/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * \r
* This file is part of Jalview.\r
- *\r
+ * \r
* Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
+ * modify it under the terms of the GNU General Public License \r
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- *\r
- * Jalview is distributed in the hope that it will be useful, but\r
- * WITHOUT ANY WARRANTY; without even the implied warranty\r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
* PURPOSE. See the GNU General Public License for more details.\r
- *\r
+ * \r
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.appletgui;\r
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;\r
\r
-public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener\r
+public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
+ ItemListener, KeyListener\r
{\r
public AlignmentPanel alignPanel;\r
\r
\r
String jalviewServletURL;\r
\r
-\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)\r
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
+ String title, boolean embedded)\r
{\r
if (applet != null)\r
{\r
showGroupConservation.setState(viewport.isShowGroupConservation());\r
showConsensusHistogram.setState(viewport.isShowConsensusHistogram());\r
showSequenceLogo.setState(viewport.isShowSequenceLogo());\r
+ normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());\r
\r
seqLimits.setState(viewport.showJVSuffix);\r
\r
{\r
RNAHelixColour.setEnabled(true);\r
}\r
- else {\r
+ else\r
+ {\r
RNAHelixColour.setEnabled(false);\r
}\r
- } else {\r
+ }\r
+ else\r
+ {\r
RNAHelixColour.setEnabled(false);\r
purinePyrimidineColour.setEnabled(false);\r
}\r
- \r
+\r
// Some JVMS send keyevents to Top frame or lowest panel,\r
// Havent worked out why yet. So add to both this frame and seqCanvas for\r
// now\r
\r
/**\r
* Load a features file onto the alignment\r
- *\r
- * @param file file URL, content, or other resolvable path\r
- * @param type is protocol for accessing data referred to by file\r
+ * \r
+ * @param file\r
+ * file URL, content, or other resolvable path\r
+ * @param type\r
+ * is protocol for accessing data referred to by file\r
*/\r
\r
public boolean parseFeaturesFile(String file, String type)\r
\r
/**\r
* Load a features file onto the alignment\r
- *\r
- * @param file file URL, content, or other resolvable path\r
- * @param type is protocol for accessing data referred to by file\r
- * @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded\r
+ * \r
+ * @param file\r
+ * file URL, content, or other resolvable path\r
+ * @param type\r
+ * is protocol for accessing data referred to by file\r
+ * @param autoenabledisplay\r
+ * when true, display features flag will be automatically enabled if\r
+ * features are loaded\r
* @return true if data parsed as a features file\r
*/\r
- public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)\r
+ public boolean parseFeaturesFile(String file, String type,\r
+ boolean autoenabledisplay)\r
{\r
- // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.\r
+ // TODO: test if importing a features file onto an alignment which already\r
+ // has features with links overwrites the original links.\r
\r
Hashtable featureLinks = new Hashtable();\r
boolean featuresFile = false;\r
try\r
{\r
featuresFile = new jalview.io.FeaturesFile(file, type)\r
- .parse(viewport.getAlignment(),\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,\r
- featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));\r
+ .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas\r
+ .getFeatureRenderer().featureColours, featureLinks,\r
+ true, viewport.applet.getDefaultParameter(\r
+ "relaxedidmatch", false));\r
} catch (Exception ex)\r
{\r
ex.printStackTrace();\r
\r
/**\r
* called by key handler and the hide all/show all menu items\r
- *\r
+ * \r
* @param toggleSeqs\r
* @param toggleCols\r
*/\r
// Hide everything by the current selection - this is a hack - we do the\r
// invert and then hide\r
// first check that there will be visible columns after the invert.\r
- if ((viewport.getColumnSelection() != null && viewport.getColumnSelection().getSelected() != null && viewport.getColumnSelection()\r
- .getSelected().size() > 0)\r
+ if ((viewport.getColumnSelection() != null\r
+ && viewport.getColumnSelection().getSelected() != null && viewport\r
+ .getColumnSelection().getSelected().size() > 0)\r
