdatasel, type);
+ initGuiWith(currentservice);
+ rdata.setSelectedIndex(rdatasel);
+ }
+ });
+ }
+ popup.show(rdata, mouse.getX(), mouse.getY());
+ }
+ }
+ @Override
+ protected void rdataAdd_actionPerformed(ActionEvent e)
+ {
+ int p;
+ if ((p=rdata.getSelectedIndex())>-1)
+ {
+ currentservice.getResultDataTypes().add(p+1, JvDataType.ANNOTATION);
+ } else {
+ currentservice.addResultDatatype(JvDataType.ANNOTATION);
+ }
+ initGuiWith(currentservice);
+ rdata.setSelectedIndex(p==-1 ? currentservice.getResultDataTypes().size()-1 : p+1);
+ }
+ @Override
+ protected void rdataNdown_actionPerformed(ActionEvent e)
+ {
+ int p;
+ if ((p=rdata.getSelectedIndex())>-1 && p<_rparam.size()-1)
+ {
+ List<JvDataType> rtypes = currentservice.getResultDataTypes();
+ JvDataType below = rtypes.get(p+1);
+ rtypes.set(p+1, rtypes.get(p));
+ rtypes.set(p, below);
+ initGuiWith(currentservice);
+ rdata.setSelectedIndex(p+1);
+ }
+ }
+ @Override
+ protected void rdataNup_actionPerformed(ActionEvent e)
+ {
+ int p;
+ if ((p=rdata.getSelectedIndex())>0)
+ {
+ List<JvDataType> rtypes = currentservice.getResultDataTypes();
+ JvDataType above = rtypes.get(p-1);
+ rtypes.set(p-1, rtypes.get(p));
+ rtypes.set(p, above);
+ initGuiWith(currentservice);
+ rdata.setSelectedIndex(p-1);
+ }
+ }
+ @Override
+ protected void rdataRem_actionPerformed(ActionEvent e)
+ {
+ if (rdata.getSelectedIndex()>-1)
+ {
+ currentservice.getResultDataTypes().remove(rdata.getSelectedIndex());
+ initGuiWith(currentservice);
+ }
+ }
private boolean updateServiceFromGui() {
- boolean valid=true;
Map<String,InputType>inputTypes = new HashMap<String, InputType>();
StringBuffer warnings=new StringBuffer();
for (String its:_iparam)
public void run()
{
+ boolean nulserv=true;
while (visible)
{
final Thread runner = Thread.currentThread();
JFrame df = new JFrame();
df.getContentPane().setLayout(new BorderLayout());
df.getContentPane().add(
- new RestServiceEditorPane(jalview.ws.rest.RestClient
- .makeShmmrRestClient().getRestDescription()),
+ (nulserv=!nulserv) ? new RestServiceEditorPane(jalview.ws.rest.RestClient
+ .makeShmmrRestClient().getRestDescription()) : new RestServiceEditorPane(),
BorderLayout.CENTER);
- df.setBounds(100, 100, 400, 600);
+ df.setBounds(100, 100, 600, 400);
df.addComponentListener(new ComponentListener()
{
@Override
public void componentShown(ComponentEvent e)
{
- // TODO Auto-generated method stub
}
@Override
public void componentResized(ComponentEvent e)
{
- // TODO Auto-generated method stub
}
@Override
public void componentMoved(ComponentEvent e)
{
- // TODO Auto-generated method stub
}
--- /dev/null
+package jalview.jbgui;
+
+import java.awt.Dimension;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+
+import jalview.gui.JvSwingUtils;
+import jalview.gui.OptsAndParamsPage;
+
+import javax.swing.*;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+import net.miginfocom.swing.MigLayout;
+
+
+public class GRestInputParamEditDialog
+{
+
+ protected JPanel dpane;
+ protected JPanel okcancel;
+ protected JList typeList;
+ protected JTextField tok;
+ protected JPanel options;
+ protected JPanel optionsPanel;
+ public GRestInputParamEditDialog()
+ {
+ jbInit();
+ }
+ protected void jbInit() {
+ dpane = new JPanel(new MigLayout("","[][][fill]","[][fill][]"));
+ dpane.setPreferredSize(new Dimension(110+100+OptsAndParamsPage.PARAM_WIDTH,400));
+ typeList = new JList();
+ typeList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ typeList.getSelectionModel().addListSelectionListener(new ListSelectionListener()
+ {
+
+ @Override
+ public void valueChanged(ListSelectionEvent e)
