| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
|---|
| 2 | UP arb.hlp |
|---|
| 3 | UP glossary.hlp |
|---|
| 4 | UP tree_shading.hlp |
|---|
| 5 | |
|---|
| 6 | #Please insert subtopic references (line starts with keyword SUB) |
|---|
| 7 | #SUB subtopic.hlp |
|---|
| 8 | |
|---|
| 9 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
|---|
| 10 | |
|---|
| 11 | #************* Title of helpfile !! and start of real helpfile ******** |
|---|
| 12 | TITLE Topology shader |
|---|
| 13 | |
|---|
| 14 | OCCURRENCE ARB_NT/Tree/Tree shading/Topology shader |
|---|
| 15 | |
|---|
| 16 | DESCRIPTION This shader uses the tree currently displayed in the main |
|---|
| 17 | tree display as a reference to shade species. |
|---|
| 18 | |
|---|
| 19 | Species at the top of that tree will be shaded with the "low" color, |
|---|
| 20 | species at the bottom with the "high" color of the active color-range. |
|---|
| 21 | |
|---|
| 22 | The intented purpose of this shader is comparing two tree topologies. |
|---|
| 23 | To do that, display one of the trees in the main window, then open a |
|---|
| 24 | second treeview using "File/New Window" and display a different tree |
|---|
| 25 | in that window. |
|---|
| 26 | |
|---|
| 27 | * The tree in the main window will always be shaded continuously. |
|---|
| 28 | |
|---|
| 29 | * Shading of trees in other windows will be non-continuous where their |
|---|
| 30 | topology differs from the topology shown in the main window. |
|---|
| 31 | This facilitates the detection of topology differences. |
|---|
| 32 | |
|---|
| 33 | The granularity of topology shading depends on the size of the reference tree. |
|---|
| 34 | Therefore modifying the settings in section 'Value phasing' is strongly |
|---|
| 35 | recommended while comparing topologies: |
|---|
| 36 | |
|---|
| 37 | * to detect local topology differences, increase the phasing frequency |
|---|
| 38 | until adjacent species are displayed in distinguishable colors. |
|---|
| 39 | Then use either of the phase-shift sliders to shift the shading. |
|---|
| 40 | * to detect global topology differences, decrease the phasing frequency. |
|---|
| 41 | |
|---|
| 42 | NOTES Whenever the tree in the main tree display changes, the shading is instantly |
|---|
| 43 | updated and refreshed in all tree displays. |
|---|
| 44 | |
|---|
| 45 | You can use the logical zoom-mode in the main tree display while the |
|---|
| 46 | topology shader is active, to shade only the zoomed part of the tree. |
|---|
| 47 | |
|---|
| 48 | EXAMPLES The range allowed for the phasing frequency is [0.01 .. 100]. |
|---|
| 49 | The number of colors available for shading is currently limited to 4096. |
|---|
| 50 | |
|---|
| 51 | When you compare trees with e.g. 500k Species, |
|---|
| 52 | |
|---|
| 53 | * using a frequency of 1.0 will shade approx. 120 adjacent species with the same color, |
|---|
| 54 | * using a frequency of 0.1 will shade approx. 1200 adjacent species with the same color and |
|---|
| 55 | * using a frequency of 10 will shade approx. 12 adjacent species with the same color. |
|---|
| 56 | |
|---|
| 57 | WARNINGS This feature will cause frequent display updates. Using it while ARB is running |
|---|
| 58 | over a remote connection may be dissatisfying. |
|---|
| 59 | |
|---|
| 60 | BUGS No bugs known |
|---|
