classdef browse < handle
% Creates the class inheritance browser GUI
% Copyright 2012 Eric Lee, Clayton Ernst, Andrew Hagen and Andreas Kotowicz
% Written for Engineering 177 Spring 2010, Final Project. Professor:
% Andy Packard, UC Berkeley.
properties (Access = private)
trees
metadata
liststr
indx
guiHan
bioinfo_toolbox = 0;
NODIRSTRING = 'No dir found. Go up.';
end
%% PUBLIC methods
methods
function obj = browse(inputdir)
if nargin==0
inputdir = '.';
end
% bioinformatics toolbox checks.
try
% Check if bioinfo toolbox exists
a = ver('bioinfo');
% Check also if network license is available.
% Need to return "errormessage", otherwise user sees an
% ugly "License checkout failed." error message.
%
try % matlab >= 2011a: `[TF, errmsg] = license('checkout',feature)`
[b, errormessage] = license('checkout', 'bioinformatics_toolbox'); %#ok<NASGU>
catch me %#ok<NASGU> % matlab <= 2010b: `result = license('checkout',feature)`
b = license('checkout', 'bioinformatics_toolbox');
end
if numel(a) > 0 && b == 1
obj.bioinfo_toolbox = 1;
end
catch me %#ok<NASGU>
obj.bioinfo_toolbox = 0;
end
if obj.bioinfo_toolbox == 0
disp('Bioinformatics Toolbox not found.');
end
% initalize data fields
ok = init_data(obj, inputdir);
% quit right away if there was a problem.
if ok == 0
return;
end
% show class viewer
if obj.bioinfo_toolbox == 1
obj.trees.view();
end
% build main gui
setup_gui(obj);
% update class listbox
update_class_listbox(obj)
% fill gui with information
displayinfo(obj, 1, obj.liststr{1});
end
function display(obj) %#ok<MANU>
display('Class Inheritance Analyzer/Browser')
end
function closefunc(src,evt,obj) %#ok<INUSL,MANU>
if ~isempty(obj.trees) && ~isempty(obj.trees.directory)
close(findobj('name',['Class Inheritance tree for ', obj.trees.directory]))
end
delete(obj.guiHan.f)
end
function KeyPressFcn_browse(src, evnt, obj) %#ok<MANU>
try % maybe not all kpfs are committed.
switch evnt.Key
case 'm'
[name, value] = get_selected_class_name(obj);
ak.create_metauml(obj.metadata{value});
otherwise
end
catch me %#ok<NASGU> % no error message - just ignore the error
end
end
function LOCALbrowseCb(src, evnt, obj) %#ok<INUSL,MANU>
% allow user to browse to different directory
start_path = get(obj.guiHan.dirH, 'String');
dialog_title = 'Please select new directory';
try
folder_name = uigetdir(start_path,dialog_title);
catch %#ok<CTCH>
folder_name = uigetdir('', dialog_title);
end
set(obj.guiHan.dirH, 'String', folder_name);
end
function LOCALdirCb(src,evt,obj)
flag = 1;
% check for keypresses if pushbotton didn't get pressed
if ~strcmp(get(src,'style'),'pushbutton')
if strcmp(evt.Key,'return')
flag = 1;
else
flag = 0;
end
end
% user didn't press the pushbutton and didn't hit 'return'
if flag == 0
return;
end
drawnow();
inputdir = get(obj.guiHan.dirH, 'String');
if isempty(inputdir)
inputdir = '.';
end
if ~isempty(obj.trees) && ~isempty(obj.trees.directory)
close(findobj('name', ['Class Inheritance tree for ', obj.trees.directory]));
end
a = dir(inputdir);
a([a.isdir] == 0) = [];
a(strcmp({a.name}, '.')) = [];
a(strcmp({a.name}, '..')) = [];
nbr_entries = numel(a);
if nbr_entries > 0
entries = cell(1, nbr_entries + 1);
for j = 1 : nbr_entries
entries{1, j+1} = a(j).name;
end
entries{1, 1} = 'Go up';
set(obj.guiHan.directoryList, 'String', entries);
else
set(obj.guiHan.directoryList, 'String', obj.NODIRSTRING, 'Value', 1);
end
% initalize data fields
ok = init_data(obj, inputdir);
% quit if there was a problem.
if ok == 0
return;
end
if obj.bioinfo_toolbox == 1
% show class viewer
obj.trees.view();
end
% update bioviewer
setup_gui_biograph_viewer(obj);
% update class listbox
update_class_listbox(obj);
% populate remaining listboxes.
