final AlignViewport viewport;\r
public AlignFrame(AlignmentI al)\r
{\r
- super();\r
- viewport = new AlignViewport(al,true,true,true,false);\r
+ viewport = new AlignViewport(al,true,true,false);\r
+\r
+ String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
+ String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
+ String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
+ if(fontName!=null && fontStyle!=null && fontSize!=null)\r
+ viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
+\r
+\r
alignPanel = new AlignmentPanel(this, viewport);\r
getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
- fontNameMenuItem.setText(viewport.getFont().getName());\r
- fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
+\r
+ // add conservation graph to alignment\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+\r
+ alignPanel.annotationPanel.adjustPanelHeight();\r
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+ alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+\r
\r
addInternalFrameListener(new InternalFrameAdapter()\r
{\r
\r
protected void saveAs_actionPerformed(ActionEvent e)\r
{\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
+ String suffix [] = null;\r
+ if(e.getActionCommand().equals("FASTA"))\r
+ suffix = new String[]{"fa", "fasta"};\r
+ else if(e.getActionCommand().equals("MSF"))\r
+ suffix = new String[]{"msf"};\r
+ else if(e.getActionCommand().equals("CLUSTAL"))\r
+ suffix = new String[]{"aln"};\r
+ else if(e.getActionCommand().equals("BLC"))\r
+ suffix = new String[]{"blc"};\r
+ else if(e.getActionCommand().equals("PIR"))\r
+ suffix = new String[]{"pir"};\r
+ else if(e.getActionCommand().equals("PFAM"))\r
+ suffix = new String[]{"pfam"};\r
+\r
+ if(e.getActionCommand().equals("XML DUMP"))\r
+ {\r
+ XMLStore store = new XMLStore();\r
+ store.store(viewport);\r
+ return;\r
+ }\r
+\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
+ , suffix, e.getActionCommand()+" file");\r
+ chooser.setFileView(new JalviewFileView());\r
chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");\r
chooser.setToolTipText("Save");\r
int value = chooser.showSaveDialog(this);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
+ if(value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
String choice = chooser.getSelectedFile().getPath();\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
htmlOutput = null;\r
}\r
\r
- protected void createJPG_actionPerformed(ActionEvent e)\r
+ protected void createPNG_actionPerformed(ActionEvent e)\r
{\r
+ alignPanel.makePNG();\r
+ }\r
\r
- int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
- int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
-\r
-\r
- if(!viewport.getWrapAlignment())\r
- {\r
- height = viewport.alignment.getHeight() * viewport.charHeight;\r
- width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
- }\r
-\r
- alignPanel.makeJPG( width, height);\r
+ protected void epsFile_actionPerformed(ActionEvent e)\r
+ {\r
+ alignPanel.makeEPS();\r
}\r
\r
\r
}catch(Exception ex){}\r
}\r
\r
- ArrayList historyList = new ArrayList();\r
- ArrayList redoList = new ArrayList();\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
+ JMenuBar jMenuBar1 = new JMenuBar();\r
\r
void updateEditMenuBar()\r
{\r
seq = (SequenceI[]) history[1];\r
viewport.setAlignment( new Alignment(seq) );\r
updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.RefreshPanels();\r
alignPanel.RefreshPanels();\r
}\r
\r
public void moveSelectedSequences(boolean up)\r
{\r
- SequenceGroup sg = viewport.getRubberbandGroup();\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
if (sg == null)\r
return;\r
\r
\r
protected void copy_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getRubberbandGroup()==null)\r
+ if(viewport.getSelectionGroup()==null)\r
return;\r
\r
- SequenceGroup sg = viewport.getRubberbandGroup();\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
\r
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
StringBuffer buffer= new StringBuffer();\r
\r
protected void pasteThis_actionPerformed(ActionEvent e)\r
{\r
+ addHistoryItem("Paste");\r
paste(false);\r
}\r
\r
int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
if (newHeight > 500)\r
newHeight = 500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
+ Desktop.addInternalFrame(af, "Copied sequences", 700, 500);\r
}\r
else\r
{\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
}\r
\r
\r
protected void delete_actionPerformed(ActionEvent e)\r
{\r
- if (viewport.getRubberbandGroup() == null)\r
+ addHistoryItem("Delete");\r
+ if (viewport.getSelectionGroup() == null)\r
return;\r
\r
- SequenceGroup sg = viewport.getRubberbandGroup();\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
for (int i=0;i < sg.sequences.size(); i++)\r
- viewport.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.getAlignment().findIndex(seq);\r
+ seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);\r
+\r
+ if(seq.getSequence().length()<1)\r
+ viewport.getAlignment().deleteSequence(seq);\r
+ else\r
+ viewport.getAlignment().getSequences().setElementAt(seq, index);\r
+ }\r
\r
+ viewport.setSelectionGroup(null);\r
viewport.alignment.deleteGroup(sg);\r
viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());\r
if(viewport.getAlignment().getHeight()<1)\r
{\r
this.setClosed(true);\r
}catch(Exception ex){}\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
\r
}\r
SequenceI[] seq = (SequenceI[]) history[1];\r
viewport.setAlignment( new Alignment(seq) );\r
updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.RefreshPanels();\r
alignPanel.RefreshPanels();\r
}\r
\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.alignment.deleteAllGroups();\r
- viewport.getSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
\r
alignPanel.RefreshPanels();\r
}\r
\r
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
- Selection sel = viewport.getSelection();\r
+ SequenceGroup sg = new SequenceGroup();\r
for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- sel.addElement( viewport.getAlignment().getSequenceAt(i));\r
+ sg.addSequence( viewport.getAlignment().getSequenceAt(i));\r
+ sg.setEndRes(viewport.alignment.getWidth());\r
+ viewport.setSelectionGroup(sg);\r
PaintRefresher.Refresh(null);\r
}\r
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setRubberbandGroup(null);\r
- viewport.getSelection().clear();\r
+ viewport.setSelectionGroup(null);\r
PaintRefresher.Refresh(null);\r
}\r
\r
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
- Selection sel = viewport.getSelection();\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)\r
- {\r
- if (sel.contains(viewport.getAlignment().getSequenceAt(i)))\r
- sel.removeElement(viewport.getAlignment().getSequenceAt(i));\r
- else\r
- sel.addElement(viewport.getAlignment().getSequenceAt(i));\r
- }\r
+ sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));\r
+\r
PaintRefresher.Refresh(null);\r
}\r
\r
int min = colSel.getMin();\r
viewport.getAlignment().trimLeft(min);\r
colSel.compensateForEdit(0,min);\r
+\r
+ if(viewport.getSelectionGroup()!=null)\r
+ viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+ if(!sg.adjustForRemoveLeft(min))\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+\r
alignPanel.RefreshPanels();\r
}\r
}\r
if (colSel.size() > 0)\r
{\r
int max = colSel.getMax();\r
- if(max>1)\r
- viewport.getAlignment().trimRight(max);\r
+ viewport.getAlignment().trimRight(max);\r
+ if(viewport.getSelectionGroup()!=null)\r
+ viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+\r
+ Vector groups = viewport.alignment.getGroups();\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.get(i);\r
+ if(!sg.adjustForRemoveRight(max))\r
+ viewport.alignment.deleteGroup(sg);\r
+ }\r
+\r
+\r
\r
alignPanel.RefreshPanels();\r
}\r
{\r
addHistoryItem("delete gapped columns");\r
viewport.getAlignment().removeGaps();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
}\r
\r
jSize--;\r
}\r
}\r
-\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
}\r
\r
\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
- JOptionPane op = new JOptionPane();\r
- JInternalFrame frame = op.createInternalFrame(this, "Find");\r
- Finder finder = new Finder(viewport, alignPanel, frame);\r
- frame.setClosable(true);\r
- frame.setContentPane(finder);\r
- frame.setSize(340,110);\r
- frame.setVisible(true);\r
- }\r
-\r
-\r
-\r
- public void fontNameMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
-\r
-\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font",\r
- "Font selection",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null,fonts\r
- ,fontNameMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontNameMenuItem.setText(selection);\r
- SetFont();\r
- }\r
+ JInternalFrame frame = new JInternalFrame();\r
+ Finder finder = new Finder(viewport, alignPanel, frame);\r
+ frame.setContentPane(finder);\r
+ Desktop.addInternalFrame(frame, "Find", 340,110);\r
\r
}\r
\r
- public void fontSizeMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ public void font_actionPerformed(ActionEvent e)\r
{\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font size",\r
- "Font size",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"1","2","4","6","8","10","12","14","16","18","20"}\r
- ,fontSizeMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontSizeMenuItem.setText(selection);\r
- SetFont();\r
- }\r
+ JInternalFrame frame = new JInternalFrame();\r
+ FontChooser fc = new FontChooser( alignPanel, frame );\r
+ frame.setContentPane(fc);\r
+ Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
}\r
\r
- public void fontStyleMenuItem_actionPerformed(ActionEvent e)\r
+ protected void fullSeqId_actionPerformed(ActionEvent e)\r
{\r
- String selection = JOptionPane.showInternalInputDialog(this,\r
