-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathicldiss.aux
128 lines (128 loc) · 8.95 KB
/
icldiss.aux
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
\relax
\citation{treeOfLifeDefine}
\citation{phylogeneticTree}
\citation{treeOfLifeDefine}
\@writefile{toc}{\contentsline {chapter}{\numberline {1}Introduction}{7}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\@writefile{toc}{\contentsline {section}{\numberline {1.1}Background}{7}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.1.1}What is tree of life}{7}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.1.2}Traditional way to visualize the tree of life}{7}}
\citation{euclidean}
\citation{multipleMonitoring}
\citation{multipleMonitoring2}
\@writefile{lof}{\contentsline {figure}{\numberline {1.1}{\ignorespaces Euclidean Drawing\relax }}{8}}
\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
\newlabel{fig:eucdeanDrawing}{{1.1}{8}}
\citation{euclidean}
\@writefile{lof}{\contentsline {figure}{\numberline {1.2}{\ignorespaces Using multiple monitor to display tree of life\relax }}{9}}
\newlabel{fig:multipleMonitoring}{{1.2}{9}}
\@writefile{lof}{\contentsline {figure}{\numberline {1.3}{\ignorespaces 2D/3D Hyperbolic view\relax }}{9}}
\newlabel{fig:Hyperbolic}{{1.3}{9}}
\@writefile{toc}{\contentsline {subsection}{\numberline {1.1.3}Interactive fractal-inspired graph}{9}}
\citation{oneZoomWebsite}
\citation{oneZoom}
\citation{oneZoom}
\citation{dataForOneZoom}
\citation{fractal1}
\citation{fractal2}
\citation{fractalWiki1}
\citation{fractalWiki2}
\citation{fractalWiki3}
\citation{fractalWiki4}
\citation{fractalMath}
\citation{fractalMath}
\@writefile{lof}{\contentsline {figure}{\numberline {1.4}{\ignorespaces An example IFIG of a 408,135-tip phylogeny of small-subunit RNAs using data from SILVA\relax }}{10}}
\newlabel{fig:oneZoomExample}{{1.4}{10}}
\@writefile{toc}{\contentsline {section}{\numberline {1.2}OneZoom Android Application}{11}}
\@writefile{toc}{\contentsline {section}{\numberline {1.3}Report outline}{11}}
\@writefile{toc}{\contentsline {chapter}{\numberline {2}OneZoom Website Software}{12}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\@writefile{toc}{\contentsline {section}{\numberline {2.1}Data processing}{12}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.1.1}Raw data format}{12}}
\@writefile{toc}{\contentsline {subsection}{\numberline {2.1.2}Node object}{13}}
\@writefile{toc}{\contentsline {section}{\numberline {2.2}Ways to decrease the amount of elements being drawn}{13}}
\@writefile{toc}{\contentsline {section}{\numberline {2.3}Software work flow}{14}}
\@writefile{toc}{\contentsline {section}{\numberline {2.4}How to use the software}{14}}
\@writefile{lof}{\contentsline {figure}{\numberline {2.1}{\ignorespaces Tree of Mammals\relax }}{15}}
\newlabel{fig:mammal}{{2.1}{15}}
\@writefile{lof}{\contentsline {figure}{\numberline {2.2}{\ignorespaces Tree of Rodents: Zoom In to the Rodent Branch\relax }}{15}}
\newlabel{fig:rodent}{{2.2}{15}}
\@writefile{lof}{\contentsline {figure}{\numberline {2.3}{\ignorespaces Zoom In the to Mouse Like Rodents Branch\relax }}{16}}
\newlabel{fig:mouseLikeRodent}{{2.3}{16}}
\@writefile{toc}{\contentsline {chapter}{\numberline {3}OneZoom Android Application}{17}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\@writefile{toc}{\contentsline {section}{\numberline {3.1}Create subclass for link node and leaf node}{17}}
\@writefile{toc}{\contentsline {section}{\numberline {3.2}User Operation Listener}{17}}
\@writefile{toc}{\contentsline {chapter}{\numberline {4}Memory Handling Issues}{19}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\@writefile{toc}{\contentsline {section}{\numberline {4.1}Problem description}{19}}
\newlabel{table:nonlin}{{\caption@xref {table:nonlin}{ on input line 423}}{19}}
\@writefile{lot}{\contentsline {table}{\numberline {4.1}{\ignorespaces Heap usage of tree with different amount of species in Chrome\relax }}{19}}
\newlabel{table:nonlin}{{\caption@xref {table:nonlin}{ on input line 462}}{20}}
\@writefile{lot}{\contentsline {table}{\numberline {4.2}{\ignorespaces Memory usage of different trees between Chrome and Firefox\relax }}{20}}
\newlabel{table:nonlin}{{\caption@xref {table:nonlin}{ on input line 480}}{20}}
\@writefile{lot}{\contentsline {table}{\numberline {4.3}{\ignorespaces Memory usage of different trees between right after initialization and a long time after initialization in Chrome \relax }}{20}}
\@writefile{toc}{\contentsline {section}{\numberline {4.2}Overview of the solution}{20}}
