Alignment Window Menus

From 7c5e7c1c51a48eab1b217a221df82748c35b76b1 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 3 Nov 2014 16:59:04 +0000 Subject: [PATCH] JAL-1152 annotation sorting preferences and help documentation --- help/help.jhm | 3 +- help/helpTOC.xml | 23 ++--- help/html/menus/alignmentMenu.html | 88 ++++++++++++-------- help/html/menus/alwannotation.html | 79 ++++++++++++++++++ ...alwannotations.html => alwannotationpanel.html} | 0 help/html/menus/alwview.html | 37 -------- help/html/menus/index.html | 2 +- resources/lang/Messages.properties | 3 +- src/jalview/analysis/AnnotationSorter.java | 36 +++++++- src/jalview/bin/Cache.java | 18 +++- src/jalview/gui/AlignFrame.java | 2 +- src/jalview/gui/AlignViewport.java | 5 +- src/jalview/gui/Preferences.java | 64 +++++++++++--- src/jalview/jbgui/GAlignFrame.java | 14 +++- src/jalview/jbgui/GPreferences.java | 79 ++++++++++++++---- 15 files changed, 332 insertions(+), 121 deletions(-) create mode 100755 help/html/menus/alwannotation.html rename help/html/menus/{alwannotations.html => alwannotationpanel.html} (100%) diff --git a/help/help.jhm b/help/help.jhm index b199dbf..7750265 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -112,13 +112,14 @@ + - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 48a2b2a..4c09e8f 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -116,17 +116,18 @@ - - - - - - - - - - - + + + + + + + + + + + + diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index a7cb733..f67faa9 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -279,39 +279,6 @@ selected, the view will automatically scroll to display the highlighted sequence position corresponding to the position under the mouse pointer in a linked alignment or structure view. -

Show Annotations
If this - is selected the "Annotation Panel" will be displayed - below the alignment. The default setting is to display the - conservation calculation, quality calculation and consensus values - as bar charts. -

Show All Annotations
- Show all available annotations on the alignment. You can selectively hide these from the Popup - or Annotation menus. (Since Jalview 2.8.2)

Hide All Annotations
- Hide all annotations on the alignment. (Since Jalview 2.8.2)

Autocalculated Annotation
Settings - for the display of autocalculated annotation. -

Apply to all groups
When - ticked, any modification to the current settings will be applied - to all autocalculated annotation.
Show Consensus Histogram
- Enable or disable the display of the histogram above the - consensus sequence.
Show Consensus Logo
Enable - or disable the display of the Consensus Logo above the consensus - sequence.
Normalise Consensus Logo
- When enabled, scales all logo stacks to the same height, - making it easier to compare symbol diversity in highly variable - regions.
Group Conservation
When - ticked, display a conservation row for all groups (only available - for protein alignments).
Apply to all groups
When - ticked, display a consensus row for all groups.

Show Sequence Features
Show or hide sequence features on this alignment.

@@ -338,6 +305,61 @@ using the mouse. +

Annotations (Since Jalview 2.8.2) +

Show Annotations
If this + is selected the "Annotation Panel" will be displayed + below the alignment. The default setting is to display the + conservation calculation, quality calculation and consensus values + as bar charts. +
Show Alignment Related
+ Show all annotations that are for the alignment as a whole (for example, Consensus, + or secondary structure prediction from alignment).
Hide Alignment Related
+ Hide all annotations that are for the alignment as a whole.
Show Sequence Related
+ Show all annotations that are for individual sequences.
Hide Sequence Related
+ Hide all annotations that are for individual sequences.
You can also selectively show or hide annotations from the Popup + or Annotation menus.
Sort by Sequence
Sort sequence-specific annotations by sequence order in the alignment + (and within that, by label).
Sort by Label
Sort sequence-specific annotations by label + (and within that, by sequence order). If neither sort order is selected, no sorting is applied, + allowing you to make a manual ordering of the annotations.
Autocalculated Annotation
Settings + for the display of autocalculated annotation. +
- Show first
  + Show autocalculated annotations above sequence-specific annotations. + Note this also applies to other annotations for the alignment, for example secondary + structure prediction from alignment.
- Show last
  + Show autocalculated / alignment annotations below sequence-specific annotations.
- Apply to all groups
  When + ticked, any modification to the current settings will be applied + to all autocalculated annotation.
- Show Consensus Histogram
  + Enable or disable the display of the histogram above the + consensus sequence.
- Show Consensus Logo
  Enable + or disable the display of the Consensus Logo above the consensus + sequence.
- Normalise Consensus Logo
  + When enabled, scales all logo stacks to the same height, + making it easier to compare symbol diversity in highly variable + regions.
- Group Conservation
  When + ticked, display a conservation row for all groups (only available + for protein alignments).
- Group Consensus
  When + ticked, display a consensus row for all groups.
+

Alignment Window Format Menu

Font...
Opens the diff --git a/help/html/menus/alwannotation.html b/help/html/menus/alwannotation.html new file mode 100755 index 0000000..2f98542 --- /dev/null +++ b/help/html/menus/alwannotation.html @@ -0,0 +1,79 @@ + + + +Alignment Window Menus + + + +
Alignment Window Annotations Menu (Since Jalview 2.8.2)
+
+
Show Alignment Related
+ Show all annotations that are for the alignment as a whole (for example, Consensus, + or secondary structure prediction from alignment)).
+
Hide Alignment Related
+ Hide all annotations that are for the alignment as a whole.
+
Show Sequence Related
+ Show all annotations that are for individual sequences.
+
Hide Sequence Related
+ Hide all annotations that are for individual sequences.
+
Show Alignment Related
+ Show all annotations that are for the alignment as a whole (for example, Consensus).
+
You can also selectively show or hide annotations from the Popup + or Annotation menus.
+
Sort by Sequence
Sort sequence-specific annotations by sequence order in the alignment + (and within that, by label).
+
Sort by Label
Sort sequence-specific annotations by label + (and within that, by sequence order). If neither sort order is selected, no sorting is applied, + allowing you to make a manual ordering of the annotations.
+
Autocalculated Annotation
Settings + for the display of autocalculated annotation. +
+
Show first
+ Show autocalculated annotations above sequence-specific annotations. + Note this also applies to other annotations for the alignment, for example secondary + structure prediction from alignment.
+
Show last
+ Show autocalculated / alignment annotations below sequence-specific annotations.
+
Apply to all groups
When + ticked, any modification to the current settings will be applied + to all autocalculated annotation.
+
Show Consensus Histogram
+ Enable or disable the display of the histogram above the + consensus sequence.
+
Show Consensus Logo
Enable + or disable the display of the Consensus Logo above the consensus + sequence.
+
Normalise Consensus Logo
+ When enabled, scales all logo stacks to the same height, + making it easier to compare symbol diversity in highly variable + regions.
+
Group Conservation
When + ticked, display a conservation row for all groups (only available + for protein alignments).
+
Group Consensus
When + ticked, display a consensus row for all groups.
+
+
+
+

+ + diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotationpanel.html similarity index 100% rename from help/html/menus/alwannotations.html rename to help/html/menus/alwannotationpanel.html diff --git a/help/html/menus/alwview.html b/help/html/menus/alwview.html index cb38708..e8fce84 100755 --- a/help/html/menus/alwview.html +++ b/help/html/menus/alwview.html @@ -38,43 +38,6 @@ All hidden Columns / Sequences / Sequences and Columns will be revealed.
Hide→(all Columns / Sequences / Selected Region / All but Selected Region)
Hides the currently selected Columns / Sequences / Region or everything but the selected Region.
Show Annotations
- If this is selected the "Annotation Panel" will be - displayed below the alignment. The default setting is to display the conservation - calculation, quality calculation and consensus values as bar charts.
Show All Annotations
- Show all available annotations on the alignment. You can selectively hide these from the Popup - or Annotation menus. (Since Jalview 2.8.2)
Hide All Annotations
- Hide all annotations on the alignment. (Since Jalview 2.8.2)
Autocalculated Annotation
Settings for the display of autocalculated annotation. -
- - Apply to all groups
  - When ticked, any modification to the current settings will be applied to all autocalculated annotation. -
- - Show Consensus Histogram
  - Enable or disable the display of the histogram above the consensus sequence. -
- - Show Consensus Logo
  - Enable or disable the display of the sequence logo above the consensus sequence. -
- Normalise Consensus Logo
  - When enabled, scales all logo stacks to the same height, - making it easier to compare symbol diversity in highly variable - regions.
- - Group Conservation
  - When ticked, display a conservation row for all groups (only available for protein alignments). -
- - Apply to all groups
  - When ticked, display a consensus row for all groups. -
-
Automatic Scrolling
When selected, the view will automatically scroll to display the highlighted sequence position corresponding to the position under the mouse diff --git a/help/html/menus/index.html b/help/html/menus/index.html index 2b51b18..7e1ed70 100755 --- a/help/html/menus/index.html +++ b/help/html/menus/index.html @@ -35,7 +35,7 @@ accessible once an alignment has been opened.

The Popup Menus are opened by clicking with the right mouse button in the alignment display area or on a sequence label in the alignment window.
-
The Annotations Menu is opened +
The Annotations Menu is opened by right-clicking on an annotation row label or in an annotation row.
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index fe04105..93977b4 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -480,10 +480,11 @@ label.edit_sequences = Edit Sequences label.sequence_details = Sequence Details label.jmol_help = Jmol Help label.all = All -label.sort_by = Sort by +label.sort_by = Sort alignment by label.sort_by_score = Sort by Score label.sort_by_density = Sort by Density label.sequence_sort_by_density = Sequence sort by Density +label.sort_ann_by = Sort annotations by label.sort_annotations_by_sequence = Sort by sequence label.sort_annotations_by_label = Sort by label label.reveal = Reveal diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java index b9e9ed5..28fa1f8 100644 --- a/src/jalview/analysis/AnnotationSorter.java +++ b/src/jalview/analysis/AnnotationSorter.java @@ -17,9 +17,43 @@ import java.util.Comparator; public class AnnotationSorter { + /** + * enum for annotation sort options. The text description is used in the + * Preferences drop-down options. The enum name is saved in the preferences + * file. + * + * @author gmcarstairs + * + */ public enum SequenceAnnotationOrder { - SEQUENCE_AND_LABEL, LABEL_AND_SEQUENCE, NONE + // Text descriptions surface in the Preferences Sort by... options + SEQUENCE_AND_LABEL("Sequence"), LABEL_AND_SEQUENCE("Label"), NONE( + "No sort"); + + private String description; + + private SequenceAnnotationOrder(String s) + { + description = s; + } + + @Override + public String toString() + { + return description; + } + + public static SequenceAnnotationOrder forDescription(String d) { + for (SequenceAnnotationOrder order : values()) + { + if (order.toString().equals(d)) + { + return order; + } + } + return null; + } } private final AlignmentI alignment; diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 2a9f53d..21a030b 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -32,8 +32,11 @@ import java.io.InputStream; import java.io.InputStreamReader; import java.text.DateFormat; import java.text.SimpleDateFormat; +import java.util.Collections; import java.util.Date; +import java.util.Enumeration; import java.util.Properties; +import java.util.TreeSet; import org.apache.log4j.ConsoleAppender; import org.apache.log4j.Level; @@ -204,13 +207,26 @@ public class Cache public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE"; + /* + * Property key/value constants + */ + public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS"; + + public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE"; + /** * Initialises the Jalview Application Log */ public static Logger log; /** Jalview Properties */ - public static Properties applicationProperties = new Properties(); + public static Properties applicationProperties = new Properties() { + // override results in properties output in alphabetical order + @Override + public synchronized Enumeration