|| (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg\r
.getEndRes()))\r
{\r
hide = true;\r
viewport.hideAllSelectedSeqs();\r
}\r
- else if (!(toggleCols && viewport.getColumnSelection().getSelected().size() > 0))\r
+ else if (!(toggleCols && viewport.getColumnSelection().getSelected()\r
+ .size() > 0))\r
{\r
viewport.showAllHiddenSeqs();\r
}\r
{\r
showSequenceLogo_actionPerformed();\r
}\r
+ else if (evt.getSource() == normSequenceLogo)\r
+ {\r
+ normSequenceLogo_actionPerformed();\r
+ }\r
else if (evt.getSource() == showConsensusHistogram)\r
{\r
showConsensusHistogram_actionPerformed();\r
{\r
showSequenceLogo_actionPerformed();\r
}\r
+ else if (source == normSequenceLogo)\r
+ {\r
+ normSequenceLogo_actionPerformed();\r
+ }\r
else if (source == showConsensusHistogram)\r
{\r
showConsensusHistogram_actionPerformed();\r
else if (source == clustalColour)\r
{\r
abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));\r
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));\r
}\r
else if (source == zappoColour)\r
{\r
{\r
changeColour(new Blosum62ColourScheme());\r
}\r
- else if (source == tcoffeeColour) {\r
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ else if (source == tcoffeeColour)\r
+ {\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
}\r
else if (source == annotationColour)\r
{\r
{\r
String annotation = new AnnotationFile().printAnnotations(\r
viewport.showAnnotation ? viewport.getAlignment()\r
- .getAlignmentAnnotation() : null, viewport.getAlignment()\r
- .getGroups(),\r
- ((Alignment) viewport.getAlignment()).alignmentProperties);\r
+ .getAlignmentAnnotation() : null, viewport\r
+ .getAlignment().getGroups(), ((Alignment) viewport\r
+ .getAlignment()).alignmentProperties);\r
\r
if (displayTextbox)\r
{\r
\r
private Hashtable getDisplayedFeatureCols()\r
{\r
- if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)\r
+ if (alignPanel.getFeatureRenderer() != null\r
+ && viewport.featuresDisplayed != null)\r
{\r
FeatureRenderer fr = alignPanel.getFeatureRenderer();\r
Hashtable fcols = new Hashtable();\r
String features;\r
if (format.equalsIgnoreCase("Jalview"))\r
{\r
- features = new FeaturesFile().printJalviewFormat(\r
- viewport.getAlignment().getSequencesArray(),\r
+ features = new FeaturesFile().printJalviewFormat(viewport\r
+ .getAlignment().getSequencesArray(),\r
getDisplayedFeatureCols());\r
}\r
else\r
{\r
- features = new FeaturesFile().printGFFFormat(\r
- viewport.getAlignment().getSequencesArray(),\r
- getDisplayedFeatureCols());\r
+ features = new FeaturesFile().printGFFFormat(viewport.getAlignment()\r
+ .getSequencesArray(), getDisplayedFeatureCols());\r
}\r
\r
if (displayTextbox)\r
{\r
- boolean frimport=false;\r
- if (features==null || features.equals("No Features Visible"))\r
+ boolean frimport = false;\r
+ if (features == null || features.equals("No Features Visible"))\r
{\r
features = "# No features visible - paste some and import them here.";\r
- frimport=true;\r
+ frimport = true;\r
}\r
\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);\r
cap.setText(features);\r
- } else {\r
- if (features==null)\r
+ }\r
+ else\r
+ {\r
+ if (features == null)\r
features = "";\r
}\r
\r
public void closeMenuItem_actionPerformed()\r
{\r
PaintRefresher.RemoveComponent(alignPanel);\r
- if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)\r
+ if (alignPanel.seqPanel != null\r
+ && alignPanel.seqPanel.seqCanvas != null)\r
{\r
PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
}\r
- if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {\r
+ if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)\r
+ {\r
PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
}\r
\r
if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
{\r
System.exit(0);\r
- } else {\r
+ }\r
+ else\r
+ {\r
}\r
viewport = null;\r
alignPanel = null;\r
}\r
\r
/**\r
- * TODO: JAL-1104\r
- * DOCUMENT ME!\r
- *\r
+ * TODO: JAL-1104 DOCUMENT ME!\r
+ * \r
* @param e\r
* DOCUMENT ME!\r
*/\r
\r
AlignViewport originalSource = getOriginatingSource(command);\r
// JBPNote Test\r
- if (originalSource!=viewport) {\r
- System.err.println("Warning: Viewport object mismatch whilst undoing");\r
+ if (originalSource != viewport)\r
+ {\r
+ System.err\r
+ .println("Warning: Viewport object mismatch whilst undoing");\r
}\r
- originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = viewport.getColumnSelection().getHiddenColumns() != null;\r
+ originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =\r
+ // viewport.getColumnSelection().getHiddenColumns()\r
+ // != null;\r
updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null,\r
- originalSource.getAlignment().getSequences());\r
+ originalSource.firePropertyChange("alignment", null, originalSource\r
+ .getAlignment().getSequences());\r
}\r
\r
/**\r
- * TODO: JAL-1104\r
- * DOCUMENT ME!\r
- *\r
+ * TODO: JAL-1104 DOCUMENT ME!\r
+ * \r
* @param e\r
* DOCUMENT ME!\r
*/\r
\r
AlignViewport originalSource = getOriginatingSource(command);\r
// JBPNote Test\r
- if (originalSource!=viewport) {\r
- System.err.println("Warning: Viewport object mismatch whilst re-doing");\r
+ if (originalSource != viewport)\r
+ {\r
+ System.err\r
+ .println("Warning: Viewport object mismatch whilst re-doing");\r
}\r
- originalSource.updateHiddenColumns(); //sethasHiddenColumns(); = viewport.getColumnSelection().getHiddenColumns() != null;\r
+ originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =\r
+ // viewport.getColumnSelection().getHiddenColumns()\r
+ // != null;\r
\r
updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null,\r
- originalSource.getAlignment().getSequences());\r
+ originalSource.firePropertyChange("alignment", null, originalSource\r
+ .getAlignment().getSequences());\r
}\r
\r
AlignViewport getOriginatingSource(CommandI command)\r
{\r
return;\r
}\r
- viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);\r
+ viewport.getAlignment().moveSelectedSequencesByOne(sg,\r
+ up ? null : viewport.getHiddenRepSequences(), up);\r
alignPanel.paintAlignment(true);\r
}\r
\r
synchronized void slideSequences(boolean right, int size)\r
{\r
- List<SequenceI>sg = new Vector<SequenceI>();\r
+ List<SequenceI> sg = new Vector<SequenceI>();\r
if (viewport.cursorMode)\r
{\r
- sg.add(viewport.getAlignment()\r
- .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
+ sg.add(viewport.getAlignment().getSequenceAt(\r
+ alignPanel.seqPanel.seqCanvas.cursorY));\r
}\r
else if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSize() != viewport.getAlignment()\r
- .getHeight())\r
+ && viewport.getSelectionGroup().getSize() != viewport\r
+ .getAlignment().getHeight())\r
{\r
sg = viewport.getSelectionGroup().getSequences(\r
viewport.getHiddenRepSequences());\r
\r
SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);\r
\r
- SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);\r
+ SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup\r
+ .size()]);\r
for (int i = 0; i < invertGroup.size(); i++)\r
seqs2[i] = invertGroup.elementAt(i);\r
\r
\r
// !newAlignment\r
addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,\r
- seqs, 0, viewport.getAlignment().getWidth(), viewport.getAlignment()));\r
+ seqs, 0, viewport.getAlignment().getWidth(),\r
+ viewport.getAlignment()));\r
\r
viewport.setEndSeq(viewport.getAlignment().getHeight());\r
viewport.getAlignment().getWidth();\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
\r
}\r
\r
\r
/**\r
* group consensus toggled\r
- *\r
+ * \r
*/\r
protected void showGroupConsensus_actionPerformed()\r
{\r
\r
/*\r
* (non-Javadoc)\r
- *\r
+ * \r
* @see\r
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt\r
* .event.ActionEvent)\r
viewport.setShowConsensusHistogram(showConsensusHistogram.getState());\r
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
}\r
+\r
/*\r
* (non-Javadoc)\r
- *\r
+ * \r
* @see\r
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt\r
* .event.ActionEvent)\r
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
}\r
\r
+ protected void normSequenceLogo_actionPerformed()\r
+ {\r
+ showSequenceLogo.setState(true);\r
+ viewport.setShowSequenceLogo(true);\r
+ viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
protected void applyAutoAnnotationSettings_actionPerformed()\r
{\r
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(\r
viewport.getSequenceSelection(),\r
viewport.getAlignmentView(true).getSequenceStrings(\r
- viewport.getGapCharacter()),\r
- viewport.getAlignment().getGroups());\r
+ viewport.getGapCharacter()), viewport.getAlignment()\r
+ .getGroups());\r
viewport.getAlignment().deleteAllGroups();\r
viewport.sequenceColours = null;\r
viewport.setSelectionGroup(null);\r
(int) (Math.random() * 255), (int) (Math.random() * 255));\r
col = col.brighter();\r
