-<html>\r
-<head><title>Alignment Annotation</title></head>\r
-<body>\r
-<p><strong>Alignment Annotation</strong></p>\r
-\r
-<p>In addition to the definition of groups and sequence features,\r
- Jalview can display symbols and graphs under the columns of an\r
- alignment, and allow you to mark particular columns of an alignment and add symbols and text \r
- in the annotation area shown below the alignment (which may be hidden if <strong>View→Show \r
- Annotation</strong> is not ticked). </p>\r
-<p>Web services can also add annotation to an alignment (see the\r
- <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic\r
- annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations \r
- File</a> dragged into the alignment window or loaded from the\r
- alignment's file menu.</p>\r
-<p><strong>Interactive Alignment Annotation</strong></p>\r
-<p>\r
-Annotation rows are added using the <strong>Annotation Label</strong>\r
-menu, which is obtained by clicking anywhere on the annotation row labels\r
-area (below the sequence ID area).\r
-</p>\r
-<ul>\r
- <li>Add New Row<br>\r
- <em>Adds a new, named annotation row (a dialog box will pop up for you to \r
- enter the label for the new row). </em> </li>\r
- <li>Hide Row<br>\r
- <em>Hides the annotation row whose label was clicked in order to bring up \r
- the menu.</em> </li>\r
- <li>Delete Row<br>\r
- <em>Deletes the annotation row whose label was clicked in order to bring up \r
- the menu.</em> </li>\r
- <li>Show All Hidden Rows<br>\r
- <em>Shows all hidden annotation rows.</em> </li>\r
- <li>Show Values in Text Box<br>\r
- <em>Opens a text box with a list of comma-separated values corresponding to \r
- the annotation (numerical or otherwise) at each position in the row. This \r
- is useful to export alignment quality measurements for further analysis.</em> \r
- </li>\r
-</ul>\r
-<p>\r
-<strong>Editing Label and secondary structure Annotation</strong></p>\r
-<p>\r
-Use the <strong>left mouse button</strong> to select a position along the row that are to\r
-be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination\r
-with the left-click will select more than one position, or a range of\r
-positions on the alignment.\r
-</p>\r
-<p>Once the desired position has been selected, use the <strong>right mouse\r
-button</strong> to open the <strong>annotation menu</strong>:</p>\r
-<ul>\r
-<li>Helix<br><em>Mark selected positions with a helix glyph (a red\r
-oval), and optional text label (see below). A\r
-dialog box will open for you to enter the text. Consecutive ovals\r
-will be rendered as an unbroken red line.</em>\r
-</li>\r
-<li>Sheet<br><em>Mark selected positions with a sheet glyph (a green\r
-arrow oriented from left to right), and optional text label (see\r
-below). A dialog box will open for you to enter the text. Consecutive\r
-arrows will be joined together to form a single green arrow.</em>\r
-</li>\r
-<li>Label<br><em>Set the text label at the selected positions. A\r
-dialog box will open for you to enter the text. If\r
-more that one consecutive position is marked with the same label, only\r
-the first position's label will be rendered.</em>\r
-</li>\r
-<li>Colour<br><em>Changes the colour of the annotation text label.</em>\r
-</li>\r
-<li>Remove Annotation<br><em>Blanks any annotation at the selected positions on\r
-the row. Note: <strong>This cannot be undone</strong></em>\r
-</li>\r
-</ul>\r
-<p>\r
-User defined annotation is stored and retrieved using <a\r
-href="../features/jalarchive.html">Jalview Archives</a>.\r
-</p>\r
-<p><em>Current Limitations</em></p>\r
-\r
-<p>In the current version of Jalview, reordering of the annotation\r
-rows is not possible. If you save \r
-your annotation as a Jalview file, however, it will be reloaded with user \r
-annotations at the top (nearest the alignment), above any of the\r
-automatically generated Conservation, Quality or consensus\r
-annotations. Finally, the Jalview GUI will not, as yet, allow you to output\r
-Jalview annotation files for the current alignment, change the line\r
-colour, display style, or create groups of quantitative annotation rows.</p>\r
-</body>\r
-</html>\r
+<html>
+<head><title>Alignment Annotation</title></head>
+<body>
+<p><strong>Alignment Annotation</strong></p>
+
+<p>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 <strong>View→Show
+ Annotation</strong> is not ticked). </p>
+<p>Web services can also add annotation to an alignment (see the
+ <a href="../webServices/jnet.html">JNet web service</a>), and as of Jalview 2.08 quantitative and symbolic
+ annotations can be added to an alignment via an <a href="annotationsFormat.html">Annotations
+ File</a> dragged into the alignment window or loaded from the
+ alignment's file menu.</p>
+<p><strong>Interactive Alignment Annotation</strong></p>
+<p>
+Annotation rows are added using the <strong>Annotation Label</strong>
+menu, which is obtained by clicking anywhere on the annotation row labels
+area (below the sequence ID area).
