Changeset 3941

Timestamp:

Nov 2, 2010, 2:06:13 PM (13 years ago)

Author:

Gregory Vincic

Message:

Refs #698. Moved method getForm(FormTemplateInterface?) and related methods to the one action that used them.

Location:

trunk/client/servlet/src/org/proteios

Files:

• action/spectrumSearch/ViewActivePeptideSearchResult.java (modified) (2 diffs)
• gui/form/FormFactory.java (modified) (53 diffs)

trunk/client/servlet/src/org/proteios/action/spectrumSearch/ViewActivePeptideSearchResult.java

@@ -1 +1 @@
 /*
- $Id$
-
- Copyright (C) 2006 Fredrik Levander, Gregory Vincic, Olle Mansson
- Copyright (C) 2007 Fredrik Levander, Gregory Vincic
-
- Files are copyright by their respective authors. The contributions to
- files where copyright is not explicitly stated can be traced with the
- source code revision system.
-
- This file is part of Proteios.
- Available at http://www.proteios.org/
-
- Proteios-2.x is free software; you can redistribute it and/or
- modify it under the terms of the GNU General Public License
- as published by the Free Software Foundation; either version 2
- of the License, or (at your option) any later version.
-
- Proteios is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place - Suite 330,
- Boston, MA  02111-1307, USA.
- */
+    $Id$
+                    
+    Copyright (C) 2006 Fredrik Levander, Gregory Vincic, Olle Mansson
+    Copyright (C) 2007 Fredrik Levander, Gregory Vincic
+    Copyright (C) 2010 Gregory Vincic
+                    
+    Files are copyright by their respective authors. The contributions to
+    files where copyright is not explicitly stated can be traced with the
+    source code revision system.
+                    
+    This file is part of Proteios.
+    Available at http://www.proteios.org/
+                    
+    Proteios-2.x is free software; you can redistribute it and/or
+    modify it under the terms of the GNU General Public License
+    as published by the Free Software Foundation; either version 2
+    of the License, or (at your option) any later version.
+                    
+    Proteios is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+                    
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place - Suite 330,
+    Boston, MA  02111-1307, USA.
+*/
 package org.proteios.action.spectrumSearch;
 
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.lang.reflect.Modifier;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
 import org.proteios.ActionLink;
 import org.proteios.action.ProteiosAction;
 import org.proteios.action.peakList.PlotFileSpectrum;
 import org.proteios.core.Annotation;
+import org.proteios.core.AnnotationSet;
 import org.proteios.core.Annotator;
 import org.proteios.core.DbControl;
@@ -51 +60 @@
 import org.proteios.gui.RowContainer;
 import org.proteios.gui.Toolbar;
+import org.proteios.gui.form.*;
 import org.proteios.gui.form.Fieldset;
-import org.proteios.gui.form.Form;
-import org.proteios.gui.form.FormFactory;
-import org.proteios.gui.form.FormTemplateImpl;
-import org.proteios.gui.form.FormTemplateInterface;
 import org.proteios.gui.layout.RowLayout;
 import org.proteios.gui.table.Table;
 import org.proteios.gui.table.TableFactory;
-
 import se.lu.thep.waf.ActionException;
+import se.lu.thep.waf.constraints.Format;
 import se.lu.thep.waf.constraints.InvalidParameterValue;
 import se.lu.thep.waf.constraints.VBoolean;
 import se.lu.thep.waf.constraints.VInteger;
+import se.lu.thep.waf.constraints.VString;
 
