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Commit 84f50977 authored by edgrif's avatar edgrif
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update for new names for bump options.

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......@@ -209,32 +209,29 @@ the properties themselves.
</td>
</tr>
<tr>
<td>overlap-mode</td>
<td>&lt; complete | overlap | position | name | oscillate | item-overlap | simple | ends-range
| complex-interleave | complex-range | complex-limit &gt;</td>
<td>bump-mode</td>
<td>&lt; unbump | overlap | start-position | alternating | all
| name | name-interleave | name-no-interleave | name-colinear | name-best-ends &gt;</td>
<td>Controls how features are arranged within their column:
<ul>
<li><b>complete:</b> draw on top - default
<li><b>overlap:</b> bump if feature coords overlap.
<li><b>position:</b> bump if features start at same coord
<li><b>name:</b> one column per homol target
<li><b>oscillate:</b> Oscillate between one column and another
<li><b>item-overlap:</b> bump if item coords overlap in canvas space
<li><b>simple:</b> one column per feature, for testing
<li><b>ends-range:</b> Sort by 5' and 3' best/biggest matches, one match per column.
<li><b>complex-interleave:</b> all features with same name in a single sub-column,
several names in one column but no 2 features overlap.
<li><b>complex-range:</b> All features with same name in a single column if they overlap the
'mark' range, all other features in a single column
<li><b>complex-limit:</b> As complex-range but constrain
matches to be colinear within range or are truncated
<li><b>unbump:</b> No bumping (default)
<li><b>overlap:</b> Bump any features overlapping each other.
<li><b>start-position:</b> Bump if features have same start coord.
<li><b>alternating:</b> Alternate features between two sub_columns, e.g. to display assemblies.
<li><b>all:</b> A sub-column for every feature.
<li><b>name:</b> A sub-column for features with the same name.
<li><b>name-interleave:</b> All features with same name in a single sub-column
but several names interleaved in each sub-column, the most compact display.
<li><b>name-no-interleave:</b> Display as for Interleave but no interleaving of different names.
<li><b>name-colinear:</b> As for No Interleave but for alignments only colinear shown.
<li><b>name-best-ends:</b> As for No Interleave but for alignments sorted by 5' and 3' best/biggest matches, one sub_column per match.
</ul>
</td>
</tr>
<tr>
<td>default-overlap-mode</td>
<td>(as for overlap-mode)</td>
<td>(as for overlap-mode)</td>
<td>default-bump-mode</td>
<td>(as for bump-mode)</td>
<td>(as for bump-mode)</td>
</tr>
<tr>
<td>bump-spacing</td>
......@@ -487,7 +484,7 @@ mode = alignment
parent-style = basic_feature_parent
colours = normal fill brown
width = 15.000000
overlap_mode = complete
bump-mode = complete
score-mode = width
min-score = 100.000000
max-score = 400.000000
......@@ -546,7 +543,7 @@ displayed:
<td>How the feature should be displayed/processed.</td>
</tr>
<tr>
<td>"overlap_mode"</td>
<td>"bump-mode"</td>
<td>How the feature should be bumped.</td>
</tr>
<tr>
......@@ -570,7 +567,7 @@ displayed:
mode = xxxxx
width = nnn.nnn
colours = normal border some colour
overlap_mode = xxxx
bump-mode = xxxx
</pre>
......@@ -584,21 +581,21 @@ Here are some examples:
mode = basic
colours = normal fill orange
width = 1.100000
overlap_mode = complete
bump-mode = complete
[blastn_est_briggsae]
mode = alignment
colours = normal fill brown
width = 15.000000
overlap_mode = complete
bump-mode = complete
[curated]
mode = transcript
colours = normal border darkblue
width = 15.000000
overlap_mode = compact_cluster
bump-mode = compact_cluster
</pre>
......@@ -657,16 +654,16 @@ frame-mode = only-1 gives the third behaviour
<pre class="example">
overlap_mode = XXXXXXX sets the initial bump mode.
bump-mode = XXXXXXX sets the initial bump mode.
overlap_mode_default = XXXXXX sets the mode that the column will be bumped with by default.
bump-mode-default = XXXXXX sets the mode that the column will be bumped with by default.
</pre>
<p>If you want the column to be initially "unbumped" but bumped with colinear lines etc when
it is bumped you just need to set overlap_mode_default, overlap_mode will be unbumped by default, e.g.</p>
it is bumped you just need to set bump-mode-default, bump-mode will be unbumped by default, e.g.</p>
<pre class="example">
overlap_mode_default = range_colinear
bump-mode-default = range_colinear
</pre>
......@@ -685,8 +682,8 @@ joined up with lines:</p>
description = Inherited method for all WABA hits.
colours = normal fill darkgreen ; normal border black
width = 6.000000
overlap_mode = complete
overlap_mode_default = range_colinear
bump-mode = complete
bump-mode-default = range_colinear
score-mode = width
score_min = 40.000000
score_max = 120.000000
......@@ -762,6 +759,12 @@ the predefined styles:
<td>Yes</td>
<td>Show peptide translation column</td>
</tr>
<tr>
<td>Assembly Path</td>
<td>Normal</td>
<td>Yes</td>
<td>Show reference sequence assembly path</td>
</tr>
</table>
<p>The rules for using these predefined styles are:
......@@ -954,24 +957,19 @@ be copied and pasted direct into a models.wrm file.
// Specifies how columns should be displayed when bumped.
?Zmap_overlap Remark Text
Overlap_mode UNIQUE Complete // Draw on top - default
Overlap // Bump by set amount if coords overlap.
Item_overlap // Bump so items do not overlap at all if coords overlap.
Start // Bump if match start at same coord.
Name // One column per match target
Oscillate // Oscillate between one column and another, useful for displaying tile paths.
Simple // One column per match, good for testing
Ends_range // Sort by 5' and 3' best/biggest matches, one match per column, very
// fmap like but better...
Compact // All features with same name in a single column, several names in one
// column but no 2 features overlap.
Compact_no_interleave // All features with same name in a single column, several names in one
// column but no interleaving of sets of features.
Range // All features with same name in a single column if they overlap the
// mark range.
Range_colinear // As for "Range" but constrain matches to be colinear across range.
?Zmap_bump Remark Text
Fixed // Cannot be changed from initial mode.
Bump_mode UNIQUE Unbump // No bumping (default)
Overlap // Bump any features overlapping each other.
Start_position // Bump if features have same start coord.
Alternating // Alternate features between two sub_columns, e.g. to display assemblies.
All // A sub-column for every feature.
Name // A sub-column for features with the same name.
Name_interleave // All features with same name in a single sub-column
// but several names interleaved in each sub-column, the most compact display.
Name_no_interleave // Display as for Interleave but no interleaving of different names.
Name_colinear // As for No Interleave but for alignments only colinear shown.
Name_best_Ends // As for No Interleave but for alignments sorted by 5' and 3' best/biggest matches, one sub_column per match.
......@@ -1025,8 +1023,8 @@ be copied and pasted direct into a models.wrm file.
Directional_ends
//
// Bumping controls display of features when there are so many in a column that they overlap.
Bump_mode #Zmap_overlap // sets current mode.
Bump_default #ZMap_overlap // sets normal bumping mode for column.
Bump_mode #Zmap_bump // sets current mode.
Bump_default #ZMap_bump // sets normal bumping mode for column.
Bump_spacing UNIQUE Float // default is 0.0, i.e. no gap between bumped features.
//
Strand_sensitive Show_up_strand
......
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