displayinfo(obj, 1, obj.liststr{1});
end
function LOCALmethCb(src, evt, obj) %#ok<MANU,INUSL>
% opens currently selected method (if it's in a separate file)
% otherwise it opens the file containing the method
selected_class = get_selected_class_name(obj);
selected_method = get_selected_method_name(obj);
% method list is empty (can happen in old matlab versions)
if isempty(selected_method)
return;
end
dd = filesep();
class_name_and_method = [selected_class dd selected_method];
class_name_and_method_private = [selected_class dd 'private' dd selected_method];
[result, which_file] = classInheritance.browse.resolvePath(class_name_and_method, class_name_and_method_private);
% found a file.
if result == 1
[pathstr, name] = fileparts(which_file); %#ok<ASGLU>
% method is in a separate file - no need to look up the
% line number
if strcmp(name, selected_method)
line_number = 0;
else
% method is inside a class file.
% read-in file and find the line where this method is
% defined
content = textread(which_file, '%s', 'delimiter', '\n');
regexp_rule = ['(.*function.*' selected_method '.*)'];
s = regexp(content, regexp_rule, 'start');
line_number = find(cellfun(@(x) ~isempty(x), s), 1);
if isempty(line_number)
line_number = 0;
end
end
% open file at correct line_number
opentoline(which_file, line_number);
end
end
function LOOCALpropLb(src, evt, obj)
% find out what item user clicked on
selected_entry = get(src, 'Value');
subdirs = get(src, 'String');
curr_dir = get(obj.guiHan.dirH, 'String');
new_dir_selected = false;
% check whether user wants to navigate up to parent level.
if selected_entry == 1 && ((~iscell(subdirs) && strcmp(subdirs, obj.NODIRSTRING) == 1) || (strcmp(subdirs{1}, 'Go up')) )
% disp('gotta ignore this.');
[parent, this_dir] = fileparts(curr_dir);
if strcmp(parent, this_dir)
return;
else
new_dir_selected = true;
new_dir = parent;
end
end
% new directory wasn't selected, so let's build it here.
if new_dir_selected == false
new_dir = [curr_dir filesep() subdirs{selected_entry}];
end
% set the new path.
set(obj.guiHan.dirH, 'String', new_dir);
% run the 'Go' callback, fake the 'return' key being pressed.
evt.Key = 'return';
LOCALdirCb(src, evt, obj);
end
function LOCALpropCb(src, evt, obj) %#ok<MANU,INUSL>
% prints help text of currently selected property to console
selected_property = get_selected_property_name(obj);
% property list might be empty
if isempty(selected_property)
return;
end
selected_class = get_selected_class_name(obj);
class_name_and_property = [selected_class '.' selected_property];
% calling 'help' is very expensive. That's why we only do it
% here once the user clicks on a property.
help_string = help(class_name_and_property);
if isempty(help_string)
disp(['No description available for: ' class_name_and_property]);
else
disp([class_name_and_property ':' help_string]);
end
end
function LOCALlistCb(src,evt,obj) %#ok<INUSL,MANU>
obj.indx = get(obj.guiHan.classH,'UserData');
[name, value] = get_selected_class_name(obj);
% check if bioinfo toolbox is available.
if obj.bioinfo_toolbox == 1
% restart class viewer if it was closed by user
if ~obj.trees.view_running()
obj.trees.view();
end
% 'trees.h' might be empty, if only one class is given.
if ~isempty(obj.trees.h)
nodes = get(obj.trees.h.Nodes);
oldind = [];
for j=1:length(nodes)
if isequal(2,nodes(j).LineWidth)
oldind = j;
end
end
if ~isempty(oldind)
set(obj.trees.h.Nodes(oldind),'LineWidth',1)
set(obj.trees.h.Nodes(oldind),'LineColor',[.3 .3 1])
end
nodename = cell(1,length(nodes));
for i=1:length(nodes); nodename{i} = nodes(i).ID; end
newind = strcmp(name,nodename);
set(obj.trees.h.Nodes(newind),'LineWidth',2)
set(obj.trees.h.Nodes(newind),'LineColor',[1 0 0])
end
end
displayinfo(obj,value,name);
end
function LOCALsearchCb(src,evt,obj)
flag = 1;
% check for keypresses if pushbotton didn't get pressed
if ~strcmp(get(src,'style'),'pushbutton')
if strcmp(evt.Key,'return')
flag = 1;
else
flag = 0;
end
end
% user didn't press the pushbutton and didn't hit 'return'
if flag == 0
return;
end
drawnow;
set(obj.guiHan.classH,'string',obj.liststr);
str=get(obj.guiHan.searchH,'string');
if isempty(str)
set(obj.guiHan.classH,'string',obj.liststr);
set(obj.guiHan.classH,'UserData',1:length(obj.metadata));
value = get(obj.guiHan.classH,'Value');
str = get(obj.guiHan.classH,'String');
name = str{value};
displayinfo(obj,value,name)
else
[strmatchs,obj.indx] = classInheritance.browse.wholewordizer(str,obj.liststr);
set(obj.guiHan.classH,'UserData',obj.indx);
if ~isempty(strmatchs)
set(obj.guiHan.classH,'string',strmatchs);
set(obj.guiHan.classH,'Value',1);
displayinfo(obj,1,strmatchs{1});
else
set(obj.guiHan.classH,'string','');
set(obj.guiHan.propH,'string','');
set(obj.guiHan.methH,'string','');
end
end
end
end
%% PRIVATE methods
methods (Access = private)
function displayinfo(obj,value,name)
% takes a class name, and puts the methods and properties in respective
% lists in the info figure.
