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
+\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
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 = "";\r
+ if(e.getActionCommand().equals("FASTA"))\r
+ suffix = "fa";\r
+ else if(e.getActionCommand().equals("MSF"))\r
+ suffix = "msf";\r
+ else if(e.getActionCommand().equals("CLUSTAL"))\r
+ suffix = "aln";\r
+ else if(e.getActionCommand().equals("BLC"))\r
+ suffix = "blc";\r
+ else if(e.getActionCommand().equals("PIR"))\r
+ suffix = "pir";\r
+ else if(e.getActionCommand().equals("PFAM"))\r
+ suffix = "pfam";\r
+\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
+ , new String[]{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
-\r
int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\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.makePNG( width, height);\r
+ }\r
+\r
+ protected void epsFile_actionPerformed(ActionEvent e)\r
+ {\r
+ int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;\r
+ int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();\r
\r
if(!viewport.getWrapAlignment())\r
{\r
width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;\r
}\r
\r
- alignPanel.makeJPG( width, height);\r
+ alignPanel.makeEPS( width, height);\r
+\r
}\r
\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
protected void delete_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem("Delete");\r
- if (viewport.getRubberbandGroup() == null)\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
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
\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
+ // JOptionPane op = new JOptionPane();\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
\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
git://source.jalview.org / jalview.git / blobdiff