Merge branch 'dev'

Conflicts:
	portal.ejb/src/main/java/org/vamdc/portal/session/queryLog/QueryStoreProcessor.java

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/QueryTreeController.java

@@ -84,7 +84,6 @@ private Integer requestableFormsCount(){
 	public List<Form> getForms() {
 		List<Form> forms= new ArrayList<Form>();
 		forms = this.getQueryData().getOrderedGuidedForm();
-		//return queryData.getUnsortedForms();
 		return forms;
 	}
 

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/fields/ProxyRangeField.java

@@ -12,7 +12,7 @@
 import org.vamdc.portal.session.queryBuilder.unitConv.UnitConverter;
 
 /**
- * Field that proxies several range fields and does intercorversion into the primary one
+ * Field that proxies several range fields and does interconversion into the primary one
  * @author doronin
  *
  */

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/fields/SuggestionImpl.java

@@ -11,8 +11,8 @@ public abstract class SuggestionImpl implements SuggestionField.Suggestion{
 	 * @return a collection that will be used for suggestion lookup
 	 */
 	protected abstract Collection<String> loadValues();
-
-	protected final Collection<String> values;
+	protected Collection<String> values;
+
 	public SuggestionImpl(){
 		this.values= loadValues();
 	}

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/forms/CollisionsForm.java

@@ -98,8 +98,9 @@ public class ProcessNameSuggest extends SuggestionImpl{
 		@Override
 		protected Collection<String> loadValues() {
 			Collection<String> result = new ArrayList<String>();
-			for (XsamsProcessCode code:XsamsProcessCode.values())
+			for (XsamsProcessCode code:XsamsProcessCode.values()){;
 				result.add(code.getProcessName());
+			}
 			return result;
 		}
 

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/formsTree/AtomsTreeForm.java

@@ -1,7 +1,6 @@
 package org.vamdc.portal.session.queryBuilder.formsTree;
 
 import org.vamdc.portal.session.queryBuilder.QueryTreeInterface;
-import org.vamdc.portal.session.queryBuilder.fields.AbstractField;
 import org.vamdc.portal.session.queryBuilder.forms.FormForFields;
 import org.vamdc.portal.session.queryBuilder.forms.AtomsForm;
 import org.vamdc.portal.session.queryBuilder.forms.Order;
@@ -13,14 +12,13 @@ public class AtomsTreeForm extends AtomsForm implements FormForFields, TreeFormI
 	private static final long serialVersionUID = 5992593235932991330L;
 	protected Integer position; 
 	private QueryTreeInterface tree;
+
 	public AtomsTreeForm(QueryTreeInterface tree) {
-		//super(tree);
 		this.tree = tree;
 		position = tree.getFormCount();
 	}
 
 	public AtomsTreeForm(QueryTreeInterface tree, String prefix) {
-		//super(tree);
 		this.tree = tree;
 		this.setPrefix(prefix);
 		position = tree.getFormCount();
@@ -30,32 +28,20 @@ public String getObject(){
 		return this.toString();
 	}
 
-	/*@Override
-	public String getView() {
-		return "/xhtml/query/queryTree/atomsForm.xhtml";
-	}*/
 
 	@Override
 	public void validate() {
-		// TODO Auto-generated method stub
 		tree.addForm(this);
 	}
-
 
-	@Override
-	public void fieldUpdated(AbstractField field) {
-		// TODO Auto-generated method stub
-	}
 
 	@Override
 	public Integer getOrder() {
-		// TODO Auto-generated method stub
 		return Order.Atoms;
 	}
 
 	@Override
 	public Boolean getQueryable() {
-		// TODO Auto-generated method stub
 		return true;
 	}
 

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/formsTree/CollisionTreeForm.java

@@ -36,7 +36,7 @@ public class CollisionTreeForm extends CollisionsForm implements FormForFields,
 	private Boolean queryable = true;
 	private SearchMode selectedMode = SearchMode.withoutReaction;
 	private QueryTreeInterface tree;
-	private final String defaultSubmitButtonValue = "Select target(s) and collider(s)";
+	private String defaultSubmitButtonValue = "Select targets and colliders";
 	private String submitButtonValue = defaultSubmitButtonValue;
 
