boolean embedded)\r
{\r
\r
- jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+ if (applet != null)\r
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
\r
try{\r
jbInit();\r
\r
if(toggleSeqs)\r
{\r
- if (sg != null && sg.getSize(false) != viewport.alignment.getHeight())\r
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
{\r
hide = true;\r
viewport.hideAllSelectedSeqs();\r
loadTree_actionPerformed();\r
else if(source==loadApplication)\r
launchFullApplication();\r
+ else if (source == loadAnnotations)\r
+ loadAnnotations();\r
+ else if (source == outputAnnotations)\r
+ outputAnnotations(true);\r
+ else if(source == outputFeatures)\r
+ outputFeatures(true, "Jalview");\r
else if(source==closeMenuItem)\r
closeMenuItem_actionPerformed();\r
else if(source==copy)\r
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().getSequences(),\r
+ viewport.getAlignment(),\r
viewport.showJVSuffix));\r
}\r
\r
+ public void loadAnnotations()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your features / annotations file here.");\r
+ cap.setAnnotationImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
+\r
+ }\r
+\r
+ public String outputAnnotations(boolean displayTextbox)\r
+ {\r
+ String annotation = new AnnotationFile().printAnnotations(\r
+ viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,\r
+ viewport.alignment.getGroups());\r
+\r
+ if(displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Annotations",\r
+ 600, 500);\r
+ cap.setText(annotation);\r
+ }\r
+\r
+ return annotation;\r
+ }\r
+\r
+ public String outputFeatures(boolean displayTextbox, String format)\r
+ {\r
+ String features;\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ features = new FeaturesFile().printJalviewFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+ else\r
+ features = new FeaturesFile().printGFFFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+\r
+\r
+ if(displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Features",\r
+ 600, 500);\r
+\r
+ cap.setText(features);\r
+ }\r
+\r
+ return features;\r
+ }\r
+\r
void launchFullApplication()\r
{\r
StringBuffer url = new StringBuffer(jalviewServletURL);\r
\r
originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null,null);\r
+ originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences());\r
}\r
\r
/**\r
originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;\r
\r
updateEditMenuBar();\r
- originalSource.firePropertyChange("alignment", null, null);\r
+ originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences());\r
}\r
\r
AlignViewport getOriginatingSource(CommandI command)\r
//For sequence removal and addition, we need to fire\r
//the property change event FROM the viewport where the\r
//original alignment was altered\r
+ AlignmentI al = null;\r
if (command instanceof EditCommand)\r
{\r
EditCommand editCommand = (EditCommand) command;\r
- AlignmentI al = editCommand.getAlignment();\r
+ al = editCommand.getAlignment();\r
Vector comps = (Vector) PaintRefresher.components\r
.get(viewport.getSequenceSetId());\r
for (int i = 0; i < comps.size(); i++)\r
}\r
}\r
}\r
- if (originalSource == null)\r
- {\r
- //The original view is closed, we must validate\r
- //the current view against the closed view first\r
- if (al != null)\r
- PaintRefresher.validateSequences(al, viewport.alignment);\r
- originalSource = viewport;\r
- }\r
+ }\r
\r
+ if (originalSource == null)\r
+ {\r
+ //The original view is closed, we must validate\r
+ //the current view against the closed view first\r
+ if (al != null)\r
+ PaintRefresher.validateSequences(al, viewport.alignment);\r
+\r
+ originalSource = viewport;\r
}\r
\r
+\r
return originalSource;\r
}\r
\r
for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.getSequences(false).contains(seq))\r
+ if (!sg.getSequences(null).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.getSequences(false).contains(temp))\r
+ if (sg.getSequences(null).contains(temp))\r
{\r
continue;\r
}\r
for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.getSequences(true).contains(seq))\r
+ if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.getSequences(true).contains(temp))\r
+ if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
{\r
continue;\r
}\r
SequenceGroup sg = viewport.getSelectionGroup();\r
copiedSequences = new StringBuffer();\r
Hashtable orderedSeqs = new Hashtable();\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.alignment.findIndex(seq);\r
copiedHiddenColumns = null;\r
\r
\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
SequenceI seq = null;\r
\r
copiedSequences.append(seq.getName() + "\t" +\r
startRes + "\t" +\r
endRes + "\t" +\r
- seq.getSequence(sg.getStartRes(),\r
+ seq.getSequenceAsString(sg.getStartRes(),\r
sg.getEndRes() + 1) + "\n");\r
}\r
\r
}\r
else\r
{\r
- for (int i = 0; i < newSeqs.length; i++)\r
- {\r
- viewport.alignment.addSequence(newSeqs[i]);\r
- }\r
-\r
- //!newAlignment\r
- addHistoryItem(new EditCommand(\r
- "Add sequences",\r
- EditCommand.PASTE,\r
- newSeqs,\r
- 0,\r
- viewport.alignment.getWidth(),\r
- viewport.alignment)\r
- );\r
-\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.firePropertyChange("alignment", null, null);\r
+ addSequences(newSeqs);\r
}\r
\r
}\r
\r
}\r
\r
+ void addSequences(SequenceI[] seqs)\r
+ {\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ viewport.alignment.addSequence(seqs[i]);\r
+ }\r
+\r
+ //!newAlignment\r
+ addHistoryItem(new EditCommand(\r
+ "Add sequences",\r
+ EditCommand.PASTE,\r
+ seqs,\r
+ 0,\r
+ viewport.alignment.getWidth(),\r
+ viewport.alignment)\r
+ );\r
+\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.alignment.getSequences());\r
+\r
+ }\r
+\r
protected void cut_actionPerformed()\r
{\r
copy_actionPerformed();\r
\r
Vector seqs = new Vector();\r
SequenceI seq;\r
- for (int i = 0; i < sg.getSize(false); i++)\r
+ for (int i = 0; i < sg.getSize(); i++)\r
{\r
seq = sg.getSequenceAt(i);\r
seqs.addElement(seq);\r