+ {
+ type_SelectionChangedActionPerformed(e);
+ };
+ });
+
+ tok = new JTextField();
+ tok.addKeyListener(new KeyListener()
+ {
+
+ @Override
+ public void keyTyped(KeyEvent e)
+ {
+ }
+
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ tokChanged_actionPerformed();
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+
+ }
+ });
+ options = new JPanel(new MigLayout("","[grow 100,fill]",""));
+ optionsPanel = new JPanel(new MigLayout("","[fill]","[fill]"));
+ JScrollPane optionView = new JScrollPane();
+ optionView.setViewportView(options);
+ JvSwingUtils.mgAddtoLayout(dpane, "Input Parameter name", new JLabel("Name"), tok, "grow,spanx 3,wrap");
+ JPanel paramsType = new JPanel(new MigLayout("","[grow 100,fill]","[grow 100,fill]"));
+ paramsType.setBorder(new TitledBorder("Select input type"));
+ JScrollPane jlistScroller=new JScrollPane();
+ jlistScroller.setViewportView(typeList);
+ paramsType.add(jlistScroller,"spanx 2,spany 2");
+ dpane.add(paramsType);
+ optionsPanel.setBorder(new TitledBorder("Set options for type"));
+ optionsPanel.add(optionView);
+ dpane.add(optionsPanel,"wrap");
+ okcancel = new JPanel(new MigLayout("","[center][center]","[]"));
+ dpane.add(okcancel,"spanx 3,wrap");
+
+ }
+ protected void tokChanged_actionPerformed()
+ {
+
+ }
+ protected void type_SelectionChangedActionPerformed(ListSelectionEvent e)
+ {
+ }
+
+}
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
import javax.swing.BoxLayout;
import javax.swing.JButton;
import javax.swing.JTabbedPane;
import javax.swing.JTextArea;
import javax.swing.JViewport;
+import javax.swing.ListSelectionModel;
import javax.swing.UIManager;
import javax.swing.border.TitledBorder;
import javax.swing.event.CaretEvent;
import javax.swing.event.CaretListener;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
+import javax.swing.event.ListSelectionListener;
import net.miginfocom.swing.MigLayout;
cpanel,
"What kind of function the service performs (e.g. alignment, analysis, search, etc).",
new JLabel("Service Action:"), action,"wrap");
- descr = new JTextArea(4, 40);
+ descr = new JTextArea(4, 60);
descrVp = new JScrollPane();
descrVp.setViewportView(descr);
JvSwingUtils.mgAddtoLayout(cpanel, "Brief description of service",
new JLabel("Description:"), descrVp,"wrap");
- url = new JTextArea(2, 20);
+ url = new JTextArea(2, 60);
urlVp = new JScrollPane();
urlVp.setViewportView(url);
JvSwingUtils
new JLabel("POST URL:"), urlVp,"wrap");
urlsuff = new JTextArea();
- urlsuff.setColumns(20);
+ urlsuff.setColumns(60);
JvSwingUtils
.mgAddtoLayout(
// Inputparams
JPanel iprmsList = new JPanel();
iprmsList.setBorder(new TitledBorder("Data input parameters"));
- iprmsList.setLayout(new MigLayout());
+ iprmsList.setLayout(new MigLayout("","[grow 90, fill][]"));
iprmVp = new JScrollPane();
iprmVp.getViewport().setView(iprms = new JList());
iprmsList.add(iprmVp);
+ iprms.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+ iprms.addMouseListener(new MouseListener()
+ {
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount()>1) {
+ iprmListSelection_doubleClicked();
+ }
+
+ }
+ });
JPanel iprmButs = new JPanel();
iprmButs.setLayout(new MigLayout());
JPanel rparamList = new JPanel();
rparamList.setBorder(new TitledBorder("Data returned by service"));
- rparamList.setLayout(new MigLayout());
+ rparamList.setLayout(new MigLayout("","[grow 90, fill][]"));
rdata = new JList();
+ rdata.setToolTipText("Right click to edit currently selected parameter.");
+ rdata.addMouseListener(new MouseListener()
+ {
+
+ @Override