- "Select font style",\r
- "Font style",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, new String[]{"plain", "bold", "italic"}\r
- ,fontStyleMenuItem.getText()).toString();\r
- if(selection!=null)\r
- {\r
- fontStyleMenuItem.setText(selection);\r
- SetFont();\r
- }\r
+ viewport.setShowFullId( fullSeqId.isSelected() );\r
\r
+ alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
+ alignPanel.RefreshPanels();\r
}\r
\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
alignPanel.RefreshPanels();\r
}\r
\r
- void SetFont()\r
- {\r
- int style = java.awt.Font.PLAIN;\r
- if(fontStyleMenuItem.getText().equals("bold"))\r
- style = java.awt.Font.BOLD;\r
- else if(fontStyleMenuItem.getText().equals("italic"))\r
- style = java.awt.Font.ITALIC;\r
-\r
- viewport.setFont(new java.awt.Font(fontNameMenuItem.getText(),\r
- style,\r
- Integer.parseInt(fontSizeMenuItem.getText())));\r
- alignPanel.RefreshPanels();\r
-\r
- }\r
-\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
alignPanel.RefreshPanels();\r
}\r
\r
- public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
+ if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())\r
+ {\r
+ annotationPanelMenuItem.setSelected(false);\r
+ return;\r
+ }\r
+ viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );\r
+ alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
}\r
\r
public void overviewMenuItem_actionPerformed(ActionEvent e)\r
protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+ if(coloursChanging)\r
+ return;\r
+\r
+ coloursChanging = true;\r
\r
viewport.setAbovePIDThreshold(false);\r
abovePIDThreshold.setSelected(false);\r
changeColour( ((ConservationColourScheme)cs).cs );\r
else\r
changeColour( cs );\r
- }\r
\r
+ coloursChanging = false;\r
+ }\r
\r
+ boolean coloursChanging = false;\r
public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
{\r
+ if(coloursChanging)\r
+ return;\r
+\r
+ coloursChanging = true;\r
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
\r
conservationMenuItem.setSelected(false);\r
else\r
changeColour( cs );\r
\r
+ coloursChanging = false;\r
}\r
\r
\r
\r
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if(viewport.getSelection().size()<2)\r
+ if(viewport.getSelectionGroup().getSize()<2)\r
JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);\r
else\r
{\r
\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)\r
+\r
+ if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)\r
|| viewport.getAlignment().getHeight()<4)\r
{\r
JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"\r
}\r
\r
TreePanel tp=null;\r
- if (viewport.getSelection() != null && viewport.getSelection().size() > 3)\r
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)\r
{\r
- tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,\r
+ tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,\r
0, viewport.alignment.getWidth());\r
}\r
else\r
g.drawString("Clustal Alignment Web Service running", 30,30);\r
}\r
}\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
+{\r
+\r
+ JInternalFrame frame = new JInternalFrame();\r
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)\r
+ {\r
+ // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
+ SequenceGroup seqs = viewport.getSelectionGroup();\r
+ if (seqs.getSize() == 1 || !viewport.alignment.isAligned())\r
+ {\r
+ JPredClient ct = new JPredClient( (SequenceI)\r
+ seqs.getSequenceAt(0));\r
+ }\r
+ else\r
+ {\r
+ int sz;\r
+ SequenceI[] msa = new SequenceI[sz=seqs.getSize()];\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
+ }\r
+\r
+ JPredClient ct = new JPredClient(msa);\r
+ }\r
+\r
+ }\r
+ else\r
+ {\r
+ Vector seqs = viewport.getAlignment().getSequences();\r
+\r
+ if (seqs.size() == 1 || !viewport.alignment.isAligned())\r
+ {\r
+ JPredClient ct = new JPredClient( (SequenceI)\r
+ seqs.elementAt(0));\r
+ }\r
+ else\r
+ {\r
+ SequenceI[] msa = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ msa[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
+\r
+ JPredClient ct = new JPredClient(msa);\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
+ // Pick the tree file\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Select a newick-like tree file");\r
+ chooser.setToolTipText("Load a tree file");\r
+ int value = chooser.showOpenDialog(null);\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ TreePanel treepanel = null;\r
+ try\r
+ {\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");\r
+ fin.parse();\r
+\r
+ if (fin.getTree() != null)\r
+ {\r
+ TreePanel tp = null;\r
+ tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
+ fin, "FromFile", choice);\r
+ Desktop.addInternalFrame(tp, title, 600, 500);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ JOptionPane.showMessageDialog(Desktop.desktop,\r
+ "Problem reading tree file",\r
+ ex.getMessage(),\r
+ JOptionPane.WARNING_MESSAGE);\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff