updated to-do task list (for week of 24 march), adding skeleton of ja…

…vadoc for project (in dist/javadoc)

VisualizationInterfaceReports/task_notes_current-todo.txt

@@ -1,27 +1,29 @@
 
 Alex's emr-vis-nlp to-do list
-(last update: mar 12)
+(last update: mar 22)
 (FYI: code available at https://github.com/omgpotatoes/emr-vis-nlp)
 (FYI: open issues being tracked at https://github.com/omgpotatoes/emr-vis-nlp/issues?state=open)
 
-
 document-grid view:
--- (backburner idea) on mouseover of terms in blown-up doc: highlight other docs which contain term? highlight sections of other docs that are relevant to the same issues? (or simplification: other terms that are strongly associated with whatever indicator the hovered term is)
--- (backburner idea) highlight piece of text before moving doc to indicate to back-end which terms are relevant
--- todo: finish fixing glyph auto movement wrt. boundary lines: regions too small to accomodate pieces?
--- (backburner todo) run force-layout before drawing to the screen (to eliminate jitter?)
-- (lower priority) revising histogram interactions: highlight on hover, or color-code all visible docs on hover of single attr's histogram? (as opposed to individual bars)
--- (low-priority backburner) rename "skew" column
-- representing multiple documents per patient:
--- idea: box around glyphs for single patient? or, patient starts as single glyph, interacting causes it to be split into constituent glyphs representing each report for patient? (constituent docs organized temporally)
-- bugfix: ensure consistent attribute ordering! indicate max cert vs min cert indicators in visualization!
-- (idea: possibly have a details pane for active document?)
+- (top priority) revisit layout: implement sorted-grid-within-grid layout, in place of the current scatterplot-within-grid layout
+-- grid-aware distortion, to control/eliminate occlusion and disorientation
+-- incorporate lightweight animation, if possible
+-- keep all document text in thumbnails w/ highlights, as opposed to only including highlights
+- (secondary priority) enhance interactive histograms: update histograms to indicate % included for active search query
+- (secondary priority) enhance term highlighting: 
+-- for active query, pulling out text snippets in which query occurs?
 
 misc:
-- take the dead code out of the master, put it in another branch
-- renaming indicators & vars; explicit/textual/?, inferred/? (backburner: how to display rules?)
--- for attr names: move from jtable to jtree? root -> vars, indicators, meta -> [specific attrs]
-- continuing to work on documentation, general refactoring
-- with respect to annotated bibliography: think about pieces of tool we're building and where it fits in with these other projects
+- (top priority) discuss interface between back-and-front-ends; refactor my ML/NLP interface, and discuss the feasibility of its implementation with Phuong
+- (secondary priority) continuing to work on documentation, general refactoring
+-- ensure that we have some high-level, big-picture documentation!
 
+other low-priority items:
+- rename "skew" column; possibly reorganize attribute selection table as a tree?
+- renaming indicators & vars; explicit/textual/?, inferred/? 
+- think about: how to display rules?
+- representing multiple documents per patient; think about how to handle this?
+-- idea: box around glyphs for single patient? or, patient starts as single glyph, interacting causes it to be split into constituent glyphs representing each report for patient? (constituent docs organized temporally)
+- (idea: possibly have a details pane for active document?)
+- keeping bibliography up-to-date: think about pieces of tool we're building and where it fits in with these other projects
 

build.xml

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project xmlns:ivy="antlib:org.apache.ivy.ant" name="emr-vis-nlp" default="run" basedir=".">
 	<description>Builds and runs the project emr-vis-nlp.</description>
+    <import file="nbproject/build-impl.xml"/>
 
 	<!-- set global properties for this build -->
 	<property name="lib.dir" value="lib" />
@@ -16,13 +17,8 @@
 		<path location="${build.dir}" />
 	</path>
 
-	<!-- retrieve libraries via ivy -->
-	<target name="resolve" description="--> retrieve dependencies with ivy">
-		<mkdir dir="${lib.dir}" />
-		<ivy:retrieve />
-	</target>
 
-	<target name="compile" depends="resolve" description="--> compile the source" >
+	<target name="compile" description="--> compile the source" >
 		<!-- Create timestamp -->
 		<tstamp/>
 		<!-- Compile the java code from ${src.dir} into ${build.dir} -->