 
@@ -139,7 +139,7 @@ public void changeCollisionType(ValueChangeEvent e){
 			break;
 
 		case withReaction:
-			this.submitButtonValue = "Select reactant(s) and product(s)";
+			this.submitButtonValue = "Select reactants and products";
 			break;				
 		}
 

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/formsTree/RadiativeForm.java

@@ -43,7 +43,6 @@ private enum NextForm{
 		private static final long serialVersionUID = 1L;
 		{
 			add(new SelectItem(NextForm.upperLowerEnergyRange,"Transition from an energy range to another one"));
-			//add(new SelectItem(NextForm.stateEnergyRange,"Transition to and from a given energy range"));
 			add(new SelectItem(NextForm.anyEnergyRange,"Any transition"));
 		}
 	};
@@ -67,9 +66,7 @@ public String getView() {
 	public void validate() {
 		if (this.selectedMode == null)
 			return;
-
-		//System.err.println("Adding next form "+selectedMode.name());
-
+
 		switch(this.selectedMode){
 		case upperLowerEnergyRange:
 			tree.addForm(new AllStatesEnergyTreeForm(tree));
@@ -129,12 +126,13 @@ public String getSubmitButtonValue(){
 
 	public void changeTransitionType(ValueChangeEvent e){
 		NextForm value = (NextForm)e.getNewValue();
+		String submitButton = "Select range";
 		switch(value){
 		case upperLowerEnergyRange:
-			this.submitButtonValue = "Configure energy range";
+			this.submitButtonValue = submitButton;
 			break;
 		case stateEnergyRange:
-			this.submitButtonValue = "Configure energy range";
+			this.submitButtonValue = submitButton;
 			break;
 		case anyEnergyRange:	
 			this.submitButtonValue = this.defaultSubmitButtonValue;

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/formsTree/ReactionCollisionForm.java

@@ -23,7 +23,6 @@ public abstract class ReactionCollisionForm extends AbstractForm implements Form
 	private QueryTreeInterface tree;
 	private Boolean queryable = true;
 
-	//private Boolean hasHiddenForm = false;
 
 	private String typeAName;
 	private String typeBName;

portal.ejb/src/main/java/org/vamdc/portal/session/queryBuilder/unitConv/WavelengthUnitConverter.java

@@ -15,6 +15,7 @@ public WavelengthUnitConverter() {
 	private static final long serialVersionUID = 3599889437685237848L;
 
 	enum WavelengthConvert implements AbstractUnitConverter.EnumConverter{
+
 		ANGSTROM("A",NonSI.ANGSTROM.getConverterTo(NonSI.ANGSTROM)),
 		NM("nm",METRE.times(1e-9).getConverterTo(NonSI.ANGSTROM)),
 		UM("um",METRE.times(1e-6).getConverterTo(NonSI.ANGSTROM)),
@@ -24,6 +25,7 @@ enum WavelengthConvert implements AbstractUnitConverter.EnumConverter{
 		WavelengthConvert(String display,javax.measure.converter.UnitConverter converter){
 			this.display = display;
 			this.convert = converter;
+			javax.measure.converter.UnitConverter c = METRE.times(1e-3).getConverterTo(NonSI.ANGSTROM);
 		}
 
 		private javax.measure.converter.UnitConverter convert;
@@ -32,12 +34,19 @@ enum WavelengthConvert implements AbstractUnitConverter.EnumConverter{
 		public String getDisplay() { return display; }
 
 		@Override
-		public Double convert(Double value) { return convert.convert(value); }
+		public Double convert(Double value) { 		
+			// return int value of double if value is an integer
+			// to prevent trailing decimal values (i.e 1.00000000001)
+			if((value - Math.round(value)) == 0 ){
+				return new Double(Math.round(convert.convert(value)));
+			}else{
+				return convert.convert(value);
+			}
+		}
 
