obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 149)

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Revision: 954
          http://obo.svn.sourceforge.net/obo/?rev=954&view=rev
Author:   mgibson
Date:     2007-10-03 14:52:29 -0700 (Wed, 03 Oct 2007)

Log Message:
-----------
well this was harder than i thought - swing swing
so there was a bug with min completion chars being 1 that completion
would be blank
but i decided really min completion chars should just be scrapped 
as its buggy in other ways and made irrelevant with the new threading
of completion
the one purpose it was serving was to hold back on preloading ontologies
(optionally) to be able to see whole ontology - by hitting arrow button with 
no input - 
as pre loading can be a real drag with many ontols - the 
post comp gui was doing it evgery time it was brought up - on a slow 
labtop (birn) it was taking forever
so now it loads up ontol with blank input on demand - once the user hits
the arrow it goes and gets
even better you can look at individual ontologies - wasnt true before
but the trick was getting the jlist to not be all blinky - as in come up 
1st blank and then a second or 2 later with terms
the problem ironically was threading - so in this one case - bringing up
completion with no input - and not from typing (delete) phenote actually
makes a non threaded call for completions so it wont be all blinky
typing to empty input is detected by turning on a flag with typing
all other comletions are threaded and cancellable

so this make min complete chars irrelevant - and actually probably better not
to use - i think i might disable it
and take it out of configurations

Modified Paths:
--------------
    phenote/trunk/conf/ncbo.cfg
    phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
    phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
    phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
    phenote/trunk/src/java/phenote/gui/field/RelationCompList.java
    phenote/trunk/src/java/phenote/gui/field/TermCompList.java
    phenote/trunk/src/java/phenote/servlet/PhenoteController.java

Modified: phenote/trunk/conf/ncbo.cfg
===================================================================

--- phenote/trunk/conf/ncbo.cfg	2007-10-03 19:15:27 UTC (rev 953)
+++ phenote/trunk/conf/ncbo.cfg	2007-10-03 21:52:29 UTC (rev 954)
@@ -56,7 +56,7 @@
     <ns:ontology name="MP" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/mammalian_phenotype.obo"/>
   </ns:field>
 
-  <ns:field name="Add'l Entity" datatag="E2"  min-completion-chars="1" enable="true" desc="To be used when using relational qualities">
+  <ns:field name="Add'l Entity" datatag="E2" enable="true" desc="To be used when using relational qualities">
     <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
     <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
     <ns:ontology name="EHDAA" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/human/human-dev-anat-abstract.obo"/>

Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java	2007-10-03 19:15:27 UTC (rev 953)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java	2007-10-03 21:52:29 UTC (rev 954)
@@ -132,6 +132,8 @@
     for (FieldConfig fieldConfig : cfg().getEnbldFieldCfgs()) {
       for (OntologyConfig oc : fieldConfig.getOntologyConfigList()) {
         try {
+          // this actually does repos synching, should only do once per obo file,
+          // but it wont download something twice as 2nd time it will be in synch
           String file = findOboUrlString(oc); // throws oex if not found
           if (!files.contains(file)) { // dont load file twice
             files.add(file);

Modified: phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-10-03 19:15:27 UTC (rev 953)
+++ phenote/trunk/src/java/phenote/gui/field/AbstractAutoCompList.java	2007-10-03 21:52:29 UTC (rev 954)
@@ -11,6 +11,7 @@
 
 import javax.accessibility.Accessible;
 import javax.accessibility.AccessibleContext;
+import javax.swing.AbstractButton;
 import javax.swing.ComboBoxModel;
 import javax.swing.InputMap;
 import javax.swing.JComboBox;
@@ -21,6 +22,8 @@
 import javax.swing.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
 import javax.swing.event.ListDataListener;
+import javax.swing.event.PopupMenuEvent;
+import javax.swing.event.PopupMenuListener;
 import javax.swing.plaf.basic.BasicComboBoxEditor;
 import javax.swing.plaf.basic.BasicComboBoxRenderer;
 import javax.swing.plaf.basic.ComboPopup;
@@ -39,7 +42,7 @@
 
