X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c1a710508c5e432e088c227d37101a6206167db7;hb=ac07859006686a2c62bcf57b24742eb610bc46f0;hp=079f31515fc7c43e013036c8b6e33dca64731f5c;hpb=c4e30ea2141be5b0622cf9cd59eac0366fa47d32;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 079f315..c1a7105 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -23,16 +23,24 @@ import java.awt.print.*; import javax.swing.*; import javax.swing.event.*; import java.util.*; -import java.awt.datatransfer.*; +import java.awt.datatransfer.*; public class AlignFrame extends GAlignFrame { final AlignmentPanel alignPanel; final AlignViewport viewport; + public static final int NEW_WINDOW_WIDTH = 700; + public static final int NEW_WINDOW_HEIGHT = 500; + public AlignFrame(AlignmentI al) { - super(); + try{ + String ip = java.net.InetAddress.getLocalHost().getHostAddress(); + if( !ip.startsWith("10.")) + alignMenu.setVisible(false); + } + catch(java.net.UnknownHostException e){} viewport = new AlignViewport(al,true,true,false); String fontName = jalview.bin.Cache.getProperty("FONT_NAME"); @@ -41,11 +49,20 @@ public class AlignFrame extends GAlignFrame if(fontName!=null && fontStyle!=null && fontSize!=null) viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) ); + // add conservation graph to alignment + viewport.updateConservation(); + viewport.updateConsensus(); alignPanel = new AlignmentPanel(this, viewport); + + alignPanel.annotationPanel.adjustPanelHeight(); + alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize()); + alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize()); + getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER); + addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameActivated(InternalFrameEvent evt) @@ -63,22 +80,23 @@ public class AlignFrame extends GAlignFrame protected void saveAs_actionPerformed(ActionEvent e) { - String suffix = ""; + String suffix [] = null; if(e.getActionCommand().equals("FASTA")) - suffix = "fa"; + suffix = new String[]{"fa", "fasta"}; else if(e.getActionCommand().equals("MSF")) - suffix = "msf"; + suffix = new String[]{"msf"}; else if(e.getActionCommand().equals("CLUSTAL")) - suffix = "aln"; + suffix = new String[]{"aln"}; else if(e.getActionCommand().equals("BLC")) - suffix = "blc"; + suffix = new String[]{"blc"}; else if(e.getActionCommand().equals("PIR")) - suffix = "pir"; + suffix = new String[]{"pir"}; else if(e.getActionCommand().equals("PFAM")) - suffix = "pfam"; + suffix = new String[]{"pfam"}; + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY") - , new String[]{suffix}, e.getActionCommand()+" file"); + , suffix, e.getActionCommand()+" file"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format."); chooser.setToolTipText("Save"); @@ -116,31 +134,12 @@ public class AlignFrame extends GAlignFrame protected void createPNG_actionPerformed(ActionEvent e) { - int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight; - int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth(); - - if(!viewport.getWrapAlignment()) - { - height = viewport.alignment.getHeight() * viewport.charHeight; - width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth; - } - - alignPanel.makePNG( width, height); + alignPanel.makePNG(); } protected void epsFile_actionPerformed(ActionEvent e) { - int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight; - int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth(); - - if(!viewport.getWrapAlignment()) - { - height = viewport.alignment.getHeight() * viewport.charHeight; - width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth; - } - - alignPanel.makeEPS( width, height); - + alignPanel.makeEPS(); } @@ -185,6 +184,7 @@ public class AlignFrame extends GAlignFrame Stack historyList = new Stack(); Stack redoList = new Stack(); + JMenuBar jMenuBar1 = new JMenuBar(); void updateEditMenuBar() { @@ -246,6 +246,8 @@ public class AlignFrame extends GAlignFrame seq = (SequenceI[]) history[1]; viewport.setAlignment( new Alignment(seq) ); updateEditMenuBar(); + viewport.updateConsensus(); + alignPanel.RefreshPanels(); alignPanel.RefreshPanels(); } @@ -355,15 +357,14 @@ public class AlignFrame extends GAlignFrame SequenceI[] newSeqs = new SequenceI[seqs.size()]; seqs.toArray(newSeqs); AlignFrame af = new AlignFrame(new Alignment(newSeqs)); - int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200; - if (newHeight > 500) - newHeight = 500; - Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight); + Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); } else { viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); + viewport.updateConservation(); + viewport.updateConsensus(); alignPanel.RefreshPanels(); } @@ -405,6 +406,8 @@ public class AlignFrame extends GAlignFrame { this.setClosed(true); }catch(Exception ex){} + viewport.updateConservation(); + viewport.updateConsensus(); alignPanel.RefreshPanels(); } @@ -417,19 +420,12 @@ public class AlignFrame extends GAlignFrame SequenceI[] seq = (SequenceI[]) history[1]; viewport.setAlignment( new Alignment(seq) ); updateEditMenuBar(); + viewport.updateConsensus(); + alignPanel.RefreshPanels(); alignPanel.RefreshPanels(); } - public void groupsMenuItem_actionPerformed(ActionEvent e) - { - GroupEditor geditor = new GroupEditor(viewport, alignPanel); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(geditor); - Desktop.addInternalFrame(frame, "Group editor", 710, 410); - frame.setResizable(false); - } - protected void deleteGroups_actionPerformed(ActionEvent e) { viewport.alignment.deleteAllGroups(); @@ -481,6 +477,18 @@ public class AlignFrame extends GAlignFrame int min = colSel.getMin(); viewport.getAlignment().trimLeft(min); colSel.compensateForEdit(0,min); + + if(viewport.getSelectionGroup()!=null) + viewport.getSelectionGroup().adjustForRemoveLeft(min); + + Vector groups = viewport.alignment.getGroups(); + for(int i=0; i 0) { int max = colSel.getMax(); - if(max>1) - viewport.getAlignment().trimRight(max); + viewport.getAlignment().trimRight(max); + if(viewport.getSelectionGroup()!