% make sure the class name has the correct format
name = classInheritance.iTree.format(name);
obj.indx = get(obj.guiHan.classH,'UserData');
indxvalue = obj.indx(value);
props=obj.metadata{indxvalue}.Properties;
meth=obj.metadata{indxvalue}.Methods;
sup=obj.metadata{indxvalue}.SuperClasses;
nbr_props = length(props);
nbr_meth = length(meth);
propstr = cell(nbr_props, 1);
for i = 1:nbr_props
% show only properties that were defined in this class
if strcmp(props{i}.DefiningClassName, name)
propstr{i, 1} = props{i}.Name;
end
end
% remove empty cells
propstr = classInheritance.browse.remove_empty_cell_entries(propstr);
methstr = cell(nbr_meth, 1);
for i = 1:nbr_meth
if strcmp(meth{i}.DefiningClassName, name)
methstr{i, 1} = meth{i}.Name;
end
end
% remove empty cells
methstr = classInheritance.browse.remove_empty_cell_entries(methstr);
supstr = cell(length(sup), 1);
for i = 1:length(sup)
supstr{i, 1} = classInheritance.iTree.unformat(sup{i}.Name);
end
set(obj.guiHan.propH, 'String', propstr);
set(obj.guiHan.methH, 'String', methstr);
set(obj.guiHan.supH, 'String', supstr);
set(obj.guiHan.propH, 'Value', 1);
set(obj.guiHan.methH, 'Value', 1);
set(obj.guiHan.supH, 'Value', 1);
nbr_props = size(propstr, 1);
nbr_meth = size(methstr, 1);
% enable / disable listboxes and their context menus
do = 'on';
if nbr_props == 0
do = 'off';
end
obj.enable_disable_listbox_and_contextmenu(obj.guiHan.propH, do);
do = 'on';
if nbr_meth == 0
do = 'off';
end
obj.enable_disable_listbox_and_contextmenu(obj.guiHan.methH, do);
% update number of entries per category
set(obj.guiHan.PropertiesH, 'String', ['Properties: ' num2str(nbr_props)]);
set(obj.guiHan.MethodsH, 'String', ['Methods: ' num2str(nbr_meth)]);
set(obj.guiHan.SuperClassesH, 'String', ['Super Classes: ' num2str(size(supstr, 1))]);
end
function [selected_property, value] = get_selected_property_name(obj)
this_list = get(obj.guiHan.propH, 'String');
if isempty(this_list)
selected_property = [];
value = 0;
return;
end
value = get(obj.guiHan.propH, 'Value');
selected_property = this_list{value};
end
function [selected_class, value] = get_selected_class_name(obj)
str = get(obj.guiHan.classH, 'String');
if isempty(str)
selected_class = [];
value = 0;
return;
end
value = get(obj.guiHan.classH, 'Value');
selected_class = str{value};
end
function [selected_method, value] = get_selected_method_name(obj)
str = get(obj.guiHan.methH, 'String');
if isempty(str)
selected_method = [];
value = 0;
return;
end
value = get(obj.guiHan.methH, 'Value');
selected_method = str{value};
end
function update_class_listbox(obj)
set(obj.guiHan.classH, 'UserData', obj.indx);
set(obj.guiHan.classH, 'Value', 1);
set(obj.guiHan.classH, 'String', obj.liststr)
nbr_classes = numel(obj.indx);
set(obj.guiHan.ClassesH, 'String', ['Classes: ' num2str(nbr_classes)]);
end
function ok = init_data(obj, inputdir)
ok = 1;
for i=1:length(obj.metadata)
clear(obj.metadata{i}.Name)
end
% clear out old data
obj.metadata = [];
% make sure to delete the trees object if one exists -
% otherwise we might get nasty errors.
