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
\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
{\r
SequenceI seq = sg.getSequenceAt(i);\r
viewport.getAlignment().getSequences().setElementAt(seq, index);\r
}\r
\r
- viewport.setRubberbandGroup(null);\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
Desktop.addInternalFrame(frame, "Change Font", 480,100);\r
}\r
\r
+ protected void fullSeqId_actionPerformed(ActionEvent e)\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
{\r
viewport.setColourText( colourTextMenuItem.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