\@writefile{lof}{\contentsline {figure}{\numberline {4.1}{\ignorespaces Work flow of building part of the tree\relax }}{21}}
\@writefile{lof}{\contentsline {figure}{\numberline {4.2}{\ignorespaces Using Bouding Box to select branch\relax }}{22}}
\newlabel{fig:screenAndBounding1}{{4.2}{22}}
\@writefile{lof}{\contentsline {figure}{\numberline {4.3}{\ignorespaces Bounding box of child1 and child2 of root\relax }}{22}}
\newlabel{fig:screenAndBounding2}{{4.3}{22}}
\@writefile{toc}{\contentsline {section}{\numberline {4.3}Creating a new data format}{23}}
\@writefile{lof}{\contentsline {figure}{\numberline {4.4}{\ignorespaces Database columns\relax }}{23}}
\@writefile{toc}{\contentsline {section}{\numberline {4.4}Dynamic adding and deleting of nodes}{24}}
\@writefile{lof}{\contentsline {figure}{\numberline {4.5}{\ignorespaces Work flow of adding nodes on the tree\relax }}{25}}
\@writefile{lof}{\contentsline {figure}{\numberline {4.6}{\ignorespaces Possibility with distance\relax }}{26}}
\@writefile{lof}{\contentsline {figure}{\numberline {4.7}{\ignorespaces Possibility with size\relax }}{26}}
\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces Work flow of deleting nodes on the tree\relax }}{27}}
\@writefile{toc}{\contentsline {section}{\numberline {4.5}Result}{27}}
\newlabel{table:nonlin}{{\caption@xref {table:nonlin}{ on input line 691}}{27}}
\@writefile{lot}{\contentsline {table}{\numberline {4.4}{\ignorespaces Comparison of memory usage before and after optimization\relax }}{27}}
\@writefile{toc}{\contentsline {chapter}{\numberline {5}Performance Issues}{28}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\@writefile{toc}{\contentsline {section}{\numberline {5.1}Loading Time}{28}}
\newlabel{table:nonlin}{{\caption@xref {table:nonlin}{ on input line 723}}{28}}
\@writefile{lot}{\contentsline {table}{\numberline {5.1}{\ignorespaces Loading Time on Android and website version before memory and performance optimizing\relax }}{28}}
\@writefile{toc}{\contentsline {subsection}{\numberline {5.1.1}Optimization result}{29}}
\@writefile{lot}{\contentsline {table}{\numberline {5.2}{\ignorespaces Result of loading time after optimizing in Android\relax }}{29}}
\newlabel{table:loadingCamparison}{{5.2}{29}}
\@writefile{toc}{\contentsline {section}{\numberline {5.2}User Interaction}{29}}
\@writefile{lof}{\contentsline {figure}{\numberline {5.1}{\ignorespaces Previous working flow of main UI thread\relax }}{29}}
\@writefile{toc}{\contentsline {subsection}{\numberline {5.2.1}Using thread and message queue to discard extra mouse move message}{29}}
\@writefile{lof}{\contentsline {figure}{\numberline {5.2}{\ignorespaces How recalculation thread deals with message\relax }}{30}}
\@writefile{toc}{\contentsline {subsection}{\numberline {5.2.2}Using idle thread to prepare nodes}{30}}
\@writefile{lof}{\contentsline {figure}{\numberline {5.3}{\ignorespaces Calculation during idle time\relax }}{31}}
\@writefile{toc}{\contentsline {subsection}{\numberline {5.2.3}Using cached bitmap to update view before calculation is done}{31}}
\@writefile{lof}{\contentsline {figure}{\numberline {5.4}{\ignorespaces How to update view\relax }}{32}}
\@writefile{toc}{\contentsline {subsection}{\numberline {5.2.4}Test use bitmap or do actual drawing}{32}}
\@writefile{lof}{\contentsline {figure}{\numberline {5.5}{\ignorespaces How to test whether to use bitmap to redraw\relax }}{33}}
\@writefile{toc}{\contentsline {subsection}{\numberline {5.2.5}Avoid duplicate drawing nodes}{33}}
\@writefile{lof}{\contentsline {figure}{\numberline {5.6}{\ignorespaces Causes of extra drawing after user interaction\relax }}{34}}
\@writefile{lof}{\contentsline {figure}{\numberline {5.7}{\ignorespaces Solve extra drawing by setting a new flag\relax }}{35}}
\@writefile{toc}{\contentsline {subsection}{\numberline {5.2.6}Draw less details first}{35}}
\@writefile{lof}{\contentsline {figure}{\numberline {5.8}{\ignorespaces Draw less details when user interaction ends, draw more details one second later\relax }}{36}}
\bibdata{icldiss}
\@writefile{toc}{\contentsline {chapter}{\numberline {6}Conclusion and Future Work}{37}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\bibcite{treeOfLifeDefine}{1}
\bibcite{phylogeneticTree}{2}
\bibcite{oneZoomWebsite}{3}
\bibcite{fractal1}{4}
\bibcite{fractalWiki3}{5}
\bibcite{euclidean}{6}
\bibcite{fractalWiki2}{7}
\bibcite{fractal2}{8}
\bibcite{multipleMonitoring2}{9}
\bibcite{fractalMath}{10}
\bibcite{fractalWiki1}{11}
\bibcite{multipleMonitoring}{12}
\bibcite{dataForOneZoom}{13}
\bibcite{oneZoom}{14}
\bibcite{fractalWiki4}{15}
\bibstyle{plain}