X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c1a710508c5e432e088c227d37101a6206167db7;hb=ac07859006686a2c62bcf57b24742eb610bc46f0;hp=00961d62988bf741f59bbf506527277d272b6703;hpb=39d42f25edeb526275d178e0259e767e7c29bd78;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 00961d6..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"); @@ -41,10 +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) @@ -76,6 +94,7 @@ public class AlignFrame extends GAlignFrame else if(e.getActionCommand().equals("PFAM")) suffix = new String[]{"pfam"}; + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY") , suffix, e.getActionCommand()+" file"); chooser.setFileView(new JalviewFileView()); @@ -227,6 +246,8 @@ public class AlignFrame extends GAlignFrame seq = (SequenceI[]) history[1]; viewport.setAlignment( new Alignment(seq) ); updateEditMenuBar(); + viewport.updateConsensus(); + alignPanel.RefreshPanels(); alignPanel.RefreshPanels(); } @@ -336,15 +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(); } @@ -386,6 +406,8 @@ public class AlignFrame extends GAlignFrame { this.setClosed(true); }catch(Exception ex){} + viewport.updateConservation(); + viewport.updateConsensus(); alignPanel.RefreshPanels(); } @@ -398,19 +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(); @@ -508,6 +523,8 @@ public class AlignFrame extends GAlignFrame { addHistoryItem("delete gapped columns"); viewport.getAlignment().removeGaps(); + viewport.updateConservation(); + viewport.updateConsensus(); alignPanel.RefreshPanels(); } @@ -528,7 +545,8 @@ public class AlignFrame extends GAlignFrame jSize--; } } - + viewport.updateConservation(); + viewport.updateConsensus(); alignPanel.RefreshPanels(); } @@ -548,17 +566,17 @@ public class AlignFrame extends GAlignFrame public void findMenuItem_actionPerformed(ActionEvent e) { - JInternalFrame frame = new JInternalFrame(); - Finder finder = new Finder(viewport, alignPanel, frame); - frame.setContentPane(finder); - Desktop.addInternalFrame(frame, "Find", 340,110); + JInternalFrame frame = new JInternalFrame(); + Finder finder = new Finder(viewport, alignPanel, frame); + frame.setContentPane(finder); + Desktop.addInternalFrame(frame, "Find", 340,110, false); + frame.setLayer(JLayeredPane.PALETTE_LAYER); } public void font_actionPerformed(ActionEvent e) { - // JOptionPane op = new JOptionPane(); JInternalFrame frame = new JInternalFrame(); FontChooser fc = new FontChooser( alignPanel, frame ); frame.setContentPane(fc); @@ -583,8 +601,31 @@ public class AlignFrame extends GAlignFrame { viewport.setWrapAlignment( wrapMenuItem.isSelected() ); alignPanel.setWrapAlignment( wrapMenuItem.isSelected() ); + scaleAbove.setVisible( wrapMenuItem.isSelected() ); + scaleLeft.setVisible( wrapMenuItem.isSelected() ); + scaleRight.setVisible( wrapMenuItem.isSelected() ); + alignPanel.RefreshPanels(); + } + + protected void scaleAbove_actionPerformed(ActionEvent e) + { + viewport.setScaleAboveWrapped(scaleAbove.isSelected()); + alignPanel.repaint(); } + protected void scaleLeft_actionPerformed(ActionEvent e) + { + viewport.setScaleLeftWrapped(scaleLeft.isSelected()); + alignPanel.repaint(); + } + + protected void scaleRight_actionPerformed(ActionEvent e) + { + viewport.setScaleRightWrapped(scaleRight.isSelected()); + alignPanel.repaint(); + } + + public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -616,9 +657,15 @@ public class AlignFrame extends GAlignFrame alignPanel.RefreshPanels(); } - public void consensusGraphMenuItem_actionPerformed(ActionEvent e) + public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() ); + if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment()) + { + annotationPanelMenuItem.setSelected(false); + return; + } + viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() ); + alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() ); } public void overviewMenuItem_actionPerformed(ActionEvent e) @@ -736,7 +783,7 @@ public class AlignFrame extends GAlignFrame sg.sequences, sg.getStartRes(), sg.getEndRes()); c.calculate(); - c.verdict(false, 