   private JComboBox jComboBox;
   private boolean changingCompletionList = false;
-  private boolean doCompletion = true;
+  private boolean settingTextExternally = false;
   private CompComboBoxModel compComboBoxModel;
   private boolean inTestMode = false;
   private AutoTextField autoTextField;
@@ -66,10 +69,14 @@
     this.getJComboBox().addActionListener(new ComboBoxActionListener());
     compListSearcher = new CompListSearcher(getCharField().getOntologyList());
     // init with all terms if config.showAllOnEmptyInput...
-    if (getMinCompChars() == 0) {
-      boolean showPopupWithComp = false; // dont show popup -
-      doCompletion(showPopupWithComp);  //we dont have a gui yet, just populating
-    }
+    // this can take a while (post comp gui) do on demand with popup menu listener
+//     if (getMinCompChars() == 0) {
+//       boolean showPopupWithComp = false; // dont show popup -
+//       doCompletion(showPopupWithComp);  //we dont have a gui yet, just populating
+//     }
+    getJComboBox().addPopupMenuListener(new CompPopupMenuListener());
+    //if (hasArrowButton())
+    //getArrowButton().addActionListener(new ArrowButtonActionListener());
   }
 
   public void setMinCompChars(int minChars) { minCompChars = minChars; }
@@ -114,15 +121,15 @@
   /** Set text in editable text field of j combo (eg from table select) */
   public void setText(String text) {
     // do not do term completion on externally set text!
-    boolean doCompletion = false;
-    setText(text,doCompletion);
+    boolean settingTextExternally = true;
+    setText(text,settingTextExternally);
   }
 
   /** text from selecting table doesnt do completion, TestPhenote does */
-  public void setText(String text, boolean doCompletion) {
-    this.doCompletion = doCompletion;
+  public void setText(String text, boolean settingTextExternally) {
+    this.settingTextExternally = settingTextExternally;
     jComboBox.getEditor().setItem(text);
-    this.doCompletion = true; // set back to default
+    this.settingTextExternally = false; // set back to default
   }
 
   /** Return text in text field */
@@ -207,7 +214,7 @@
       // but this is needed from mouse release on selection set text
       // is called and will cause completion list to come up after sel
       // w/o it
-      doCompletion = false;
+      settingTextExternally = true;
       //this is problematic for syns & such where string is diff than term name
       // JComboBox sets this text AFTER got event and set to name
       //super.setText(text); 
@@ -219,7 +226,7 @@
       }
       else
         super.setText(getCurrentTermRelName()); // set to term name with syn select
-      doCompletion = true;
+      settingTextExternally = false;
     }
 
     protected void processKeyEvent(KeyEvent e) {
@@ -251,8 +258,13 @@
   }
 
   private void doCompletion(boolean showPopup) {
+    doCompletion(showPopup,true); // thread
+  }
+
+  /** This completion is threaded */
+  private void doCompletion(boolean showPopup, boolean thread) {
     this.setHasChangedMultipleValues(true);
-    if (!doCompletion) // flag set if text filled in externally (from table sel)
+    if (settingTextExternally) // flag set if text filled in externally (from table sel)
       return;
     // too soon - text field doesnt have text yet.... hmmmm....
     String input = getText();
@@ -262,7 +274,9 @@
     // if input is empty will return whole list (if configged)
     //log().debug("got new completion request for input "+input+" time "+time());
     listSearchListener.showPopup = showPopup;
-    /*List<CompletionTerm> l =*/ getSearchItems(input,listSearchListener);
+    // fires thread
+    /*List<CompletionTerm> l =*/ 
+    getSearchItems(input,listSearchListener,thread);
     //log().debug("got search items for input "+input+" milsec: "+time());
 //    changingCompletionList = true;
 //     // could just do comboBoxModel.setList(l); ???
@@ -287,8 +301,11 @@
       compComboBoxModel = new CompComboBoxModel(results);
       jComboBox.setModel(compComboBoxModel);
       changingCompletionList = false;
-      if (showPopup) //only show popup on key events actually only do com      
+      if (showPopup) { //only show popup on key events actually only do com
+        doingPopupForCompletion = true; // otherwise doComp endless loop
         jComboBox.showPopup();
+        doingPopupForCompletion = false;
+      }
       //jComboBox.revalidate();
       //jComboBox.repaint();
       //getUIJList().repaint();
@@ -328,7 +345,7 @@
   }
 
