Java TreeView User's Manual

$Revision: 1.26 $, covers Java TreeView 1.1.5

Alok Saldanha

$Revision: 1.26 $, covers Java TreeView 1.1.5

Table of Contents

1. Installation and Introduction
General Instructions
Overview of Java TreeView
Getting Started
Selection in Java TreeView
2. Feature Reference
Command Line Options
Useful JVM Arguments
Main Program options
Dendrogram export options
Document Settings
Global Settings
Url Presets
Dendrogram Color Presets
Karyoscope Coordinates Presets
Url Settings
Dendrogram Font Settings
Dendrogram Pixel Settings
Karyoscope Coordinates Settings
Karyoscope Averaging Settings
Export of Selected Genes and Data to Tab-Delimited Text
Export of Dendrograms
Bounding Box
Java Treeview Modes
Informational Panels
Selection in Dendrogram
Url Linking in Dendrogram
Coloring Gene Names and Array Names
Creating a Scatterplot
Cursor hinting in Karyoscope
Zooming in Karyoscope
Selection Highlighting in Karyoscope
File Formats
Minimal File Requirements
Generalized CDT File
Coordinates Files for Karyoscope
Tree Files
3. Troubleshooting
Installation Problems
Unzipping Distribution
Running Launcher Files
Url Related Issues
Url Linking in Windows
Url Linking on OSX
Export Problems
Export of Gene Summary
Giant Postscript Files
Giant GIF Files
Miscellaneous Problems
Out of Memory
Displaying Annotations
Switching browsers
Strange drawing of dendrogram branch lines
Crashing on Mac Os X

List of Figures

1.1. Contents of Java TreeView Distribution Archive
2.1. Url Presets Dialog
2.2. Dendrogram Color Presets Dialog
2.3. Karyoscope Coordinates Presets Dialog
2.4. Url Settings Dialog
2.5. Dendrogram Font Settings Dialog
2.6. Dendrogram Pixel Settings Dialog
2.7. Karyoscope Settings Dialog
2.8. Karyoscope Averaging Settings Dialog
2.9. Dendrogram Export Dialog
2.10. Dendrogram Component Layout
2.11. Scatterplot Component Layout
2.12. Creating a Scatterplot
2.13. Karyoscope Component Layout
2.14. Alignment Component Layout
2.15. File Formats in Java TreeView
2.16. Screenshot of Generalized CDT file in Excel
2.17. Screenshot of a Tree File in Excel
3.1. Screenshot of Running Java TreeView from the Command Line with 800 Megs of RAM

List of Tables

2.1. CDT Column Headers With Special Meaning
2.2. CDT Row Headers With Special Meaning
2.3. GTR/ATR Column Headers With Special Meaning