Alignment Annotation

From: jprocter Date: Fri, 31 Aug 2007 14:05:40 +0000 (+0000) Subject: added CSV export of annotation rows to application. X-Git-Tag: Release_2_4~288 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=990fd5f012601024aaeeb09e2901791d242636c4;p=jalview.git added CSV export of annotation rows to application. --- diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 0c0ccfc..98599e2 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -1,87 +1,90 @@ - -Alignment Annotation - -

Alignment Annotation

- -

In addition to the definition of groups and sequence features, - Jalview can display symbols and graphs under the columns of an - alignment, and allow you to mark particular columns of an alignment and add symbols and text - in the annotation area shown below the alignment (which may be hidden if View→Show - Annotation is not ticked).

Web services can also add annotation to an alignment (see the - JNet web service), and as of Jalview 2.08 quantitative and symbolic - annotations can be added to an alignment via an Annotations - File dragged into the alignment window or loaded from the - alignment's file menu.

Interactive Alignment Annotation

-Annotation rows are added using the Annotation Label -menu, which is obtained by clicking anywhere on the annotation row labels -area (below the sequence ID area). -

Add New Row
- Adds a new, named annotation row (a dialog box will pop up for you to - enter the label for the new row).
Hide Row
- Hides the annotation row whose label was clicked in order to bring up - the menu.
Delete Row
- Deletes the annotation row whose label was clicked in order to bring up - the menu.
Show All Hidden Rows
- Shows all hidden annotation rows.
Show Values in Text Box
- Opens a text box with a list of comma-separated values corresponding to - the annotation (numerical or otherwise) at each position in the row. This - is useful to export alignment quality measurements for further analysis. -

-Editing Label and secondary structure Annotation

-Use the left mouse button to select a position along the row that are to -be annotated - these regions will be coloured red. Control and shift in combination -with the left-click will select more than one position, or a range of -positions on the alignment. -

Once the desired position has been selected, use the right mouse -button to open the annotation menu:

Helix
Mark selected positions with a helix glyph (a red -oval), and optional text label (see below). A -dialog box will open for you to enter the text. Consecutive ovals -will be rendered as an unbroken red line. -
Sheet
Mark selected positions with a sheet glyph (a green -arrow oriented from left to right), and optional text label (see -below). A dialog box will open for you to enter the text. Consecutive -arrows will be joined together to form a single green arrow. -
Label
Set the text label at the selected positions. A -dialog box will open for you to enter the text. If -more that one consecutive position is marked with the same label, only -the first position's label will be rendered. -
Colour
Changes the colour of the annotation text label. -
Remove Annotation
Blanks any annotation at the selected positions on -the row. Note: This cannot be undone -

-User defined annotation is stored and retrieved using Jalview Archives. -

Current Limitations

- -

In the current version of Jalview, reordering of the annotation -rows is not possible. If you save -your annotation as a Jalview file, however, it will be reloaded with user -annotations at the top (nearest the alignment), above any of the -automatically generated Conservation, Quality or consensus -annotations. Finally, the Jalview GUI will not, as yet, allow you to output -Jalview annotation files for the current alignment, change the line -colour, display style, or create groups of quantitative annotation rows.

- - + +Alignment Annotation + +

Alignment Annotation

+ +

In addition to the definition of groups and sequence features, + Jalview can display symbols and graphs under the columns of an + alignment, and allow you to mark particular columns of an alignment and add symbols and text + in the annotation area shown below the alignment (which may be hidden if View→Show + Annotation is not ticked).

Web services can also add annotation to an alignment (see the + JNet web service), and as of Jalview 2.08 quantitative and symbolic + annotations can be added to an alignment via an Annotations + File dragged into the alignment window or loaded from the + alignment's file menu.