   // no longer returns List<CompletionTerm>, a thread sends list to listener
-  protected abstract void getSearchItems(String input,SearchListener l);
+  protected abstract void getSearchItems(String input,SearchListener l,boolean thread);
 //     if (isRelationshipList()) return termSearcher.getStringMatchRelations(input);
 //     else return termSearcher.getStringMatchTerms(input);}
 
@@ -365,7 +382,31 @@
     return null; // ex?
   }
 
+  /** This is the button pressed to see the list
+      so in theory youre not supposed to delve into the innards of the jcombo
+      but in practice ya need to, need to know when that button is pressed when the
+      user hasnt entered anything, and AbstractButton is not plaf specific (hopefully) */
+  private AbstractButton getArrowButton() {
+    for (Component c : getJComboBox().getComponents()) {
+      if (c instanceof AbstractButton) return (AbstractButton)c; 
+    }
+    return null; // ex?
+  }
 
+  private boolean hasArrowButton() { return getArrowButton() != null; }
+
+  private class ArrowButtonActionListener implements ActionListener {
+    public void actionPerformed(ActionEvent e) {
+      log().debug("arrow has been pressed jcombo vis? "+getJComboBox().isPopupVisible());
+      if (!getJComboBox().isPopupVisible()) return;
+      getJComboBox().hidePopup(); // ???
+      if (getText() == null || getText().length() == 0) {
+        doCompletion(true); // --> doNonThreadedCompletion
+      }      
+    }
+  }
+  
+
   // for TestPhenote
   public void doMouseOver(int itemNumber) {
     //System.out.println("AutoComboBox.doMouseOver not implemented yet");
@@ -486,6 +527,27 @@
       return dimension;
     }
   }
+
+  private boolean doingPopupForCompletion = false;
+
+  /** If user hits arrow on completion field with nothing typed in, all terms
+      should then be listed */
+  private class CompPopupMenuListener implements PopupMenuListener {
+    public void popupMenuCanceled(PopupMenuEvent e) {}
+    public void	popupMenuWillBecomeInvisible(PopupMenuEvent e) {}
+    public void	popupMenuWillBecomeVisible(PopupMenuEvent e) {
+      //log().debug("popup will become visible "+getText()+" disable? "+doingPopupForCompletion+" popup vis? "+getJComboBox().isPopupVisible());
+      if (doingPopupForCompletion) return;
+      if (getText() != null && getText().length() > 0) 
+        return;
+      // popup already coming dont do another
+      boolean showPopup = false;
+      // dont do threaded as need to wait for results before continuing with popup
+      // if threaded and popup then its blinky (2 popups, 1st one is blank)
+      boolean doThreaded = false;
+      doCompletion(showPopup,doThreaded);
+    }
+  }
   