-/**
- * @author gregory
- */
 public class ViewActivePeptideSearchResult
-    extends ProteiosAction<ViewActivePeptideSearchResult>
+extends ProteiosAction<ViewActivePeptideSearchResult>
 {
-  public static final VInteger VSEARCHRESULTID = new VInteger(
-    "active.searchresult.id", 1, true);
-  public static final VBoolean VKEEPORIGINALSPECTRUM = new VBoolean(
-    "keepOriginalSpectrum", false);
-
-
-  @Override
-  public void runMe()
-      throws ActionException, InvalidParameterValue
-  {
-    verifySessionAttributes(VSEARCHRESULTID);
-    /***********************************************************************
-     * Properties
-     */
-    Integer ssId = getSessionAttribute(VSEARCHRESULTID);
-    String massCutoffLowStr = getValidString(PlotFileSpectrum.VMASSCUTOFFLOWSTR);
-    String massCutoffHighStr = getValidString(PlotFileSpectrum.VMASSCUTOFFHIGHSTR);
-    Boolean keepOriginalSpectrum = getValidBoolean(VKEEPORIGINALSPECTRUM);
-    log.debug("ssId = " + ssId);
-    log.debug("massCutoffLowStr = \"" + massCutoffLowStr + "\"");
-    log.debug("massCutoffHighStr = \"" + massCutoffHighStr + "\"");
-    log.debug("(1) keepOriginalSpectrum = " + keepOriginalSpectrum);
-    if (keepOriginalSpectrum == null)
-    {
-      keepOriginalSpectrum = true;
-    }
-    log.debug("(2) keepOriginalSpectrum = " + keepOriginalSpectrum);
-    // Only show one spectrum view if no mass range parameters
-    if ((massCutoffLowStr == null || massCutoffLowStr.equals(""))
-      && (massCutoffHighStr == null || massCutoffHighStr.equals("")))
-    {
-      keepOriginalSpectrum = false;
-    }
-    log.debug("(3) keepOriginalSpectrum = " + keepOriginalSpectrum);
-    DbControl dc = newDbControl();
-    ItemFactory factory = new ItemFactory(dc);
-    TableFactory tableFactory = getTableFactory();
-    SearchResult ss = factory.getById(SearchResult.class, ssId);
-    Form mainForm = new Form("Search Result");
-    Fieldset fs=new Fieldset();
-    fs.setTitle("Search Result");
-    mainForm.addFieldset(fs);
-    FormTemplateImpl formTemplate = new FormTemplateImpl();
-    formTemplate.setItemObject(ss);
-    formTemplate.setReadOnlyForm(true);
-    FormFactory formFactory = getFormFactory();
-    Form form = formFactory.getForm(formTemplate);
-    // Peptides:
-    ItemQuery<Peptide> peptideQuery = Peptide.getQuery();
-    peptideQuery.restrict(Restrictions.eq(Hql.property("searchResult"), Hql
-      .entity(ss)));
-    tableFactory.reset();
-    tableFactory.setItemClass(Peptide.class);
-    tableFactory.setQuery(peptideQuery);
-    ActionLink rowAction = getActionFactory().getActionLink(
-      ViewExternalId.class, "View");
-    tableFactory.setColumnAction("AccessionNumber", rowAction);
-    Table peptideTable = tableFactory.build();
-    peptideTable.setTitle("Peptides");
-    peptideTable.setToolbar(null);
-    /***********************************************************************
-     * Annotations table
-     */
-    Annotator anna = new Annotator(getItemFactory(dc));
-    tableFactory.reset();
-    tableFactory.setItemClass(Annotation.class);
-    ItemQuery<Annotation> annotationQuery = anna.getAnnotationSet(ss)
-      .getAnnotations();
-    tableFactory.setQuery(annotationQuery);
-    Table annotationsTable = tableFactory.build();
-    ColumnContainer cc = new ColumnContainer();
-    cc.add(annotationsTable);
-    /**
-     * Spectrum plot
-     */
-    ItemQuery<Hit> hitQuery = Hit.getQuery();
-    hitQuery.restrict(Restrictions.eq(Hql.property("identificationResultFile"), Hql
-      .entity(ss.getSpectrumSearch().getResultFile())));
-    File peakListFile = null;
-    ItemResultIterator<Hit> hitit = hitQuery.iterate(dc);
-    if (hitit.hasNext()) peakListFile = hitit.next().getPeakListFile();
-    if (peakListFile == null)
-    {
-      ItemQuery<File> fileQuery = File.getQuery();
-      fileQuery.restrict(Restrictions.eq(Hql.property("name"),
-        Expressions.parameter("name")));
-      fileQuery.setParameter("name", ss.getSpectrumSearch().getInputSpectrumFileName(), null);
-      ItemResultIterator<File> fileit = fileQuery.iterate(dc);
-      if (fileit.hasNext()) peakListFile = fileit.next();
-    }
-    if (peakListFile!=null)
-    {
-      /***********************************************************************
-       * Spectrum plot
-       */
-      String spectrumId = Integer.toString(ss.getInputSpectrumId());
-      PlotFileSpectrum plotFileSpectrum = new PlotFileSpectrum();
-      ImageMap imageMap;
-      Image plotOriginal = null;
-      if (keepOriginalSpectrum)
-      {
-        plotOriginal = new Image();
-        ActionLink viewOriginalAction = getActionFactory().getActionLink(
-          PlotFileSpectrum.class, "ViewOriginal");
-        viewOriginalAction.addParameter(FormFactory.VID, peakListFile.getId());
-        viewOriginalAction.addParameter(PlotFileSpectrum.VSPECTRUMID, spectrumId);
-        plotOriginal.setViewAction(viewOriginalAction);
-        plotOriginal.setHeight(PlotFileSpectrum.HEIGHT);
-        plotOriginal.setWidth(PlotFileSpectrum.WIDTH);
-        // Add mass annotation image map
-        imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc, peakListFile.getId(), spectrumId,
-          (String) null, (String) null);
-        plotOriginal.setImageMap(imageMap);
-      }
-      Image plot = new Image();
-      ActionLink viewAction = getActionFactory().getActionLink(
-        PlotFileSpectrum.class, "View");
-      viewAction.addParameter(FormFactory.VID, peakListFile.getId());
-      viewAction.addParameter(PlotFileSpectrum.VSPECTRUMID, spectrumId);
-      viewAction.addParameter(PlotFileSpectrum.VMASSCUTOFFLOWSTR, massCutoffLowStr);
-      viewAction.addParameter(PlotFileSpectrum.VMASSCUTOFFHIGHSTR, massCutoffHighStr);
-      plot.setViewAction(viewAction);
-      plot.setHeight(PlotFileSpectrum.HEIGHT);
-      plot.setWidth(PlotFileSpectrum.WIDTH);
-      // Add mass annotation image map
-      imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc, peakListFile.getId(), spectrumId,
-        massCutoffLowStr, massCutoffHighStr);
-      plot.setImageMap(imageMap);
-      /***********************************************************************
-       * Spectrum mass range selection form
-       */
-      Form massRangeSelectionForm = getFormFactory().getSpectrumMassRangeSelectionForm(massCutoffLowStr, massCutoffHighStr, spectrumId);
-      Toolbar toolbar = new Toolbar();
-      massRangeSelectionForm.setToolbar(toolbar);
-      //
-      ActionLink zoomWithOriginalAction = getActionLink(ViewActivePeptideSearchResult.class, "ZoomedAndOriginalSpectrum");
-      //zoomWithOriginalAction.addParameter(FormFactory.VID, peakListFile.getId());
-      zoomWithOriginalAction.addParameter(VKEEPORIGINALSPECTRUM, true);
-      toolbar.add(zoomWithOriginalAction);
-      //
-      ActionLink zoomAction = getActionLink(ViewActivePeptideSearchResult.class, "ZoomedSpectrum");
-      //zoomAction.addParameter(FormFactory.VID, peakListFile.getId());
-      zoomAction.addParameter(VKEEPORIGINALSPECTRUM, false);
-      toolbar.add(zoomAction);
-      // Row container for plot and properties form
-      RowContainer rc = new RowContainer();
-      if (plotOriginal != null)
-      {
-        rc.add(plotOriginal);
-      }
-      rc.add(plot);
-      rc.add(massRangeSelectionForm);
-      cc.add(rc);
-    }
-    /***********************************************************************
-     * Layout
-     */
-    RowLayout layout = getLayoutFactory().getRowLayout();
-    layout.add(mainForm);
-    layout.add(form);
-    layout.add(cc);
-    layout.add(peptideTable);
-    setLayout(layout);
-  }
+    public static final VInteger VSEARCHRESULTID = new VInteger("active.searchresult.id", 1, true);
+    public static final VBoolean VKEEPORIGINALSPECTRUM = new VBoolean("keepOriginalSpectrum", false);
+    public static final VBoolean VREADONLYFORM = new VBoolean("readOnlyForm",false);
+                    
+    /**
+        * List<String> of excluded getter methods declared in current class. If a
+        * getter accessor method is included in this list, when a generic form for
+        * an object is created with getForm(), no field will be added to the form
+        * for an instance variable (if any) corresponding to the getter method.
+    */
+    private List<String> excludedDeclMethods = new ArrayList<String>();
+        
+    @Override
+    public void runMe()
+    throws ActionException, InvalidParameterValue
+    {
+        Integer ssId;
+        String massCutoffLowStr;
+        String massCutoffHighStr;
+        Boolean keepOriginalSpectrum;
+        DbControl dc;
+        ItemFactory factory;
+        TableFactory tableFactory;
+        SearchResult ss;
+        Form mainForm;
+        Fieldset fs;
+        FormTemplateImpl formTemplate;
+        Form form;
+        ItemQuery<Peptide> peptideQuery;
+        ActionLink rowAction;
+        Table peptideTable;
+        Annotator anna;
+        ItemQuery<Annotation> annotationQuery;
+        Table annotationsTable;
+        ColumnContainer cc;
+        ItemQuery<Hit> hitQuery;
+        File peakListFile;
+        ItemResultIterator<Hit> hitit;
+        ItemQuery<File> fileQuery;
+        ItemResultIterator<File> fileit;
+        // Define
+        initExcludedDeclMethods();
+                
+        verifySessionAttributes(VSEARCHRESULTID);
+        ssId = getSessionAttribute(VSEARCHRESULTID);
+        massCutoffLowStr = getValidString(PlotFileSpectrum.VMASSCUTOFFLOWSTR);
+        massCutoffHighStr = getValidString(PlotFileSpectrum.VMASSCUTOFFHIGHSTR);
+        keepOriginalSpectrum = getValidBoolean(VKEEPORIGINALSPECTRUM);
+        if (keepOriginalSpectrum == null)
+        {
+            keepOriginalSpectrum = true;
+        }
+        // Only show one spectrum view if no mass range parameters
+        if ((massCutoffLowStr == null || massCutoffLowStr.equals(""))
+        && (massCutoffHighStr == null || massCutoffHighStr.equals("")))
+        {
+            keepOriginalSpectrum = false;
+        }
+        log.debug("keepOriginalSpectrum = " + keepOriginalSpectrum);
+        dc = newDbControl();
+        factory = getItemFactory(dc);
+        tableFactory = getTableFactory();
+        ss = factory.getById(SearchResult.class, ssId);
+        mainForm = new Form("Search Result");
+        fs=new Fieldset();
+        fs.setTitle("Search Result");
+        mainForm.addFieldset(fs);
+        formTemplate = new FormTemplateImpl();
+        formTemplate.setItemObject(ss);
+        formTemplate.setReadOnlyForm(true);
+        form = getForm(formTemplate);
+        // Peptides:
+        peptideQuery = Peptide.getQuery();
+        peptideQuery.restrict(Restrictions.eq(Hql.property("searchResult"), Hql.entity(ss)));
+        tableFactory.reset();
+        tableFactory.setItemClass(Peptide.class);
+        tableFactory.setQuery(peptideQuery);
+        rowAction = getActionFactory().getActionLink(ViewExternalId.class, "View");
+        tableFactory.setColumnAction("AccessionNumber", rowAction);
+        peptideTable = tableFactory.build();
+        peptideTable.setTitle("Peptides");
+        peptideTable.setToolbar(null);
+        // Annotations
+        anna = new Annotator(getItemFactory(dc));
+        tableFactory.reset();
+        tableFactory.setItemClass(Annotation.class);
+        annotationQuery = anna.getAnnotationSet(ss).getAnnotations();
+        tableFactory.setQuery(annotationQuery);
+        annotationsTable = tableFactory.build();
+        cc = new ColumnContainer();
+        cc.add(annotationsTable);
+        // Plot
+        hitQuery = Hit.getQuery();
+        hitQuery.restrict(Restrictions.eq(Hql.property("identificationResultFile"), Hql
+        .entity(ss.getSpectrumSearch().getResultFile())));
+        peakListFile = null;
+        hitit = hitQuery.iterate(dc);
+        if (hitit.hasNext()) 
+        {
+            peakListFile = hitit.next().getPeakListFile();
+        }
+        if (peakListFile == null)
+        {
+            fileQuery = File.getQuery();
+            fileQuery.restrict(Restrictions.eq(Hql.property("name"),
+            Expressions.parameter("name")));
+            fileQuery.setParameter("name", ss.getSpectrumSearch().getInputSpectrumFileName(), null);
+            fileit = fileQuery.iterate(dc);
+            if (fileit.hasNext()) peakListFile = fileit.next();
+        }
+        if (peakListFile!=null)
+        {
+            String spectrumId = Integer.toString(ss.getInputSpectrumId());
+            PlotFileSpectrum plotFileSpectrum = new PlotFileSpectrum();
+            ImageMap imageMap;
+            Image plotOriginal = null;
+            if (keepOriginalSpectrum)
+            {
+                plotOriginal = new Image();
+                ActionLink viewOriginalAction = getActionFactory().getActionLink(
+                PlotFileSpectrum.class, "ViewOriginal");
+                viewOriginalAction.addParameter(FormFactory.VID, peakListFile.getId());
+                viewOriginalAction.addParameter(PlotFileSpectrum.VSPECTRUMID, spectrumId);
+                plotOriginal.setViewAction(viewOriginalAction);
+                plotOriginal.setHeight(PlotFileSpectrum.HEIGHT);
+                plotOriginal.setWidth(PlotFileSpectrum.WIDTH);
+                // Add mass annotation image map
+                imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc, peakListFile.getId(), spectrumId,
+                (String) null, (String) null);