+ public void mouseReleased(MouseEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mousePressed(MouseEvent arg0)
+ {
+
+ }
+
+ @Override
+ public void mouseExited(MouseEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent arg0)
+ {
+ if (arg0.getButton()==MouseEvent.BUTTON3)
+ {
+ rdata_rightClicked(arg0);
+ }
+
+ }
+ });
rdataVp = new JScrollPane();
rdataVp.getViewport().setView(rdata);
rparamList.add(rdataVp);
// Parse flat-text to a service
- urldesc = new JTextArea(4,50);
+ urldesc = new JTextArea(4,60);
urldesc.setEditable(true);
urldesc.setWrapStyleWord(true);
urldescVp = new JScrollPane();
parseResVp = new JScrollPane();
parseResVp.setViewportView(parseRes);
parseRes.setWrapStyleWord(true);
- parseRes.setColumns(40);
+ parseRes.setColumns(60);
parseWarnings = new JPanel(new MigLayout("","[grow 100, fill]", "[grow 100, fill]"));
parseWarnings.setBorder(new TitledBorder("Parsing errors"));
parseWarnings.setToolTipText("<html>"+JvSwingUtils.wrapTooltip("Results of parsing the RSBS representation")+"</html>");
}
+ protected void rdata_rightClicked(MouseEvent arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void iprmListSelection_doubleClicked()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
protected void hSeparable_actionPerformed(ActionEvent arg0)
{
// TODO Auto-generated method stub
package jalview.ws.rest;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.Option;
import jalview.ws.rest.params.SeqGroupIndexVector;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.nio.charset.Charset;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
* not used yet
*/
boolean replaceids;
- public enum molType { NUC, PROT, MIX}
+ public enum molType { NUC, PROT, MIX;
+
+ public static Collection<String> toStringValues()
+ {
+ Collection<String> c = new ArrayList<String>();
+ for (molType type:values())
+ {
+ c.add(type.toString());
+ }
+ return c;
+ }}
public String token;
public int min=1;
public int max=0; // unbounded
* @return true if property was set
*/
public abstract boolean configureProperty(String tok, String val, StringBuffer warnings);
-
+
/**
* Get unique key for this type of parameter in a URL encoding.
* @return the string that prefixes an input parameter of InputType<T> type in the string returned from getURLEncodedParameter
warnings.append("Invalid value for parameter "+mtch.group(1).toLowerCase()+" '"+mtch.group(2)+"' (expected an integer)\n");
}
- valid = valid && configureProperty(mtch.group(1), mtch.group(2), warnings);
+ if (!configureProperty(mtch.group(1), mtch.group(2), warnings)) {
+ if (warnings.length()==0)
+ {
+ warnings.append("Failed to configure InputType :"+getURLtokenPrefix()+" with property string: '"+mtch.group(0)+"'\n (token is '"+mtch.group(1)+"' and value is '"+mtch.group(2)+"')\n");
+ }
+ valid=false;
+ }
}
}
return valid;
prms.add("min='"+min+"'");
}
if (max!=0) {
- prms.add("min='"+max+"'");
+ prms.add("max='"+max+"'");
}
}
+
+ public abstract List<OptionI> getOptions();
+ public List<OptionI> getBaseOptions()
+ {
+ ArrayList<OptionI> opts = new ArrayList<OptionI>();
+ opts.add(new IntegerParameter("min","Minimum number of data of this type",true,1,min,0,-1));
+ opts.add(new IntegerParameter("max","Maximum number of data of this type",false,0,max,0,-1));
+ return opts;
+ }
+ /**
+ * make a copy of this InputType
+ * @return
+ * may not be needed
+ public abstract InputType copy();
+ */
+
+ /**
+ * parse a set of configuration options
+ * @param currentSettings - modified settings originally from getOptions
+ * @throws InvalidArgumentException thrown if currentSettings contains invalid options for this type.