for (SequenceI sq : gps[g].getSequences(null))\r
- viewport.setSequenceColour(\r
- sq, col)\r
- ;\r
+ viewport.setSequenceColour(sq, col);\r
}\r
PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
alignPanel.updateAnnotation();\r
\r
addHistoryItem(trimRegion);\r
\r
-\r
-\r
- for (SequenceGroup sg:viewport.getAlignment().getGroups())\r
+ for (SequenceGroup sg : viewport.getAlignment().getGroups())\r
{\r
if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
|| (!trimLeft && !sg.adjustForRemoveRight(column)))\r
}\r
\r
RemoveGapColCommand removeGapCols = new RemoveGapColCommand(\r
- "Remove Gapped Columns", seqs, start, end, viewport.getAlignment());\r
+ "Remove Gapped Columns", seqs, start, end,\r
+ viewport.getAlignment());\r
\r
addHistoryItem(removeGapCols);\r
\r
\r
/**\r
* create a new view derived from the current view\r
- *\r
+ * \r
* @param viewtitle\r
* @return frame for the new view\r
*/\r
{\r
if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)\r
{\r
- newal.addAnnotation(viewport.getAlignment().getAlignmentAnnotation()[i]);\r
+ newal.addAnnotation(viewport.getAlignment()\r
+ .getAlignmentAnnotation()[i]);\r
}\r
}\r
}\r
}\r
\r
/**\r
- *\r
+ * \r
* @return list of feature groups on the view\r
*/\r
public String[] getFeatureGroups()\r
\r
/**\r
* get sequence feature groups that are hidden or shown\r
- *\r
+ * \r
* @param visible\r
* true is visible\r
* @return list\r
\r
/**\r
* Change the display state for the given feature groups\r
- *\r
+ * \r
* @param groups\r
* list of group strings\r
* @param state\r
overview.getPreferredSize().height + 50);\r
\r
frame.pack();\r
- final AlignmentPanel ap=alignPanel;\r
+ final AlignmentPanel ap = alignPanel;\r
frame.addWindowListener(new WindowAdapter()\r
{\r
@Override\r
public void windowClosing(WindowEvent e)\r
{\r
- if (ap!=null) {\r
+ if (ap != null)\r
+ {\r
ap.setOverviewPanel(null);\r
}\r
};\r
}\r
viewport.setGlobalColourScheme(cs);\r
\r
-\r
if (alignPanel.getOverviewPanel() != null)\r
{\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
}\r
\r
jalview.structure.StructureSelectionManager\r
- .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(\r
- alignPanel);\r
+ .getStructureSelectionManager(viewport.applet)\r
+ .sequenceColoursChanged(alignPanel);\r
\r
alignPanel.paintAlignment(true);\r
}\r
{\r
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
AlignmentSorter.sortByID(viewport.getAlignment());\r
- addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));\r
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder,\r
+ viewport.getAlignment()));\r
alignPanel.paintAlignment(true);\r
}\r
\r
\r
if ((viewport.getSelectionGroup() != null && viewport\r
.getSelectionGroup().getSize() > 1)\r
- || (viewport.getSelectionGroup() == null && viewport.getAlignment()\r
- .getHeight() > 1))\r
+ || (viewport.getAlignment().getHeight() > 1))\r
{\r
final TreePanel tp = new TreePanel(alignPanel, type, pwType);\r
\r
\r
/**\r
* sort the alignment using the given treePanel\r
- *\r
+ * \r
* @param treePanel\r
* tree used to sort view\r
* @param title\r
/**\r
* Do any automatic reordering of the alignment and add the necessary bits to\r
* the menu structure for the new tree\r
- *\r
+ * \r
* @param treePanel\r
* @param title\r
*/\r
};\r
});\r
}\r
+\r
public boolean sortBy(AlignmentOrder alorder, String undoname)\r
{\r
- SequenceI[] oldOrder = viewport.getAlignment()\r
- .getSequencesArray();\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
if (viewport.applet.debug)\r
{\r
- System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");\r
+ System.err.println("Sorting " + alorder.getOrder().size()\r
+ + " in alignment '" + getTitle() + "'");\r
}\r
AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
- if (undoname!=null)\r
+ if (undoname != null)\r
{\r
- addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment()));\r
+ addHistoryItem(new OrderCommand(undoname, oldOrder,\r
+ viewport.getAlignment()));\r
}\r
alignPanel.paintAlignment(true);\r
return true;\r
g.drawString("Build date: " + builddate, x, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
g.drawString(\r
- "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",\r
+ "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",\r
x, y += fh * 1.5);\r
- g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);\r
+ g.drawString(\r
+ "Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.",\r