+                plotOriginal.setImageMap(imageMap);
+            }
+            Image plot = new Image();
+            ActionLink viewAction = getActionFactory().getActionLink(
+            PlotFileSpectrum.class, "View");
+            viewAction.addParameter(FormFactory.VID, peakListFile.getId());
+            viewAction.addParameter(PlotFileSpectrum.VSPECTRUMID, spectrumId);
+            viewAction.addParameter(PlotFileSpectrum.VMASSCUTOFFLOWSTR, massCutoffLowStr);
+            viewAction.addParameter(PlotFileSpectrum.VMASSCUTOFFHIGHSTR, massCutoffHighStr);
+            plot.setViewAction(viewAction);
+            plot.setHeight(PlotFileSpectrum.HEIGHT);
+            plot.setWidth(PlotFileSpectrum.WIDTH);
+            // Add mass annotation image map
+            imageMap = plotFileSpectrum.fetchMassPeakAnnotationToolTips(dc, peakListFile.getId(), spectrumId,
+            massCutoffLowStr, massCutoffHighStr);
+            plot.setImageMap(imageMap);
+            // Spectrum mass range selection form
+            Form massRangeSelectionForm = getFormFactory().getSpectrumMassRangeSelectionForm(massCutoffLowStr, massCutoffHighStr, spectrumId);
+            Toolbar toolbar = new Toolbar();
+            massRangeSelectionForm.setToolbar(toolbar);
+                                                
+            ActionLink zoomWithOriginalAction = getActionLink(ViewActivePeptideSearchResult.class, "ZoomedAndOriginalSpectrum");
+            zoomWithOriginalAction.addParameter(VKEEPORIGINALSPECTRUM, true);
+            toolbar.add(zoomWithOriginalAction);
+                                                
+            ActionLink zoomAction = getActionLink(ViewActivePeptideSearchResult.class, "ZoomedSpectrum");
+            zoomAction.addParameter(VKEEPORIGINALSPECTRUM, false);
+            toolbar.add(zoomAction);
+            // Row container for plot and properties form
+            RowContainer rc = new RowContainer();
+            if (plotOriginal != null)
+            {
+                rc.add(plotOriginal);
+            }
+            rc.add(plot);
+            rc.add(massRangeSelectionForm);
+            cc.add(rc);
+        }
+                                
+        RowLayout layout = getLayoutFactory().getRowLayout();
+        layout.add(mainForm);
+        layout.add(form);
+        layout.add(cc);
+        layout.add(peptideTable);
+        setLayout(layout);
+    }
+        
+    /**
+        Get generic form for object.
+                                                
+        @param template template for generic form
+        @return Form for editing the object
+    */
+    private Form getForm(FormTemplateInterface formTemplate)
+    {
+        /***********************************************************************
+            Analyze object class
+        */
+                                                
+        /*
+            Get class from formTemplate itemObject or itemClass.
+        */
+        Object itemObject = null;
+        Class<? extends Object> itemClass = null;
+        if (formTemplate.getItemObject() != null)
+        {
+            itemObject = formTemplate.getItemObject();
+            itemClass = itemObject.getClass();
+        }
+        else if (formTemplate.getItemClass() != null)
+        {
+            itemClass = formTemplate.getItemClass();
+        }
+        /*
+            Add optional extra formTemplate list of methods to be excluded.
+        */
+        if (formTemplate != null && formTemplate.getExcludedDeclMethods() != null)
+        {
+            addExcludedDeclMethods(formTemplate.getExcludedDeclMethods());
+        }
+        String clsName = new String("");
+        if (itemClass != null)
+        {
+            clsName = itemClass.getSimpleName();
+        }
+                                                
+        /***********************************************************************
+            Main fieldset
+        */
+        Fieldset mainFS = new Fieldset();
+        String mainFsName = new String("Properties");
+        mainFS.setTitle(mainFsName);
+        /*
+            Add forward actionId field as first field, for external use.
+        */
+        TextField<String> fwdactionF = new ForwardField();
+        mainFS.add(fwdactionF);
+        /*
+            Get item id, if any.
+        */
+        int itemId = 0;
+        String getIdMethodName = "getId";
+        Method getIdMethod = fetchPublicMethodForObject(getIdMethodName,
+        itemClass);
+        if (getIdMethod != null && itemObject != null)
+        {
+            try
+            {
+                Object[] arguments = new Object[] {};
+                Object retobj = getIdMethod.invoke(itemObject, arguments);
+                String idStr = retobj.toString();
+                itemId = Integer.parseInt(idStr);
+            }
+            catch (InvocationTargetException e)
+            {
+                itemId = 0;
+            }
+            catch (IllegalAccessException e)
+            {
+                itemId = 0;
+            }
+            catch (java.lang.NumberFormatException e)
+            {
+                itemId = 0;
+            }
+        }
+        /*
+            Add itemId field idF (hidden) if itemId value ok.
+        */
+        if (itemId > 0)
+        {
+            TextField<Integer> idF = new ItemIdField().setHidden(true);
+            mainFS.add(idF);
+            idF.setLabel("ItemId");
+            idF.setValue(itemId);
+            idF.setDisabled(true);
+        }
+        /*
+            Add class name field cnF.
+        */
+        String classNameFull = new String("");
+        if (itemClass != null)
+        {
+            classNameFull = itemClass.getName();
+        }
+        TextField<String> cnF = new ClassNameField();
+        mainFS.add(cnF);
+        cnF.setHidden(true);
+        cnF.setLabel("ClassName");
+        cnF.setValue(classNameFull);
+        cnF.setDisabled(true);
+        /*
+            Add readOnlyForm field rofF (hidden).
+        */
+        TextField<Boolean> rofF = newHiddenReadOnlyFormField();
+        mainFS.add(rofF);
+        rofF.setLabel("ReadOnlyForm");
+        rofF.setValue(formTemplate.isReadOnlyForm());
+        rofF.setDisabled(true);
+        /*
+            Keep track on whether public setter methods exist, in order to know
+            if a "Save" button should be added.
+        */
+        boolean hasSetterMethods = false;
+        /*
+            Methods, declared and inherited
+        */
+        Method[] methodArr = new Method[0];
+        if (itemClass != null)
+        {
+            methodArr = itemClass.getMethods();
+        }
+                                                
+        /*
+            Methods declared in object class (not inherited)
+        */
+        Method[] declaredMethodArr = new Method[0];
+        if (itemClass != null)
+        {
+            declaredMethodArr = itemClass.getDeclaredMethods();
+        }
+        for (int i = 0; i < declaredMethodArr.length; i++)
+        {
+            Method method = declaredMethodArr[i];
+            String modStr = methodModifierString(method);
+            String methodName = method.getName();
+            String methodReturnType = method.getReturnType().getName();
+            /*
+                Only process declared methods not in exclude list.
+            */
+            if (!getExcludedDeclMethods().contains(methodName))
+            {
+                String attrName = new String("");
+                String attrValueStr = new String("");
+                String returnTypeStr = new String("");
+                boolean returnTypeOK = false;
+                Class<?> returnTypeOfGetterMethod = null;
+                /*
+                    Check if getter access method.
+                */
+                if (methodName.startsWith("get"))
+                {
+                    /*
+                        Assume that attribute name can optained by skipping "get"
+                        in method name.
+                    */
+                    attrName = methodName.substring(3);
+                    // int methodMod = declaredMethodArr[i].getModifiers();
+                    if (method.getReturnType().getName().equals("int") || method
+                    .getReturnType().getName().equals("java.lang.Integer") || method
+                    .getReturnType().getName().equals("float") || method
+                    .getReturnType().getName().equals("java.lang.Float") || method
+                    .getReturnType().getName().equals("double") || method
+                    .getReturnType().getName().equals("java.lang.Double") || method
+                    .getReturnType().getName().equals("java.lang.String") || method
+                    .getReturnType().getName().equals("java.util.Date"))
+                    {
+                        returnTypeOfGetterMethod = method.getReturnType();
+                        returnTypeStr = method.getReturnType().getName();
+                        returnTypeOK = true;
+                    }
+                }
+                else if (methodName.startsWith("is"))
+                {
+                    /*
+                        Assume that attribute name can optained by skipping "is"
+                        in method name.
+                    */
+                    attrName = methodName.substring(2);
+                    // int methodMod = declaredMethodArr[i].getModifiers();
+                    if (method.getReturnType().getName().equals("boolean") || method
+                    .getReturnType().getName().equals("java.lang.Boolean"))
+                    {
+                        returnTypeOfGetterMethod = method.getReturnType();
+                        returnTypeStr = method.getReturnType().getName();
+                        returnTypeOK = true;
+                    }
+                }
+                if (returnTypeOK)
+                {
+                    if (itemObject != null)
+                    {
+                        try
+                        {
+                            Object[] arguments = new Object[] {};
+                            Object retobj = method
+                            .invoke(itemObject, arguments);
+                            if (retobj != null)
+                            {
+                                /*
+                                    Return date values in "YYYY-MM-DD HH:mm:ss"
+                                    24-hour format.
+                                */
+                                if (method.getReturnType().getName().equals(
+                                "java.util.Date"))
+                                {
+                                    SimpleDateFormat dateFormat = Format.TIMESTAMP
+                                    .getPattern();
+                                    attrValueStr = dateFormat
+                                    .format((Date) retobj);
+                                }
+                                else
+                                {
+                                    attrValueStr = retobj.toString();
+                                }
+                            }
+                        }
+                        catch (InvocationTargetException e)
+                        {
+                            log
+                            .warn("FormFactory::getFormImpl(): InvocationTargetException when invoking method \"" + methodName + "\":" + e);
+                        }
+                        catch (IllegalAccessException e)
+                        {
+                            log
+                            .warn("FormFactory::getFormImpl(): IllegalAccessException when invoking method \"" + methodName + "\":" + e);
+                        }
+                        log
+                        .debug("FormFactory::getFormImpl(): methodName = \"" + methodName + "\"  returnTypeOfGetterMethod = \"" + returnTypeOfGetterMethod + "\" attrValueStr = \"" + attrValueStr + "\"");
+                    }
+                    /*
+                        Check if public accessor method for setting value exists.
+                    */
+                    boolean isSettable = false;
+                    String publMethodName = new String("set" + attrName);
+                    if (!formTemplate.isReadOnlyForm())
+                    {
+                        if (fetchPublicMethodForObject(publMethodName,
+                        itemClass) != null)
+                        {
+                            isSettable = true;
+                        }
+                    }
+                    log
+                    .debug("FormFactory::getFormImpl(): attrName = \"" + attrName + "\" publMethodName = \"" + publMethodName + "\" isSettable = " + isSettable);
+                    /*
+                        Use TextArea for Description, else TextField
+                    */
+                    if (attrName.equals("Description"))
+                    {
+                        /*
+                            Value text area
+                        */
+                        TextArea valueF = null;
+                        if (!isSettable)
+                        {
+                            valueF = newValueTextArea("", String.class);
+                        }
+                        else
+                        {
+                            hasSetterMethods = true;
+                            valueF = newValueTextArea(publMethodName,
