added genus and species to drop-down with common name

ChangeLog.md

@@ -6,6 +6,7 @@ Features
 
 - Add option to suppress calculation of non-canonical splice site [2509](https://github.com/GMOD/Apollo/issues/2509).
 - Added the ability to sync the gene and transcript name with the click of a button [2519](https://github.com/GMOD/Apollo/issues/2519).
+- Added organism and species to menus [2537](https://github.com/GMOD/Apollo/pull/2537).
 
 Bug Fixes
 

src/gwt/org/bbop/apollo/gwt/client/MainPanel.java

@@ -3,12 +3,15 @@
 import com.google.gwt.core.client.GWT;
 import com.google.gwt.core.client.JavaScriptObject;
 import com.google.gwt.core.client.Scheduler;
+import com.google.gwt.dom.client.Document;
 import com.google.gwt.dom.client.Element;
+import com.google.gwt.dom.client.OptionElement;
 import com.google.gwt.event.dom.client.ChangeEvent;
 import com.google.gwt.event.dom.client.ClickEvent;
 import com.google.gwt.event.logical.shared.SelectionEvent;
 import com.google.gwt.http.client.*;
 import com.google.gwt.json.client.*;
+import com.google.gwt.safehtml.shared.SafeHtmlUtils;
 import com.google.gwt.uibinder.client.UiBinder;
 import com.google.gwt.uibinder.client.UiField;
 import com.google.gwt.uibinder.client.UiHandler;
@@ -24,6 +27,7 @@
 import org.bbop.apollo.gwt.client.rest.*;
 import org.bbop.apollo.gwt.shared.FeatureStringEnum;
 import org.bbop.apollo.gwt.shared.GlobalPermissionEnum;
+import org.bbop.apollo.gwt.shared.OrganismComparator;
 import org.bbop.apollo.gwt.shared.PermissionEnum;
 import org.gwtbootstrap3.client.ui.*;
 import org.gwtbootstrap3.client.ui.Anchor;
@@ -34,9 +38,7 @@
 import org.gwtbootstrap3.extras.bootbox.client.Bootbox;
 import org.gwtbootstrap3.extras.bootbox.client.callback.ConfirmCallback;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 /**
  * Created by ndunn on 12/18/14.
@@ -657,6 +659,16 @@ public static void updateGenomicViewer(boolean forceReload, boolean forceUrl) {
         }
     }
 
+    private String capitalize(String input){
+      return input.substring(0,1).toUpperCase(Locale.ROOT) + input.substring(1).toLowerCase(Locale.ROOT);
+    }
+
+    private String createSpace(int length){
+      StringBuffer buffer = new StringBuffer();
+      for(int i = 0 ; i < length ; i++) { buffer.append("&nbsp;");}
+      return buffer.toString();
+    }
+
     public void setAppState(AppStateInfo appStateInfo) {
         trackPanel.clear();
 
@@ -673,6 +685,8 @@ public void setAppState(AppStateInfo appStateInfo) {
             organismInfoList = appStateInfo.getOrganismList();
         }
 
+        Collections.sort(organismInfoList, new OrganismComparator() );
+
         commonDataDirectory = appStateInfo.getCommonDataDirectory();
         currentSequence = appStateInfo.getCurrentSequence();
         currentOrganism = appStateInfo.getCurrentOrganism();
@@ -681,8 +695,20 @@ public void setAppState(AppStateInfo appStateInfo) {
 
         organismListBox.clear();
         for (OrganismInfo organismInfo : organismInfoList) {
-            organismListBox.addItem(organismInfo.getName(), organismInfo.getId());
-            if (currentOrganism.getId().equals(organismInfo.getId())) {
+//           Element listElement = organismListBox.getElement();
+          String display = organismInfo.getName();
+            if(organismInfo.getGenus()!=null && organismInfo.getSpecies()!=null) {
+//              display = "<i>"+capitalize(organismInfo.getGenus()) + " " + organismInfo.getSpecies()+ "</i> (" + display + ")";
+              display = capitalize(organismInfo.getGenus()) + " " + organismInfo.getSpecies()+ " (" + display + ")";
+            }
+
+            // allows an html option
+//          OptionElement optionElement = Document.get().createOptionElement();
+//          optionElement.setInnerSafeHtml(SafeHtmlUtils.fromTrustedString(display));
+//          optionElement.setValue(organismInfo.getId());
+            organismListBox.addItem(display, organismInfo.getId());
+//          listElement.appendChild(optionElement);
+          if (currentOrganism.getId().equals(organismInfo.getId())) {
                 organismListBox.setSelectedIndex(organismListBox.getItemCount() - 1);
 
                 // fixes #2319

src/gwt/org/bbop/apollo/gwt/client/OrganismPanel.java

@@ -27,6 +27,7 @@
 import org.bbop.apollo.gwt.client.rest.OrganismRestService;
 import org.bbop.apollo.gwt.client.rest.RestService;
 import org.bbop.apollo.gwt.shared.FeatureStringEnum;
+import org.bbop.apollo.gwt.shared.OrganismComparator;
 import org.bbop.apollo.gwt.shared.track.SequenceTypeEnum;
 import org.gwtbootstrap3.client.ui.*;
 import org.gwtbootstrap3.client.ui.Button;
@@ -38,6 +39,7 @@
 import java.util.ArrayList;
 import java.util.Comparator;
 import java.util.List;
+import java.util.Locale;
 