 }
 

Modified: phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2007-10-03 19:15:27 UTC (rev 953)
+++ phenote/trunk/src/java/phenote/gui/field/CompListSearcher.java	2007-10-03 21:52:29 UTC (rev 954)
@@ -10,6 +10,7 @@
 import org.apache.log4j.Logger;
 
 import org.geneontology.util.AbstractTaskDelegate;
+import org.geneontology.swing.BackgroundUtil;
 import org.geneontology.util.TaskDelegate;
 import org.geneontology.oboedit.datamodel.OBOClass;
 import org.geneontology.oboedit.datamodel.OBOProperty;
@@ -31,7 +32,7 @@
   //private boolean searchAll=false;
   private List<Ontology> ontologyList = new ArrayList<Ontology>(3);
   private SearchParamsI searchParams = SearchParams.inst(); // singleton
-  private String previousInput = "";
+  private String previousInput = null;
   private List<CompletionTerm> previousCompList = new ArrayList<CompletionTerm>();
 
   /** Ontology - the initial ontology to search, setOntology changes this,
@@ -77,22 +78,27 @@
 
   private CompTaskDelegate compTaskDelegate = null;
 
-  /** Returns a List of CompletionTerms from ontology that contain input string
-      constrained by compParams. compParams specifies syns,terms,defs,& obs 
+  /** Makes a List of CompletionTerms from ontology that contain input string
+      constrained by compParams. Gives this list to SearchListener, does search
+      in background thread if thread is true.  compParams specifies syns,terms,defs,& obs 
       should input be just part of search params? called by servlet & standalone now */
-  public /*List<CompletionTerm>*/ void getStringMatchTermList(String input,
-                                                     SearchListener lis) {
+  public void getStringMatchTermList(String input,SearchListener lis,boolean threaded) {
 
     //new org.jdesktop.swingworker.SwingWorker();
     // kill old task!
     if (compTaskDelegate!=null) compTaskDelegate.cancel();
-    compTaskDelegate = new CompTaskDelegate(input,lis);
-    org.geneontology.swing.BackgroundUtil.scheduleTask(compTaskDelegate);
-    
+    // THREADED
+    if (threaded) {
+      compTaskDelegate = new CompTaskDelegate(input,lis);
+      BackgroundUtil.scheduleTask(compTaskDelegate);
+    }
+    // NON THREADED - null task, results sent to listener synchronously
+    else {
+      getSearchTermList(input,lis,null);
+    }
   }
 
-  private class CompTaskDelegate
-    extends AbstractTaskDelegate<List<CompletionTerm>> {
+  private class CompTaskDelegate extends AbstractTaskDelegate<List<CompletionTerm>> {
 
     private String input;
     private SearchListener searchListener;
@@ -104,57 +110,9 @@
 
     public void execute() {
       try {
-      List<CompletionTerm> searchTerms = new ArrayList<CompletionTerm>();
-      
-      // if no input should phenote give no terms? or all terms?
-      boolean nothingForNothing = false; // get from FieldConfig!!
-      if (nothingForNothing && isBlank(input)) {
-        results = searchTerms; // empty
-        searchListener.newResults(results);
-        return;
-      }
-      
-      // optimization - if user has only typed one more letter (common case)
-      // use previous search list
-      try {
-        if (input.startsWith(previousInput) 
-            && input.length() == previousInput.length() + 1) {
-          searchTerms = searchPreviousList(input,previousCompList,this);
-        }
-        
-        else {
-          // gets term set for currently selected ontology(s)
-          //Set ontologyTermList = getCurrentOntologyTermSet();
-          // THIS IS WRONG! or is it?
-          for (Ontology ontology : ontologyList) {
-            Collection<OBOClass> ontologyTermList = ontology.getSortedTerms(); // non obsolete
-            List<CompletionTerm> l =
-              getSearchTermList(input,ontologyTermList,this);
-            searchTerms.addAll(l);
-            
-            // if obsoletes set then add them in addition to regulars
-            if (searchParams.searchObsoletes()) {
-              ontologyTermList = ontology.getSortedObsoleteTerms();
-              List<CompletionTerm> obsoletes =
-                getSearchTermList(input,ontologyTermList,this);
-              searchTerms.addAll(obsoletes);
-            }
-          } 
-        
-        }
-      
-      } 
-      catch (CancelEx x) { return; } // task has been cancelled
-
-      previousInput = input;
-      previousCompList = searchTerms;
-      //return searchTerms;
-      //setResults(searchTerms);
-      results = searchTerms;
-      if (!isCancelled())
-        searchListener.newResults(results); // send off results
-
-      } catch (RuntimeException x) {
+        getSearchTermList(input,searchListener,this);
+      } // TaskDelegates dont yet deal with runtime exceptions
+      catch (RuntimeException x) {
         log().error("got runtime exception in completion "+x);
       }
     