\r
\r
// If the cut affects all sequences, remove highlighted columns\r
- if (sg.getSize(false) == viewport.alignment.getHeight())\r
+ if (sg.getSize() == viewport.alignment.getHeight())\r
{\r
viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
sg.getEndRes() + 1);\r
\r
SequenceI [] seqs;\r
if(viewport.getSelectionGroup()!=null)\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
else\r
seqs = viewport.alignment.getSequencesArray();\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
new RemoveGapColCommand("Remove Gapped Columns",\r
seqs,\r
start, end,\r
- viewport.getGapCharacter());\r
+ viewport.alignment);\r
\r
addHistoryItem(removeGapCols);\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(true);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
seqs,\r
start, end,\r
- viewport.getGapCharacter()));\r
+ viewport.alignment));\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
\r
else\r
newal = new Alignment(viewport.alignment.getSequencesArray());\r
\r
+ if(viewport.alignment.getAlignmentAnnotation()!=null)\r
+ {\r
+ for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)\r
+ {\r
+ if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+ {\r
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+ }\r
+ }\r
+ }\r
+\r
AlignFrame newaf = new AlignFrame(newal,\r
viewport.applet,\r
"",\r
frame.add(overview);\r
// +50 must allow for applet frame window\r
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.preferredSize().width,\r
- overview.preferredSize().height + 50);\r
+ overview.getPreferredSize().width,\r
+ overview.getPreferredSize().height + 50);\r
\r
frame.pack();\r
frame.addWindowListener(new WindowAdapter()\r
}\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(\r
+ sg.getSequences(viewport.hiddenRepSequences),\r
+ sg.getWidth());\r
}\r
else\r
{\r
|| cs instanceof Blosum62ColourScheme)\r
{\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
}\r
else\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
+ sg.getSequences(viewport.hiddenRepSequences), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
if (viewport.getSelectionGroup()!=null\r
- && viewport.getSelectionGroup().getSize(false) > 1)\r
+ && viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\r
}\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize(false) < 4 &&\r
- viewport.getSelectionGroup().getSize(false) > 0)\r
+ viewport.getSelectionGroup().getSize() < 4 &&\r
+ viewport.getSelectionGroup().getSize() > 0)\r
|| viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
\r
protected void avTreeBlosumMenuItem_actionPerformed()\r
{\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
}\r
\r
void NewTreePanel(String type, String pwType, String title)\r
}\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize(false) > 1)\r
+ viewport.getSelectionGroup().getSize() > 1)\r
|| (viewport.getSelectionGroup() == null\r
&& viewport.alignment.getHeight() > 1))\r
{\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
cap.setText("Paste your Newick tree file here.");\r
- cap.treeImport = true;\r
+ cap.setTreeImport();\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
protected MenuBar alignFrameMenuBar = new MenuBar();\r
protected Menu fileMenu = new Menu("File");\r
protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
- protected MenuItem loadTree = new MenuItem("Load Associated Tree");\r
+ protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+ protected MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+ protected MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+ protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
protected MenuItem closeMenuItem = new MenuItem("Close");\r
protected Menu editMenu = new Menu("Edit");\r
protected Menu viewMenu = new Menu("View");\r
loadApplication.addActionListener(this);\r
\r
loadTree.addActionListener(this);\r
+ loadAnnotations.addActionListener(this);\r
+ outputFeatures.addActionListener(this);\r
+ outputAnnotations.addActionListener(this);\r
selectAllSequenceMenuItem.addActionListener(this);\r
deselectAllSequenceMenuItem.addActionListener(this);\r
invertSequenceMenuItem.addActionListener(this);\r
averageDistanceTreeMenuItem.addActionListener(this);\r
neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
neighbourTreeMenuItem.addActionListener(this);\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setBackground(Color.white);\r
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setText("Status bar");\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
alignFrameMenuBar.add(helpMenu);\r
+\r
fileMenu.add(inputText);\r
+ fileMenu.add(loadTree);\r
+ fileMenu.add(loadAnnotations);\r
+\r
+ fileMenu.addSeparator();\r
fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(outputFeatures);\r
+ fileMenu.add(outputAnnotations);\r
+\r
if(jalviewServletURL!=null)\r
fileMenu.add(loadApplication);\r
+\r
fileMenu.addSeparator();\r
- fileMenu.add(loadTree);\r
fileMenu.add(closeMenuItem);\r
+\r
editMenu.add(undoMenuItem);\r
editMenu.add(redoMenuItem);\r
editMenu.add(cut);\r
editMenu.add(copy);\r
editMenu.add(pasteMenu);\r
editMenu.add(delete);\r
- editMenu.addSeparator();\r
+ editMenu.addSeparator();\r
editMenu.add(remove2LeftMenuItem);\r
editMenu.add(remove2RightMenuItem);\r
editMenu.add(removeGappedColumnMenuItem);\r
embeddedCalculate.addMouseListener(this);\r
embeddedHelp.addMouseListener(this);\r
\r
- // setVisible(false);\r
fileMenu.remove(closeMenuItem);\r
fileMenu.remove(3); // Seperator\r
\r
viewport.applet.setLayout(new BorderLayout());\r
viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
- // viewport.applet.validate();\r
\r
- alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
+ alignPanel.setSize(viewport.applet.getSize().width, viewport.applet.getSize().height\r
- embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
\r
viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
git://source.jalview.org / jalview.git / blobdiff