 /**
  * Created by ndunn on 12/17/14.
@@ -181,10 +183,14 @@ public void callback(boolean result) {
         TextColumn<OrganismInfo> organismNameColumn = new TextColumn<OrganismInfo>() {
             @Override
             public String getValue(OrganismInfo organism) {
+                String display = organism.getName();
                 if (organism.getObsolete()) {
-                    return "(obs) " + organism.getName();
+                    display = "(obs) " + display;
                 }
-                return organism.getName();
+                if(organism.getGenus()!=null && organism.getSpecies()!=null){
+                  display = organism.getGenus() + " " + organism.getSpecies() +  " ("+display  +")";
+                }
+                return display ;
             }
         };
         Column<OrganismInfo, Number> annotationsNameColumn = new Column<OrganismInfo, Number>(new NumberCell()) {
@@ -262,12 +268,12 @@ public void onDoubleClick(DoubleClickEvent event) {
 
         ColumnSortEvent.ListHandler<OrganismInfo> sortHandler = new ColumnSortEvent.ListHandler<OrganismInfo>(organismInfoList);
         dataGrid.addColumnSortHandler(sortHandler);
-        sortHandler.setComparator(organismNameColumn, new Comparator<OrganismInfo>() {
-            @Override
-            public int compare(OrganismInfo o1, OrganismInfo o2) {
-                return o1.getName().compareTo(o2.getName());
-            }
-        });
+        sortHandler.setComparator(organismNameColumn, new OrganismComparator());
+//            @Override
+//            public int compare(OrganismInfo o1, OrganismInfo o2) {
+//                return o1.getName().compareTo(o2.getName());
+//            }
+//        });
         sortHandler.setComparator(annotationsNameColumn, new Comparator<OrganismInfo>() {
             @Override
             public int compare(OrganismInfo o1, OrganismInfo o2) {
@@ -298,10 +304,21 @@ static void filterList() {
             return ;
         }
         for (OrganismInfo organismInfo : organismInfoList) {
-            if (organismInfo.getName().toLowerCase().contains(text.toLowerCase())) {
-                    filteredOrganismInfoList.add(organismInfo);
+          String searchText = text.toLowerCase(Locale.ROOT);
+              if(organismInfo.getGenus()!=null && organismInfo.getSpecies()!=null){
+                if (organismInfo.getGenus().toLowerCase().contains(searchText)
+                  || organismInfo.getSpecies().toLowerCase(Locale.ROOT).contains(searchText)
+                  || organismInfo.getName().toLowerCase(Locale.ROOT).contains(searchText)
+                ) {
+                  filteredOrganismInfoList.add(organismInfo);
+                }
+              }
+              else{
+                if (organismInfo.getName().toLowerCase().contains(searchText)) {
+                  filteredOrganismInfoList.add(organismInfo);
+                }
+              }
             }
-        }
     }
 
     public void loadOrganismInfo() {
@@ -313,11 +330,8 @@ public void loadOrganismInfo(OrganismInfo organismInfo) {
             setNoSelection();
             return;
         }
-
         setTextEnabled(organismInfo.isEditable());
-
-        GWT.log("loadOrganismInfo setValue " + organismInfo.getPublicMode());
-        Boolean isEditable = organismInfo.isEditable() || MainPanel.getInstance().isCurrentUserAdmin();
+        boolean isEditable = organismInfo.isEditable() || MainPanel.getInstance().isCurrentUserAdmin();
 
         organismName.setText(organismInfo.getName());
         organismName.setEnabled(isEditable);

src/gwt/org/bbop/apollo/gwt/client/OrganismPanel.ui.xml

@@ -100,7 +100,7 @@
                 </gwt:FormPanel>
                 <b:Row addStyleNames="{style.searchRow}">
                     <b:Column size="MD_4">
-                        <b:TextBox placeholder="Search" ui:field="nameSearchBox"/>
+                        <b:TextBox placeholder="Search common name" ui:field="nameSearchBox"/>
                     </b:Column>
                     <b:Column size="MD_4">
                         <b:ButtonGroup dataToggle="BUTTONS">

src/gwt/org/bbop/apollo/gwt/shared/OrganismComparator.java

@@ -0,0 +1,26 @@
+package org.bbop.apollo.gwt.shared;
+
+import org.bbop.apollo.gwt.client.dto.OrganismInfo;
+
+import java.util.Comparator;
+
+public class OrganismComparator implements Comparator<OrganismInfo> {
+  @Override
+  public int compare(OrganismInfo o1, OrganismInfo o2) {
+    if(o1.getGenus()==null && o2.getGenus()!=null) return 1 ;
+    if(o1.getGenus()!=null && o2.getGenus()==null) return -1 ;
+    if(o1.getGenus()!=null && o2.getGenus()!=null){
+      if(!o1.getGenus().equalsIgnoreCase(o2.getGenus())) return o1.getGenus().compareToIgnoreCase(o2.getGenus());
+      if(o1.getGenus().equalsIgnoreCase(o2.getGenus())) {
+        if(o1.getSpecies()==null && o2.getSpecies()!=null) return 1 ;
+        if(o1.getSpecies()!=null && o2.getSpecies()==null) return -1 ;
+        if(o1.getSpecies()==null && o2.getSpecies()==null) return o1.getName().compareToIgnoreCase(o2.getName());
+        if(!o1.getSpecies().equalsIgnoreCase(o2.getSpecies())) {
+          return o1.getSpecies().compareToIgnoreCase(o2.getSpecies());
+        }
+      }
+    }
+    return o1.getName().compareToIgnoreCase(o2.getName());
+  }
+
+}