=null) + viewport.getSelectionGroup().adjustForRemoveRight(max); + + Vector groups = viewport.alignment.getGroups(); + for(int i=0; i 3) - { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType, + final TreePanel tp; + if (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize() > 3) + { + tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, + pwType, 0, viewport.alignment.getWidth()); - } - else - { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); - } + } + else + { + tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), + type, pwType, 0, viewport.alignment.getWidth()); + } + + addTreeMenuItem(tp, title); Desktop.addInternalFrame(tp, title, 600, 500); } + void addTreeMenuItem(final TreePanel treePanel, String title) + { + final JMenuItem item = new JMenuItem(title); + sortByTreeMenu.add(item); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addHistoryItem("sort"); + AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); + alignPanel.RefreshPanels(); + } + }); + + treePanel.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt) + { + sortByTreeMenu.remove(item); + }; + }); + } public void clustalAlignMenuItem_actionPerformed(ActionEvent e) @@ -997,47 +1079,49 @@ if ( viewport.getConservationSelected() ) Thread t = new Thread(ct); t.start(); frame.setContentPane(ct); - Desktop.addInternalFrame(frame, title, 300, 80); + Desktop.addInternalFrame(frame, title, 320, 90); } class ClustalThread extends JPanel implements Runnable { - Image [] image; - int imageIndex = 0; + Image image; + int angle = 0; boolean webServiceRunning = false; JInternalFrame frame; public ClustalThread(JInternalFrame frame) { this.frame = frame; - image = new Image[9]; - for(int i=0; i<9; i++) + + java.net.URL url = getClass().getResource("/images/logo.gif"); + if (url != null) { - java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif"); - if (url != null) + image = java.awt.Toolkit.getDefaultToolkit().createImage(url); + MediaTracker mt = new MediaTracker(this); + mt.addImage(image, 0); + try { - image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url); - MediaTracker mt = new MediaTracker(this); - mt.addImage(image[i], i); - try{mt.waitForID(i);} - catch(Exception ex){} + mt.waitForID(0); } + catch (Exception ex) + {} } - DNATwirler twirler = new DNATwirler(); - twirler.start(); + + ImageSpinner spinner = new ImageSpinner(); + spinner.start(); webServiceRunning = true; } - class DNATwirler extends Thread + class ImageSpinner extends Thread { public void run() { while(webServiceRunning) { try{ - Thread.sleep(100); - imageIndex++; - imageIndex %=9; + Thread.sleep(10); + angle+=1; + angle %=360; repaint(); } catch(Exception ex){} @@ -1066,10 +1150,9 @@ if ( viewport.getConservationSelected() ) if (alignment != null) { AlignFrame af = new AlignFrame(new Alignment(alignment)); - af.clustalColour.setSelected(true); - af.clustalColour_actionPerformed(null); - Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"), - 700, 500); // JBPNote - is there a new window geom. property ? + Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); + af.clustalColour_actionPerformed(null); + af.clustalColour.setSelected(true); } else JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error", @@ -1081,17 +1164,109 @@ if ( viewport.getConservationSelected() ) }catch(Exception ex){} } - public void paintComponent(Graphics g) + public void paintComponent(Graphics g1) { + Graphics2D g = (Graphics2D)g1; g.setColor(Color.white); g.fillRect(0,0,getWidth(), getHeight()); if(image!=null) { - g.drawImage(image[imageIndex],10,10,this); + + g.rotate (Math.toRadians(angle), 28, 28); + + g.drawImage(image,10,10,this); + g.rotate (-Math.toRadians(angle), 28, 28 ); } g.setFont(new Font("Arial", Font.BOLD, 12)); g.setColor(Color.black); - g.drawString("Clustal Alignment Web Service running", 30,30); + g.drawString("Clustal Alignment Web Service running", 60,30); } } + protected void jpred_actionPerformed(ActionEvent e) +{ + + JInternalFrame frame = new JInternalFrame(); + if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0) + { + // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface! + SequenceGroup seqs = viewport.getSelectionGroup(); + if (seqs.getSize() == 1 || !viewport.alignment.isAligned()) + { + JPredClient ct = new JPredClient( (SequenceI) + seqs.getSequenceAt(0)); + } + else + { + int sz; + SequenceI[] msa = new SequenceI[sz=seqs.getSize()]; + for (int i = 0; i < sz; i++) + { + msa[i] = (SequenceI) seqs.getSequenceAt(i); + } + + JPredClient ct = new JPredClient(msa); + } + + } + else + { + Vector seqs = viewport.getAlignment().getSequences(); + + if (seqs.size() == 1 || !viewport.alignment.isAligned()) + { + JPredClient ct = new JPredClient( (SequenceI) + seqs.elementAt(0)); + } + else + { + SequenceI[] msa = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + msa[i] = (SequenceI) seqs.elementAt(i); + } + + JPredClient ct = new JPredClient(msa); + } + + } + } + + protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { + // Pick the tree file + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY")); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Select a newick-like tree file"); + chooser.setToolTipText("Load a tree file"); + int value = chooser.showOpenDialog(null); + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + TreePanel treepanel = null; + try + { + jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File"); + fin.parse(); + + if (fin.getTree() != null) + { + TreePanel tp = null; + tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), + fin, "FromFile", choice); + Desktop.addInternalFrame(tp, title, 600, 500); + addTreeMenuItem(tp, title); + } + } + catch (Exception ex) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "Problem reading tree file", + ex.getMessage(), + JOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); + } + } + } + }