+ x + 50, y += fh + 8);\r
g.drawString(\r
"Development managed by The Barton Group, University of Dundee, Scotland, UK.",\r
x, y += fh);\r
MenuItem buriedColour = new MenuItem();\r
\r
MenuItem purinePyrimidineColour = new MenuItem();\r
+\r
MenuItem RNAInteractionColour = new MenuItem();\r
+\r
MenuItem RNAHelixColour = new MenuItem();\r
\r
MenuItem userDefinedColour = new MenuItem();\r
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
\r
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
- Menu autoAnnMenu=new Menu();\r
- CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();\r
+\r
+ Menu autoAnnMenu = new Menu();\r
+\r
+ CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();\r
+\r
CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
+\r
CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
+\r
CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
+\r
CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
\r
+ CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();\r
+\r
private void jbInit() throws Exception\r
{\r
\r
BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
BLOSUM62Colour.addActionListener(this);\r
tcoffeeColour.setLabel("T-Coffee Scores");\r
- tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided\r
+ tcoffeeColour.setEnabled(false); // it will enabled only if a score file is\r
+ // provided\r
tcoffeeColour.addActionListener(this);\r
- avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem\r
+ .setLabel("Average Distance Using BLOSUM62");\r
avDistanceTreeBlosumMenuItem.addActionListener(this);\r
njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
njTreeBlosumMenuItem.addActionListener(this);\r
showGroupConservation.setLabel("Group Conservation");\r
showConsensusHistogram.setLabel("Show Consensus Histogram");\r
showSequenceLogo.setLabel("Show Consensus Logo");\r
+ normSequenceLogo.setLabel("Normalise Consensus Logo");\r
applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
applyAutoAnnotationSettings.setState(true);\r
autoAnnMenu.setLabel("Autocalculated Annotation");\r
autoAnnMenu.add(applyAutoAnnotationSettings);\r
autoAnnMenu.add(showConsensusHistogram);\r
autoAnnMenu.add(showSequenceLogo);\r
+ autoAnnMenu.add(normSequenceLogo);\r
autoAnnMenu.addSeparator();\r
autoAnnMenu.add(showGroupConservation);\r
autoAnnMenu.add(showGroupConsensus);\r
* Attach the alignFrame panels after embedding menus, if necessary. This used\r
* to be called setEmbedded, but is now creates the dropdown menus in a\r
* platform independent manner to avoid OSX/Mac menu appendage daftness.\r
- *\r
+ * \r
* @param reallyEmbedded\r
* true to attach the view to the applet area on the page rather than\r
* in a new window\r
@Override\r
public void focusLost(FocusEvent e)\r
{\r
- if (me.viewport.applet.currentAlignFrame==me) {\r
- me.viewport.applet.currentAlignFrame = null;\r
- }}\r
+ if (me.viewport.applet.currentAlignFrame == me)\r
+ {\r
+ me.viewport.applet.currentAlignFrame = null;\r
+ }\r
+ }\r
\r
@Override\r
public void focusGained(FocusEvent e)\r
* structures in the original jmol window. Note This method doesn't work\r
* without an additional javascript library to exchange messages between the\r
* distinct applets. See http://issues.jalview.org/browse/JAL-621\r
- *\r
+ * \r
* @param viewer\r
* JmolViewer instance\r
* @param sequenceIds\r
// TODO: search for a jmv that involves viewer\r
if (jmv == null)\r
{ // create a new viewer/jalview binding.\r
- jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});\r
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]\r
+ { seqs });\r
}\r
return jmv;\r
\r
}\r
+\r
/**\r
* bind a pdb file to a sequence in the current view\r
- *\r
+ * \r
* @param sequenceId\r
* - sequenceId within the dataset.\r
* @param pdbEntryString\r
if (applet.useXtrnalSviewer)\r
{\r
// register the association(s) and quit, don't create any windows.\r
- if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {\r
- System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");\r
+ if (StructureSelectionManager.getStructureSelectionManager(applet)\r
+ .setMapping(seqs, chains, pdb.getFile(), protocol) == null)\r
+ {\r
+ System.err.println("Failed to map " + pdb.getFile() + " ("\r
+ + protocol + ") to any sequences");\r
}\r
return;\r
}\r
}\r
\r
/**\r
- * modify the current selection, providing the user has not made a selection already.\r