 		@Override
 		public EnumConverter[] getValues() { return WavelengthConvert.values(); }
 
-
 	}
 
 }

portal.ejb/src/main/java/org/vamdc/portal/session/queryLog/QueryStoreProcessor.java

@@ -46,7 +46,7 @@ public QueryStoreResponse getResponse() {
 		} catch (InterruptedException e) {
 			log.debug(e);
 			result = new QueryStoreResponse(QueryStoreResponse.STATUS_ERROR, "", e.getMessage());
-		} catch (ExecutionException e) {			
+		} catch (ExecutionException e) {		
 			log.debug(e);
 			result = new QueryStoreResponse(QueryStoreResponse.STATUS_ERROR, "", e.getMessage());
 		}catch (NullPointerException e) {

portal.war/src/main/webapp/layout/template.xhtml

@@ -4,8 +4,9 @@
 	xmlns:ui="http://java.sun.com/jsf/facelets"
 	xmlns:f="http://java.sun.com/jsf/core"
 	xmlns:h="http://java.sun.com/jsf/html"
+	xmlns:s="http://jboss.com/products/seam/taglib"
 	xmlns:a="http://richfaces.org/a4j"
-	xmlns:s="http://jboss.com/products/seam/taglib" contentType="text/html">
+	 contentType="text/html">
 	<html>
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />

portal.war/src/main/webapp/queryTree.xhtml

@@ -5,33 +5,29 @@
 	xmlns:ui="http://java.sun.com/jsf/facelets"
 	xmlns:f="http://java.sun.com/jsf/core"
 	xmlns:h="http://java.sun.com/jsf/html"
-	xmlns:rich="http://richfaces.org/rich"
 	xmlns:a4j="http://richfaces.org/a4j"
 	xmlns:c="http://java.sun.com/jstl/core"
+	xmlns:rich="http://richfaces.org/rich"
 	template="/layout/template.xhtml">
-	
-	
+
+
 	<ui:define name="body">
 		<c:if test="#{disclaimer.value == false}">
-			 <ui:include src="/xhtml/disclaimer/disclaimerValidation.xhtml" />
+			<ui:include src="/xhtml/disclaimer/disclaimerValidation.xhtml" />
 		</c:if>
 		<c:if test="#{disclaimer.value == true}">
-			<a4j:outputPanel width="460" id="formPanel">
-				<h:panelGrid>
+			<a4j:outputPanel id="formPanel">
+				<h:panelGrid width="50%">
 					<c:forEach items="#{queryTree.forms}" var="form">
 						<a4j:include viewId="#{form.view}" />
-					</c:forEach>				
-					<rich:spacer width="460" />				
+					</c:forEach>
+
 				</h:panelGrid>
-				<a4j:outputPanel width="460" id="buttons">
-			<ui:include src="/xhtml/query/queryTree/actionButtons.xhtml" />
-			</a4j:outputPanel>
-
-			</a4j:outputPanel>
-			<a4j:outputPanel id="nodeTree">
-				<rich:spacer width="460" />			
+				<a4j:outputPanel id="buttons">
+					<ui:include src="/xhtml/query/queryTree/actionButtons.xhtml" />
+				</a4j:outputPanel>
+
 			</a4j:outputPanel>
-			<a4j:outputPanel id="asyncForm" />
 		</c:if>
 	</ui:define>
 

portal.war/src/main/webapp/stylesheet/style.css

@@ -104,7 +104,7 @@ table.radio input[type=radio] {
 }
 
 .content {
-	padding: 1%;
+	padding: 0.5em;
 	width : 100%;
 }
 
@@ -116,7 +116,7 @@ table.radio input[type=radio] {
 	margin-left:5px;
 }
 .narrowfield{
-	width: 70px;
+	width: 60px;
 	margin-top:0px;
 	margin-bottom:0px;
 	margin-right:5px;
@@ -140,10 +140,10 @@ table.radio input[type=radio] {
 }
 