+ */
+ public void configureFromArgumentI(List<ArgumentI> currentSettings) throws InvalidArgumentException
+ {
+ ArrayList<String> urltoks = new ArrayList<String>();
+ String rg;
+ for (ArgumentI arg: currentSettings)
+ {
+ if (arg instanceof ParameterI)
+ {
+ rg=arg.getName()+"='"+arg.getValue()+"'";
+ } else {
+ // TODO: revise architecture - this is counter intuitive - options with different values to their names are actually parameters
+ rg=(arg.getValue().length()>0) ? (arg.getValue().equals(arg.getName()) ? arg.getName():arg.getName()+"='"+arg.getValue()+"'")
+ : arg.getName();
+ }
+ if (rg.length()>0) {
+ urltoks.add(rg);
+ }
+ }
+ StringBuffer warnings;
+ if (!configureFromURLtokenString(urltoks, warnings=new StringBuffer()))
+ {
+ throw new InvalidArgumentException(warnings.toString());
+ }
+ }
+ protected OptionI createMolTypeOption(String name, String descr,
+ boolean req, molType curType, molType defType)
+ {
+ return new Option(name,descr, req, defType==null ? "" : defType.toString(), curType==null ? "" : curType.toString(),molType.toStringValues(),
+ null);
+ }
}
\ No newline at end of file
{
super();
this.details = new UIinfo();
- details.Action = action;
- details.description = description;
- details.Name = name;
- this.postUrl = postUrl;
- this.urlSuffix = urlSuffix;
- this.inputParams = inputParams;
+ details.Action = action == null ? "" : action;
+ details.description = description == null ? "" : description;
+ details.Name = name == null ? "" : name;
+ this.postUrl = postUrl == null ? "" : postUrl;
+ this.urlSuffix = urlSuffix == null ? "" : urlSuffix;
+ if (inputParams != null)
+ {
+ this.inputParams = inputParams;
+ }
this.hseparable = hseparable;
this.vseparable = vseparable;
this.gapCharacter = gapCharacter;
/**
* input info given as key/value pairs - mapped to post arguments
*/
- Map<String, InputType> inputParams = new HashMap<String,InputType>();
+ Map<String, InputType> inputParams = new HashMap<String, InputType>();
/**
* assigns the given inputType it to its corresponding input parameter token
public RestServiceDescription(RestServiceDescription toedit)
{
- // Rather then do the above, we cheat and use our human readable serialization code to clone everything
+ // Rather then do the above, we cheat and use our human readable
+ // serialization code to clone everything
this(toedit.toString());
/**
- if (toedit == null)
- {
- return;
- }
- /**
- urlSuffix = toedit.urlSuffix;
- postUrl = toedit.postUrl;
- hseparable = toedit.hseparable;
- vseparable = toedit.vseparable;
- gapCharacter = toedit.gapCharacter;
- details = new RestServiceDescription.UIinfo();
- details.Action = toedit.details.Action;
- details.description = toedit.details.description;
- details.Name = toedit.details.Name;
- for (InputType itype: toedit.inputParams.values())
- {
- inputParams.put(itype.token, itype.clone());
-
- }
-
- */
+ * if (toedit == null) { return; } /** urlSuffix = toedit.urlSuffix; postUrl
+ * = toedit.postUrl; hseparable = toedit.hseparable; vseparable =
+ * toedit.vseparable; gapCharacter = toedit.gapCharacter; details = new
+ * RestServiceDescription.UIinfo(); details.Action = toedit.details.Action;
+ * details.description = toedit.details.description; details.Name =
+ * toedit.details.Name; for (InputType itype: toedit.inputParams.values()) {
+ * inputParams.put(itype.token, itype.clone());
+ *
+ * }
+ */
// TODO Implement copy constructor NOW*/
}
return null;
java.util.ArrayList<String> jv = new ArrayList<String>();
int cp = 0, pos, escape;
- boolean wasescaped = false;
+ boolean wasescaped = false,wasquoted=false;
String lstitem = null;
while ((pos = list.indexOf(separator, cp)) >= cp)
{
- escape = (pos>0 && list.charAt(pos - 1) == '\\') ? -1 : 0;
- if (wasescaped)
+
+ escape = (pos > 0 && list.charAt(pos - 1) == '\\') ? -1 : 0;
+ if (wasescaped || wasquoted)
{
// append to previous pos
jv.set(jv.size() - 1,
