");
- webService.add(webServiceNoServices);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortLengthMenuItem);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- sort.add(sortByTreeMenu);
- calculateTree.add(averageDistanceTreeMenuItem);
- calculateTree.add(neighbourTreeMenuItem);
- calculateTree.add(avDistanceTreeBlosumMenuItem);
- calculateTree.add(njTreeBlosumMenuItem);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
- addSequenceMenu.add(addFromFile);
- addSequenceMenu.add(addFromText);
- addSequenceMenu.add(addFromURL);
- this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
- statusPanel.add(statusBar, null);
- this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
- jMenu3.add(showAllColumns);
- jMenu3.add(showAllSeqs);
- jMenu3.add(showAllhidden);
- hideMenu.add(hideSelColumns);
- hideMenu.add(hideSelSequences);
- hideMenu.add(hideAllSelection);
- hideMenu.add(hideAllButSelection);
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /**
+ * Generate the reverse sequence (or reverse complement if the flag is true)
+ * and add it to the alignment
+ *
+ * @param complement
+ */
+ protected void showReverse_actionPerformed(boolean complement)
+ {
+ }
+
+ /**
+ * Try to run script in a Groovy console, having first ensured that this
+ * alignframe is set as currentAlignFrame in Desktop
+ */
+ protected void runGroovy_actionPerformed()
+ {
+
+ }
+
+ /**
+ * Adds the given action listener and key accelerator to the given menu item.
+ * Also saves in a lookup table to support lookup of action by key stroke.
+ *
+ * @param keyStroke
+ * @param menuItem
+ * @param actionListener
+ */
+ protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
+ JMenuItem menuItem, ActionListener actionListener)
+ {
+ menuItem.setAccelerator(keyStroke);
+ accelerators.put(keyStroke, menuItem);
+ menuItem.addActionListener(actionListener);
+ }
+
+ /**
+ * Action on clicking sort annotations by type.
+ *
+ * @param sortOrder
+ */
+ protected void sortAnnotations_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking Show all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void showAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(true, forSequences, forAlignment);
+ }
+
+ /**
+ * Action on clicking Hide all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void hideAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(false, forSequences, forAlignment);
+ }
+
+ /**
+ * Set the visibility of annotations to true or false. Can act on
+ * sequence-related annotations, or alignment-related, or both.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
+ {
- formatMenu.add(font);
- formatMenu.addSeparator();
- formatMenu.add(wrapMenuItem);
- formatMenu.add(scaleAbove);
- formatMenu.add(scaleLeft);
- formatMenu.add(scaleRight);
- formatMenu.add(seqLimits);
- formatMenu.add(idRightAlign);
- formatMenu.add(hiddenMarkers);
- formatMenu.add(viewBoxesMenuItem);
- formatMenu.add(viewTextMenuItem);
- formatMenu.add(colourTextMenuItem);
- formatMenu.add(renderGapsMenuItem);
- formatMenu.add(centreColumnLabelsMenuItem);
- formatMenu.add(showNonconservedMenuItem);
- selectMenu.add(findMenuItem);
- selectMenu.addSeparator();
- selectMenu.add(selectAllSequenceMenuItem);
- selectMenu.add(deselectAllSequenceMenuItem);
- selectMenu.add(invertSequenceMenuItem);
- selectMenu.add(invertColSel);
- selectMenu.add(createGroup);
- selectMenu.add(unGroup);
- selectMenu.add(grpsFromSelection);
- selectMenu.add(deleteGroups);
- // TODO - determine if the listenToViewSelections button is needed : see bug
- // JAL-574
- // selectMenu.addSeparator();
- // selectMenu.add(listenToViewSelections);
}
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
@@ -2055,13 +2406,6 @@ public class GAlignFrame extends JInternalFrame
}
- protected void showSeqFeaturesHeight_actionPerformed(
- ActionEvent actionEvent)
- {
- // TODO Auto-generated method stub
-
- }
-
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
@@ -2096,10 +2440,6 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void showProducts_actionPerformed(ActionEvent e)
- {
- }
-
protected void buildSortByAnnotationScoresMenu()
{
}
@@ -2141,6 +2481,11 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
protected void closeMenuItem_actionPerformed(boolean b)
{
}
@@ -2221,19 +2566,19 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void PCAMenuItem_actionPerformed(ActionEvent e)
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
}
@@ -2241,131 +2586,86 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void clustalColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void zappoColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void taylorColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void helixColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void strandColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void turnColour_actionPerformed(ActionEvent e)
- {
- }
-
- protected void buriedColour_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
- protected void userDefinedColour_actionPerformed(ActionEvent e)
+ protected void printMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ protected void findMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ protected void abovePIDThreshold_actionPerformed(boolean selected)