+                            returnTypeOfGetterMethod);
+                        }
+                        mainFS.add(valueF);
+                        valueF.setLabel(attrName);
+                        valueF.setValue(attrValueStr);
+                    }
+                    else
+                    {
+                        /*
+                            Value field
+                        */
+                        TextField<String> valueF = null;
+                        if (!isSettable)
+                        {
+                            valueF = getFormFactory().newValueField("", String.class);
+                        }
+                        else
+                        {
+                            hasSetterMethods = true;
+                            valueF = getFormFactory().newValueField(publMethodName,
+                            returnTypeOfGetterMethod);
+                        }
+                        mainFS.add(valueF);
+                        valueF.setLabel(attrName);
+                        valueF.setValue(attrValueStr);
+                    }
+                }
+            }
+        }
+                                                
+        /*
+            Check if object supports method getAnnotationSet().
+        */
+        Fieldset annotationFS = null;
+        Method[] methodGeneralArr = new Method[0];
+        if (itemClass != null)
+        {
+            methodGeneralArr = itemClass.getMethods();
+        }
+        for (int i = 0; i < methodGeneralArr.length; i++)
+        {
+            Method method = methodGeneralArr[i];
+            // String modStr = methodModifierString(method);
+            String methodName = method.getName();
+            if (methodName.equals("getAnnotationSet"))
+            {
+                /***************************************************************
+                    Annotation fieldset
+                */
+                annotationFS = new Fieldset();
+                annotationFS.setTitle("Annotations");
+                /*
+                    Get DbControl
+                */
+                DbControl dc = getDbControlForObject(itemObject);
+                /*
+                    Fetch annotations
+                */
+                if (itemObject != null)
+                {
+                    try
+                    {
+                        Object[] arguments = new Object[] {};
+                        Object retobj = method.invoke(itemObject, arguments);
+                        AnnotationSet as = (AnnotationSet) retobj;
+                        for (Annotation a : as.getAnnotations().list(dc))
+                        {
+                            /*
+                                Only add annotations that contain something.
+                            */
+                            String value = joinAnnotationValues(a);
+                            if (value != null && !value.equals(""))
+                            {
+                                /*
+                                    Value (description) field - optional scroll
+                                    bar
+                                */
+                                TextArea descrF = new DescriptionField();
+                                descrF.setDisabled(true);
+                                descrF
+                                .setLabel(a.getAnnotationType().getName());
+                                descrF.setValue(value);
+                                annotationFS.add(descrF);
+                            }
+                        }
+                    }
+                    catch (InvocationTargetException e)
+                    {
+                        log
+                        .warn("FormFactory::getFormImpl(): InvocationTargetException when invoking method \"" + methodName + "\":" + e);
+                    }
+                    catch (IllegalAccessException e)
+                    {
+                        log
+                        .warn("FormFactory::getFormImpl(): IllegalAccessException when invoking method \"" + methodName + "\":" + e);
+                    }
+                }
+            }
+        }
+        /***********************************************************************
+            Form
+        */
+        String formName = new String("newForm");
+        if (clsName != null && clsName.length() > 0)
+        {
+            formName = clsName.substring(0, 1).toLowerCase() + clsName
+            .substring(1, clsName.length()) + "Form";
+        }
+        Form form = new Form(formName);
+        form.setTitle(clsName);
+        /***********************************************************************
+            Add fieldsets to form
+        */
+        form.addFieldset(mainFS);
+        if (annotationFS != null)
+        {
+            form.addFieldset(annotationFS);
+        }
+        /*
+            Return generated form.
+        */
+        return form;
+    }
+        
+    /**
+        Get DbControl for object.
+                                                
+        @return DbControl for the object
+    */
+    public DbControl getDbControlForObject(Object itemObject)
+    {
+        /*
+            Get class from itemObject.
+        */
+        Class<? extends Object> cls = null;
+        if (itemObject != null)
+        {
+            cls = itemObject.getClass();
+        }
+        if (cls == null)
+        {
+            return null;
+        }
+        String clsName = cls.getSimpleName();
+        /*
+            Check if object supports method getDbControl().
+        */
+        DbControl dc = null;
+        Method[] methodGeneralArr = cls.getMethods();
+        for (int i = 0; i < methodGeneralArr.length; i++)
+        {
+            Method method = methodGeneralArr[i];
+            String methodName = method.getName();
+            if (methodName.equals("getDbControl"))
+            {
+                /*
+                    Get DbControl for object
+                */
+                try
+                {
+                    Object[] arguments = new Object[] {};
+                    Object retobj = method.invoke(itemObject, arguments);
+                    dc = (DbControl) retobj;
+                }
+                catch (InvocationTargetException e)
+                {
+                    log
+                    .warn("FormFactory::getDbControlForObject(): InvocationTargetException when invoking method \"" + methodName + "\":" + e);
+                }
+                catch (IllegalAccessException e)
+                {
+                    log
+                    .warn("FormFactory::getDbControlForObject(): IllegalAccessException when invoking method \"" + methodName + "\":" + e);
+                }
+            }
+        }
+        /*
+            Return DbControl.
+        */
+        return dc;
+    }
+                        
+    /**
+        @param a annotation
+        @return String
+    */
+    private String joinAnnotationValues(Annotation a)
+    {
+        List<?> values = a.getValues();
+        StringBuilder sb = new StringBuilder();
+        for (Object o : values)
+        sb.append(o);
+        return sb.toString();
+    }
+                        
+    /**
+        Get list of excluded getter methods declared in current class.
+                                                
+        @return List<String> of excluded getter methods.
+    */
+    public List<String> getExcludedDeclMethods()
+    {
+        return this.excludedDeclMethods;
+    }
+                        
+    /**
+        Set list of excluded getter methods declared in current class.
+                                                
+        @param excludedDeclMethods List<String> of excluded getter methods to
+        set.
+    */
+    public void setExcludedDeclMethods(List<String> excludedDeclMethods)
+    {
+        this.excludedDeclMethods = excludedDeclMethods;
+    }
+                        
+    /**
+        Add list of excluded getter methods declared in current class.
+                                                
+        @param excludedDeclMethods List<String> of excluded getter methods to to
+        add.
+    */
+    public void addExcludedDeclMethods(List<String> excludedDeclMethods)
+    {
+        for (String exclMethod : excludedDeclMethods)
+        {
+            /*
+                Add excluded method if not already in list.
+            */
+            if (!getExcludedDeclMethods().contains(exclMethod))
+            {
+                getExcludedDeclMethods().add(exclMethod);
+            }
+        }
+    }
+        
+    /**
+        Initializes list of excluded getter methods declared in current class.
+    */
+    public void initExcludedDeclMethods()
+    {
+        /*
+            Initialize list of excluded declared methods.
+        */
+        getExcludedDeclMethods().add("getType");
+        getExcludedDeclMethods().add("getQuery");
+        getExcludedDeclMethods().add("getNew");
+        getExcludedDeclMethods().add("getById");
+        getExcludedDeclMethods().add("isUsed");
+        getExcludedDeclMethods().add("isRemoved");
+        getExcludedDeclMethods().add("getAnnotatableParents");
+    }
+             
+    /**
+        Fetch public method for object, or null if not found.
+                                                
+        @param publMethodName String Name of public method to search for.
+        @return Method public method for object with desired name, or null if not
+        found.
+    */
+    private Method fetchPublicMethodForObject(String publMethodName,
+    Class<? extends Object> cls)
+    {
+        if (cls == null)
+        {
+            return null;
+        }
+        String clsName = cls.getSimpleName();
+        /*
+            Check if object supports public method with desired name.
+        */
+        Method publMethod = null;
+        Method[] methodGeneralArr = cls.getMethods();
+        for (int i = 0; i < methodGeneralArr.length; i++)
+        {
+            Method method = methodGeneralArr[i];
+            String methodName = method.getName();
+            if (methodName.equals(publMethodName))
+            {
+                /*
+                    Check if method is public.
+                */
+                int methodMod = method.getModifiers();
+                if (Modifier.isPublic(methodMod))
+                {
+                    publMethod = method;
+                }
+            }
+        }
+        return publMethod;
+    }
+                        
+    /**
+        Returns a String corresponding to the method modifier: "static",
+        "public", "protected", or "private".
+                                                
+        @param method
+        @return String for method modifier
+    */
+    private String methodModifierString(Method method)
+    {
+        String modStr = new String("");
+        int methodMod = method.getModifiers();
+        if (Modifier.isStatic(methodMod))
+        {
+            modStr = new String("static");
+        }
+        else if (Modifier.isPublic(methodMod))
+        {
+            modStr = new String("public");
+        }
+        else if (Modifier.isProtected(methodMod))
+        {
+            modStr = new String("protected");
+        }
+        else if (Modifier.isPrivate(methodMod))
+        {
+            modStr = new String("private");
+        }
+        return modStr;
+    }
+    private TextArea newValueTextArea(String setValueMethodName,
+    Class<?> valueClass)
+    {
+        log
+        .debug("FormFactory::newValueTextArea(): setValueMethodName = \"" + setValueMethodName + "\" valueClass.getSimpleName() = \"" + valueClass
+        .getSimpleName() + "\"");
+        String setValueMethodSignature = null;
+        if (setValueMethodName != null && !setValueMethodName.equals(""))
+        {
+            /*
+                Set valid parameter name to signature of single-argument setter
+                method, if existing, in order to separate between arguments of
+                primitive types like boolean, int, float, and double, from those
+                of wrapper class types like Boolean, Integer, Float, and Double.
+            */
+            setValueMethodSignature = setValueMethodName + ":" + valueClass
+            .getSimpleName();
+            if (valueClass == String.class)
+            {
+                VString vSetterMethodParam = new VString(
+                setValueMethodSignature, 0, 65535, false);
+                TextArea valueF = new TextArea(vSetterMethodParam);
+                valueF.setLabel("");
+                valueF.setDisabled(false);
+                return valueF;
+            }
+            VString vSetterMethodParam = new VString("null", 0, 65535, false);
+            TextArea valueF = new TextArea(vSetterMethodParam);
+            valueF.setLabel("");
+            valueF.setDisabled(false);
+            return valueF;
+        }
+        VString vSetterMethodParam = new VString("null", 0, 65535, false);
+        TextArea valueF = new TextArea(vSetterMethodParam);
+        valueF.setLabel("");
+        valueF.setDisabled(true);
+        return valueF;
+    }
+        
+    private TextField<Boolean> newHiddenReadOnlyFormField()
+    {
+        TextField<Boolean> field = new TextField<Boolean>(VREADONLYFORM)
+        .setHidden(true);
+        return field;
+    }
 }