+</p>
+<ul>
+ <li>Add New Row<br>
+ <em>Adds a new, named annotation row (a dialog box will pop up for you to
+ enter the label for the new row). </em> </li>
+ <li>Hide Row<br>
+ <em>Hides the annotation row whose label was clicked in order to bring up
+ the menu.</em> </li>
+ <li>Delete Row<br>
+ <em>Deletes the annotation row whose label was clicked in order to bring up
+ the menu.</em> </li>
+ <li>Show All Hidden Rows<br>
+ <em>Shows all hidden annotation rows.</em> </li>
+ <li><strong>Export Annotation</strong> <em>(Application only)</em><br>
+ <em>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). </em> </li>
+ <li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
+ <em>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.</em>
+ </li>
+</ul>
+<p>
+<strong>Editing Label and secondary structure Annotation</strong></p>
+<p>
+Use the <strong>left mouse button</strong> to select a position along the row that are to
+be annotated - these regions will be coloured red. <strong>Control</strong> and <strong>shift</strong> in combination
+with the left-click will select more than one position, or a range of
+positions on the alignment.
+</p>
+<p>Once the desired position has been selected, use the <strong>right mouse
+button</strong> to open the <strong>annotation menu</strong>:</p>
+<ul>
+<li>Helix<br><em>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.</em>
+</li>
+<li>Sheet<br><em>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.</em>
+</li>
+<li>Label<br><em>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.</em>
+</li>
+<li>Colour<br><em>Changes the colour of the annotation text label.</em>
+</li>
+<li>Remove Annotation<br><em>Blanks any annotation at the selected positions on
+the row. Note: <strong>This cannot be undone</strong></em>
+</li>
+</ul>
+<p>
+User defined annotation is stored and retrieved using <a
+href="../features/jalarchive.html">Jalview Archives</a>.
+</p>
+<p><em>Current Limitations</em></p>
+
+<p>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.</p>
+</body>
+</html>
-<html>\r
-<head>\r
-<title>Annotation Panel Menus</title>\r
-</head>\r
-<body>\r
-<p><strong>Annotation Panel Menus</strong></p>\r
-<ul>\r
- <li> <strong>Annotation Label Popup Menu</strong><br>\r
- <em>This menu is opened by clicking anywhere on the annotation row labels \r
- area (below the sequence ID area).</em> \r
- <ul>\r
- <li><strong> Add New Row</strong><br>\r
- <em>Adds a new, named annotation row (a dialog box will pop up for you \r
- to enter the label for the new row). </em> </li>\r
- <li><strong>Hide Row</strong><br>\r
- <em>Hides the annotation row whose label was clicked in order to bring \r
- up the menu.</em> </li>\r
- <li><strong>Delete Row</strong><br>\r
- <em>Deletes the annotation row whose label was clicked in order to bring \r
- up the menu.</em> </li>\r
- <li><strong>Show All Hidden Rows</strong><br>\r
+<html>
+<head>
+<title>Annotation Panel Menus</title>
+</head>
+<body>
+<p><strong>Annotation Panel Menus</strong></p>
+<ul>
+ <li> <strong>Annotation Label Popup Menu</strong><br>
+ <em>This menu is opened by clicking anywhere on the annotation row labels
+ area (below the sequence ID area).</em>
+ <ul>
+ <li><strong> Add New Row</strong><br>
+ <em>Adds a new, named annotation row (a dialog box will pop up for you
+ to enter the label for the new row). </em> </li>
+ <li><strong>Hide Row</strong><br>
+ <em>Hides the annotation row whose label was clicked in order to bring
+ up the menu.</em> </li>
+ <li><strong>Delete Row</strong><br>
+ <em>Deletes the annotation row whose label was clicked in order to bring
+ up the menu.</em> </li>
+ <li><strong>Show All Hidden Rows</strong><br>
<em>Shows all hidden annotation rows.</em> </li>
<li><strong>Export Annotation</strong> <em>(Application only)</em><br>
- <em>Annotations can be saved to file or output to a text window in the
- Jalview annotations format. </em> </li>
+ <em>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). </em> </li>
<li><strong>Show Values in Text Box</strong> <em>(applet only)</em><br>
<em>Opens a text box with a list of comma-separated values corresponding
to the annotation (numerical or otherwise) at each position in the row.
</li>
</ul>
<em>The following additional entries are avalable when the popup menu is opened on a consensus sequence annotation row:</em>
- <ul>\r
- <li><strong>Ignore Gaps in Consensus</strong><br>\r
- If this checkbox is selected, all consensus calculations performed in \r
- the current Alignment window will be done without counting gaps as a consensus \r
- character.</li>\r
- <li><strong>Copy Consensus Sequence</strong><br>\r
- Copies the consensus sequence to the clipboard in Fasta format, to allow \r
- the consensus sequence to be added to an alignment. Note the copied sequence \r
- is not accessible to other programs if Jalview is running as an applet \r
- in a web page.</li>\r
- </ul>\r
- </li>\r
- <li><strong>Annotation Popup Menu<br>\r
- </strong><em>This menu is opened when right-clicking on the selected positions \r
- of an annotation.</em> \r
- <ul>\r
- <li><strong>Helix</strong><br>\r
- <em>Mark selected positions with a helix glyph (a red oval), and optional \r
- text label (see below). Consecutive ovals will be rendered as an unbroken \r
- red line.</em> </li>\r
- <li><strong>Sheet</strong><br>\r
- <em>Mark selected positions with a sheet glyph (a green arrow oriented \r
- from left to right), and optional text label (see below). Consecutive \r
- arrows will be joined together to form a single green arrow.</em> </li>\r
- <li><strong>Label</strong><br>\r
- <em>Sets the text label at the selected positions. If more that one consecutive \r
- position is marked with the same label, only the first position's label \r
- will be rendered.</em> </li>\r
- <li><strong>Colour</strong><br>\r
- <em>Changes the colour of the annotation text label.</em> </li>\r
- <li><strong>Remove Annotation</strong><br>\r
- <em>Blanks any annotation at the selected positions on the row. Note: \r
- <strong>This cannot be undone</strong></em> </li>\r
- </ul>\r
- </li>\r
-</ul>\r
-</body>\r
-</html>\r
+ <ul>
+ <li><strong>Ignore Gaps in Consensus</strong><br>
+ If this checkbox is selected, all consensus calculations performed in
+ the current Alignment window will be done without counting gaps as a consensus
+ character.</li>
+ <li><strong>Copy Consensus Sequence</strong><br>
+ 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.</li>
+ </ul>
+ </li>
+ <li><strong>Annotation Popup Menu<br>
+ </strong><em>This menu is opened when right-clicking on the selected positions
+ of an annotation.</em>
+ <ul>
+ <li><strong>Helix</strong><br>
+ <em>Mark selected positions with a helix glyph (a red oval), and optional
+ text label (see below). Consecutive ovals will be rendered as an unbroken
+ red line.</em> </li>
+ <li><strong>Sheet</strong><br>
+ <em>Mark selected positions with a sheet glyph (a green arrow oriented
+ from left to right), and optional text label (see below). Consecutive
+ arrows will be joined together to form a single green arrow.</em> </li>
+ <li><strong>Label</strong><br>
+ <em>Sets the text label at the selected positions. If more that one consecutive
+ position is marked with the same label, only the first position's label
+ will be rendered.</em> </li>
+ <li><strong>Colour</strong><br>
+ <em>Changes the colour of the annotation text label.</em> </li>
+ <li><strong>Remove Annotation</strong><br>
+ <em>Blanks any annotation at the selected positions on the row. Note:
+ <strong>This cannot be undone</strong></em> </li>
+ </ul>
+ </li>
+</ul>
+</body>
+</html>
import jalview.datamodel.*;\r
import jalview.io.*;\r
\r
+/**\r
+ * \r
+ * GUI dialog for exporting features or alignment annotations depending upon which method is called.\r
+ * \r
+ * @author AMW\r
+ *\r
+ */\r
public class AnnotationExporter\r
extends JPanel\r
{\r
{\r
this.ap = ap;\r
features = true;\r
+ CSVFormat.setVisible(false);\r
frame.setTitle("Export Features");\r
}\r
\r
this.ap = ap;\r
features = false;\r
GFFFormat.setVisible(false);\r
+ CSVFormat.setVisible(true);\r
this.annotations = annotations;\r
this.sequenceGroups = sequenceGroups;\r
this.alignmentProperties = alProperties;\r
}\r
else\r
{\r
- text = new AnnotationFile().printAnnotations(\r
+ if (CSVFormat.isSelected())\r
+ {\r
+ text = new AnnotationFile().printCSVAnnotations(annotations);\r
+ } else {\r
+ text = new AnnotationFile().printAnnotations(\r
annotations,\r
sequenceGroups,\r
alignmentProperties);\r
+ }\r
}\r
\r
try\r
}\r
else if (!features)\r
{\r
- text = new AnnotationFile().printAnnotations(\r
+ if (CSVFormat.isSelected())\r
+ {\r
+ text = new AnnotationFile().printCSVAnnotations(annotations);\r
+ } else {\r
+ text = new AnnotationFile().printAnnotations(\r
annotations,\r
sequenceGroups,\r
alignmentProperties);\r
+ }\r
}\r
\r
CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
jalviewFormat.setText("Jalview");\r
GFFFormat.setOpaque(false);\r
GFFFormat.setText("GFF");\r
+ CSVFormat.setOpaque(false);\r
+ CSVFormat.setText("CSV(Spreadsheet)");\r
jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);\r
jLabel1.setText("Format: ");\r
this.setBackground(Color.white);\r
jPanel3.add(jLabel1);\r
jPanel3.add(jalviewFormat);\r
jPanel3.add(GFFFormat);\r
+ jPanel3.add(CSVFormat);\r
buttonGroup.add(jalviewFormat);\r
buttonGroup.add(GFFFormat);\r
+ buttonGroup.add(CSVFormat);\r
this.add(jPanel3, null);\r
this.add(jPanel1, null);\r
}\r
ButtonGroup buttonGroup = new ButtonGroup();\r
JRadioButton jalviewFormat = new JRadioButton();\r
JRadioButton GFFFormat = new JRadioButton();\r
+ JRadioButton CSVFormat = new JRadioButton();\r
JLabel jLabel1 = new JLabel();\r
JPanel jPanel3 = new JPanel();\r
FlowLayout flowLayout1 = new FlowLayout();\r
al.setProperty(key,value);\r
}\r
}\r
+\r
+ /**\r
+ * Write annotations as a CSV file of the form 'label, value, value, ...' for each row.\r
+ * @param annotations\r
+ * @return CSV file as a string.\r
+ */\r
+ public String printCSVAnnotations(AlignmentAnnotation[] annotations)\r
+ {\r
+ StringBuffer sp = new StringBuffer();\r
+ for (int i=0; i<annotations.length; i++)\r
+ {\r
+ String atos = annotations[i].toString();\r
+ int p = 0;\r
+ do {\r
+ int cp = atos.indexOf("\n", p);\r
+ sp.append(annotations[i].label);\r
+ sp.append(",");\r
+ if (cp>p)\r
+ {\r
+ sp.append(atos.substring(p, cp+1));\r
+ } else {\r
+ sp.append(atos.substring(p));\r
+ sp.append("\n");\r
+ }\r
+ p = cp+1;\r
+ } while (p>0);\r
+ }\r
+ return sp.toString();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / commitdiff