if isobject(obj.trees)
delete(obj.trees);
end
obj.trees = [];
% make sure we catch all possible errors in iTree
try
obj.trees = classInheritance.iTree(inputdir);
catch me
switch me.identifier
case 'classInheritance:iTreeClassNOTFOUND'
disp('Error: No class found. If if you think this is a mistake, please check if class name is correct or try again using full path to class.');
otherwise
disp('unkown error:');
disp(me.message);
end
ok = 0;
return;
end
obj.metadata = obj.trees.metalist;
obj.indx = 1:length(obj.metadata);
obj.liststr = cell(1,length(obj.metadata));
for i = 1:length(obj.metadata)
obj.liststr{i} = classInheritance.iTree.unformat(obj.metadata{i}.Name);
end
end
function setup_gui_biograph_viewer(obj)
if obj.bioinfo_toolbox == 1
% set name and windowbuttondown function of class viewer
child_handles = allchild(0);
names = get(child_handles, 'Name');
k = strncmp('Biograph Viewer', names, 15);
obj.guiHan.bioH = child_handles(k);
set(obj.guiHan.bioH, 'Name',['Class Inheritance tree for ', obj.trees.directory]);
set(obj.guiHan.bioH, 'WindowButtonDownFcn',{})
end
end
function setup_gui(obj)
% builds the GUI
left = 10;
bottom = 100;
width = 855;
height = 470;
obj.guiHan.f = figure('Position',[left bottom width height],'menubar','none','name','Class Information');
searchBox = uipanel('Title','Search','units','pixel','BackgroundColor','white','Position',[10 420 315 40]);
dirBox = uipanel('Title','Directory','units','pixel','BackgroundColor','white','Position',[330 420 315 40]);
infoBox = uipanel('Title','Class Information','units','pixel','BackgroundColor','white','Position',[10 10 642 400]);
obj.guiHan.searchH = uicontrol('style','edit','position',[5 5 200 20],'parent',searchBox);
obj.guiHan.dirH = uicontrol('style','edit','position',[5 5 200 20],'parent',dirBox,'string',obj.trees.fullpath);
obj.guiHan.searchButtonH = uicontrol('style','pushbutton' ,'position',[210 5 100 20],'string','Search','parent',searchBox);
% list box for quickly browsing through subdirectories.
list_box_width = 200;
obj.guiHan.directoryList = uicontrol('style', 'listbox', ...
'position', [width-list_box_width 0 list_box_width height], ...
'string', obj.NODIRSTRING, 'Parent', obj.guiHan.f, ...
'Callback', {@LOOCALpropLb obj}, ...
'TooltipString', 'Browse through directories by clicking on them.');
obj.guiHan.dirsearchButtonH = uicontrol('style', 'pushbutton', ...
'position', [210 5 45 20], 'string', 'Go', ...
'parent', dirBox, 'TooltipString', 'Inspect this directory');
obj.guiHan.browsedirButtonH = uicontrol('style', 'pushbutton', ...
'position', [256 5 53 20], 'string', 'Browse', ...
'parent', dirBox, 'TooltipString', 'Browse to different directory');
% panels used as encasing for both the listbox, and the text
% above it.
uipanel('units','pixel','position',[3 3 154 380],'parent',infoBox);
uipanel('units','pixel','position',[163 3 154 380],'parent',infoBox);
uipanel('units','pixel','position',[323 3 154 380],'parent',infoBox);
uipanel('units','pixel','position',[483 3 154 380],'parent',infoBox);
% labels
obj.guiHan.ClassesH = uicontrol('style','text','position',[5 365 150 15],'String','Classes','parent',infoBox);
obj.guiHan.PropertiesH = uicontrol('style','text','position',[165 365 150 15],'String','Properties','parent',infoBox);
obj.guiHan.MethodsH = uicontrol('style','text','position',[325 365 150 15],'String','Methods','parent',infoBox);
obj.guiHan.SuperClassesH = uicontrol('style','text','position',[485 365 150 15],'String','Super Classes','parent',infoBox);
% listboxes below
obj.guiHan.classH = uicontrol('style','listbox','position',[5 5 150 355],'parent',infoBox);
obj.guiHan.propH = uicontrol('style','listbox','position',[165 5 150 355],'parent',infoBox);
obj.guiHan.methH = uicontrol('style','listbox','position',[325 5 150 355],'parent',infoBox);
obj.guiHan.supH = uicontrol('style','listbox','position',[485 5 150 355],'parent',infoBox);
% context menus for listboxes
cmenu = uicontextmenu;
uimenu(cmenu, 'Label', 'Print property description to console', 'Callback', {@LOCALpropCb obj});
set(obj.guiHan.propH, 'UIContextMenu', cmenu);