100); + c.verdict(false, viewport.ConsPercGaps); ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); sg.cs = ccs; @@ -746,16 +793,16 @@ public class AlignFrame extends GAlignFrame } - if ( viewport.getAbovePIDThreshold()) + if ( viewport.getAbovePIDThreshold() ) { - int threshold = 0; - threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background"); + // int threshold = 0; + // threshold = Desktop.setPIDSliderSource(alignPanel, cs, "Background"); Desktop.hideConservationSlider(); - if (cs instanceof ResidueColourScheme) - ( (ResidueColourScheme) cs).setThreshold(threshold); - else if (cs instanceof ScoreColourScheme) - ( (ScoreColourScheme) cs).setThreshold(threshold); + // if (cs instanceof ResidueColourScheme) + // ( (ResidueColourScheme) cs).setThreshold(threshold); + // else if (cs instanceof ScoreColourScheme) + // ( (ScoreColourScheme) cs).setThreshold(threshold); viewport.setGlobalColourScheme(cs); @@ -780,14 +827,13 @@ if ( viewport.getConservationSelected() ) al.getWidth()); c.calculate(); - c.verdict(false, 100); + c.verdict(false, viewport.ConsPercGaps); ccs = new ConservationColourScheme(c, cs); - int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, - "Background"); + // int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background"); - ccs.inc = threshold; + // ccs.inc = threshold; viewport.setGlobalColourScheme(ccs); @@ -798,6 +844,16 @@ if ( viewport.getConservationSelected() ) alignPanel.RefreshPanels(); } + protected void modifyPID_actionPerformed(ActionEvent e) + { + Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); + } + + protected void modifyConservation_actionPerformed(ActionEvent e) + { + Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme, "Background"); + } + protected void conservationMenuItem_actionPerformed(ActionEvent e) { @@ -855,10 +911,7 @@ if ( viewport.getConservationSelected() ) JInternalFrame frame = new JInternalFrame(); UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null); frame.setContentPane(chooser); - Desktop.addInternalFrame(frame,"User defined colours", 450,540 ); - frame.setResizable(false); - frame.setIconifiable(false); - frame.setMaximizable(false); + Desktop.addInternalFrame(frame,"User defined colours", 450,540, false ); } public void PIDColour_actionPerformed(ActionEvent e) @@ -896,24 +949,12 @@ if ( viewport.getConservationSelected() ) alignPanel.RefreshPanels(); } - public void sortTreeOrderMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem("sort"); - if(viewport.getCurrentTree()==null) - return; - - AlignmentSorter.sortByTree(viewport.getAlignment(), viewport.getCurrentTree()); - alignPanel.RefreshPanels(); - } - public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { RedundancyPanel sp = new RedundancyPanel(alignPanel); JInternalFrame frame = new JInternalFrame(); frame.setContentPane(sp); - Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100); - frame.setMaximizable(false); - frame.setResizable(false); + Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false); } @@ -987,22 +1028,48 @@ if ( viewport.getConservationSelected() ) return; } - TreePanel tp=null; - if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 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) @@ -1012,47 +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){} @@ -1081,10 +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", @@ -1096,25 +1164,72 @@ 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); } } - public void jpredMenuItem_actionPerformed(ActionEvent e) + 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 { - // JInternalFrame frame = new JInternalFrame(); -// JPredClient ct = new JPredClient((SequenceI) - /// viewport.getAlignment().getSequences().elementAt(0)); + 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 @@ -1140,6 +1255,7 @@ if ( viewport.getConservationSelected() ) tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), fin, "FromFile", choice); Desktop.addInternalFrame(tp, title, 600, 500); + addTreeMenuItem(tp, title); } } catch (Exception ex)