trunk/client/servlet/src/org/proteios/gui/form/FormFactory.java

@@ -1 +1 @@
 /*
     $Id$
-                
+                        
     Copyright (C) 2006, 2007 Fredrik Levander, Gregory Vincic, Olle Mansson
-                
+                        
     Files are copyright by their respective authors. The contributions to
     files where copyright is not explicitly stated can be traced with the
     source code revision system.
-                
+                        
     This file is part of Proteios.
     Available at http://www.proteios.org/
-                
+                        
     proteios-2.x is free software; you can redistribute it and/or
     modify it under the terms of the GNU General Public License
     as published by the Free Software Foundation; either version 2
     of the License, or (at your option) any later version.
-                
+                        
     Proteios is distributed in the hope that it will be useful,
     but WITHOUT ANY WARRANTY; without even the implied warranty of
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     GNU General Public License for more details.
-                
+                        
     You should have received a copy of the GNU General Public License
     along with this program; if not, write to the Free Software
@@ -68 +68 @@
     private HttpServletRequest request = null;
     private SessionControl sc = null;
-    /**
-        * List<String> of excluded getter methods declared in current class. If a
-        * getter accessor method is included in this list, when a generic form for
-        * an object is created with getForm(), no field will be added to the form
-        * for an instance variable (if any) corresponding to the getter method.
-    */
-    private List<String> excludedDeclMethods = new ArrayList<String>();
+        
     private Localizer locale = null;
     private String forwardActionId = null;
@@ -124 +118 @@
     public static final VBoolean VISMICROTITREPLATE = new VBoolean("isMicrotitrePlate", false);
     public static final VString VRANDOMSTRING = new VString("randomString", 1,15, true);
-    public static final VBoolean VREADONLYFORM = new VBoolean("readOnlyForm",false);
     public static final VBoolean VCONFIRM = new VBoolean("confirm", false);
     public static final VString VCONFIRMMESSAGE = new VString("confirmMessage",0, 255, false);
@@ -173 +166 @@
     private static final org.apache.log4j.Logger log = org.apache.log4j.LogManager
     .getLogger("org.proteios.gui.form");
-                
+                        
     /**
         Default constructor. Initializes list excludedDeclMethods.
@@ -182 +175 @@
             Initialize list excludedDeclMethods.
         */
-        initExcludedDeclMethods();
-    }
                 
-    /**
-        Get list of excluded getter methods declared in current class.
-                                
-        @return List<String> of excluded getter methods.
-    */
-    public List<String> getExcludedDeclMethods()
-    {
-        return this.excludedDeclMethods;
-    }
-                
-    /**
-        Set list of excluded getter methods declared in current class.
-                                
-        @param excludedDeclMethods List<String> of excluded getter methods to
-        set.
-    */
-    public void setExcludedDeclMethods(List<String> excludedDeclMethods)
-    {
-        this.excludedDeclMethods = excludedDeclMethods;
-    }
-                
-    /**
-        Add list of excluded getter methods declared in current class.
-                                
-        @param excludedDeclMethods List<String> of excluded getter methods to to
-        add.
-    */
-    public void addExcludedDeclMethods(List<String> excludedDeclMethods)
-    {
-        for (String exclMethod : excludedDeclMethods)
-        {
-            /*
-                Add excluded method if not already in list.
-            */
-            if (!getExcludedDeclMethods().contains(exclMethod))
-            {
-                getExcludedDeclMethods().add(exclMethod);
-            }
-        }
-    }
-                
+    }
+                        
     public void setActionFactory(ActionFactory af)
     {
         this.actionFactory = af;
     }
-                
+                        
     public String getForwardActionId()
     {
         return this.forwardActionId;
     }
-                
+                        
     public void setForwardActionId(String forwardActionId)
     {
         this.forwardActionId = forwardActionId;
     }
-                
+                        
     public String getSortColumnKey()
     {
         return this.sortColumnKey;
     }
-                
+                        
     public void setSortColumnKey(String sortColumnKey)
     {
         this.sortColumnKey = sortColumnKey;
     }
-                
+                        
     public Integer getFilterListSize()
     {
         return this.filterListSize;
     }
-                
+                        
     public void setFilterListSize(Integer filterListSize)
     {
         this.filterListSize = filterListSize;
     }
-                
+                        
     public List<String> getFilterKeyColumnList()
     {
         return this.filterKeyColumnList;
     }
-                
+                        
     public void setFilterKeyColumnList(List<String> filterKeyColumnList)
     {
         this.filterKeyColumnList = filterKeyColumnList;
     }
-                
+                        
     public HashMap<String, String> getFilterClassColumnHashMap()
     {
         return this.filterClassColumnHashMap;
     }
-                
+                        
     public void setFilterClassColumnHashMap(
     HashMap<String, String> filterClassColumnHashMap)
@@ -281 +233 @@
         this.filterClassColumnHashMap = filterClassColumnHashMap;
     }
-                
+                        
     public HashMap<String, String> getFilterConditionColumnHashMap()
     {
         return this.filterConditionColumnHashMap;
     }
-                
+                        
     public void setFilterConditionColumnHashMap(
     HashMap<String, String> filterConditionColumnHashMap)
@@ -292 +244 @@
         this.filterConditionColumnHashMap = filterConditionColumnHashMap;
     }
-                
+                        
     public HashMap<String, String> getFilterValueColumnHashMap()
     {
         return this.filterValueColumnHashMap;
     }
-                
+                        
     public void setFilterValueColumnHashMap(
     HashMap<String, String> filterValueColumnHashMap)
@@ -303 +255 @@
         this.filterValueColumnHashMap = filterValueColumnHashMap;
     }
-                
-    /**
-        Initializes list of excluded getter methods declared in current class.
-    */
-    public void initExcludedDeclMethods()
-    {
-        /*
-            Initialize list of excluded declared methods.
-        */
-        getExcludedDeclMethods().add("getType");
-        getExcludedDeclMethods().add("getQuery");
-        getExcludedDeclMethods().add("getNew");
-        getExcludedDeclMethods().add("getById");
-        getExcludedDeclMethods().add("isUsed");
-        getExcludedDeclMethods().add("isRemoved");
-        getExcludedDeclMethods().add("getAnnotatableParents");
-    }
-                
+                        
     public HttpServletRequest getRequest()
     {
         return request;
     }
-                
+                        
     public void setRequest(HttpServletRequest request)
     {
         this.request = request;
     }
-                
+                        
     public void modifyForPopup(Fieldset fs)
     {
         actionFactory.modifyForPopup(fs);
     }
-                
+                        
     private FileField newFileField()
     {
@@ -342 +277 @@
         return fileF;
     }
-                
+                        
     public TextField<Integer> newIdField()
     {
@@ -350 +285 @@
         return idF;
     }
-                
-    private TextField<String> newValueField(String setValueMethodName,
+                        
+    public TextField<String> newValueField(String setValueMethodName,
     Class<?> valueClass)
     {
@@ -382 +317 @@
         return valueF;
     }
-                
-    private TextArea newValueTextArea(String setValueMethodName,
-    Class<?> valueClass)
-    {
-        log
-        .debug("FormFactory::newValueTextArea(): setValueMethodName = \"" + setValueMethodName + "\" valueClass.getSimpleName() = \"" + valueClass
-        .getSimpleName() + "\"");
-        String setValueMethodSignature = null;
-        if (setValueMethodName != null && !setValueMethodName.equals(""))
-        {
-            /*
-                Set valid parameter name to signature of single-argument setter
-                method, if existing, in order to separate between arguments of
-                primitive types like boolean, int, float, and double, from those
-                of wrapper class types like Boolean, Integer, Float, and Double.
-            */
-            setValueMethodSignature = setValueMethodName + ":" + valueClass
-            .getSimpleName();
-            if (valueClass == String.class)
-            {
-                VString vSetterMethodParam = new VString(
-                setValueMethodSignature, 0, 65535, false);
-                TextArea valueF = new TextArea(vSetterMethodParam);
-                valueF.setLabel("");
-                valueF.setDisabled(false);
-                return valueF;
-            }
-            VString vSetterMethodParam = new VString("null", 0, 65535, false);
-            TextArea valueF = new TextArea(vSetterMethodParam);
-            valueF.setLabel("");
-            valueF.setDisabled(false);
-            return valueF;
-        }
-        VString vSetterMethodParam = new VString("null", 0, 65535, false);
-        TextArea valueF = new TextArea(vSetterMethodParam);
-        valueF.setLabel("");
-        valueF.setDisabled(true);
-        return valueF;
-    }
-                
+                        
     public TextField<Integer> newHiddenItemIdField()
     {
@@ -427 +323 @@
         return field;
     }
-                
-    private TextField<Boolean> newHiddenReadOnlyFormField()
-    {
-        TextField<Boolean> field = new TextField<Boolean>(VREADONLYFORM)
-        .setHidden(true);
-        return field;
-    }
-                
+                        
     private TextField<Integer> newHiddenIntegerField(VInteger vInteger)
     {
@@ -441 +330 @@
         return field;
     }
-                
+                        
     private TextField<String> newHiddenStringField(VString vString)
     {
@@ -448 +337 @@
         return field;
     }
-                
+                        
     public <D extends BasicItem<?>, E extends ProteiosAction<?>> Form getAnnotationsForm(
     DbControl dc, D item, Class<E> forwardAction)
@@ -498 +387 @@
         return form;
     }
-                
+                        
     /**
         @return Hidden
@@ -508 +397 @@
         return field;
     }
-                
+                        
     /**
         Form for user preferences configuration settings. Arguments
@@ -514 +403 @@
         holders for current values for the notification configuration and table
         preferences configuration form fields.
-                                
+                                                
         @param nc NotificationConfiguration object (need not be stored in
         database) with default field values.
@@ -532 +421 @@
         return form;
     }
-                
+                        
     /**
         Fieldset for notification configuration settings. Argument
         NotificationConfiguration is place holder for current values for the
         notification configuration form fields.
-                                
+                                                
         @param nc NotificationConfiguration object (need not be stored in
         database) with default field values.
@@ -589 +478 @@
         return properties;
     }
-                
+                        
     /**
         Creates a select box for notification mode.
-                                
+                                                
         @param modeValue int Mode value for default selection.
         @return Select<VInteger> Select box for notification mode selection
@@ -617 +506 @@
         return modeS;
     }
-                
+                        
     /**
         Fieldset for table preferences configuration settings. Argument
         TablePreferencesConfiguration is place holder for current values for the
         table preferences configuration form fields.
-                                
+                                                
         @param tpc TablePreferencesConfiguration object (need not be stored in
         database) with default field values.
@@ -652 +541 @@
         return properties;
     }
-                
+                        
     /**
         Creates a select box for table preferences mode.
-                                
+                                                
         @param modeValue int Mode value for default selection.
         @return Select<VInteger> Select box for table preferences mode selection
@@ -680 +569 @@
         return modeS;
     }
-                
+                        
+    /**
+        @param a annotation
+        @return String
+    */
+    private String joinAnnotationValues(Annotation a)
+    {
+        List<?> values = a.getValues();
+        StringBuilder sb = new StringBuilder();
+        for (Object o : values)
+        sb.append(o);
+        return sb.toString();
+    }
+        
     /**
         This will probably be removed when fixint #691
@@ -779 +681 @@
         return form;
     }
-                
+                        
     /**
         @param hit Current Hit
@@ -995 +897 @@
         return form;
     }
-                
-    /**
-        @param a annotation
-        @return String
-    */
-    private String joinAnnotationValues(Annotation a)
-    {
-        List<?> values = a.getValues();
-        StringBuilder sb = new StringBuilder();
-        for (Object o : values)
-        sb.append(o);
-        return sb.toString();
-    }
-                
+                        
     /**
         Returns a form for selecting spectrum mass range limits.
-                                
+                                                
         @param massCutoffLow String The lower cutoff mass value.
         @param massCutoffHigh String The upper cutoff mass value.
@@ -1057 +946 @@
         return form;
     }
-                
+                        
     /**
         Returns a form with spectrum properties for a spectrum obtained from a
         spectrum file.
-                                
+                                                
         @param spectrumFile File Core file with spectrum.
         @param spectrumId String Spectrum id string.
@@ -1270 +1159 @@
         return form;
     }
-                
+                        
     /**
         Returns a form with spectrum file instrument data for a spectrum file.
-                                
+                                                
         @param spectrumFileInstrumentList List<SpectrumFileInstrumentInterface>
         Spectrum file instrument list.
@@ -1458 +1347 @@
         return form;
     }
-                
+                        
     /**
         Adds a table row to a table. A "value" argument that is null will be
         represented as an empty string, otherwise by its toString() value.
-                                
+                                                
         @param table Table The table to add a row to.
         @param nameKey String Property key string.
@@ -1499 +1388 @@
         table.addRow(row);
     }
-                
+                        