{
}
- /*
- * protected void covariationColour_actionPerformed(ActionEvent e) { }
- */
-
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
{
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
- protected void printMenuItem_actionPerformed(ActionEvent e)
+ protected void createGroup_actionPerformed(ActionEvent e)
{
}
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ protected void unGroup_actionPerformed(ActionEvent e)
{
}
- protected void findMenuItem_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed(ActionEvent e)
{
}
- protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed(ActionEvent e)
{
}
- public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
+ protected void delete_actionPerformed(ActionEvent e)
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ protected void pasteNew_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
- protected void deleteGroups_actionPerformed(ActionEvent e)
- {
- }
-
- protected void createGroup_actionPerformed(ActionEvent e)
- {
- }
-
- protected void unGroup_actionPerformed(ActionEvent e)
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed(boolean selected)
{
}
- protected void cut_actionPerformed(ActionEvent e)
+ protected void hmmBuild_actionPerformed(boolean withDefaults)
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ protected void hmmSearch_actionPerformed(boolean withDefaults)
{
}
- protected void pasteNew_actionPerformed(ActionEvent e)
+ protected void jackhmmer_actionPerformed(boolean b)
{
}
- protected void pasteThis_actionPerformed(ActionEvent e)
+ protected void addDatabase_actionPerformed()
+ throws FileFormatException, IOException
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ protected void hmmAlign_actionPerformed(boolean withDefaults)
{
}
@@ -2390,33 +2690,25 @@ public class GAlignFrame extends JInternalFrame
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ public void createSVG(java.io.File f)
{
}
- /**
- * Template method to handle the 'load T-Coffee scores' menu event.
- *
- * Subclasses override this method to provide a custom action.
- *
- * @param event
- * The raised event
- */
- protected void loadScores_actionPerformed(ActionEvent event)
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
}
/**
- * Template method to handle the 'Color T-Coffee scores' menu event.
+ * Template method to handle the 'load T-Coffee scores' menu event.
*
* Subclasses override this method to provide a custom action.
*
* @param event
* The raised event
*/
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+ protected void loadScores_actionPerformed(ActionEvent event)
{
}
@@ -2433,15 +2725,23 @@ public class GAlignFrame extends JInternalFrame
{
}
+ protected void filterByEValue_actionPerformed()
+ {
+ }
+
+ protected void filterByScore_actionPerformed()
+ {
+ }
+
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
}
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
}
@@ -2463,7 +2763,7 @@ public class GAlignFrame extends JInternalFrame
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
}
@@ -2483,17 +2783,16 @@ public class GAlignFrame extends JInternalFrame
}
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
-
}
- public void rnahelicesColour_actionPerformed(ActionEvent e)
+ public void annotationColumn_actionPerformed(ActionEvent e)
{
-
}
public void associatedData_actionPerformed(ActionEvent e)
+ throws IOException, InterruptedException
{
}
@@ -2583,7 +2882,7 @@ public class GAlignFrame extends JInternalFrame
}
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
}
@@ -2603,7 +2902,7 @@ public class GAlignFrame extends JInternalFrame
}
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
}
@@ -2617,4 +2916,77 @@ public class GAlignFrame extends JInternalFrame
{
}
+
+ protected void expand_newalign(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected boolean isShowAutoCalculatedAbove()
+ {
+ return showAutoCalculatedAbove;
+ }
+
+ protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
+ {
+ this.showAutoCalculatedAbove = showAutoCalculatedAbove;
+ }
+
+ protected SequenceAnnotationOrder getAnnotationSortOrder()
+ {
+ return annotationSortOrder;
+ }
+
+ protected void setAnnotationSortOrder(
+ SequenceAnnotationOrder annotationSortOrder)
+ {
+ this.annotationSortOrder = annotationSortOrder;
+ }
+
+ public Map getAccelerators()
+ {
+ return this.accelerators;
+ }
+
+ /**
+ * Returns the selected index of the tabbed pane, or -1 if none selected
+ * (including the case where the tabbed pane has not been made visible).
+ *
+ * @return
+ */
+ public int getTabIndex()
+ {
+ return tabbedPane.getSelectedIndex();
+ }
+
+ public JPanel getStatusPanel()
+ {
+ return statusPanel;
+ }
+
+ /**
+ * Sets a reference to the containing split frame. Also makes the 'toggle
+ * split view' menu item visible and checked.
+ *
+ * @param sf
+ */
+ public void setSplitFrame(SplitContainerI sf)
+ {
+ this.splitFrame = sf;
+ if (sf != null)
+ {
+ this.showComplementMenuItem.setVisible(true);
+ this.showComplementMenuItem.setState(true);
+ }
+ }
+
+ public SplitContainerI getSplitViewContainer()
+ {
+ return this.splitFrame;
+ }
+
+ protected void showComplement_actionPerformed(boolean complement)
+ {
+ }
}