Interactive Alignment Annotation

+Annotation rows are added using the Annotation Label +menu, which is obtained by clicking anywhere on the annotation row labels +area (below the sequence ID area). +

Add New Row
+ Adds a new, named annotation row (a dialog box will pop up for you to + enter the label for the new row).
Hide Row
+ Hides the annotation row whose label was clicked in order to bring up + the menu.
Delete Row
+ Deletes the annotation row whose label was clicked in order to bring up + the menu.
Show All Hidden Rows
+ Shows all hidden annotation rows.
Export Annotation (Application only)
+ Annotations can be saved to file or output to a text window in either the + Jalview annotations format or as a spreadsheet style set of comma separated values (CSV).
Show Values in Text Box (applet only)
+ Opens a text box with a list of comma-separated values corresponding + to the annotation (numerical or otherwise) at each position in the row. + This is useful to export alignment quality measurements for further analysis. +

+Editing Label and secondary structure Annotation

+Use the left mouse button to select a position along the row that are to +be annotated - these regions will be coloured red. Control and shift in combination +with the left-click will select more than one position, or a range of +positions on the alignment. +

Once the desired position has been selected, use the right mouse +button to open the annotation menu:

Helix
Mark selected positions with a helix glyph (a red +oval), and optional text label (see below). A +dialog box will open for you to enter the text. Consecutive ovals +will be rendered as an unbroken red line. +
Sheet
Mark selected positions with a sheet glyph (a green +arrow oriented from left to right), and optional text label (see +below). A dialog box will open for you to enter the text. Consecutive +arrows will be joined together to form a single green arrow. +
Label
Set the text label at the selected positions. A +dialog box will open for you to enter the text. If +more that one consecutive position is marked with the same label, only +the first position's label will be rendered. +
Colour
Changes the colour of the annotation text label. +
Remove Annotation
Blanks any annotation at the selected positions on +the row. Note: This cannot be undone +

+User defined annotation is stored and retrieved using Jalview Archives. +

Current Limitations

+ +

In the current version of Jalview, reordering of the annotation +rows is not possible. If you save +your annotation as a Jalview file, however, it will be reloaded with user +annotations at the top (nearest the alignment), above any of the +automatically generated Conservation, Quality or consensus +annotations. Finally, the Jalview GUI will not, as yet, allow you to output +Jalview annotation files for the current alignment, change the line +colour, display style, or create groups of quantitative annotation rows.

+ + diff --git a/help/html/menus/alwannotations.html b/help/html/menus/alwannotations.html index 7b9b0d5..c633546 100755 --- a/help/html/menus/alwannotations.html +++ b/help/html/menus/alwannotations.html @@ -1,28 +1,28 @@ - - -Annotation Panel Menus - - -

Annotation Panel Menus

Annotation Label Popup Menu
- This menu is opened by clicking anywhere on the annotation row labels - area (below the sequence ID area). -
- Add New Row
  - Adds a new, named annotation row (a dialog box will pop up for you - to enter the label for the new row).
- Hide Row
  - Hides the annotation row whose label was clicked in order to bring - up the menu.
- Delete Row
  - Deletes the annotation row whose label was clicked in order to bring - up the menu.
- Show All Hidden Rows
  + + +Annotation Panel Menus + + +
  Annotation Panel Menus
  +
  - Annotation Label Popup Menu
    + This menu is opened by clicking anywhere on the annotation row labels + area (below the sequence ID area). +
    - Add New Row
      + Adds a new, named annotation row (a dialog box will pop up for you + to enter the label for the new row).
    - Hide Row
      + Hides the annotation row whose label was clicked in order to bring + up the menu.
    - Delete Row
      + Deletes the annotation row whose label was clicked in order to bring + up the menu.
    - Show All Hidden Rows
      Shows all hidden annotation rows.
    - Export Annotation (Application only)
      - Annotations can be saved to file or output to a text window in the - Jalview annotations format.
    - Show Values in Text Box (applet only)
      Opens a text box with a list of comma-separated values corresponding to the annotation (numerical or otherwise) at each position in the row. @@ -30,41 +30,41 @@
    The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row: -
    -
    Ignore Gaps in Consensus
    - If this checkbox is selected, all consensus calculations performed in - the current Alignment window will be done without counting gaps as a consensus - character.
    -
    Copy Consensus Sequence
    - Copies the consensus sequence to the clipboard in Fasta format, to allow - the consensus sequence to be added to an alignment. Note the copied sequence - is not accessible to other programs if Jalview is running as an applet - in a web page.
    -
    -
  - - +
  +
  Ignore Gaps in Consensus
  + If this checkbox is selected, all consensus calculations performed in + the current Alignment window will be done without counting gaps as a consensus + character.
  +
  Copy Consensus Sequence
  + Copies the consensus sequence to the clipboard in Fasta format, to allow + the consensus sequence to be added to an alignment. Note the copied sequence + is not accessible to other programs if Jalview is running as an applet + in a web page.
  +
  +
+ + diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java index 41689c5..ab3f0d1 100755 --- a/src/jalview/gui/AnnotationExporter.java +++ b/src/jalview/gui/AnnotationExporter.java @@ -28,6 +28,13 @@ import javax.swing.*; import jalview.datamodel.*; import jalview.io.*; +/** + * + * GUI dialog for exporting features or alignment annotations depending upon which method is called. + * + * @author AMW + * + */ public class AnnotationExporter extends JPanel { @@ -61,6 +68,7 @@ public class AnnotationExporter { this.ap = ap; features = true; + CSVFormat.setVisible(false); frame.setTitle("Export Features"); } @@ -72,6 +80,7 @@ public class AnnotationExporter this.ap = ap; features = false; GFFFormat.setVisible(false); + CSVFormat.setVisible(true); this.annotations = annotations; this.sequenceGroups = sequenceGroups; this.alignmentProperties = alProperties; @@ -110,10 +119,15 @@ public class AnnotationExporter } else { - text = new AnnotationFile().printAnnotations( + if (CSVFormat.isSelected()) + { + text = new AnnotationFile().printCSVAnnotations(annotations); + } else { + text = new AnnotationFile().printAnnotations( annotations, sequenceGroups, alignmentProperties); + } } try @@ -153,10 +167,15 @@ public class AnnotationExporter } else if (!features) { - text = new AnnotationFile().printAnnotations( + if (CSVFormat.isSelected()) + { + text = new AnnotationFile().printCSVAnnotations(annotations); + } else { + text = new AnnotationFile().printAnnotations( annotations, sequenceGroups, alignmentProperties); + } } CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -214,6 +233,8 @@ public class AnnotationExporter jalviewFormat.setText("Jalview"); GFFFormat.setOpaque(false); GFFFormat.setText("GFF"); + CSVFormat.setOpaque(false); + CSVFormat.setText("CSV(Spreadsheet)"); jLabel1.setHorizontalAlignment(SwingConstants.TRAILING); jLabel1.setText("Format: "); this.setBackground(Color.white); @@ -226,8 +247,10 @@ public class AnnotationExporter jPanel3.add(jLabel1); jPanel3.add(jalviewFormat); jPanel3.add(GFFFormat); + jPanel3.add(CSVFormat); buttonGroup.add(jalviewFormat); buttonGroup.add(GFFFormat); + buttonGroup.add(CSVFormat); this.add(jPanel3, null); this.add(jPanel1, null); } @@ -239,6 +262,7 @@ public class AnnotationExporter ButtonGroup buttonGroup = new ButtonGroup(); JRadioButton jalviewFormat = new JRadioButton(); JRadioButton GFFFormat = new JRadioButton(); + JRadioButton CSVFormat = new JRadioButton(); JLabel jLabel1 = new JLabel(); JPanel jPanel3 = new JPanel(); FlowLayout flowLayout1 = new FlowLayout(); diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 4acd2a1..577b7e4 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -882,4 +882,33 @@ public class AnnotationFile al.setProperty(key,value); } } + + /** + * Write annotations as a CSV file of the form 'label, value, value, ...' for each row. + * @param annotations + * @return CSV file as a string. + */ + public String printCSVAnnotations(AlignmentAnnotation[] annotations) + { + StringBuffer sp = new StringBuffer(); + for (int i=0; ip) + { + sp.append(atos.substring(p, cp+1)); + } else { + sp.append(atos.substring(p)); + sp.append("\n"); + } + p = cp+1; + } while (p>0); + } + return sp.toString(); + } }