- * @param sel - sequences from this alignment\r
- * @param csel - columns to be selected on the alignment\r
+ * modify the current selection, providing the user has not made a selection\r
+ * already.\r
+ * \r
+ * @param sel\r
+ * - sequences from this alignment\r
+ * @param csel\r
+ * - columns to be selected on the alignment\r
*/\r
public void select(SequenceGroup sel, ColumnSelection csel)\r
{\r
{\r
alignPanel.seqPanel.scrollTo(row, column);\r
}\r
+\r
public void scrollToRow(int row)\r
{\r
alignPanel.seqPanel.scrollToRow(row);\r
}\r
+\r
public void scrollToColumn(int column)\r
{\r
alignPanel.seqPanel.scrollToColumn(column);\r
}\r
+\r
/**\r
* @return the alignments unique ID.\r
*/\r
- public String getSequenceSetId() {\r
+ public String getSequenceSetId()\r
+ {\r
return viewport.getSequenceSetId();\r
}\r
\r
-\r
/**\r
* Load the (T-Coffee) score file from the specified url\r
- *\r
- * @param source File/URL/T-COFFEE score file contents\r
+ * \r
+ * @param source\r
+ * File/URL/T-COFFEE score file contents\r
* @throws IOException\r
* @return true if alignment was annotated with data from source\r
- * @throws SAXException \r
- * @throws ParserConfigurationException \r
- * @throws ExceptionFileFormatOrSyntax \r
- * @throws ExceptionLoadingFailed \r
- * @throws ExceptionPermissionDenied \r
- * @throws InterruptedException \r
- * @throws ExceptionUnmatchedClosingParentheses \r
+ * @throws SAXException\r
+ * @throws ParserConfigurationException\r
+ * @throws ExceptionFileFormatOrSyntax\r
+ * @throws ExceptionLoadingFailed\r
+ * @throws ExceptionPermissionDenied\r
+ * @throws InterruptedException\r
+ * @throws ExceptionUnmatchedClosingParentheses\r
*/\r
- public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses {\r
-\r
- TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));\r
- if( !file.isValid()) {\r
- // TODO: raise dialog for gui\r
- System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());\r
- System.err.println("Origin was:\n"+source);\r
- return false;\r
- }\r
-\r
- /*\r
- * check that the score matrix matches the alignment dimensions\r
- */\r
- AlignmentI aln;\r
- if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {\r
- // TODO: raise a dialog box here rather than bomb out.\r
- System.err.println("The scores matrix does not match the alignment dimensions");\r
-\r
- }\r
-\r
- // TODO add parameter to indicate if matching should be done\r
- if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
- {\r
- alignPanel.fontChanged();\r
- tcoffeeColour.setEnabled(true);\r
- // switch to this color\r
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
- return true;\r
- } else {\r
- System.err.println("Problems resolving T-Coffee scores:");\r
- if (file.getWarningMessage()!=null) {\r
- System.err.println(file.getWarningMessage());\r
- }\r
- }\r
- return false;\r
- }\r
+ public boolean loadScoreFile(String source) throws IOException,\r
+ ExceptionFileFormatOrSyntax, ParserConfigurationException,\r
+ SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,\r
+ InterruptedException, ExceptionUnmatchedClosingParentheses\r
+ {\r
+\r
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source,\r
+ AppletFormatAdapter.checkProtocol(source));\r
+ if (!file.isValid())\r
+ {\r
+ // TODO: raise dialog for gui\r
+ System.err.println("Problems parsing T-Coffee scores: "\r
+ + file.getWarningMessage());\r
+ System.err.println("Origin was:\n" + source);\r
+ return false;\r
+ }\r
+\r
+ /*\r
+ * check that the score matrix matches the alignment dimensions\r
+ */\r
+ AlignmentI aln;\r
+ if ((aln = viewport.getAlignment()) != null\r
+ && (aln.getHeight() != file.getHeight() || aln.getWidth() != file\r
+ .getWidth()))\r
+ {\r
+ // TODO: raise a dialog box here rather than bomb out.\r
+ System.err\r
+ .println("The scores matrix does not match the alignment dimensions");\r
\r
+ }\r
+\r
+ // TODO add parameter to indicate if matching should be done\r
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
+ {\r
+ alignPanel.fontChanged();\r
+ tcoffeeColour.setEnabled(true);\r
+ // switch to this color\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ System.err.println("Problems resolving T-Coffee scores:");\r
+ if (file.getWarningMessage() != null)\r
+ {\r
+ System.err.println(file.getWarningMessage());\r
+ }\r
+ }\r
+ return false;\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff