X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ab5fb17bdb6ac808581b722f15788bac4ed33ef1;hb=48555d99e5255063a40ed1818a9090dd88f9a665;hp=76c483eb066e7e46c8150c8b5e47edb2503c0fa5;hpb=f0ade845a8f610bc402051d617cec4cfebe9e58a;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 76c483e..ab5fb17 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -70,7 +70,7 @@ public class AlignFrame extends GAlignFrame protected void htmlMenuItem_actionPerformed(ActionEvent e) { - HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme()); + HTMLOutput htmlOutput = new HTMLOutput(viewport); htmlOutput = null; } @@ -331,24 +331,36 @@ public class AlignFrame extends GAlignFrame public void setGapCharMenuItem_actionPerformed(ActionEvent e) { - String thisChar = "-"; - String nextChar = "."; - if(viewport.getGapCharacter().equals("-")) + char thisChar = '-'; + char nextChar = '.'; + if(viewport.getGapCharacter()=='-') { - thisChar = "."; - nextChar = "-"; + thisChar = '.'; + nextChar = '-'; } setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\""); viewport.setGapCharacter(thisChar); + alignPanel.RefreshPanels(); + } + + public void findMenuItem_actionPerformed(ActionEvent e) + { + JOptionPane op = new JOptionPane(); + JInternalFrame frame = op.createInternalFrame(this, "Find"); + Finder finder = new Finder(viewport, alignPanel, frame); + frame.setContentPane(finder); + frame.setSize(300,110); + frame.setVisible(true); } + public void fontNameMenuItem_actionPerformed(ActionEvent e) { String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames(); - String selection = JOptionPane.showInputDialog(this, + String selection = JOptionPane.showInternalInputDialog(this, "Select font", "Font selection", JOptionPane.QUESTION_MESSAGE, @@ -364,7 +376,7 @@ public class AlignFrame extends GAlignFrame public void fontSizeMenuItem_actionPerformed(ActionEvent e) { - String selection = JOptionPane.showInputDialog(this, + String selection = JOptionPane.showInternalInputDialog(this, "Select font size", "Font size", JOptionPane.QUESTION_MESSAGE, @@ -379,7 +391,7 @@ public class AlignFrame extends GAlignFrame public void fontStyleMenuItem_actionPerformed(ActionEvent e) { - String selection = JOptionPane.showInputDialog(this, + String selection = JOptionPane.showInternalInputDialog(this, "Select font style", "Font style", JOptionPane.QUESTION_MESSAGE, @@ -395,8 +407,8 @@ public class AlignFrame extends GAlignFrame protected void colourTextMenuItem_actionPerformed(ActionEvent e) { - viewport.setColourText( colourTextMenuItem.isSelected() ); - alignPanel.RefreshPanels(); + viewport.setColourText( colourTextMenuItem.isSelected() ); + alignPanel.RefreshPanels(); } void SetFont() @@ -417,7 +429,7 @@ public class AlignFrame extends GAlignFrame protected void wrapMenuItem_actionPerformed(ActionEvent e) { viewport.setWrapAlignment( wrapMenuItem.isSelected() ); - alignPanel.setWrapAlignment( wrapMenuItem.isSelected() ); + alignPanel.RefreshPanels(); } @@ -434,6 +446,13 @@ public class AlignFrame extends GAlignFrame } + protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + { + viewport.setRenderGaps(renderGapsMenuItem.isSelected()); + alignPanel.RefreshPanels(); + } + + public void consensusGraphMenuItem_actionPerformed(ActionEvent e) { alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() ); @@ -460,7 +479,7 @@ public class AlignFrame extends GAlignFrame }catch(java.lang.OutOfMemoryError ex) { - JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!" + JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!" +"\nTry reducing the font size.", "Out of memory", JOptionPane.WARNING_MESSAGE); } @@ -470,7 +489,8 @@ public class AlignFrame extends GAlignFrame protected void noColourmenuItem_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme(null, false); + viewport.setGlobalColourScheme( null ); + alignPanel.setColourScheme(); } @@ -481,52 +501,58 @@ public class AlignFrame extends GAlignFrame public void zappoColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme(new ZappoColourScheme() ); + alignPanel.setColourScheme( ); } public void taylorColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme(new TaylorColourScheme() ); + alignPanel.setColourScheme( ); } public void hydrophobicityColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme( new HydrophobicColourScheme() ); + alignPanel.setColourScheme( ); } public void helixColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme( new HelixColourScheme() ); + alignPanel.setColourScheme(); } public void strandColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme(new