}
cp = pos + seplen;
wasescaped = escape == -1;
+ if (!wasescaped)
+ {
+ // last separator may be in an unmatched quote
+ if (java.util.regex.Pattern.matches("('[^']*')*[^']*'",lstitem))
+ {
+ wasquoted=true;
+ }
+ }
+
}
if (cp < list.length())
{
String c = list.substring(cp);
- if (wasescaped)
+ if (wasescaped || wasquoted)
{
// append final separator
jv.set(jv.size() - 1, lstitem + separator + c);
{
if (list[i] != null)
{
- if (v.length()>0)
+ if (v.length() > 0)
{
v.append(separator);
}
return true;
}
;
- boolean valid=true;
+ boolean valid = true;
String val = null;
int i;
for (String prop : props)
}
if (prop.equals("gapCharacter"))
{
- if (val == null || val.length()==0 || val.length() > 1)
+ if (val == null || val.length() == 0 || val.length() > 1)
{
- valid=false;
+ valid = false;
warnings.append((warnings.length() > 0 ? "\n" : "")
+ ("Invalid service property: gapCharacter=' ' (single character) - was given '"
+ val + "'"));
}
if (prop.equals("returns"))
{
- int l=warnings.length();
+ int l = warnings.length();
_configureOutputFormatFrom(val, warnings);
- valid = (l!=warnings.length());
+ valid = (l != warnings.length());
}
}
return valid;
private String _genOutputFormatString()
{
String buff = "";
- if (resultData==null)
+ if (resultData == null)
{
return "";
}
private void _configureOutputFormatFrom(String outstring,
StringBuffer warnings)
{
- if (outstring.indexOf(";")==-1) {
+ if (outstring.indexOf(";") == -1)
+ {
// we add a token, for simplicity
- outstring = outstring+";";
+ outstring = outstring + ";";
}
StringTokenizer st = new StringTokenizer(outstring, ";");
String tok = "";
details.Name = list[0];
details.Action = list[1];
details.description = list[2];
- invalid|=!configureFromServiceInputProperties(list[3], warnings);
+ invalid |= !configureFromServiceInputProperties(list[3], warnings);
if (list.length > 5)
{
urlSuffix = list[4];
}
else
{
- urlSuffix = null;
- invalid |= !configureFromInputParamEncodedUrl(list[4], warnings);
+ if (list.length > 4)
+ {
+ urlSuffix = null;
+ invalid |= !configureFromInputParamEncodedUrl(list[4], warnings);
+ }
}
return !invalid;
}
iprmparams = iprm.substring(colon + 1);
iprm = iprm.substring(0, colon);
}
- valid = parseTypeString(prms.group(0), tok, iprm, iprmparams, iparams, warnings);
+ valid = parseTypeString(prms.group(0), tok, iprm, iprmparams,
+ iparams, warnings);
}
if (valid)
{
return valid;
}
- public static boolean parseTypeString(String fullstring, String tok, String iprm, String iprmparams,
- Map<String, InputType> iparams, StringBuffer warnings)
+ public static Class[] getInputTypes()
{
- boolean valid=true;
- InputType jinput;
// TODO - find a better way of maintaining this classlist
- for (Class type : new Class[]
+ return new Class[]
{ jalview.ws.rest.params.Alignment.class,
jalview.ws.rest.params.AnnotationFile.class,
SeqGroupIndexVector.class,
jalview.ws.rest.params.SeqIdVector.class,
jalview.ws.rest.params.SeqVector.class,
- jalview.ws.rest.params.Tree.class })
+ jalview.ws.rest.params.Tree.class };
+ }
+
+ public static boolean parseTypeString(String fullstring, String tok,
+ String iprm, String iprmparams, Map<String, InputType> iparams,
+ StringBuffer warnings)
+ {
+ boolean valid = true;
+ InputType jinput;
+ for (Class type : getInputTypes())
{
try
{
ArrayList<String> al = new ArrayList<String>();
for (String prprm : separatorListToArray(iprmparams, ","))
{
+ // hack to ensure that strings like "sep=','" containing unescaped commas as values are concatenated
al.add(prprm.trim());
}
if (!jinput.configureFromURLtokenString(al, warnings))
{
valid = false;
- warnings.append("Failed to parse '" + fullstring
- + "' as a " + jinput.getURLtokenPrefix()
- + " input tag.\n");
+ warnings.append("Failed to parse '" + fullstring + "' as a "
+ + jinput.getURLtokenPrefix() + " input tag.\n");
}
else
{
jinput.token = tok;
iparams.put(tok, jinput);
- valid=true;
+ valid = true;
}
break;
}
return valid;
}
-
public static void main(String argv[])
{
+ // test separator list
+ try {
+ assert(separatorListToArray("foo=',',min='foo',max='1,2,3',fa=','", ",").length==4);
+ if (separatorListToArray("minsize='2', sep=','", ",").length==2)
+ {
+ assert(false);
+ }
+
+ } catch (AssertionError x)
+ {
+ System.err.println("separatorListToArray is faulty.");
+ }
if (argv.length == 0)
{
if (!testRsdExchange("Test using default Shmmr service",
return jobId + urlSuffix;
}
- private List<JvDataType> resultData=new ArrayList<JvDataType>();
+ private List<JvDataType> resultData = new ArrayList<JvDataType>();
/**
*
{
return resultData;
}
-
+
}
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.Option;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
import java.net.URLEncoder;
import java.nio.charset.Charset;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
/**
* input data as a file upload rather than inline content
*/
- public boolean writeAsFile;
+ public boolean writeAsFile=false;
@Override
public ContentBody formatForInput(RestJob rj)
}
return false;
}
+ @Override
+ public List<OptionI> getOptions()
+ {
+ List<OptionI> lst = getBaseOptions();
+ lst.add(new BooleanOption("jvsuffix","Append jalview style /start-end suffix to ID", false, false, jvsuffix, null));
+ lst.add(new BooleanOption("writeasfile","Append jalview style /start-end suffix to ID", false, false, writeAsFile, null));
+
+ lst.add(new Option("format",
+ "Alignment upload format", true, "FASTA",
+ format, Arrays.asList(jalview.io.FormatAdapter.WRITEABLE_FORMATS), null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type,
+ null));
+
+ return lst;
+ }
+
}
\ No newline at end of file
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.Option;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
}
return false;
}
+ @Override
+ public List<OptionI> getOptions()
+ {
+ // TODO - consider disregarding base options here.
+ List<OptionI> lst = getBaseOptions();
+ lst.add(new Option("format",
+ "Alignment annotation upload format", true, JVANNOT,
+ format, Arrays.asList(new String[]
+ { JVANNOT, CSVANNOT}), null));
+ return lst;
+ }
}
package jalview.ws.rest.params;
+import jalview.ws.params.OptionI;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
warnings.append("IMPLEMENTATION ERROR: No Properties to configure for a Constant parameter.");
return false;
}
+
+ @Override
+ public List<OptionI> getOptions()
+ {
+ // empty list - this parameter isn't configurable, so don't try.
+ return new ArrayList<OptionI>();
+ }
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.Option;
import jalview.ws.rest.AlignmentProcessor;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import java.util.Vector;
// assume that alignment is properly ordered so groups form consecutive
// blocks
ArrayList<int[]> gl = new ArrayList<int[]>();
- int p=0;
+ int p = 0;
for (SequenceGroup sg : (Vector<SequenceGroup>) al.getGroups())
{
- if (sg.getSize()<minsize)
+ if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException("Group contains less than "+minsize+" sequences.");
+ throw new NoValidInputDataException("Group contains less than "
+ + minsize + " sequences.");
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
gl.add(se);
}
}
- // are there any more sequences ungrouped that should be added as a single remaining group ? - these might be at the start or the end
- if (gl.size()>0)
+ // are there any more sequences ungrouped that should be added as a single
+ // remaining group ? - these might be at the start or the end
+ if (gl.size() > 0)
{
- int[] tail=gl.get(0);
- if (tail[0]>0) {
- if (1+tail[0]>minsize)
+ int[] tail = gl.get(0);
+ if (tail[0] > 0)
{
- gl.add(0,new int[] { 0,tail[0]-1});
- } else {
- // lets be intelligent here - if the remaining sequences aren't enough to make a final group, then don't make one.
- // throw new NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
+ if (1 + tail[0] > minsize)
+ {
+ gl.add(0, new int[]
+ { 0, tail[0] - 1 });
+ }
+ else
+ {
+ // lets be intelligent here - if the remaining sequences aren't enough
+ // to make a final group, then don't make one.
+ // throw new
+ // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
+ }
}
- } else {
- tail=gl.get(gl.size()-1);
- if (1+tail[1]<al.getHeight())
+ else
+ {
+ tail = gl.get(gl.size() - 1);
+ if (1 + tail[1] < al.getHeight())
{
- if (al.getHeight()-(1+tail[1])>minsize) {
- gl.add(new int[] { tail[1]+1, al.getHeight()-1});
- } else {
- // lets be intelligent here - if the remaining sequences aren't enough to make a final group, then don't make one.
- // throw new NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
+ if (al.getHeight() - (1 + tail[1]) > minsize)
+ {
+ gl.add(new int[]
+ { tail[1] + 1, al.getHeight() - 1 });
+ }
+ else
+ {
+ // lets be intelligent here - if the remaining sequences aren't
+ // enough to make a final group, then don't make one.
+ // throw new
+ // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
}
}
}
- } else {
- gl.add(new int[] { 0, al.getHeight()-1});
}
- if (min>=0 && gl.size()<min)
+ else
{
- throw new NoValidInputDataException("Not enough sequence groups for input. Need at least "+min+" groups (including ungrouped regions).");
+ gl.add(new int[]
+ { 0, al.getHeight() - 1 });
}
- if (max>0 && gl.size()>max)
+ if (min >= 0 && gl.size() < min)
{
- throw new NoValidInputDataException("Too many sequence groups for input. Need at most "+max+" groups (including ungrouped regions).");
+ throw new NoValidInputDataException(
+ "Not enough sequence groups for input. Need at least " + min
+ + " groups (including ungrouped regions).");
+ }
+ if (max > 0 && gl.size() > max)
+ {
+ throw new NoValidInputDataException(
+ "Too many sequence groups for input. Need at most " + max
+ + " groups (including ungrouped regions).");
}
int[][] vals = gl.toArray(new int[gl.size()][]);
int[] srt = new int[gl.size()];
}
/**
- * set minimum number of sequences allowed in a partition. Default is 1 sequence.
- * @param i (number greater than 1)
+ * set minimum number of sequences allowed in a partition. Default is 1
+ * sequence.
+ *
+ * @param i
+ * (number greater than 1)
*/
public void setMinsize(int i)
{
- if (minsize>=1)
- {
- minsize=i;
- } else {
- minsize=1;
- }
+ if (minsize >= 1)
+ {
+ minsize = i;
+ }
+ else
+ {
+ minsize = 1;
+ }
}
+
@Override
public List<String> getURLEncodedParameter()
{
ArrayList<String> prms = new ArrayList<String>();
super.addBaseParams(prms);
- prms.add("minsize='"+ minsize+"'");
- prms.add("sep='"+ sep+"'");
- if (type!=null)
+ prms.add("minsize='" + minsize + "'");
+ prms.add("sep='" + sep + "'");
+ if (type != null)
{
- prms.add("type='"+type+"'");
+ prms.add("type='" + type + "'");
}
return prms;
}
if (tok.startsWith("sep"))
{
- sep=val;
+ sep = val;
return true;
}
if (tok.startsWith("minsize"))
{
- try {
- minsize=Integer.valueOf(val);
- if (minsize>=0)
- return true;
+ try
+ {
+ minsize = Integer.valueOf(val);
+ if (minsize >= 0)
+ return true;
} catch (Exception x)
{
-
+
}
- warnings.append("Invalid minsize value '"+val+"'. Must be a positive integer.\n");
+ warnings.append("Invalid minsize value '" + val
+ + "'. Must be a positive integer.\n");
}
if (tok.startsWith("type"))
{
- try {
- type=molType.valueOf(val);
+ try
+ {
+ type = molType.valueOf(val);
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '"+val+"'. Must be one of (");
- for (molType v:molType.values())
+ warnings.append("Invalid molecule type '" + val
+ + "'. Must be one of (");
+ for (molType v : molType.values())
{
- warnings.append(" "+v);
+ warnings.append(" " + v);
}
warnings.append(")\n");
}
return false;
}
+ @Override
+ public List<OptionI> getOptions()
+ {
+ List<OptionI> lst = getBaseOptions();
+ lst.add(new Option("sep",