 .rightColumn {
-	width: 250px;
-	align: right;
+	width: 270px;
+	/*align: right;
 	text-align: right;
-	float: right;
+	float: right;*/
 }
 
 .queryMenuPanel{
@@ -180,7 +180,7 @@ table.radio input[type=radio] {
 .queryForms{
 	height: 100%;
 	vertical-align: top;
-	width : 410px;
+	width : 460px;
 	/*max-width : 410px;*/
 }
 
@@ -270,19 +270,33 @@ table.radio input[type=radio] {
 	background-color: inherit;
 }
 
-.collisionSpecies{
+.collisionSpeciesText{
 	text-decoration:none;
 	border-bottom:1px dotted #D4CFC7;
 }
 
+
+.collisionSpeciesSelectionForm{
+	width : 49%;
+	float : left;
+}
+
+
 .roundButton {
 	-moz-border-radius: 10px;
 	border-radius: 10px;
 }
 
 .largeButton{
-	width : 100px;
+	width : 110px;
 	font-weight : bold;	
+	padding : 1px;
+}
+
+.largerButton{
+	width : 220px;
+	font-weight : bold;	
+	padding : 1px;
 }
 
 .buttonArea .largeButton{
@@ -411,4 +425,4 @@ table.radio input[type=radio] {
 .important{
 	text-decoration : underline;
 	font-weight : bold;
-}
+}

portal.war/src/main/webapp/xhtml/query/fields/proxyRangeField.xhtml

@@ -15,7 +15,6 @@
 		</h:selectOneMenu>
 	</h:panelGroup>
 	<h:panelGroup>
-		<rich:spacer width="" />
 		<h:inputText value="#{field.userLoValue}" styleClass="narrowfield" tabindex="10">
 			<a4j:support event="onkeyup" reRender="nodeTree,buttonArea,conv#{field.id}"/>
 		</h:inputText>

portal.war/src/main/webapp/xhtml/query/fields/rangeField.xhtml

@@ -14,7 +14,6 @@
 		</h:outputText>
 	</h:panelGroup>
 	<h:panelGroup>
-		<rich:spacer width="10" />
 		<h:inputText value="#{field.loValue}" styleClass="narrowfield" tabindex="10">
 			<a4j:support event="onkeyup" reRender="nodeTree,buttonArea"/>
 		</h:inputText>

portal.war/src/main/webapp/xhtml/query/forms/collisionsForm.xhtml

@@ -1,4 +1,5 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <ui:composition xmlns="http://www.w3.org/1999/xhtml"
 	xmlns:s="http://jboss.com/products/seam/taglib"
 	xmlns:ui="http://java.sun.com/jsf/facelets"
@@ -43,7 +44,7 @@
 				</f:facet>
 
 				<h:column>
-					<h:outputText value="#{species.title}" id="cspecies#{species.id}" styleClass="collisionSpecies">
+					<h:outputText value="#{species.title}" id="cspecies#{species.id}" styleClass="collisionSpeciesText">
 						<rich:toolTip value="#{species.summary}" styleClass="toolTip"
 						direction="bottom-left" />
 					</h:outputText>

portal.war/src/main/webapp/xhtml/query/forms/moleculesForm.xhtml

@@ -13,11 +13,11 @@
 		<ui:include src="/xhtml/query/forms/formTitle.xhtml" />
 
 		<a4j:form ajaxSubmit="true">
-			<c:forEach items="#{form.fields}" var="field">
-				<h:panelGrid columns="2" columnClasses="leftColumn,rightColumn">
-					<ui:include src="#{field.view}" />
-				</h:panelGrid>
-			</c:forEach>
+			<h:panelGrid columns="2" columnClasses="leftColumn,rightColumn">
+				<c:forEach items="#{form.fields}" var="field">				
+						<ui:include src="#{field.view}" />				
+				</c:forEach>
+			</h:panelGrid>
 		</a4j:form>
 
 		<a4j:form ajaxSubmit="true" rendered="#{! form.molecules.isEmpty()}">