import javax.swing.*;\r
import javax.swing.event.*;\r
import java.util.*;\r
-import java.awt.datatransfer.*;\r
+import java.awt.datatransfer.*;\r
\r
\r
public class AlignFrame extends GAlignFrame\r
final AlignViewport viewport;\r
public AlignFrame(AlignmentI al)\r
{\r
- super();\r
viewport = new AlignViewport(al,true,true,false);\r
\r
String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
if(fontName!=null && fontStyle!=null && fontSize!=null)\r
viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
\r
+ // add conservation graph to alignment\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+\r
\r
alignPanel = new AlignmentPanel(this, viewport);\r
+\r
+ alignPanel.annotationPanel.adjustPanelHeight();\r
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+ alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+\r
getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
\r
+\r
addInternalFrameListener(new InternalFrameAdapter()\r
{\r
public void internalFrameActivated(InternalFrameEvent evt)\r
\r
protected void saveAs_actionPerformed(ActionEvent e)\r
{\r
- String suffix = "";\r
+ String suffix [] = null;\r
if(e.getActionCommand().equals("FASTA"))\r
- suffix = "fa";\r
+ suffix = new String[]{"fa", "fasta"};\r
else if(e.getActionCommand().equals("MSF"))\r
- suffix = "msf";\r
+ suffix = new String[]{"msf"};\r
else if(e.getActionCommand().equals("CLUSTAL"))\r
- suffix = "aln";\r
+ suffix = new String[]{"aln"};\r
else if(e.getActionCommand().equals("BLC"))\r
- suffix = "blc";\r
+ suffix = new String[]{"blc"};\r
else if(e.getActionCommand().equals("PIR"))\r
- suffix = "pir";\r
+ suffix = new String[]{"pir"};\r
else if(e.getActionCommand().equals("PFAM"))\r
- suffix = "pfam";\r
+ suffix = new String[]{"pfam"};\r
+\r
\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")\r
- , new String[]{suffix}, e.getActionCommand()+" file");\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
seq = (SequenceI[]) history[1];\r
viewport.setAlignment( new Alignment(seq) );\r
updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.RefreshPanels();\r
alignPanel.RefreshPanels();\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
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
\r
- public void groupsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- GroupEditor geditor = new GroupEditor(viewport, alignPanel);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(geditor);\r
- Desktop.addInternalFrame(frame, "Group editor", 710, 410);\r
- frame.setResizable(false);\r
- }\r
-\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.alignment.deleteAllGroups();\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 font_actionPerformed(ActionEvent e)\r
{\r
- // JOptionPane op = new JOptionPane();\r
JInternalFrame frame = new JInternalFrame();\r
FontChooser fc = new FontChooser( alignPanel, frame );\r
frame.setContentPane(fc);\r
{\r
viewport.setWrapAlignment( wrapMenuItem.isSelected() );\r
alignPanel.setWrapAlignment( wrapMenuItem.isSelected() );\r
+ scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
+ scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
+ scaleRight.setVisible( wrapMenuItem.isSelected() );\r
+ alignPanel.RefreshPanels();\r
+ }\r
+\r
+ protected void scaleAbove_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void scaleLeft_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ protected void scaleRight_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.isSelected());\r
+ alignPanel.repaint();\r
}\r
\r
\r
+\r
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setShowBoxes( viewBoxesMenuItem.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
\r
class ClustalThread extends JPanel implements Runnable\r
{\r
- Image [] image;\r
- int imageIndex = 0;\r
+ Image image;\r
+ int angle = 0;\r
boolean webServiceRunning = false;\r
JInternalFrame frame;\r
public ClustalThread(JInternalFrame frame)\r
{\r
this.frame = frame;\r
- image = new Image[9];\r
- for(int i=0; i<9; i++)\r
+\r
+ java.net.URL url = getClass().getResource("/images/logo.gif");\r
+ if (url != null)\r
{\r
- java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");\r
- if (url != null)\r
+ image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+ MediaTracker mt = new MediaTracker(this);\r
+ mt.addImage(image, 0);\r
+ try\r
{\r
- image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image[i], i);\r
- try{mt.waitForID(i);}\r
- catch(Exception ex){}\r
+ mt.waitForID(0);\r
}\r
+ catch (Exception ex)\r
+ {}\r
}\r
- DNATwirler twirler = new DNATwirler();\r
- twirler.start();\r
+\r
+ ImageSpinner spinner = new ImageSpinner();\r
+ spinner.start();\r
webServiceRunning = true;\r
}\r
\r
- class DNATwirler extends Thread\r
+ class ImageSpinner extends Thread\r
{\r
public void run()\r
{\r
while(webServiceRunning)\r
{\r
try{\r
- Thread.sleep(100);\r
- imageIndex++;\r
- imageIndex %=9;\r
+ Thread.sleep(10);\r
+ angle+=1;\r
+ angle %=360;\r
repaint();\r
}\r
catch(Exception ex){}\r
}catch(Exception ex){}\r
}\r
\r
- public void paintComponent(Graphics g)\r
+ public void paintComponent(Graphics g1)\r
{\r
+ Graphics2D g = (Graphics2D)g1;\r
g.setColor(Color.white);\r
g.fillRect(0,0,getWidth(), getHeight());\r
if(image!=null)\r
{\r
- g.drawImage(image[imageIndex],10,10,this);\r
+\r
+ g.rotate (Math.toRadians(angle), 28, 28);\r
+\r
+ g.drawImage(image,10,10,this);\r
+ g.rotate (-Math.toRadians(angle), 28, 28 );\r
}\r
g.setFont(new Font("Arial", Font.BOLD, 12));\r
g.setColor(Color.black);\r
- g.drawString("Clustal Alignment Web Service running", 30,30);\r
+ g.drawString("Clustal Alignment Web Service running", 60,30);\r
}\r
}\r
- public void jpredMenuItem_actionPerformed(ActionEvent e)\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
- // JInternalFrame frame = new JInternalFrame();\r
-// JPredClient ct = new JPredClient((SequenceI)\r
- /// viewport.getAlignment().getSequences().elementAt(0));\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
git://source.jalview.org / jalview.git / blobdiff