+ "Separator character between elements of vector", true, ",",
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
+ lst.add(new IntegerParameter("minsize", "Minimum size of partition allowed by service", true, 1, minsize, 1,0));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type, molType.MIX));
+ return lst;
+ }
+
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.Option;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.http.entity.mime.content.StringBody;
/**
- * input a list of sequence IDs separated by some separator
+ * input a list of sequence IDs separated by some separator
+ *
* @author JimP
- *
+ *
*/
-public class SeqIdVector extends InputType {
+public class SeqIdVector extends InputType
+{
public SeqIdVector()
{
- super(new Class[] { AlignmentI.class} );
+ super(new Class[]
+ { AlignmentI.class });
}
/**
* separator for list of sequence IDs - default is ','
*/
- String sep=",";
+ String sep = ",";
+
molType type;
+
@Override
- public ContentBody formatForInput(RestJob rj) throws UnsupportedEncodingException, NoValidInputDataException
+ public ContentBody formatForInput(RestJob rj)
+ throws UnsupportedEncodingException, NoValidInputDataException
{
StringBuffer idvector = new StringBuffer();
- boolean list=false;
- for (SequenceI seq:rj.getSequencesForInput(token, type))
+ boolean list = false;
+ for (SequenceI seq : rj.getSequencesForInput(token, type))
{
if (list)
{
idvector.append(seq.getName());
}
return new StringBody(idvector.toString());
- }
+ }
+
@Override
public List<String> getURLEncodedParameter()
{
ArrayList<String> prms = new ArrayList<String>();
super.addBaseParams(prms);
- prms.add("sep='"+ sep+"'");
- prms.add("type='"+type+"'");
+ prms.add("sep='" + sep + "'");
+ if (type!=null)
+ {
+ prms.add("type='"+type+"'");
+ }
return prms;
}
+
@Override
public String getURLtokenPrefix()
{
return "SEQIDS";
}
+
@Override
- public boolean configureProperty(String tok, String val, StringBuffer warnings)
+ public boolean configureProperty(String tok, String val,
+ StringBuffer warnings)
{
if (tok.startsWith("sep"))
{
- sep=val;
+ sep = val;
return true;
}
if (tok.startsWith("type"))
{
- try {
- type=molType.valueOf(val);
+ try
+ {
+ type = molType.valueOf(val);
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '"+val+"'. Must be one of (");
- for (molType v:molType.values())
+ warnings.append("Invalid molecule type '" + val
+ + "'. Must be one of (");
+ for (molType v : molType.values())
{
- warnings.append(" "+v);
+ warnings.append(" " + v);
}
warnings.append(")\n");
}
}
return false;
}
+
+ @Override
+ public List<OptionI> getOptions()
+ {
+ List<OptionI> lst = getBaseOptions();
+ lst.add(new Option("sep",
+ "Separator character between elements of vector", true, ",",
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type,
+ null));
+ return lst;
+ }
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.simple.Option;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.StringBody;
+import org.jmol.util.ArrayUtil;
/**
* input a list of sequences separated by some separator
ArrayList<String> prms = new ArrayList<String>();
super.addBaseParams(prms);
prms.add("sep='"+ sep+"'");
- prms.add("type='"+type+"'");
+ if (type!=null)
+ {
+ prms.add("type='"+type+"'");
+ }
return prms;
}
return false;
}
+ @Override
+ public List<OptionI> getOptions()
+ {
+ List<OptionI> lst = getBaseOptions();
+ lst.add(new Option("sep",
+ "Separator character between elements of vector", true, ",",
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type,
+ molType.MIX));
+
+ return lst;
+ }
+
}
\ No newline at end of file
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
import jalview.ws.rest.InputType;
import jalview.ws.rest.RestJob;
import jalview.ws.rest.RestServiceDescription;
return true;
}
+ @Override
+ public List<OptionI> getOptions()
+ {
+ return getBaseOptions();
+ }
+
}
\ No newline at end of file
git://source.jalview.org / jalview.git / commitdiff