From 9683bef56f117100bb60a1606de66f73b7e31fbe Mon Sep 17 00:00:00 2001 From: Shawn Laffan Date: Fri, 29 Apr 2016 10:21:53 +1000 Subject: [PATCH] Remove the glade folder All the requisite files are now in the ui folder. Move strip_redundant_text.pl across in case it is needed. Updates issue #413. --- bin/glade/biodiverse.glade | 1801 ---- bin/glade/biodiverse.glade.bak | 9449 --------------------- bin/glade/biodiverse.gladep | 8 - bin/glade/biodiverse.gladep.bak | 8 - bin/glade/drag-resize.png | Bin 638 -> 0 bytes bin/glade/merge.xslt | 284 - bin/glade/selector.png | Bin 705 -> 0 bytes bin/{glade => ui}/strip_redundant_text.pl | 0 8 files changed, 11550 deletions(-) delete mode 100644 bin/glade/biodiverse.glade delete mode 100644 bin/glade/biodiverse.glade.bak delete mode 100644 bin/glade/biodiverse.gladep delete mode 100644 bin/glade/biodiverse.gladep.bak delete mode 100755 bin/glade/drag-resize.png delete mode 100644 bin/glade/merge.xslt delete mode 100644 bin/glade/selector.png rename bin/{glade => ui}/strip_redundant_text.pl (100%) diff --git a/bin/glade/biodiverse.glade b/bin/glade/biodiverse.glade deleted file mode 100644 index ea5f0462b..000000000 --- a/bin/glade/biodiverse.glade +++ /dev/null @@ -1,1801 +0,0 @@ - - - - - - True - False - window1 - - - True - True - False - True - 1 - 1 - 1 - - - True - False - - - True - False - vertical - icons - False - - - True - False - True - Select (S or B) - - - True - True - True - True - Select (S or B) - - - True - False - selector.png - - - - - - - False - - - - - True - False - True - Pan (C) - - - True - True - True - True - Pan (C) - - - True - False - drag-resize.png - - - - - - - False - - - - - True - False - Zoom In (Z) - - - True - True - True - True - Zoom In (Z) - - - True - False - gtk-zoom-in - - - - - - - False - - - - - True - False - Zoom Out (X) - - - True - True - True - True - Zoom Out (X) - - - True - False - gtk-zoom-out - - - - - - - False - - - - - True - False - Zoom to Fit (V) - - - True - True - True - True - Zoom to Fit (V) - - - True - False - gtk-zoom-fit - - - - - - - False - - - - - True - False - - - False - - - - - True - False - - - True - False - ttb - - - True - False - Display - True - - - False - - - True - False - Overlays... - True - - - - - True - False - - - - - True - False - Set the display stretch. -Uses minimum to maximum by default -but you can also set percentile ranges. - Colour stretch - True - - - True - False - - - True - False - min-max - True - True - True - - - - - True - False - 5-95 - True - True - radio_colour_stretch0 - - - - - True - False - 2.5-97.5 - True - radio_colour_stretch0 - - - - - True - False - min-95 - True - True - radio_colour_stretch0 - - - - - True - False - min-97.5 - True - True - radio_colour_stretch0 - - - - - True - False - 5-max - True - True - radio_colour_stretch0 - - - - - True - False - 2.5-max - True - True - radio_colour_stretch0 - - - - - - - - - True - False - Hue will display all hues (colours) from blue to red. - -Sat will display a single colour with saturation varying from -white to a maximum saturation at the selected colour. - -Grey will use grey scale. - -Colours are scaled using percentiles defined in the colour stretch menu. - Colour mode - True - - - True - False - - - True - False - Display all hues (colours) from blue to red. - Hue - True - True - - - - - True - False - Display a single colour with saturation varying from white to a selected maximum. - Sat... - True - True - menuitem_spatial_colour_mode_hue - - - - - True - False - Display as grey scale. - Grey - True - True - menuitem_spatial_colour_mode_hue - - - - - - - - - True - False - Control the highlighting of neighbours on the grid. - Nbr highlighting - True - - - True - False - - - True - False - Both - True - True - True - - - - - True - False - Set1 - True - True - menuitem_nbr_highlight_all - - - - - True - False - Set2 - True - True - menuitem_nbr_highlight_all - - - - - True - False - Off - True - True - menuitem_nbr_highlight_all - - - - - - - - - True - False - - - - - True - False - Set the colour for cells that were excluded from the analysis, typically using a definition query. - Set excluded cell colour - True - - - - - True - False - Set the colour of cells when the index value is undefined. - Set undefined value colour - True - - - - - True - False - Choose the colour used for the cell outlines - Set cell outline colour - True - - - - - True - False - Show or hide the cell outlines - Show cell outlines - True - True - - - - - True - False - - - - - True - False - Show or hide the legend - Show legend - True - True - - - - - True - False - Set the width of the tree branches. -Does not affect the vertical connectors. - Set tree branch line widths - True - - - - - - - - - - - False - - - - - False - True - 0 - - - - - True - False - - - True - True - 181 - - - True - False - - - True - True - automatic - - - True - False - - - True - False - - - True - False - 2 - - - True - False - 5 - 0 - - - True - True - 5 - never - automatic - - - True - True - - - - - - - True - False - Calculations to run for each neighbourhood - True - - - label_item - - - - - 1 - 2 - GTK_FILL - - - - - True - True - True - - - True - False - 12 - - - True - False - 4 - 4 - 3 - 2 - 4 - - - True - False - True - Define a second set of neighbours for use in the analyses. -A typical use is for comparative analyses like species turnover. - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - 1 - Neighbour set 2 - right - - - 2 - 3 - GTK_FILL - - - - - - True - False - 0 - <b>Name</b> - True - right - - - GTK_FILL - - - - - - True - False - 0 - none - - - 1 - 3 - 2 - 3 - GTK_FILL - GTK_FILL - - - - - True - False - 0 - none - - - 1 - 3 - 1 - 2 - GTK_FILL - GTK_SHRINK | GTK_FILL - - - - - True - False - True - Use this to run the analysis for only a subset of the groups. -Note that it will still search the full data set for neighbours. - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - 1 - Definition query - right - - - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - none - - - 1 - 3 - 3 - 4 - GTK_FILL - GTK_FILL - - - - - True - False - True - Specify the first set of neighbours to use in the analysis. - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - 1 - Neighbour set 1 - right - - - 1 - 2 - GTK_FILL - - - - - - True - False - - - True - True - ● - True - Spatial1 - False - False - True - True - - - True - True - 0 - - - - - True - True - True - True - Set analysis options - right - - - True - False - gtk-properties - - - - - False - False - 1 - - - - - 1 - 3 - - - - - - - - - - True - False - show/hide the parameters section - Parameters - - - label_item - - - - - GTK_SHRINK | GTK_FILL - - - - - True - True - 0 - - - - - True - False - edge - - - Go! - True - True - True - False - Generates a new output, or overwrites an existing one (CTRL-G) - 2 - True - - - False - False - 0 - - - - - False - False - 1 - - - - - - - - - True - True - 0 - - - - - True - True - - - - - True - True - - - True - False - 2 - 0.0099999997764825821 - none - - - True - False - 2 - 2 - - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - False - 0 - none - - - GTK_FILL - GTK_FILL - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - - - True - False - <b>Output</b> - True - - - label_item - - - - - True - True - - - - - True - False - 2 - 0.0099999997764825821 - none - - - True - False - - - True - False - 2 - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - True - - - True - False - 2 - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - - GTK_FILL - - - - - True - False - 0 - none - - - - - False - True - - - - - True - False - 0 - none - - - False - True - - - - - - - True - True - 0 - - - - - - - True - False - <b>Tree</b> - True - - - label_item - - - - - True - True - - - - - True - True - - - - - True - True - 0 - - - - - True - False - - - True - False - Lists and indices: - - - False - False - 0 - - - - - True - False - True - - - False - False - 1 - - - - - True - False - True - - - False - False - 2 - - - - - True - False - - - False - False - 3 - - - - - True - False - Tree plot: - - - False - False - 4 - - - - - True - False - True - Select tree to display - 0 - True - - - - False - False - 5 - - - - - False - False - 1 - - - - - True - True - 1 - - - - - 3 - - - - - - - - True - False - dialog2 - dialog - - - True - False - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - False - False - 0 - - - - - gtk-ok - -5 - True - True - True - False - True - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - - - True - False - <b>Select column types</b> - - True - - - False - False - 0 - - - - - True - True - automatic - never - - - True - False - 5 - 6 - 5 - 20 - 5 - - - True - True - 0 - num - True - - - 1 - 2 - GTK_FILL - - - - - - True - True - 0 - x - True - - - 2 - 3 - GTK_FILL - - - - - - True - False - 0 - y - - - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - species - - - 4 - 5 - GTK_FILL - - - - - - True - False - 1 - Ignore - - - 1 - 2 - GTK_FILL - - - - - - True - False - 1 - Label - - - 2 - 3 - GTK_FILL - - - - - - True - False - 1 - Group - - - 3 - 4 - GTK_FILL - - - - - - True - True - False - ignore - True - True - - - 2 - 3 - 1 - 2 - GTK_FILL - - - - - - True - True - False - use as label - True - True - - - 2 - 3 - 2 - 3 - GTK_FILL - - - - - - True - True - False - True - True - - - 3 - 4 - 3 - 4 - GTK_FILL - - - - - - True - True - False - True - True - - - 3 - 4 - 2 - 3 - GTK_FILL - - - - - - True - True - False - True - True - - - 3 - 4 - 1 - 2 - GTK_FILL - - - - - - True - True - False - True - True - - - 4 - 5 - 1 - 2 - GTK_FILL - - - - - - True - True - False - True - True - - - 4 - 5 - 2 - 3 - GTK_FILL - - - - - - True - True - False - True - True - - - 4 - 5 - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - Cell size - - - 4 - 5 - GTK_FILL - - - - - - True - False - 0 - Cell snap - - - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 3 0 100 1 10 0 - 1 - True - - - 1 - 2 - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 5 0 100 1 10 0 - 1 - True - - - 1 - 2 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 2 - 3 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 2 - 3 - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 3 - 4 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 3 - 4 - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 4 - 5 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 4 - 5 - 5 - 6 - GTK_FILL - - - - - - True - False - 0 - - - True - True - False - True - True - - - - - 1 - 2 - 1 - 2 - GTK_FILL - - - - - - True - False - <b>Column</b> - True - - - GTK_FILL - - - - - - True - False - 0 - - - True - True - False - True - True - radiobutton2 - - - - - 1 - 2 - 2 - 3 - GTK_FILL - - - - - - True - False - - - True - True - False - True - True - radiobutton2 - - - - - 1 - 2 - 3 - 4 - - - - - - - True - True - False - use as group - True - True - - - 2 - 3 - 3 - 4 - - - - - - - - - True - True - 1 - - - - - True - True - 2 - - - - - - - 300 - True - False - Please wait... - True - center - True - True - - - True - False - 5 - 10 - - - True - False - Progress - True - - - False - False - 0 - - - - - True - False - 0.10000000149 - - - False - False - 1 - - - - - - diff --git a/bin/glade/biodiverse.glade.bak b/bin/glade/biodiverse.glade.bak deleted file mode 100644 index 4eb437b3d..000000000 --- a/bin/glade/biodiverse.glade.bak +++ /dev/null @@ -1,9449 +0,0 @@ - - - - - - True - False - Save changes? - True - mouse - True - gtk-dialog-warning - dialog - - - True - False - - - True - False - end - - - -9 - True - True - True - - - - True - False - 0 - 0 - - - True - False - 2 - - - True - False - gtk-delete - - - False - False - 0 - - - - - True - False - _Discard changes - True - - - False - False - 1 - - - - - - - - - False - False - 0 - - - - - -6 - True - True - True - True - True - False - - - - True - False - 0 - 0 - - - True - False - 2 - - - True - False - gtk-cancel - - - False - False - 0 - - - - - True - False - Do_n't close - True - - - False - False - 1 - - - - - - - - - False - False - 1 - - - - - -8 - True - True - False - - - - True - False - 0 - 0 - - - True - False - 2 - - - True - False - gtk-save - - - False - False - 0 - - - - - True - False - _Save - True - - - False - False - 1 - - - - - - - - - False - False - 2 - - - - - False - True - end - 0 - - - - - True - False - - - True - False - 12 - 0 - none - - - True - False - 12 - - - True - False - gtk-dialog-warning - 6 - - - - - - - False - False - 0 - - - - - True - False - <b> Save changes before closing? </b> - True - - - False - False - 1 - - - - - False - False - 2 - - - - - - - True - False - Name output - True - center - dialog - - - True - False - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - False - False - 0 - - - - - gtk-ok - -5 - True - True - True - False - True - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - - - True - False - New name - - - False - False - 0 - - - - - True - True - False - False - True - True - - - True - True - 1 - - - - - True - True - 2 - - - - - - - True - False - Export - True - center - normal - - - True - False - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - False - False - 0 - - - - - gtk-ok - -5 - True - True - True - False - True - - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - 5 - - - True - False - 5 - - - True - False - 0 - none - - - True - False - 12 - - - True - False - 2 - 3 - 3 - - - - - - - - - - - - - - - - True - False - Options - True - - - label_item - - - - - False - True - 0 - - - - - True - False - 0 - none - - - True - False - save - - - - - True - False - Filename - True - - - label_item - - - - - True - True - 1 - - - - - True - True - 0 - - - - - True - True - 2 - - - - - - - True - False - Export Basedata - True - mouse - True - gtk-dialog-question - dialog - - - True - False - - - True - False - end - - - _Groups - -9 - True - True - False - True - - - - False - False - 0 - - - - - _Labels - -8 - True - True - False - True - - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - - - True - False - 12 - 0 - none - - - True - False - 12 - - - True - False - gtk-dialog-question - 6 - - - - - - - False - False - 0 - - - - - True - False - What to export? - True - - - False - False - 1 - - - - - False - False - 2 - - - - - - - True - False - Import Data - True - center - True - gtk-add - dialog - - - True - False - 5 - - - True - False - - - True - False - 0 - 3 - Note: you can import more than one file at a time so long as the order of the columns is the same. - - - False - False - 0 - - - - - True - False - - - False - True - 9 - 1 - - - - - True - False - True - - - True - False - - - True - False - 0 - 5 - Target Data Set - - - False - False - 0 - - - - - True - False - DEFAULT - - - True - True - 1 - - - - - True - True - 0 - - - - - True - False - - - True - False - 0 - 3 - 3 - - - New - True - True - False - True - Check to off to import new data to an existing Basedata set - True - True - - - - - False - False - 0 - - - - - True - True - True - True - Name for a new data set - ● - 20 - False - False - True - True - - - True - True - 1 - - - - - True - True - 1 - - - - - False - False - 2 - - - - - True - False - True - - - True - False - - - True - True - 0 - - - - - One Basedata per file - True - True - False - If checked then each imported file is assigned to a separate basedata. These will be created if they do not exist, and will use the file names as the basedata names (excluding the directory components). Turn off the New checkbox above if you want to import into existing basedatas (they will be created if they do not exist). - True - - - True - True - 1 - - - - - False - True - 3 - - - - - True - False - - - False - True - 9 - 4 - - - - - True - False - - - True - False - 5 - Format - right - - - False - False - 0 - - - - - True - False - Select the type of input data you wish to use. - 0 - Text -Raster -Shapefile -Spreadsheet - - - False - False - 54 - 1 - - - - - False - False - 5 - - - - - 550 - 240 - True - False - vertical - True - - - True - True - end - 6 - - - - - True - False - - - False - True - 9 - 7 - - - - - True - True - 0 - - - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - False - False - 0 - - - - - -5 - True - True - True - True - False - - - True - False - 0 - 0 - - - True - False - 2 - - - True - False - Next - True - - - False - False - 0 - - - - - True - False - gtk-go-forward - - - False - False - 1 - - - - - - - - - False - False - 1 - - - - - False - False - end - 1 - - - - - - - False - 5 - Import options - center-on-parent - dialog - - - True - False - 2 - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - False - False - 0 - - - - - -5 - True - True - True - True - False - - - True - False - 0 - 0 - - - True - False - 2 - - - True - False - gtk-go-forward - - - False - False - 0 - - - - - True - False - Next - True - - - False - False - 1 - - - - - - - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - 0 - none - - - True - False - 0 - 12 - - - True - False - 2 - 3 - 3 - - - - - - - - - - - - - - - - True - False - <b>Options</b> - True - - - label_item - - - - - False - True - 2 - - - - - - - True - False - Spatial Index - True - center - dialog - - - True - False - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - - - False - False - 0 - - - - - gtk-ok - -5 - True - True - True - False - True - - - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - 3 - - - True - False - <b>Spatial Index</b> - True - - - False - False - 0 - - - - - _Use Index - True - True - False - True - True - - - - False - False - 1 - - - - - True - False - - - True - False - 10 - - - 127 - True - True - False - False - True - True - 100000 9.9999997473799998e-005 10000000 1 10 0 - 1 - 4 - - - - - False - False - 0 - - - - - True - False - index unit size (in map units, currently applies to all axes) - - - False - False - 1 - - - - - True - True - 2 - - - - - True - True - 2 - - - - - - - True - False - Import Matrix - True - True - gtk-add - dialog - - - True - False - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - False - False - 0 - - - - - gtk-ok - -5 - True - True - True - False - True - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - - - True - False - - - True - False - 0 - Name - - - False - False - 5 - 0 - - - - - True - True - False - False - True - True - - - True - True - 1 - - - - - False - True - 3 - 0 - - - - - True - False - 7 - Input File: - - - False - False - 1 - - - - - 550 - 240 - True - False - - - True - True - 2 - - - - - True - True - 2 - - - - - - - True - False - Re-order Columns - True - center - dialog - - - True - False - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - - False - False - 0 - - - - - gtk-ok - -5 - True - True - True - False - True - - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - - - True - False - <b>Re-order Columns</b> - (for example so latitude and longitude are in the correct X-Y order) -<i>Tip:</i> You can also drag to re-arrange - - True - center - - - False - False - 0 - - - - - True - False - - - True - False - 0 - - - True - False - 12 - 5 - - - 71 - 270 - True - True - automatic - automatic - in - - - True - True - - - - - - - - - True - False - Labels - True - - - label_item - - - - - True - True - 0 - - - - - True - False - 0 - 0 - - - True - False - 5 - start - - - gtk-go-up - True - True - True - False - True - - - - False - False - 0 - - - - - gtk-go-down - True - True - True - False - True - - - - False - False - 1 - - - - - - - False - False - 1 - - - - - True - False - 0 - - - True - False - 6 - - - 71 - 270 - True - True - automatic - automatic - in - - - True - True - - - - - - - - - True - False - Groups - True - - - label_item - - - - - True - True - 2 - - - - - True - True - 1 - - - - - True - True - 2 - - - - - - - True - False - Run Exclusions - True - center - dialog - - - True - False - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - False - False - 0 - - - - - gtk-ok - -5 - True - True - True - False - True - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - - - True - False - <b>Dataset Exclusions</b> -Filtering (excluding) records may cause unpredictable results in existing analysis outputs so this is disabled for BaseDatas with existing outputs. - -Numeric conditions are assessed using less than or equal to or greater than or equal to. - - - True - center - True - - - False - False - 0 - - - - - True - False - 10 - - - True - False - 0 - - - True - False - 12 - - - True - False - - - True - False - 8 - 3 - 5 - 1 - - - True - False - False - True - True - - - 1 - 2 - 6 - 7 - GTK_FILL - - - - - - True - True - False - False - True - True - 1 1 100000 10 10 0 - 1 - True - - - 2 - 3 - 7 - 8 - - - - - - True - False - False - True - True - - - 1 - 2 - 7 - 8 - GTK_FILL - - - - - - True - False - 0 - Min Range - - - 7 - 8 - GTK_FILL - - - - - - True - True - False - False - True - True - 1000 0 100000 10 1 0 - 1 - True - - - 2 - 3 - 6 - 7 - - - - - - True - False - 0 - Max Range - - - 6 - 7 - GTK_FILL - - - - - - True - False - 0 - Min Variety - - - 1 - 2 - GTK_FILL - - - - - - True - True - False - False - True - True - 0.10000000149 0 1 0.10000000000000001 0.001 0 - 1 - 2 - True - - - 2 - 3 - 5 - 6 - - - - - - True - False - False - True - True - - - 1 - 2 - 5 - 6 - GTK_FILL - - - - - - True - False - 0 - Min Redundancy - - - 5 - 6 - GTK_FILL - - - - - - True - False - False - True - True - - - 1 - 2 - 1 - 2 - GTK_FILL - - - - - - True - True - False - False - True - True - 0.10000000000000001 0 1 0.10000000000000001 0.001 0 - 1 - 2 - True - - - 2 - 3 - 4 - 5 - - - - - - True - True - False - False - True - True - 1 1 100000 10 10 0 - 1 - True - - - 2 - 3 - 3 - 4 - - - - - - True - True - False - False - True - True - 1 1 100000 10 10 0 - 1 - True - - - 2 - 3 - 2 - 3 - - - - - - True - True - False - False - True - True - 1 1 100000 1 10 0 - 1 - True - - - 2 - 3 - 1 - 2 - - - - - - True - False - False - True - True - - - 1 - 2 - 4 - 5 - GTK_FILL - - - - - - True - False - False - True - True - - - 1 - 2 - 3 - 4 - GTK_FILL - - - - - - True - False - False - True - True - - - 1 - 2 - 2 - 3 - GTK_FILL - - - - - - True - False - False - True - True - - - 1 - 2 - GTK_FILL - - - - - - True - True - False - False - True - True - 1 1 100000 1 10 0 - 1 - True - - - 2 - 3 - - - - - - True - False - 0 - Max Redundancy - - - 4 - 5 - GTK_FILL - - - - - - True - False - 0 - Min Samples - - - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - Max Samples - - - 2 - 3 - GTK_FILL - - - - - - True - False - 0 - Max Variety - - - GTK_FILL - - - - - - True - True - 0 - - - - - True - False - 0 - - - True - False - - - True - False - - - Use? - True - True - False - True - - - True - True - 0 - - - - - True - False - True - 0 - Filter text: - - - True - True - 1 - - - - - True - True - True - ● - False - False - True - True - - - True - True - 2 - - - - - True - True - 0 - - - - - True - False - - - Negate -the filter - True - True - False - True - - - True - False - 0 - - - - - 6 - True - False - - - False - True - 1 - - - - - True - False - Regex -modifiers: - - - False - False - 5 - 2 - - - - - True - True - ● - False - False - True - True - - - True - True - 3 - - - - - True - True - 1 - - - - - - - True - False - <b>Text matching</b> - True - - - label_item - - - - - True - True - 1 - - - - - 12 - True - False - - - False - True - 2 - - - - - True - False - 0 - - - True - False - - - Use? - True - True - False - True - - - True - True - 0 - - - - - Negate the filter - True - True - False - True - - - False - False - 1 - - - - - True - False - - - True - True - 2 - - - - - - - True - False - <b>Use a list from a file</b> - True - - - label_item - - - - - True - True - 3 - - - - - Delete empty groups - True - True - False - Delete groups made empty by the deletion of all their labels - True - True - - - True - True - 4 - - - - - - - - - True - False - <b>Labels</b> (eg. species) - True - - - label_item - - - - - True - True - 0 - - - - - True - False - 0 - - - True - False - 12 - - - True - False - - - True - False - 6 - 3 - 5 - 1 - - - True - False - 0 - Max Variety (Richness) - - - GTK_FILL - - - - - - True - False - 0 - Max Samples - - - 2 - 3 - GTK_FILL - - - - - - True - False - 0 - Min Samples - - - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - Min Redundancy - - - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 1 1 100000 1 10 0 - 1 - True - - - 2 - 3 - - - - - - True - False - False - True - True - - - 1 - 2 - 1 - 2 - GTK_FILL - - - - - - True - False - False - True - True - - - 1 - 2 - 2 - 3 - GTK_FILL - - - - - - True - False - False - True - True - - - 1 - 2 - 3 - 4 - GTK_FILL - - - - - - True - False - False - True - True - - - 1 - 2 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 1 1 100000 1 10 0 - 1 - True - - - 2 - 3 - 1 - 2 - - - - - - True - True - False - False - True - True - 1 1 100000 1 10 0 - 1 - True - - - 2 - 3 - 2 - 3 - - - - - - True - True - False - False - True - True - 1 1 100000 1 10 0 - 1 - True - - - 2 - 3 - 3 - 4 - - - - - - True - True - False - False - True - True - 0.10000000000000001 0 1 0.001 0.001 0 - 1 - 2 - True - - - 2 - 3 - 4 - 5 - - - - - - True - False - False - True - True - - - 1 - 2 - GTK_FILL - - - - - - True - False - 0 - Max Redundancy - - - 5 - 6 - GTK_FILL - - - - - - True - False - False - True - True - - - 1 - 2 - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 0.10000000000000001 0 1 0.001 0.001 0 - 1 - 2 - True - - - 2 - 3 - 5 - 6 - - - - - - True - False - 0 - Min Variety (Richness) - - - 1 - 2 - GTK_FILL - - - - - - False - True - 0 - - - - - True - False - - - False - True - 10 - 1 - - - - - True - False - 0 - none - - - True - False - 12 - - - True - False - - - - - - - True - False - True - Exclude groups using a definition query. -This is specified in the same manner -as in the spatial analyses. - <b>Definition query</b> - True - - - label_item - - - - - True - True - 2 - - - - - Delete empty labels - True - True - False - True - Delete labels made empty by the deletion of all groups they occur in - True - True - - - False - True - 3 - - - - - - - - - True - False - <b>Groups</b> (eg. cells) - True - - - label_item - - - - - True - True - 1 - - - - - True - True - 1 - - - - - True - True - 2 - - - - - - - True - False - Biodiverse response - True - center - dialog - - - True - False - - - True - False - end - - - gtk-yes - -8 - True - True - False - True - - - - False - False - 0 - - - - - gtk-no - -9 - True - True - False - True - - - - False - False - 1 - - - - - gtk-cancel - -6 - True - True - True - True - True - False - True - - - - False - False - 2 - - - - - False - True - end - 0 - - - - - True - False - <b>Question</b> -Do you want to continue? - True - center - True - - - True - True - 2 - - - - - - - True - False - dialog2 - dialog - - - True - False - - - True - False - end - - - gtk-cancel - -6 - True - True - True - False - True - - - False - False - 0 - - - - - gtk-ok - -5 - True - True - True - False - True - - - False - False - 1 - - - - - False - True - end - 0 - - - - - True - False - - - True - False - <b>Select column types</b> - - True - - - False - False - 0 - - - - - True - True - automatic - never - - - True - False - 5 - 6 - 5 - 20 - 5 - - - True - True - 0 - num - True - - - 1 - 2 - GTK_FILL - - - - - - True - True - 0 - x - True - - - 2 - 3 - GTK_FILL - - - - - - True - False - 0 - y - - - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - species - - - 4 - 5 - GTK_FILL - - - - - - True - False - 1 - Ignore - - - 1 - 2 - GTK_FILL - - - - - - True - False - 1 - Label - - - 2 - 3 - GTK_FILL - - - - - - True - False - 1 - Group - - - 3 - 4 - GTK_FILL - - - - - - True - True - False - ignore - True - True - - - 2 - 3 - 1 - 2 - GTK_FILL - - - - - - True - True - False - use as label - True - True - - - 2 - 3 - 2 - 3 - GTK_FILL - - - - - - True - True - False - True - True - - - 3 - 4 - 3 - 4 - GTK_FILL - - - - - - True - True - False - True - True - - - 3 - 4 - 2 - 3 - GTK_FILL - - - - - - True - True - False - True - True - - - 3 - 4 - 1 - 2 - GTK_FILL - - - - - - True - True - False - True - True - - - 4 - 5 - 1 - 2 - GTK_FILL - - - - - - True - True - False - True - True - - - 4 - 5 - 2 - 3 - GTK_FILL - - - - - - True - True - False - True - True - - - 4 - 5 - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - Cell size - - - 4 - 5 - GTK_FILL - - - - - - True - False - 0 - Cell snap - - - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 3 0 100 1 10 0 - 1 - True - - - 1 - 2 - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 5 0 100 1 10 0 - 1 - True - - - 1 - 2 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 2 - 3 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 2 - 3 - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 3 - 4 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 3 - 4 - 5 - 6 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 4 - 5 - 4 - 5 - GTK_FILL - - - - - - True - True - False - False - True - True - 2 0 100 1 10 0 - 1 - True - - - 4 - 5 - 5 - 6 - GTK_FILL - - - - - - True - False - 0 - - - True - True - False - True - True - - - - - 1 - 2 - 1 - 2 - GTK_FILL - - - - - - True - False - <b>Column</b> - True - - - GTK_FILL - - - - - - True - False - 0 - - - True - True - False - True - True - radiobutton2 - - - - - 1 - 2 - 2 - 3 - GTK_FILL - - - - - - True - False - - - True - True - False - True - True - radiobutton2 - - - - - 1 - 2 - 3 - 4 - - - - - - - True - True - False - use as group - True - True - - - 2 - 3 - 3 - 4 - - - - - - - - - True - True - 1 - - - - - True - True - 2 - - - - - - - 386 - True - False - Info for 1111 2222 - False - - - True - False - - - True - False - - - True - False - 5 - Data - - - False - False - 0 - - - - - True - False - True - - - False - False - 1 - - - - - True - False - 5 - - - Re-use - True - True - False - Overwrite this dialog instead of opening a new ones - True - True - True - - - - - False - False - 2 - - - - - False - True - 0 - - - - - True - True - automatic - automatic - in - - - True - True - - - - - True - True - 1 - - - - - True - False - 3 - 5 - end - - - Copy - True - True - True - False - Copy list to clipboard - True - - - False - False - 0 - - - - - Close All - True - True - True - False - True - - - False - False - 1 - - - - - Close - True - True - True - False - Shortcut: Press Escape - True - - - - False - False - 2 - - - - - False - False - 2 - - - - - - - 1000 - 600 - True - False - Biodiverse - True - - - - True - False - - - True - False - - - True - False - _File - True - - - False - - - New project - True - False - False - - - - - True - False - gtk-new - 1 - - - - - - - Open project - True - False - False - - - - - True - False - gtk-open - 1 - - - - - - - Save project - True - False - True - Save the project to file (all basedatas, trees and matrices) - False - - - - - True - False - gtk-save - 1 - - - - - - - Save project as - True - False - Save the project to a new file (all basedatas, trees and matrices) - False - - - - True - False - gtk-save-as - 1 - - - - - - - True - False - - - - - True - False - True - Set the directory to use for default file loading and saving - Set _Working Directory - True - - - - - - - True - False - - - - - gtk-quit - True - False - True - True - - - - - - - - - - True - False - Manipulate basedata objects - _Basedata - True - - - False - - - True - False - View _Labels - True - - - - - - - True - False - Exclude groups and labels using simple criteria - Run _exclusions - True - - - - - - - True - False - - - - - True - False - Import data onto a new or existing basedata object - _Import - True - - - - - - - True - False - Open from Biodiverse format - _Open - True - - - - - - - True - False - Delete selected basedata from project - _Delete - True - - - - - - - True - False - Save selected basedata to external Biodiverse format file - _Save as - True - - - - - - - True - False - - - - - True - False - Basic descriptors of the selected BaseData - Describe - True - - - - - - True - False - Rename the selected basedata object - _Rename - True - - - - - - True - False - Duplicate the basedata object, including outputs - Du_plicate - True - - - - - - True - False - Duplicate the basedata object, without the outputs - Duplicate without outputs - True - - - - - - - True - False - You forgot to set the correct order when importing, for example you have latitude as the x-axis, and longitude as the y-axis. -This will create a new basedata with the corrected axis orders. - Duplicate with re-ordered axes - True - - - - - - True - False - Create a new basedata with the labels and groups transposed - - labels become groups and groups become labels - Transpose - True - - - - - - True - False - Merge groups and labels from another basedata into the selected basedata. - Merge into - True - - - - - - True - False - Rename basedata labels. WIll not work if basedata has existing outputs. - Rename labels - True - - - - - - True - False - Rename basedata groups. WIll not work if basedata has existing outputs. - Rename groups - True - - - - - - True - False - Convert all sample counts to binary. -All non-zero values will be set to 1 - Binarise sample counts - True - - - - - - True - False - Attach properties (e.g. species traits) to the groups or labels. -It will only work if your basedata has no analysis outputs, -as these might have used existing properties. -If that is the case then randomisations would be invalidated for those analyses. - Attach group or label properties - True - - - - - - True - False - Attach the current label ranges as properties for each label. -This is useful to maintain the overall ranges used in endemism calculations if you later delete groups using the Run Exclusions dialog. - Attach label ranges as properties - True - - - - - - True - False - Attach the current label sample counts as abundance properties for each label. -This is useful to maintain the overall abundances used in rarity calculations if you later delete groups using the Run Exclusions dialog. - Attach label abundances as properties - True - - - - - - True - False - - - - - True - False - Create tree from labels - True - - - - - - True - False - Extract any trees used as analysis args for this BaseData and add them to the project. -Skips any trees already in the project. - Extract embedded trees - True - - - - - - True - False - Extract any matrices used as analysis args for this BaseData and add them to the project. -Skips any matrices already in the project. - Extract embedded matrices - True - - - - - - True - False - - - - - True - False - Remove BaseData labels not in the selected tree - Trim to match tree nodes - True - - - - - - True - False - Remove BaseData labels not in the selected matrix - Trim to match matrix elements - True - - - - - - True - False - Trim BaseData labels that occur as nodes in the tree - Trim using tree nodes - True - - - - - - True - False - Trim BaseData labels that occur as elements in the matrix - Trim using matrix elements - True - - - - - - True - False - - - - - True - False - Export the groups to a file, eg site by species matrix - Export _groups - True - - - - - - True - False - Export the groups to a file, eg species by site matrix - Export _labels - True - - - - - - - - - - True - False - Manipulate similarity matrices - _Matrices - True - - - False - - - True - False - Import a matrix from a supported format - _Import - True - - - - - - - True - False - Open from Biodiverse format - _Open - True - - - - - - - True - False - _Delete - True - - - - - - - True - False - Save selected matrix to external Biodiverse format file - _Save as - True - - - - - - - True - False - - - - - True - False - Basic descriptors of the selected matrix - Describe - True - - - - - - True - False - Rename the selected matrix - Rename - True - - - - - - True - False - - - - - True - False - Runs a cluster analysis using link_average linkage function. -Assumes a dissimilarity matrix, so take care. - Convert matrix to tree - True - - - - - - True - False - Remove any elements not found in the selected basedata - Trim to match basedata - True - - - - - - True - False - - - - - True - False - Export matrix - True - - - - - - - - - - True - False - Manipulate trees - _Trees - True - - - False - - - True - False - Import a phylogeny from a supported format (eg nexus) - _Import - True - - - - - - True - False - Open from Biodiverse format - _Open - True - - - - - - True - False - _Delete - True - - - - - - True - False - Save selected tree to external Biodiverse format file - _Save as - True - - - - - - True - False - - - - - True - False - Basic descriptors of the selected tree - Describe - True - - - - - - True - False - Rename the selected tree - Rename - True - - - - - - True - False - Clear any values cached on the tree. Can reduce memory usage for large trees. - Clear cached values - True - - - - - - True - False - - - - - True - False - Convert tree to matrix - True - - - - - - True - False - Delete tree nodes not in the selected basedata object - Trim to match basedata - True - - - - - - True - False - Create a new tree where the branch lengths are divided by their ranges. -This can help interpret phylogenetic endemism and related analyses. - Convert to range weighted branches - True - - - - - - True - False - All non-zero branches will be assigned the same length. -The sum of all branches will be the same as in the original tree. - Convert to equalised branch lengths - True - - - - - - True - False - Rescale all branches by some factor. -Creates a new tree. - Rescale branch lengths - - - - - - True - False - Re-sort branches so they are in order of their total number of descendents. -This cannot be undone. - Ladderise - True - - - - - True - False - - - - - True - False - Export the tree to other supported format - Export tree - True - - - - - - - - - - True - False - Run analyses on the selected Basedata object - _Analyses - True - - - False - - - True - False - Run a moving window analysis on the selected basedata object - _Spatial - True - - - - - - - True - False - Run a cluster analysis on the selected basedata object - _Cluster - True - - - - - - - True - False - True - Run a region grower analysis on the selected basedata object - Region _Grower - True - - - - - - - True - False - Run a randomisation analysis using cluster and spatial results in the selected Basedata object - _Randomisation - True - - - - - - - True - False - - - - - True - False - Build a spatial index for the selected BaseData - Build Spatial _Index... - True - - - - - - - True - False - Delete the spatial index in the selected BaseData - Delete Spatial Index - True - - - - - - - - - - True - False - _Help - True - - - False - - - gtk-help - True - False - Go to the main online help - True - True - - - - - - - True - False - List the available calculations and indices (uses selected BaseData) - List calculations and indices - True - - - - - - True - False - How to specify spatial conditions - Specifying spatial conditions - True - - - - - - True - False - View the release notes (online) - Release Notes - True - - - - - - True - False - - - - - True - False - Go to the Google Groups mailing list - Mailing list - True - - - - - - True - False - Go to the Biodiverse blog - Blog - True - - - - - - True - False - Citation details if you use Biodiverse. - How to cite Biodiverse - True - - - - - - True - False - Check online for updates - Check for updates - True - - - - - - True - False - - - - - gtk-about - True - False - True - True - - - - - - - - - - False - False - 0 - - - - - True - False - both-horiz - - - True - False - - - True - False - 5 - Basedata - - - - - False - - - - - True - False - - - True - False - - - - - - False - - - - - True - False - - - True - True - False - Delete selected BaseData - none - - - - True - False - gtk-delete - 2 - - - - - - - False - - - - - True - False - - - True - True - False - Save selected BaseData to Biodiverse format - none - - - - True - False - - - True - False - gtk-save - - - - - - - - - False - - - - - True - False - - - True - True - False - Add new BaseData from Biodiverse format file - none - - - - True - False - gtk-open - - - - - - - False - - - - - True - False - - - True - True - False - Import new BaseData from file - none - - - - True - False - gtk-add - 2 - - - - - - - False - - - - - True - False - - - False - - - - - True - False - - - True - False - 5 - Matrix - True - - - - - False - - - - - True - False - - - True - False - - - - - - False - - - - - True - False - - - True - True - False - Delete matrix - none - - - - True - False - Delete selected matrix - gtk-delete - 2 - - - - - - - False - - - - - True - False - - - True - True - False - Save selected matrix to Biodiverse format - none - - - - True - False - gtk-save - - - - - - - False - - - - - True - False - - - True - True - False - Add new matrix from Biodiverse format file - none - - - - True - False - gtk-open - - - - - - - False - - - - - True - False - - - True - True - False - Import new matrix from file - none - - - - True - False - 0 - 0 - - - True - False - 2 - - - True - False - gtk-add - 2 - - - False - False - 0 - - - - - True - False - True - - - False - False - 1 - - - - - - - - - - - False - - - - - True - False - - - False - - - - - True - False - - - True - False - 5 - Tree - - - - - False - - - - - True - False - - - True - False - - - - - - False - - - - - True - False - - - True - True - False - Delete tree - none - - - - True - False - Delete selected tree - gtk-delete - 2 - - - - - - - False - - - - - True - False - - - True - True - False - Save selected tree to Biodiverse format - none - - - - True - False - gtk-save - - - - - - - False - - - - - True - False - - - True - True - False - Add new tree from Biodiverse format file - none - - - - True - False - gtk-open - - - - - - - False - - - - - True - False - - - True - True - False - Import tree(s) from file - none - - - - True - False - 0 - 0 - - - True - False - 2 - - - True - False - gtk-add - 2 - - - False - False - 0 - - - - - True - False - True - - - False - False - 1 - - - - - - - - - - - False - - - - - False - False - 1 - - - - - True - False - - - False - False - end - 3 - - - - - - - True - False - Select Overlay - True - - - True - False - - - True - False - 3 - <b>Overlays</b> -<i>Currently only shapefiles are supported</i> - True - center - - - False - False - 0 - - - - - True - True - automatic - automatic - in - - - True - True - - - - - True - True - 1 - - - - - True - False - - - True - False - Select overlay colour - - - False - False - 0 - - - - - True - True - True - 3 - #000011116969 - - - False - False - 1 - - - - - Reset colour to default - True - True - True - - - False - False - 2 - - - - - True - True - 2 - - - - - True - False - 5 - 5 - end - - - gtk-add - True - True - True - True - True - Add a new shapefile to the list - True - - - False - False - 0 - - - - - gtk-delete - True - True - True - True - True - Delete selected file from the list - True - - - False - False - 1 - - - - - gtk-clear - True - True - True - True - True - Clears the overlay from the current display - True - - - False - False - 2 - - - - - gtk-cancel - True - True - True - True - True - Use selected file. -Merely closes the window if no file is selected. - True - - - - False - False - 3 - - - - - gtk-ok - True - True - True - True - True - Use selected file. -Merely closes the window if no file is selected. - True - - - - False - False - 4 - - - - - False - False - 3 - - - - - - - 300 - True - False - Please wait... - True - center - True - True - - - True - False - 5 - 10 - - - True - False - Progress - True - - - False - False - 0 - - - - - True - False - 0.10000000149 - - - False - False - 1 - - - - - - - True - False - window1 - - - True - True - False - True - 1 - 1 - 1 - - - True - False - - - True - True - in - - - True - True - False - - - - - True - True - 0 - - - - - True - False - - - False - True - 4 - 1 - - - - - True - False - 0.92000001668930054 - 1 - - - True - False - 3 - 7 - start - - - Show - True - True - True - False - Display selected item - True - - - False - False - 0 - - - - - Export... - True - True - True - False - Export to other format - True - - - False - False - 1 - - - - - Rename - True - True - True - True - True - Rename selected item -(not yet implemented for for randomisations) - True - - - False - False - 2 - - - - - Describe - True - True - True - True - True - Describe the selected basedata object -(Outputs cannot yet be described) - True - - - False - False - 3 - - - - - True - False - - - False - False - 4 - - - - - Delete... - True - True - True - False - Delete item - True - - - False - False - 5 - - - - - - - False - True - 2 - - - - - - - True - False - - - 26 - True - False - Outputs - - - False - False - 0 - - - - - False - tab - - - - - True - False - - - True - False - vertical - icons - False - - - True - False - True - Select (S or B) - - - True - True - True - True - Select (S or B) - - - True - False - selector.png - - - - - - - False - - - - - True - False - True - Pan (C) - - - True - True - True - True - Pan (C) - - - True - False - drag-resize.png - - - - - - - False - - - - - True - False - Zoom In (Z) - - - True - True - True - True - Zoom In (Z) - - - True - False - gtk-zoom-in - - - - - - - False - - - - - True - False - Zoom Out (X) - - - True - True - True - True - Zoom Out (X) - - - True - False - gtk-zoom-out - - - - - - - False - - - - - True - False - Zoom to Fit (V) - - - True - True - True - True - Zoom to Fit (V) - - - True - False - gtk-zoom-fit - - - - - - - False - - - - - True - False - - - False - - - - - True - False - - - True - False - ttb - - - True - False - Display - True - - - False - - - True - False - Overlays... - True - - - - - True - False - - - - - True - False - Sets the colour stretch for analysis results. - Colour stretch - True - - - True - False - - - True - False - min-max - True - True - True - - - - - True - False - 5-95 - True - True - radio_dendro_colour_stretch0 - - - - - True - False - 2.5-97.5 - True - radio_dendro_colour_stretch0 - - - - - True - False - min-95 - True - True - radio_dendro_colour_stretch0 - - - - - True - False - min-97.5 - True - True - radio_dendro_colour_stretch0 - - - - - True - False - 5-max - True - True - radio_dendro_colour_stretch0 - - - - - True - False - 2.5-max - True - True - radio_dendro_colour_stretch0 - - - - - - - - - True - False - This is only settable when the plot has continuous values (i.e. not the cluster option) - Colour mode - True - - - True - False - - - True - False - Display all hues (colours) from blue to red - -Colours are scaled relative to all index values across all nodes in the dendrogram. - Hue - True - True - - - - - True - False - Display a single colour with saturation varying from white to a selected maximum. - -Colours are currently taken from the outer ring. - Sat... - True - True - menuitem_cluster_colour_mode_hue - - - - - True - False - Grey - True - True - menuitem_cluster_colour_mode_hue - - - - - - - - - True - False - - - - - True - False - Set the colour for cells that were excluded from the analysis, typically using a definition query. - Set excluded cell colour - True - - - - - True - False - Set the colour of cells when the index value is undefined. - Set undefined value colour - True - - - - - True - False - Set the outline colour of the grid cells. - Set cell outline colour - True - - - - - True - False - Show or hide cell outlines. - Show cell outlines - True - True - - - - - True - False - - - - - True - False - Plot by - True - - - False - - - True - False - Length - True - True - - - - - - True - False - Depth - True - plot_length - - - - - - - - - - True - False - Should the grouping be done by length or depth? - -This allows decoupling of node selection from the tree display so trees with many reversals can be more easily plotted by depth, but selections still use the branch lengths. - -This setting has no effect on the slider bar. It always groups using the plot method, selecting whichever branches it crosses. - Group by - True - - - False - - - True - False - Length - True - True - - - - - - True - False - Depth - True - group_length - - - - - - - - - - True - False - Highlight groups under this node when hovering over the node - Highlight groups on map? - True - True - - - - - - True - False - Highlight paths on the tree associated with groups on the map when you hover the mouse over them - Highlight node paths for groups? - True - True - - - - - - True - False - When deselected, the slider bar will not change the display colours. - Use the slider bar to select nodes for colouring? - True - True - - - - - True - False - Show or hide the legend -(continous values only) - Show legend - True - True - - - - - True - False - Set the width of the tree branches. -Does not affect the vertical connectors. - - Set tree branch line widths - True - - - - - - - - - - - False - - - - - False - True - 0 - - - - - True - False - - - True - True - - - True - False - - - True - True - automatic - - - True - False - - - True - False - - - True - False - 2 - - - True - False - 5 - 0 - - - True - True - 5 - never - automatic - - - True - True - - - - - - - True - False - Calculations to run for each cluster node (optional) - True - - - label_item - - - - - 1 - 2 - GTK_FILL - - - - - True - True - True - - - True - False - 12 - - - True - False - 7 - 8 - 3 - 2 - 4 - - - - - - - - - - - - - - - - - - - - - True - False - - - 30 - True - False - - - True - True - 0 - - - - - True - False - 1 - explanation - True - True - - - True - True - 1 - - - - - 2 - 3 - 1 - 2 - - - - - True - False - 0 - none - - - 2 - 3 - 5 - 6 - GTK_FILL - GTK_FILL - - - - - True - False - True - Use this to run the analysis for only a subset of the groups. -It will ignore groups that do not satisfy the query and they -will not be part of the results - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - Definition query - - - 5 - 6 - GTK_FILL - - - - - - True - False - Specify the set of neighbours that will be used when constructing the matrix. - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - Spatial conditions -set 1 - - - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - <b>Name</b> - True - right - - - GTK_FILL - - - - - - True - True - True - Spatial1 - False - False - True - True - - - 2 - 3 - - - - - - True - False - 0 - none - - - 2 - 3 - 3 - 4 - GTK_FILL - GTK_FILL - - - - - True - False - True - What dissimilarity metric to use? - 0 - Metric - right - - - 1 - 2 - GTK_FILL - - - - - - True - False - True - How should similarities between newly merged groups -and all other groups be calculated? - 0 - Linkage - right - - - 2 - 3 - GTK_FILL - - - - - - True - False - Specify a second set of neighbours to use in the analysis. -Builds a second matrix that will be used when the first one is fully clustered. -It is a good idea to set this to include all neighbours to ensure clustering will complete properly. -In this way each group has the full set of neighbours so therefore there is a balanced matrix for clustering. -An unbalanced set of matrices is not guaranteed to complete clustering due to missing dissimilarities. - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - Spatial conditions -set 2 - - - 4 - 5 - GTK_FILL - - - - - - True - False - 0 - none - - - 2 - 3 - 4 - 5 - GTK_FILL - GTK_FILL - - - - - True - False - - - 30 - True - False - - - True - True - 0 - - - - - True - False - Control the random number sequence -used in the event of a tie when more -than one pair of elements can be merged. - 1 - PRNG seed: - True - - - True - True - 1 - - - - - True - True - The system default will be used if the value is zero. - ● - 15 - False - False - True - True - 0 0 10000000000 1 0 0 - 1 - True - - - True - True - 2 - - - - - 2 - 3 - 2 - 3 - GTK_FILL - GTK_FILL - - - - - True - False - - - 2 - 3 - 6 - 7 - - - - - True - False - (Optional) -Select a set of indices to determine the ordering of clustering when there is more than one pair to choose from. - 0 - Tie breakers - - - 6 - 7 - GTK_FILL - GTK_FILL - - - - - True - False - 0 - - - True - False - - - Do not -use caching - True - True - False - True - Don't use caching when building the matrix. -This reduces memory requirements -but can slow down processing. - True - - - True - True - 0 - - - - - Build matrices -and then stop - True - True - False - True - Just build the matrices -and don't actually cluster. - True - - - True - True - 1 - - - - - Output matrices -direct to text files - True - True - False - True - Output the matrices direct to a text formatted sparse matrix file or files. -Will not cluster if set and matrices will not be displayable via the project. - True - - - True - True - 2 - - - - - Output matrices -direct to GDM -compatible format - True - True - False - True - Only if the "Output -matrices to text files" - option is checked. - True - - - True - True - 3 - - - - - Keep spatial -neighbours output - True - True - False - True - The spatial output is used to define the set of -neighbouring groups used for matrix building. -Use this if you want to better understand how -your results were generated. - True - - - True - True - 4 - - - - - Do not clone matrices -before clustering - True - True - False - True - This will save memory, but you cannot then -view the matrix as it is destroyed as part -of clustering. It will not be added to the BaseData object. -Matrix exporting is also slowed, as the -system must rebuild the matrices each time you export. - True - - - True - True - 5 - - - - - Clear singleton -nodes from tree - True - True - False - True - Singletons are terminal nodes -connected directly to the root. -Clearing them is useful -for RegionGrower analyses. - True - - - True - True - 6 - - - - - - - False - Options - True - - - label_item - - - - - 3 - 7 - 8 - GTK_FILL - - - - - - - - - - - - True - False - Show/hide the parameters section - Parameters - - - label_item - - - - - GTK_SHRINK | GTK_FILL - - - - - True - True - 0 - - - - - True - False - edge - - - Go! - True - True - True - False - Generates a new output, or overwrites an existing one (CTRL-G) - 2 - True - - - False - False - 0 - - - - - False - False - 1 - - - - - - - - - True - True - 0 - - - - - True - True - - - - - True - True - - - True - False - - - True - False - 0.019999999552965164 - 2 - <b>Map</b> - True - - - False - False - 0 - - - - - True - False - 0.0099999997764825821 - none - - - True - False - - - True - False - 2 - 2 - - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - False - 0 - none - - - GTK_FILL - GTK_FILL - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - True - 0 - - - - - - - True - True - 1 - - - - - False - True - - - - - True - False - 2 - 0.0099999997764825821 - none - - - True - False - - - True - False - 2 - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - True - - - True - False - 2 - - - True - False - 0 - none - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - - GTK_FILL - - - - - False - True - - - - - True - False - 0 - none - - - False - True - - - - - GTK_FILL - - - - - True - True - 0 - - - - - - - True - False - <b>Dendrogram</b> - True - - - label_item - - - - - True - True - - - - - True - True - - - - - True - True - 0 - - - - - True - False - both - - - True - False - - - True - False - True - - - - - False - - - - - True - False - - - False - - - - - True - False - - - True - False - immediate - True - - - - - False - - - - - True - False - - - False - - - - - True - False - - - True - False - Clusters to colour - - - - - False - - - - - True - False - - - True - True - True - This value determines how many descendent nodes will be selected to be coloured when you click on a node. - -All siblings are included in the selection, so if the tree topology results in more than this number then the next lowest number will be selected. -For example, if 7 nodes are to be coloured but the system finds a 7th and 8th node are siblings then it will select their parent instead, resulting in 6 selected nodes. - -This setting has no effect on the slider bar. - ● - 2 - True - False - False - True - True - 6 1 13 1 1 0 - 1 - True - - - - - False - - - - - False - False - 1 - - - - - True - True - 1 - - - - - 1 - - - - - True - False - - - True - False - Spatial1 - - - False - False - 0 - - - - - True - True - False - Close - none - False - - - True - False - gtk-close - 1 - - - - - False - False - 1 - - - - - 1 - False - tab - - - - - True - False - - - True - False - vertical - icons - False - - - True - False - True - Select (S or B) - - - True - True - True - True - Select (S or B) - - - True - False - selector.png - - - - - - - False - - - - - True - False - True - Pan (C) - - - True - True - True - True - Pan (C) - - - True - False - drag-resize.png - - - - - - - False - - - - - True - False - Zoom In (Z) - - - True - True - True - True - Zoom In (Z) - - - True - False - gtk-zoom-in - - - - - - - False - - - - - True - False - Zoom Out (X) - - - True - True - True - True - Zoom Out (X) - - - True - False - gtk-zoom-out - - - - - - - False - - - - - True - False - Zoom to Fit (V) - - - True - True - True - True - Zoom to Fit (V) - - - True - False - gtk-zoom-fit - - - - - - - False - - - - - True - False - - - True - False - ttb - - - True - False - Display - - - False - - - True - False - False - Grid - True - - - - - True - False - Show or hide the legend - Show legend - True - True - - - - - True - False - Overlays... - True - - - - - True - False - - - - - True - False - False - Tree - True - - - - - True - False - True - Plot branches using their lengths. - Length - True - True - - - - - True - False - True - Plot branches as a function of depth from the root node. - Depth - True - phylogeny_plot_length - - - - - True - False - Highlight groups under this node when hovering on the node - Highlight groups on map? - True - True - - - - - True - False - Highlight paths on the tree for groups when you hover the mouse on them - Highlight node paths for groups? - True - True - - - - - True - False - Set the width of the tree branches. -Does not affect the vertical connectors. - Set tree branch line widths - True - - - - - - - - - - - False - - - - - False - True - 0 - - - - - True - True - - - True - True - - - True - True - 83 - - - True - True - Sorting this list also sorts the rows of the matrix (if one is displayed). - in - - - True - True - 0 - False - - - - - False - True - - - - - True - True - in - - - True - True - Sorting this list also sorts the columns of the matrix. - - - - - True - True - - - - - False - True - - - - - True - False - - - True - False - 2 - 2 - - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - False - 0 - none - - - True - False - <b>Matrix</b> - True - - - label_item - - - - - GTK_FILL - GTK_FILL - - - - - True - True - 0 - - - - - True - True - - - - - False - True - - - - - True - True - - - True - False - 0 - none - - - True - False - - - True - False - 2 - 2 - - - - - - True - False - 0 - none - - - GTK_FILL - GTK_FILL - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - True - 0 - - - - - - - True - False - <b>Grid</b> - True - - - label_item - - - - - False - True - - - - - True - False - 2 - 0.0099999997764825821 - none - - - True - False - - - True - False - 2 - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - True - - - True - False - 2 - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - - GTK_FILL - - - - - True - False - 0 - none - - - - - False - True - - - - - True - False - 0 - none - - - True - True - - - - - GTK_FILL - - - - - True - True - 0 - - - - - - - True - False - <b>Tree</b> - True - - - label_item - - - - - True - True - - - - - True - True - - - - - True - True - 1 - - - - - 2 - - - - - True - False - - - True - False - Labels - Set1 - - - False - False - 0 - - - - - True - True - False - Close - none - False - - - True - False - gtk-close - 1 - - - - - False - False - 1 - - - - - 2 - False - tab - - - - - True - False - - - True - False - vertical - icons - False - - - True - False - True - Select (S or B) - - - True - True - True - True - Select (S or B) - - - True - False - selector.png - - - - - - - False - - - - - True - False - True - Pan (C) - - - True - True - True - True - Pan (C) - - - True - False - drag-resize.png - - - - - - - False - - - - - True - False - Zoom In (Z) - - - True - True - True - True - Zoom In (Z) - - - True - False - gtk-zoom-in - - - - - - - False - - - - - True - False - Zoom Out (X) - - - True - True - True - True - Zoom Out (X) - - - True - False - gtk-zoom-out - - - - - - - False - - - - - True - False - Zoom to Fit (V) - - - True - True - True - True - Zoom to Fit (V) - - - True - False - gtk-zoom-fit - - - - - - - False - - - - - True - False - - - False - - - - - True - False - - - True - False - ttb - - - True - False - Display - True - - - False - - - True - False - Overlays... - True - - - - - True - False - - - - - True - False - Set the display stretch. -Uses minimum to maximum by default -but you can also set percentile ranges. - Colour stretch - True - - - True - False - - - True - False - min-max - True - True - True - - - - - True - False - 5-95 - True - True - radio_colour_stretch0 - - - - - True - False - 2.5-97.5 - True - radio_colour_stretch0 - - - - - True - False - min-95 - True - True - radio_colour_stretch0 - - - - - True - False - min-97.5 - True - True - radio_colour_stretch0 - - - - - True - False - 5-max - True - True - radio_colour_stretch0 - - - - - True - False - 2.5-max - True - True - radio_colour_stretch0 - - - - - - - - - True - False - Hue will display all hues (colours) from blue to red. - -Sat will display a single colour with saturation varying from -white to a maximum saturation at the selected colour. - -Grey will use grey scale. - -Colours are scaled using percentiles defined in the colour stretch menu. - Colour mode - True - - - True - False - - - True - False - Display all hues (colours) from blue to red. - Hue - True - True - - - - - True - False - Display a single colour with saturation varying from white to a selected maximum. - Sat... - True - True - menuitem_spatial_colour_mode_hue - - - - - True - False - Display as grey scale. - Grey - True - True - menuitem_spatial_colour_mode_hue - - - - - - - - - True - False - Control the highlighting of neighbours on the grid. - Nbr highlighting - True - - - True - False - - - True - False - Both - True - True - True - - - - - True - False - Set1 - True - True - menuitem_nbr_highlight_all - - - - - True - False - Set2 - True - True - menuitem_nbr_highlight_all - - - - - True - False - Off - True - True - menuitem_nbr_highlight_all - - - - - - - - - True - False - - - - - True - False - Set the colour for cells that were excluded from the analysis, typically using a definition query. - Set excluded cell colour - True - - - - - True - False - Set the colour of cells when the index value is undefined. - Set undefined value colour - True - - - - - True - False - Choose the colour used for the cell outlines - Set cell outline colour - True - - - - - True - False - Show or hide the cell outlines - Show cell outlines - True - True - - - - - True - False - - - - - True - False - Show or hide the legend - Show legend - True - True - - - - - True - False - Set the width of the tree branches. -Does not affect the vertical connectors. - Set tree branch line widths - True - - - - - - - - - - - False - - - - - False - True - 0 - - - - - True - False - - - True - True - 181 - - - True - False - - - True - True - automatic - - - True - False - - - True - False - - - True - False - 2 - - - True - False - 5 - 0 - - - True - True - 5 - never - automatic - - - True - True - - - - - - - True - False - Calculations to run for each neighbourhood - True - - - label_item - - - - - 1 - 2 - GTK_FILL - - - - - True - True - True - - - True - False - 12 - - - True - False - 4 - 4 - 3 - 2 - 4 - - - True - False - True - Define a second set of neighbours for use in the analyses. -A typical use is for comparative analyses like species turnover. - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - 1 - Neighbour set 2 - right - - - 2 - 3 - GTK_FILL - - - - - - True - False - 0 - <b>Name</b> - True - right - - - GTK_FILL - - - - - - True - False - 0 - none - - - 1 - 3 - 2 - 3 - GTK_FILL - GTK_FILL - - - - - True - False - 0 - none - - - 1 - 3 - 1 - 2 - GTK_FILL - GTK_SHRINK | GTK_FILL - - - - - True - False - True - Use this to run the analysis for only a subset of the groups. -Note that it will still search the full data set for neighbours. - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - 1 - Definition query - right - - - 3 - 4 - GTK_FILL - - - - - - True - False - 0 - none - - - 1 - 3 - 3 - 4 - GTK_FILL - GTK_FILL - - - - - True - False - True - Specify the first set of neighbours to use in the analysis. - -Use the checkbox to show/hide the edit box to free up screen real estate. - 0 - 1 - Neighbour set 1 - right - - - 1 - 2 - GTK_FILL - - - - - - True - False - - - True - True - ● - True - Spatial1 - False - False - True - True - - - True - True - 0 - - - - - True - True - True - True - Set analysis options - right - - - True - False - gtk-properties - - - - - False - False - 1 - - - - - 1 - 3 - - - - - - - - - - True - False - show/hide the parameters section - Parameters - - - label_item - - - - - GTK_SHRINK | GTK_FILL - - - - - True - True - 0 - - - - - True - False - edge - - - Go! - True - True - True - False - Generates a new output, or overwrites an existing one (CTRL-G) - 2 - True - - - False - False - 0 - - - - - False - False - 1 - - - - - - - - - True - True - 0 - - - - - True - True - - - - - True - True - - - True - False - 2 - 0.0099999997764825821 - none - - - True - False - 2 - 2 - - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - False - 0 - none - - - GTK_FILL - GTK_FILL - - - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - - - True - False - <b>Output</b> - True - - - label_item - - - - - True - True - - - - - True - False - 2 - 0.0099999997764825821 - none - - - True - False - - - True - False - 2 - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - GTK_FILL - - - - - True - True - - - True - False - 2 - - - True - False - 0 0 0 0 0 0 - - - 1 - 2 - - GTK_FILL - - - - - True - False - 0 - none - - - - - False - True - - - - - True - False - 0 - none - - - False - True - - - - - - - True - True - 0 - - - - - - - True - False - <b>Tree</b> - True - - - label_item - - - - - True - True - - - - - True - True - - - - - True - True - 0 - - - - - True - False - - - True - False - Lists and indices: - - - False - False - 0 - - - - - True - False - True - - - False - False - 1 - - - - - True - False - True - - - False - False - 2 - - - - - True - False - - - False - False - 3 - - - - - True - False - Tree plot: - - - False - False - 4 - - - - - True - False - True - Select tree to display - 0 - True - - - - False - False - 5 - - - - - False - False - 1 - - - - - True - True - 1 - - - - - 3 - - - - - True - False - - - True - False - Cluster1 - - - False - False - 0 - - - - - True - True - False - Close - none - False - - - True - False - gtk-close - 1 - - - - - False - False - 1 - - - - - 3 - False - tab - - - - - True - False - 5 - 3 - - - True - True - True - - - True - False - 12 - - - True - False - 7 - 6 - 2 - 2 - 4 - - - True - False - 0 - 1 - Randomise -function - right - - - 1 - 2 - GTK_FILL - - - - - - True - False - 0 - <b>Data set</b> - True - right - - - GTK_FILL - - - - - - True - False - - - 1 - 2 - GTK_FILL - - - - - True - False - - - 1 - 2 - 1 - 2 - GTK_FILL - - - - - True - False - 0 - 1 - Iterations - right - - - 2 - 3 - GTK_FILL - - - - - - True - True - False - False - True - True - 1 1 1000000 100 1000 0 - 1 - True - - - 1 - 2 - 2 - 3 - - - - - - True - True - Prefix used for resulting output lists. -All parameters will be ignored if prefix is already in use. -(They will be set to the original values used for this prefix). -The widget label will turn red if that is the case. - Rand1 - False - False - True - True - - - 1 - 2 - 4 - 6 - - - - - - True - False - Prefix used for resulting output lists. -All parameters will be ignored if prefix is already in use. -(They will be set to the original values used for this prefix). -This text will turn red if that is the case. - 0 - <b>List prefix</b> - True - - - 4 - 6 - GTK_FILL - - - - - - True - False - Specify seed value for pseudo-random number sequence. -Set to "undef" or leave blank to use system seed. - 0 - 1 - PRNG seed - right - - - 3 - 4 - GTK_FILL - - - - - - True - True - Specify seed value for pseudo-random number sequence. -Set to undef or leave blank to use system seed. - False - False - True - True - - - 1 - 2 - 3 - 4 - - - - - - - - - - True - False - Setup - - - label_item - - - - - True - True - 0 - - - - - True - True - True - - - True - False - 12 - - - True - False - 2 - 3 - 3 - - - - - - - - - - - - - - - - True - False - Parameters - - - label_item - - - - - True - True - 1 - - - - - True - False - - - Randomise! - True - True - True - False - Run randomisations (CTRL-G) - 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