cmenu = uicontextmenu;
uimenu(cmenu, 'Label', 'Open method in editor', 'Callback', {@LOCALmethCb obj});
set(obj.guiHan.methH, 'UIContextMenu', cmenu);
% assign Callbacks and other functions
set(obj.guiHan.f,'CloseRequestFcn',{@closefunc obj})
set(obj.guiHan.f,'KeyPressFcn',{@KeyPressFcn_browse obj})
set(obj.guiHan.classH, 'Callback',{@LOCALlistCb obj});
set(obj.guiHan.searchH, 'KeyPressFcn',{@LOCALsearchCb obj});
set(obj.guiHan.dirH,'KeyPressFcn',{@LOCALdirCb obj},'Interruptible','off');
set(obj.guiHan.dirsearchButtonH,'Callback',{@LOCALdirCb obj},'Interruptible','off');
set(obj.guiHan.browsedirButtonH,'Callback',{@LOCALbrowseCb obj},'Interruptible','off');
set(obj.guiHan.searchButtonH,'Callback',{@LOCALsearchCb obj});
% update bioviewer
setup_gui_biograph_viewer(obj);
end
end
%% STATIC methods, for this class only
methods (Static = true, Access = protected)
function [strg,indx] = wholewordizer(sadword,str)
% searches a cellarray of strings (str) for partial match of a single string (sadword)
% returns a cell array of strings that match as well as their index in str
% accounts of partial words and ignores upper case
hits = 0;
indx = [];
strg = {};
strL = cell(size(str));
sadword = lower(sadword);
for i = 1:length(str)
strL{i} = lower(str{i});
end
for i = 1:length(strL)
if ~isempty(strfind(strL{i},sadword));
hits = hits + 1;
strg = {strg{:} str{i}};
indx = [indx i];
end
end
end
function this_cell = remove_empty_cell_entries(this_cell)
% checks for empty cells and removes them
indices = cellfun(@(x) isempty(x), this_cell, 'UniformOutput', true);
this_cell(indices) = [];
end
function enable_disable_listbox_and_contextmenu(handle, on_off)
% the listbox itself
set(handle, 'Enable', on_off);
% disable the Uimenu entries that belong to the uicontextmenu
% of the listbox
set(get(get(handle, 'UIContextMenu'), 'Children'), 'Enable', on_off);
end
end
%% STATIC methods
methods (Static = true)
function [result, absPathname] = resolvePath(class_and_method, class_and_method_private)
% returns the absolute path for a class/method combination
% "which(class_and_method)" will fail here most of the time.
% the idea for this function is hijacked from:
% toolbox/matlab/codetools/edit.m
result = 0;
absPathname = [];
% "helpUtils.splitClassInformation" needs to be called
% differently for the different Matlab version. I'm using try /
% catch here which seems easier than checking for the
% appropriate matlab version.
%
% Call to 'splitClassInformation' with matlab <= 2012b:
% [classInfo, whichTopic, malformed] = splitClassInformation(topic, helpPath, implementor, justChecking)
% Call to 'splitClassInformation' with matlab == 2013a:
% function [classInfo, whichTopic, malformed] = splitClassInformation(topic, helpPath, justChecking)
%
try % works with matlab versions <= 2012b
[classInfo, whichTopic] = helpUtils.splitClassInformation(class_and_method, '', true, false);
catch me %#ok<NASGU> matlab == 2013a (and matlab >= 2013a?)
[classInfo, whichTopic] = helpUtils.splitClassInformation(class_and_method, '', false);
end
% try again with possible 'private' path
if isempty(classInfo)
try % works with matlab versions <= 2012b
[classInfo, whichTopic] = helpUtils.splitClassInformation(class_and_method_private, '', true, false); %#ok<ASGLU>
catch me %#ok<NASGU> matlab == 2013a (and matlab >= 2013a?)
[classInfo, whichTopic] = helpUtils.splitClassInformation(class_and_method_private, '', false); %#ok<ASGLU>
end
end
if exist(whichTopic, 'file') == 2
result = 1;
absPathname = whichTopic;
return;
end
% user should never see this message, because he / she can only
% select methods that do exist. The only reason for not finding
% this method is, that this is an abstract method.
% maybe we should think about reading out the method properties
% (abstract, strict, etc) so we can show them to the user.
disp(['Could not find file for class/method: ' class_and_method]);
disp('This is probably an abstract method.');
end
end
end
% Class Inheritance Browser Copyright Clayton Ernst, Andrew Hagen, Eric Lee and Andreas Kotowicz 2012.