@@ -162,7 +120,69 @@
 
   } // end CompTask inner class
 
+  /** task is null for non threaded case. if threaded/nonnull checks to see if task
+      is cancelled - when done passes results to SearchListener */
+  private void getSearchTermList(String input, SearchListener searchListener,
+                                 TaskDelegate task) {
+    List<CompletionTerm> searchTerms = new ArrayList<CompletionTerm>();
+    
+    // if no input should phenote give no terms? or all terms?
+    boolean nothingForNothing = false; // get from FieldConfig!!
+    if (nothingForNothing && isBlank(input)) {
+      //results = searchTerms; // empty
+      searchListener.newResults(searchTerms);
+      return;
+    }
+    
+    // optimization - if user has only typed one more letter (common case)
+    // use previous search list - i think this even works with threaded
+    try {
+      if (previousInput != null && input.startsWith(previousInput) 
+          && input.length() == previousInput.length() + 1) {
+        searchTerms = searchPreviousList(input,previousCompList,task);
+      }
+      
+      else {
+        // gets term set for currently selected ontology(s)
+        //Set ontologyTermList = getCurrentOntologyTermSet();
+        // THIS IS WRONG! or is it?
+        for (Ontology ontology : ontologyList) {
+          Collection<OBOClass> ontologyTermList = ontology.getSortedTerms(); // non obsolete
+          List<CompletionTerm> l =
+            getOntSearchTermList(input,ontologyTermList,task);
+          searchTerms.addAll(l);
+          
+          // if obsoletes set then add them in addition to regulars
+          if (searchParams.searchObsoletes()) {
+            ontologyTermList = ontology.getSortedObsoleteTerms();
+            List<CompletionTerm> obsoletes =
+              getOntSearchTermList(input,ontologyTermList,task);
+            searchTerms.addAll(obsoletes);
+          }
+        } 
+        
+      }
+      
+    } 
+    catch (CancelEx x) { return; } // task has been cancelled
+    
+    previousInput = input;
+    previousCompList = searchTerms;
+    //return searchTerms;
+    //setResults(searchTerms);
+    //results = searchTerms; // does task need results?
+    if (!isCancelled(task))
+      searchListener.newResults(searchTerms); // send off results
 
+  }
+
+  /** for non threaded context task will be null and returns false, otherwise
+      queries task */
+  private boolean isCancelled(TaskDelegate task) {
+    if (task == null) return false;
+    return task.isCancelled();
+  }
+
   private boolean isBlank(String s) {
     return s == null || s.equals("");
   }
@@ -170,8 +190,10 @@
 
   private class CancelEx extends Exception {}
 
-  /** helper fn for CompTaskDelegate */
-  private List<CompletionTerm> getSearchTermList(String input,
+  
+
+  /** helper fn for CompTaskDelegate, does search for terms from a single ontology */
+  private List<CompletionTerm> getOntSearchTermList(String input,
                                                  Collection<OBOClass> ontologyTermList,
                                                  TaskDelegate task) throws CancelEx {
     SearchTermList searchTermList = new SearchTermList();
@@ -182,7 +204,7 @@
     for (OBOClass oboClass : ontologyTermList) {
     //for (int i=0; i<ontologyTermList.size(); i++) {
 