     /**
         Returns a form with spectrum file contact data for a spectrum file.
-                                
+                                                
         @param spectrumContact Spectrum file contact
         data.
@@ -1585 +1474 @@
         return form;
     }
-                    
+                            
     /**
         Returns a form for adding spectrum file sample data for a spectrum file.
-                                
+                                                
         @param project Project The project in whose directory a new output
         directory is created.
@@ -1678 +1567 @@
         return form;
     }
-                
+                        
     private <D extends Object> TextField<D> newTextField(String name, D value)
     {
@@ -1687 +1576 @@
         return field;
     }
-                
+                        
     public Form getPeakListSetForm(PeakListSet pls)
     {
@@ -1755 +1644 @@
         return form;
     }
-                
+                        
     public Form getExportPeakListSetForm(PeakListSet pls)
     {
@@ -1802 +1691 @@
         return form;
     }
-                
+                        
     private void addAnnotationsAsFields(Fieldset to, Annotatable item,
     DbControl dc)
@@ -1817 +1706 @@
         }
     }
-                
+                        
     public Fieldset getProteinAssemblyFieldset(Project project)
     {
@@ -1840 +1729 @@
         return properties;
     }
-                
+                        
     public Select<VString> selectLocalSampleIdWithAllOption(DbControl dc,
     Project project)
@@ -1854 +1743 @@
         return select;
     }
-                
+                        
     private Select<VInteger> newSelectLabel(LabeledExtract le, DbControl dc)
     {
@@ -1875 +1764 @@
         return select;
     }
-                
+                        
     /**
         Creates and adds a hidden field with an Integer value to the given form.
@@ -1887 +1776 @@
         form.getFieldsets().get(0).add(field);
     }
-                
+                        
     /**
         Creates and adds a hidden field with an Integer value to the given table.
@@ -1899 +1788 @@
         table.add(field);
     }
-                
+                        
     public Fieldset getUsedSampleFieldset(Sample sample)
     {
@@ -1917 +1806 @@
         return fs;
     }
-                
+                        
     public Fieldset getUsedExtractFieldset(Extract extract)
     {
@@ -1932 +1821 @@
         return fs;
     }
-                
+                        
     public Fieldset getUsedLabeledExtractFieldset(LabeledExtract extract)
     {
@@ -1950 +1839 @@
         return fs;
     }
-                
+                        
     public Form getSecondaryLabeledExtractForm(LabeledExtract extract,
     DbControl dc, LabeledExtract fromExtract)
@@ -2013 +1902 @@
         return form;
     }
-                
+                        
     public Form getSetFilterForm(String filterName, String filterClass,
     String filterCondition, String filterValue)
@@ -2107 +1996 @@
         return form;
     }
-                
+                        
     private void addFilterSettingsToFieldset(Fieldset fs)
     {
@@ -2171 +2060 @@
         }
     }
-                
+                        
     public TextField<Float> newOriginalQuantityField()
     {
@@ -2179 +2068 @@
         return field;
     }
-                
+                        
     public TextField<Float> newRemainingQuantityField(Float remainingQuantity)
     {
@@ -2190 +2079 @@
         return field;
     }
-                
-    /**
-        Get generic form for object.
-                                
-        @param template template for generic form
-        @return Form for editing the object
-    */
-    public Form getForm(FormTemplateInterface formTemplate)
-    {
-        /***********************************************************************
-            Analyze object class
-        */
-                                
-        /*
-            Get class from formTemplate itemObject or itemClass.
-        */
-        Object itemObject = null;
-        Class<? extends Object> itemClass = null;
-        if (formTemplate.getItemObject() != null)
-        {
-            itemObject = formTemplate.getItemObject();
-            itemClass = itemObject.getClass();
-        }
-        else if (formTemplate.getItemClass() != null)
-        {
-            itemClass = formTemplate.getItemClass();
-        }
-        /*
-            Add optional extra formTemplate list of methods to be excluded.
-        */
-        if (formTemplate != null && formTemplate.getExcludedDeclMethods() != null)
-        {
-            addExcludedDeclMethods(formTemplate.getExcludedDeclMethods());
-        }
-        String clsName = new String("");
-        if (itemClass != null)
-        {
-            clsName = itemClass.getSimpleName();
-        }
-                                
-        /***********************************************************************
-            Main fieldset
-        */
-        Fieldset mainFS = new Fieldset();
-        String mainFsName = new String("Properties");
-        mainFS.setTitle(mainFsName);
-        /*
-            Add forward actionId field as first field, for external use.
-        */
-        TextField<String> fwdactionF = new ForwardField();
-        mainFS.add(fwdactionF);
-        /*
-            Get item id, if any.
-        */
-        int itemId = 0;
-        String getIdMethodName = "getId";
-        Method getIdMethod = fetchPublicMethodForObject(getIdMethodName,
-        itemClass);
-        if (getIdMethod != null && itemObject != null)
-        {
-            try
-            {
-                Object[] arguments = new Object[] {};
-                Object retobj = getIdMethod.invoke(itemObject, arguments);
-                String idStr = retobj.toString();
-                itemId = Integer.parseInt(idStr);
-            }
-            catch (InvocationTargetException e)
-            {
-                itemId = 0;
-            }
-            catch (IllegalAccessException e)
-            {
-                itemId = 0;
-            }
-            catch (java.lang.NumberFormatException e)
-            {
-                itemId = 0;
-            }
-        }
-        /*
-            Add itemId field idF (hidden) if itemId value ok.
-        */
-        if (itemId > 0)
-        {
-            TextField<Integer> idF = newHiddenItemIdField();
-            mainFS.add(idF);
-            idF.setLabel("ItemId");
-            idF.setValue(itemId);
-            idF.setDisabled(true);
-        }
-        /*
-            Add class name field cnF.
-        */
-        String classNameFull = new String("");
-        if (itemClass != null)
-        {
-            classNameFull = itemClass.getName();
-        }
-        TextField<String> cnF = new ClassNameField();
-        mainFS.add(cnF);
-        cnF.setHidden(true);
-        cnF.setLabel("ClassName");
-        cnF.setValue(classNameFull);
-        cnF.setDisabled(true);
-        /*
-            Add readOnlyForm field rofF (hidden).
-        */
-        TextField<Boolean> rofF = newHiddenReadOnlyFormField();
-        mainFS.add(rofF);
-        rofF.setLabel("ReadOnlyForm");
-        rofF.setValue(formTemplate.isReadOnlyForm());
-        rofF.setDisabled(true);
-        /*
-            Keep track on whether public setter methods exist, in order to know
-            if a "Save" button should be added.
-        */
-        boolean hasSetterMethods = false;
-        /*
-            Methods, declared and inherited
-        */
-        Method[] methodArr = new Method[0];
-        if (itemClass != null)
-        {
-            methodArr = itemClass.getMethods();
-        }
-                                
-        /*
-            Methods declared in object class (not inherited)
-        */
-        Method[] declaredMethodArr = new Method[0];
-        if (itemClass != null)
-        {
-            declaredMethodArr = itemClass.getDeclaredMethods();
-        }
-        for (int i = 0; i < declaredMethodArr.length; i++)
-        {
-            Method method = declaredMethodArr[i];
-            String modStr = methodModifierString(method);
-            String methodName = method.getName();
-            String methodReturnType = method.getReturnType().getName();
-            /*
-                Only process declared methods not in exclude list.
-            */
-            if (!getExcludedDeclMethods().contains(methodName))
-            {
-                String attrName = new String("");
-                String attrValueStr = new String("");
-                String returnTypeStr = new String("");
-                boolean returnTypeOK = false;
-                Class<?> returnTypeOfGetterMethod = null;
-                /*
-                    Check if getter access method.
-                */
-                if (methodName.startsWith("get"))
-                {
-                    /*
-                        Assume that attribute name can optained by skipping "get"
-                        in method name.
-                    */
-                    attrName = methodName.substring(3);
-                    // int methodMod = declaredMethodArr[i].getModifiers();
-                    if (method.getReturnType().getName().equals("int") || method
-                    .getReturnType().getName().equals("java.lang.Integer") || method
-                    .getReturnType().getName().equals("float") || method
-                    .getReturnType().getName().equals("java.lang.Float") || method
-                    .getReturnType().getName().equals("double") || method
-                    .getReturnType().getName().equals("java.lang.Double") || method
-                    .getReturnType().getName().equals("java.lang.String") || method
-                    .getReturnType().getName().equals("java.util.Date"))
-                    {
-                        returnTypeOfGetterMethod = method.getReturnType();
-                        returnTypeStr = method.getReturnType().getName();
-                        returnTypeOK = true;
-                    }
-                }
-                else if (methodName.startsWith("is"))
-                {
-                    /*
-                        Assume that attribute name can optained by skipping "is"
-                        in method name.
-                    */
-                    attrName = methodName.substring(2);
-                    // int methodMod = declaredMethodArr[i].getModifiers();
-                    if (method.getReturnType().getName().equals("boolean") || method
-                    .getReturnType().getName().equals("java.lang.Boolean"))
-                    {
-                        returnTypeOfGetterMethod = method.getReturnType();
-                        returnTypeStr = method.getReturnType().getName();
-                        returnTypeOK = true;
-                    }
-                }
-                if (returnTypeOK)
-                {
-                    if (itemObject != null)
-                    {
-                        try
-                        {
-                            Object[] arguments = new Object[] {};
-                            Object retobj = method
-                            .invoke(itemObject, arguments);
-                            if (retobj != null)
-                            {
-                                /*
-                                    Return date values in "YYYY-MM-DD HH:mm:ss"
-                                    24-hour format.
-                                */
-                                if (method.getReturnType().getName().equals(
-                                "java.util.Date"))
-                                {
-                                    SimpleDateFormat dateFormat = Format.TIMESTAMP
-                                    .getPattern();
-                                    attrValueStr = dateFormat
-                                    .format((Date) retobj);
-                                }
-                                else
-                                {
-                                    attrValueStr = retobj.toString();
-                                }
-                            }
-                        }
-                        catch (InvocationTargetException e)
-                        {
-                            log
-                            .warn("FormFactory::getFormImpl(): InvocationTargetException when invoking method \"" + methodName + "\":" + e);
-                        }
-                        catch (IllegalAccessException e)
-                        {
-                            log
-                            .warn("FormFactory::getFormImpl(): IllegalAccessException when invoking method \"" + methodName + "\":" + e);
-                        }
-                        log
-                        .debug("FormFactory::getFormImpl(): methodName = \"" + methodName + "\"  returnTypeOfGetterMethod = \"" + returnTypeOfGetterMethod + "\" attrValueStr = \"" + attrValueStr + "\"");
-                    }