StrandColourScheme() ); + alignPanel.setColourScheme( ); } public void turnColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme(new TurnColourScheme() ); + alignPanel.setColourScheme( ); } public void buriedColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme( new BuriedColourScheme() ); + alignPanel.setColourScheme( ); } protected void conservationMenuItem_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() ); + viewport.setConservationSelected(conservationMenuItem.isSelected()); conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() ); + alignPanel.setColourScheme(); } - - public void conservationColourIncMenuItem_actionPerformed(ActionEvent e) { ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel); @@ -539,14 +565,15 @@ public class AlignFrame extends GAlignFrame public void abovePIDColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme(new PIDColourScheme()); + alignPanel.setColourScheme( ); } public void userDefinedColour_actionPerformed(ActionEvent e) { JInternalFrame frame = new JInternalFrame(); - UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel ); + UserDefinedColours chooser = new UserDefinedColours( frame, viewport ); frame.setContentPane(chooser); Desktop.addInternalFrame(frame,"User defined colours", 450,540 ); frame.setResizable(false); @@ -556,20 +583,22 @@ public class AlignFrame extends GAlignFrame public void PIDColour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme(new PIDColourScheme() ); + alignPanel.setColourScheme( ); } public void BLOSUM62Colour_actionPerformed(ActionEvent e) { - alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() ); + viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) ); + alignPanel.setColourScheme(); } protected void schemeKeyMenuItem_actionPerformed(ActionEvent e) { - ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() ); + ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() ); Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320); } @@ -591,7 +620,7 @@ public class AlignFrame extends GAlignFrame public void sortGroupMenuItem_actionPerformed(ActionEvent e) { addHistoryItem("sort"); - AlignmentSorter.sortGroups(viewport.getAlignment()); + AlignmentSorter.sortByGroup(viewport.getAlignment()); AlignmentSorter.sortGroups(viewport.getAlignment()); alignPanel.RefreshPanels(); } @@ -614,7 +643,7 @@ public class AlignFrame extends GAlignFrame public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { if(viewport.getSelection().size()<2) - JOptionPane.showMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE); else { JInternalFrame frame = new JInternalFrame(); @@ -628,7 +657,7 @@ public class AlignFrame extends GAlignFrame if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0) || viewport.getAlignment().getHeight()<4) { - JOptionPane.showMessageDialog(this, "Principal component analysis must take\n" + JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n" +"at least 4 input sequences.", "Sequence selection insufficient", JOptionPane.WARNING_MESSAGE); @@ -642,7 +671,7 @@ public class AlignFrame extends GAlignFrame Desktop.addInternalFrame(frame, "Principal component analysis", 400, 400); }catch(java.lang.OutOfMemoryError ex) { - JOptionPane.showMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!", + JOptionPane.showInternalMessageDialog(this, "Too many sequences selected\nfor Principal Component Analysis!!", "Out of memory", JOptionPane.WARNING_MESSAGE); } @@ -694,7 +723,7 @@ public class AlignFrame extends GAlignFrame public void clustalAlignMenuItem_actionPerformed(ActionEvent e) { - JOptionPane.showMessageDialog(this, "Jalview is currently being reengineered" + JOptionPane.showInternalMessageDialog(this, "Jalview is currently being reengineered" +"\nwithin the Barton Group, Dundee University." +"\nThis will be available as a web service 2005", "Web service", JOptionPane.INFORMATION_MESSAGE); @@ -702,7 +731,7 @@ public class AlignFrame extends GAlignFrame public void pdbTest_actionPerformed(ActionEvent e) { - String reply = JOptionPane.showInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE); + String reply = JOptionPane.showInternalInputDialog(this, "Enter pdb code", "PDB test viewer", JOptionPane.QUESTION_MESSAGE); String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u"; if (reply.length()>1) @@ -730,4 +759,15 @@ public class AlignFrame extends GAlignFrame } + + public void doKeyPressed(KeyEvent evt) + { + + System.out.println(evt.getKeyChar()); + if(evt.isControlDown() && evt.getKeyChar()=='f') + findMenuItem_actionPerformed(null); + + } + + }