-      if (i++ % 50 == 0 && task.isCancelled()) throw new CancelEx(); 
+      if (i++ % 50 == 0 && isCancelled(task)) throw new CancelEx(); 
       CompletionTerm ct = new CompletionTerm(oboClass);
       // if input is blank then add all terms (list all terms on empty input)
       // matches records the kind of hit in CompTerm
@@ -203,7 +225,7 @@
     SearchTermList newList = new SearchTermList();
     //for (CompletionTerm ct : prevList) {
     for (int i=0; i<prevList.size(); i++) {
-      if (i % 50 == 0 && task.isCancelled()) throw new CancelEx();
+      if (i % 50 == 0 && isCancelled(task)) throw new CancelEx();
       CompletionTerm ct = prevList.get(i);
       ct.resetMatchState(); // reusing ct has stale match state from previous search
       if (ct.matches(input,searchParams))

Modified: phenote/trunk/src/java/phenote/gui/field/RelationCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/RelationCompList.java	2007-10-03 19:15:27 UTC (rev 953)
+++ phenote/trunk/src/java/phenote/gui/field/RelationCompList.java	2007-10-03 21:52:29 UTC (rev 954)
@@ -41,7 +41,7 @@
       return; // debug stack trace?
     }
     currentRel = rel;
-    setText(rel.getName(),false); // eventually .getName()
+    setText(rel.getName());
   }
   /** Throws exception if there isnt a current relation - for relation lists
       (post comp), if the user
@@ -91,9 +91,10 @@
       just term */ 
   protected void setCharFieldValue(CharFieldValue value) {}
 
-  protected void getSearchItems(String input, SearchListener l)  {
-    // for now not threading and just sending results to listener - 
-    // relations are short lists - dont need threaded optimization
+  /** for now not threading and just sending results to listener - 
+      relations are short lists - dont need threaded optimization
+      so boolean thread is ignored */
+  protected void getSearchItems(String input, SearchListener l, boolean thread)  {
     l.newResults(getCompListSearcher().getStringMatchRelations(input));
   }
 

Modified: phenote/trunk/src/java/phenote/gui/field/TermCompList.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-10-03 19:15:27 UTC (rev 953)
+++ phenote/trunk/src/java/phenote/gui/field/TermCompList.java	2007-10-03 21:52:29 UTC (rev 954)
@@ -116,8 +116,8 @@
   }
 
   /** now threaded so cant return - set AbAutoCompList when done */
-  protected void getSearchItems(String input,SearchListener l) {
-    /*return*/ getCompListSearcher().getStringMatchTermList(input,l);
+  protected void getSearchItems(String input,SearchListener l,boolean thread) {
+    /*return*/ getCompListSearcher().getStringMatchTermList(input,l,thread);
   }
 
   /**
@@ -156,7 +156,7 @@
     else
       this.setForegroundColor(this.getEnabledTextColor());
     String val = term == null ? "" : term.getName();
-    setText(val, false); // no completion
+    setText(val); // no completion with setText fyi
   }
 
   /**

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteController.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2007-10-03 19:15:27 UTC (rev 953)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteController.java	2007-10-03 21:52:29 UTC (rev 954)
@@ -72,8 +72,11 @@
     //List<CompletionTerm> termList = null;
     SearchListener searchListener = new ContSearchListener(ontologyName,field,form);
     try {
-      //termList = its now threaded - term list returned to SearchListener
-      getCompListSearcher(ontologyName).getStringMatchTermList(userInput,searchListener);
+      //termList = its now optionally threaded - term list returned to SearchListener
+      // Christian - set this boolean to false to turn off threading
+      boolean thread = true;
+      getCompListSearcher(ontologyName).getStringMatchTermList(userInput,searchListener,
+                                                               thread);
     } catch (OntologyException e) {
       // Todo: Add this error as an error completion list
       LOG.error(e.getMessage(), e);


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obo-svn-commit Mailing List for Open Biomedical Ontologies (Page 149)

obo-svn-commit — sends mail for all commits to svn repository