-                    /*
-                        Check if public accessor method for setting value exists.
-                    */
-                    boolean isSettable = false;
-                    String publMethodName = new String("set" + attrName);
-                    if (!formTemplate.isReadOnlyForm())
-                    {
-                        if (fetchPublicMethodForObject(publMethodName,
-                        itemClass) != null)
-                        {
-                            isSettable = true;
-                        }
-                    }
-                    log
-                    .debug("FormFactory::getFormImpl(): attrName = \"" + attrName + "\" publMethodName = \"" + publMethodName + "\" isSettable = " + isSettable);
-                    /*
-                        Use TextArea for Description, else TextField
-                    */
-                    if (attrName.equals("Description"))
-                    {
-                        /*
-                            Value text area
-                        */
-                        TextArea valueF = null;
-                        if (!isSettable)
-                        {
-                            valueF = newValueTextArea("", String.class);
-                        }
-                        else
-                        {
-                            hasSetterMethods = true;
-                            valueF = newValueTextArea(publMethodName,
-                            returnTypeOfGetterMethod);
-                        }
-                        mainFS.add(valueF);
-                        valueF.setLabel(attrName);
-                        valueF.setValue(attrValueStr);
-                    }
-                    else
-                    {
-                        /*
-                            Value field
-                        */
-                        TextField<String> valueF = null;
-                        if (!isSettable)
-                        {
-                            valueF = newValueField("", String.class);
-                        }
-                        else
-                        {
-                            hasSetterMethods = true;
-                            valueF = newValueField(publMethodName,
-                            returnTypeOfGetterMethod);
-                        }
-                        mainFS.add(valueF);
-                        valueF.setLabel(attrName);
-                        valueF.setValue(attrValueStr);
-                    }
-                }
-            }
-        }
-                                
-        /*
-            Check if object supports method getAnnotationSet().
-        */
-        Fieldset annotationFS = null;
-        Method[] methodGeneralArr = new Method[0];
-        if (itemClass != null)
-        {
-            methodGeneralArr = itemClass.getMethods();
-        }
-        for (int i = 0; i < methodGeneralArr.length; i++)
-        {
-            Method method = methodGeneralArr[i];
-            // String modStr = methodModifierString(method);
-            String methodName = method.getName();
-            if (methodName.equals("getAnnotationSet"))
-            {
-                /***************************************************************
-                    Annotation fieldset
-                */
-                annotationFS = new Fieldset();
-                annotationFS.setTitle("Annotations");
-                /*
-                    Get DbControl
-                */
-                DbControl dc = getDbControlForObject(itemObject);
-                /*
-                    Fetch annotations
-                */
-                if (itemObject != null)
-                {
-                    try
-                    {
-                        Object[] arguments = new Object[] {};
-                        Object retobj = method.invoke(itemObject, arguments);
-                        AnnotationSet as = (AnnotationSet) retobj;
-                        for (Annotation a : as.getAnnotations().list(dc))
-                        {
-                            /*
-                                Only add annotations that contain something.
-                            */
-                            String value = joinAnnotationValues(a);
-                            if (value != null && !value.equals(""))
-                            {
-                                /*
-                                    Value (description) field - optional scroll
-                                    bar
-                                */
-                                TextArea descrF = new DescriptionField();
-                                descrF.setDisabled(true);
-                                descrF
-                                .setLabel(a.getAnnotationType().getName());
-                                descrF.setValue(value);
-                                annotationFS.add(descrF);
-                            }
-                        }
-                    }
-                    catch (InvocationTargetException e)
-                    {
-                        log
-                        .warn("FormFactory::getFormImpl(): InvocationTargetException when invoking method \"" + methodName + "\":" + e);
-                    }
-                    catch (IllegalAccessException e)
-                    {
-                        log
-                        .warn("FormFactory::getFormImpl(): IllegalAccessException when invoking method \"" + methodName + "\":" + e);
-                    }
-                }
-            }
-        }
-        /***********************************************************************
-            Form
-        */
-        String formName = new String("newForm");
-        if (clsName != null && clsName.length() > 0)
-        {
-            formName = clsName.substring(0, 1).toLowerCase() + clsName
-            .substring(1, clsName.length()) + "Form";
-        }
-        Form form = new Form(formName);
-        form.setTitle(clsName);
-        /***********************************************************************
-            Add fieldsets to form
-        */
-        form.addFieldset(mainFS);
-        if (annotationFS != null)
-        {
-            form.addFieldset(annotationFS);
-        }
-        /*
-            Return generated form.
-        */
-        return form;
-    }
-                
-    /**
-        Get DbControl for object.
-                                
-        @return DbControl for the object
-    */
-    public DbControl getDbControlForObject(Object itemObject)
-    {
-        /*
-            Get class from itemObject.
-        */
-        Class<? extends Object> cls = null;
-        if (itemObject != null)
-        {
-            cls = itemObject.getClass();
-        }
-        if (cls == null)
-        {
-            return null;
-        }
-        String clsName = cls.getSimpleName();
-        /*
-            Check if object supports method getDbControl().
-        */
-        DbControl dc = null;
-        Method[] methodGeneralArr = cls.getMethods();
-        for (int i = 0; i < methodGeneralArr.length; i++)
-        {
-            Method method = methodGeneralArr[i];
-            String methodName = method.getName();
-            if (methodName.equals("getDbControl"))
-            {
-                /*
-                    Get DbControl for object
-                */
-                try
-                {
-                    Object[] arguments = new Object[] {};
-                    Object retobj = method.invoke(itemObject, arguments);
-                    dc = (DbControl) retobj;
-                }
-                catch (InvocationTargetException e)
-                {
-                    log
-                    .warn("FormFactory::getDbControlForObject(): InvocationTargetException when invoking method \"" + methodName + "\":" + e);
-                }
-                catch (IllegalAccessException e)
-                {
-                    log
-                    .warn("FormFactory::getDbControlForObject(): IllegalAccessException when invoking method \"" + methodName + "\":" + e);
-                }
-            }
-        }
-        /*
-            Return DbControl.
-        */
-        return dc;
-    }
-                
-    /**
-        Fetch public method for object, or null if not found.
-                                
-        @param publMethodName String Name of public method to search for.
-        @return Method public method for object with desired name, or null if not
-        found.
-    */
-    private Method fetchPublicMethodForObject(String publMethodName,
-    Class<? extends Object> cls)
-    {
-        if (cls == null)
-        {
-            return null;
-        }
-        String clsName = cls.getSimpleName();
-        /*
-            Check if object supports public method with desired name.
-        */
-        Method publMethod = null;
-        Method[] methodGeneralArr = cls.getMethods();
-        for (int i = 0; i < methodGeneralArr.length; i++)
-        {
-            Method method = methodGeneralArr[i];
-            String methodName = method.getName();
-            if (methodName.equals(publMethodName))
-            {
-                /*
-                    Check if method is public.
-                */
-                int methodMod = method.getModifiers();
-                if (Modifier.isPublic(methodMod))
-                {
-                    publMethod = method;
-                }
-            }
-        }
-        return publMethod;
-    }
-                
-    /**
-        Returns a String corresponding to the method modifier: "static",
-        "public", "protected", or "private".
-                                
-        @param method
-        @return String for method modifier
-    */
-    private String methodModifierString(Method method)
-    {
-        String modStr = new String("");
-        int methodMod = method.getModifiers();
-        if (Modifier.isStatic(methodMod))
-        {
-            modStr = new String("static");
-        }
-        else if (Modifier.isPublic(methodMod))
-        {
-            modStr = new String("public");
-        }
-        else if (Modifier.isProtected(methodMod))
-        {
-            modStr = new String("protected");
-        }
-        else if (Modifier.isPrivate(methodMod))
-        {
-            modStr = new String("private");
-        }
-        return modStr;
-    }
-                
+                        
     private Localizer getLocale()
     {
         return locale;
     }
-                
+                        
     public void setLocale(Localizer locale)
     {
         this.locale = locale;
     }
-                
+                        
     //Cleaning up from here        
-            
+                    
     /**
         Form for new Protocol item. The difference between calling
@@ -2729 +2102 @@
         a convenient place holder for default values for the Protocol form
         fields.
-                                
+                                                
         @param protocol Protocol object (need not be stored in database) with
         default field values.
@@ -2814 +2187 @@
         return form;
     }
-                
+                        
     public Form getForm(Class<?> cls)
     {
@@ -2904 +2277 @@
             loginF.setDisabled(true);
             fs.add(fs.size()-2, loginF); // After the itemId field
-                                    
+                                                            
             TextField<String> emailF = new EmailField();
             fs.add(fs.size()-1, emailF);
-                                                
+                                                                        
             TextField<String> phoneF = new PhoneField();
             fs.add(phoneF);
-                                                
+                                                                        
             TextField<String> addressF = new AddressField();
             fs.add(addressF);
-                                                
+                                                                        
             TextField<String> organisationF = new OrganisationField();
             fs.add(organisationF);
-                                                
+                                                                        
             if (obj != null)
             {
@@ -3247 +2620 @@
         return form;
     }
-                
+                        
     /**
         Creates a select box for protocols. If the class for which the protocol
@@ -3255 +2628 @@
         if the protocol is tagged to be removed. However, no other protocols
         tagged to be removed should be included in the list.
-                                
+                                                
         @param cls Class Class for which a protocol should be selected.
         @param obj Object Optional object with attached protocol for setting
@@ -3362 +2735 @@
         return protocolS;
     }
-                
+                        
     public void setSc(SessionControl sc)
     {