X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=3177bfcb3dc8292e83ffa5da8efd9ae30ab1607c;hb=1d123ffc99d3e9fb14dd1440adcd8d60a938722f;hp=62d69d00aa38ecb2e5ec035bb4741478894afd08;hpb=714aae012ecf6cb27e602eaafdb6458b885dc80c;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 62d69d0..3177bfc 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -3,16 +3,15 @@ package jalview.gui; import jalview.datamodel.*; import jalview.analysis.*; import jalview.schemes.*; +import java.awt.*; import javax.swing.*; import java.awt.event.*; - +import jalview.io.*; +import MCview.*; public class PopupMenu extends JPopupMenu { JMenu groupMenu = new JMenu(); - JMenuItem copyGroup = new JMenuItem(); - JMenuItem moveGroup = new JMenuItem(); - JMenuItem deleteSequences = new JMenuItem(); JMenuItem analyze = new JMenuItem(); JMenu defineMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); @@ -25,7 +24,7 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem(); + protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); @@ -39,9 +38,13 @@ public class PopupMenu extends JPopupMenu JMenu residueMenu = new JMenu(); JMenuItem annotateResidue = new JMenuItem(); - SequenceI sequence; + Sequence sequence; + JMenuItem unGroupMenuItem = new JMenuItem(); + JMenuItem pdbMenuItem = new JMenuItem(); + JMenuItem outline = new JMenuItem(); + JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - public PopupMenu(AlignmentPanel ap, SequenceI seq) + public PopupMenu(AlignmentPanel ap, Sequence seq) { /////////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -73,15 +76,42 @@ public class PopupMenu extends JPopupMenu catch(Exception e) { e.printStackTrace(); } - SequenceGroup sg = ap.av.getRubberbandGroup(); + SequenceGroup sg = ap.av.getSelectionGroup(); if(sg!=null) - groupName.setText( sg.getName() ); + { + groupName.setText(sg.getName()); + if(sg.cs instanceof ZappoColourScheme) + zappoColour.setSelected(true); + else if(sg.cs instanceof TaylorColourScheme) + taylorColour.setSelected(true); + else if (sg.cs instanceof PIDColourScheme) + PIDColour.setSelected(true); + else if (sg.cs instanceof Blosum62ColourScheme) + BLOSUM62Colour.setSelected(true); + else if (sg.cs instanceof UserColourScheme) + userDefinedColour.setSelected(true); + else if (sg.cs instanceof HydrophobicColourScheme) + hydrophobicityColour.setSelected(true); + else if (sg.cs instanceof HelixColourScheme) + helixColour.setSelected(true); + else if (sg.cs instanceof StrandColourScheme) + strandColour.setSelected(true); + else if (sg.cs instanceof TurnColourScheme) + turnColour.setSelected(true); + else if (sg.cs instanceof BuriedColourScheme) + buriedColour.setSelected(true); + else if (sg.cs instanceof ClustalxColourScheme) + clustalColour.setSelected(true); + else + noColourmenuItem.setSelected(true); + + if (sg.cs instanceof ConservationColourScheme) + conservationMenuItem.setSelected(true); + } + if(seq!=null) - { residueMenu.setVisible(false); - sequenceName.setText( sequence.getName() ); - } else sequenceMenu.setVisible(false); @@ -89,30 +119,6 @@ public class PopupMenu extends JPopupMenu private void jbInit() throws Exception { groupMenu.setText("Group"); - copyGroup.setText("Copy region to new Alignment"); - copyGroup.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copyGroup_actionPerformed(e); - } - }); - moveGroup.setText("Move sequences to new Alignment"); - moveGroup.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - moveGroup_actionPerformed(e); - } - }); - deleteSequences.setText("Delete sequences"); - deleteSequences.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deleteSequences_actionPerformed(e); - } - }); analyze.setText("Analyze"); analyze.addActionListener(new java.awt.event.ActionListener() { @@ -130,6 +136,7 @@ public class PopupMenu extends JPopupMenu groupName_actionPerformed(e); } }); + groupAnnotation.setEnabled(false); groupAnnotation.setText("Annotation"); groupAnnotation.addActionListener(new java.awt.event.ActionListener() { @@ -139,7 +146,7 @@ public class PopupMenu extends JPopupMenu } }); sequenceMenu.setText("Sequence"); - sequenceName.setText("sequenceName"); + sequenceName.setText("Edit name"); sequenceName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -148,23 +155,59 @@ public class PopupMenu extends JPopupMenu } }); residueMenu.setText("Residue"); + annotateResidue.setEnabled(false); + annotateResidue.setActionCommand("annotate residue"); annotateResidue.setText("annotate residue???"); PIDColour.setFocusPainted(false); + unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + unGroupMenuItem_actionPerformed(e); + } + }); + pdbMenuItem.setText("View PDB structure"); + pdbMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pdbMenuItem_actionPerformed(e); + } + }); + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outline_actionPerformed(e); + } + }); + nucleotideMenuItem.setText("Nucleotide"); + nucleotideMenuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + nucleotideMenuItem_actionPerformed(e); + } + }); add(groupMenu); this.add(sequenceMenu); this.add(residueMenu); groupMenu.add(defineMenu); - groupMenu.addSeparator(); - groupMenu.add(copyGroup); - groupMenu.add(moveGroup); - groupMenu.add(deleteSequences); + groupMenu.add(unGroupMenuItem); groupMenu.addSeparator(); groupMenu.add(analyze); defineMenu.add(groupName); defineMenu.add(groupAnnotation); defineMenu.addSeparator(); + defineMenu.add(outline); + defineMenu.addSeparator(); defineMenu.add(noColourmenuItem); defineMenu.add(clustalColour); + defineMenu.add(BLOSUM62Colour); + defineMenu.add(PIDColour); + defineMenu.add(zappoColour); defineMenu.add(taylorColour); defineMenu.add(hydrophobicityColour); @@ -172,18 +215,19 @@ public class PopupMenu extends JPopupMenu defineMenu.add(strandColour); defineMenu.add(turnColour); defineMenu.add(buriedColour); + defineMenu.add(nucleotideMenuItem); + defineMenu.add(userDefinedColour); - defineMenu.add(PIDColour); - defineMenu.add(BLOSUM62Colour); + defineMenu.addSeparator(); defineMenu.add(abovePIDColour); defineMenu.add(conservationMenuItem); sequenceMenu.add(sequenceName); + sequenceMenu.add(pdbMenuItem); residueMenu.add(annotateResidue); noColourmenuItem.setText("None"); - noColourmenuItem.setSelected(true); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -192,7 +236,6 @@ public class PopupMenu extends JPopupMenu } }); - clustalColour.setSelected(false); clustalColour.setText("Clustalx colours"); clustalColour.addActionListener(new java.awt.event.ActionListener() { @@ -201,7 +244,7 @@ public class PopupMenu extends JPopupMenu clustalColour_actionPerformed(e); } }); - zappoColour.setText("Zappo colour scheme"); + zappoColour.setText("Zappo"); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -209,7 +252,7 @@ public class PopupMenu extends JPopupMenu zappoColour_actionPerformed(e); } }); - taylorColour.setText("Taylor colour scheme"); + taylorColour.setText("Taylor"); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -217,7 +260,7 @@ public class PopupMenu extends JPopupMenu taylorColour_actionPerformed(e); } }); - hydrophobicityColour.setText("By hydrophobicity"); + hydrophobicityColour.setText("Hydrophobicity"); hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -249,7 +292,7 @@ public class PopupMenu extends JPopupMenu turnColour_actionPerformed(e); } }); - buriedColour.setText("Buried index"); + buriedColour.setText("Buried Index"); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -257,7 +300,7 @@ public class PopupMenu extends JPopupMenu buriedColour_actionPerformed(e); } }); - abovePIDColour.setText("Above PID threshold only"); + abovePIDColour.setText("Above % Identity"); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -265,7 +308,7 @@ public class PopupMenu extends JPopupMenu abovePIDColour_actionPerformed(e); } }); - userDefinedColour.setText("User defined colours"); + userDefinedColour.setText("User Defined"); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -281,7 +324,7 @@ public class PopupMenu extends JPopupMenu PIDColour_actionPerformed(e); } }); - BLOSUM62Colour.setText("BLOSUM62 score"); + BLOSUM62Colour.setText("BLOSUM62"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -289,7 +332,7 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(e); } }); - conservationMenuItem.setText("By conservation"); + conservationMenuItem.setText("Conservation"); conservationMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -304,13 +347,18 @@ public class PopupMenu extends JPopupMenu void refresh() { - ap.seqPanel.seqCanvas.paintFlag=true; + SequenceGroup sg = getGroup(); + SuperGroup superG = ap.av.alignment.getSuperGroup( sg ); + if( superG !=null) + superG.setSuperGroupProperties( sg ); + ap.seqPanel.repaint(); } protected void clustalColour_actionPerformed(ActionEvent e) { - getGroup().cs = new ClustalxColourScheme(); + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth()); refresh(); } @@ -357,40 +405,46 @@ public class PopupMenu extends JPopupMenu refresh(); } + public void nucleotideMenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } -/* -public void conservationColourIncMenuItem_actionPerformed(ActionEvent e) -{ -ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel); -JInternalFrame frame = new JInternalFrame(); -frame.setContentPane(cip); -Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90); -frame.setMaximizable(false); - - }*/ protected void abovePIDColour_actionPerformed(ActionEvent e) { - SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs ); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(sp); - Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400,90); - frame.setMaximizable(false); + SequenceGroup sg = getGroup(); + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); + if (sg.cs instanceof ResidueColourScheme) + ( (ResidueColourScheme)sg. cs).setThreshold(threshold); + else if (sg.cs instanceof ScoreColourScheme) + ( (ScoreColourScheme) sg.cs).setThreshold(threshold); + + SliderPanel.showPIDSlider(); + + + } + else // remove PIDColouring + { + ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; + rcs.setThreshold(0); + sg.cs = rcs; + } + + refresh(); } protected void userDefinedColour_actionPerformed(ActionEvent e) { - JInternalFrame frame = new JInternalFrame(); - UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup()); - frame.setContentPane(chooser); - Desktop.addInternalFrame(frame,"User defined colours", 450,540 ); - frame.setResizable(false); - frame.setIconifiable(false); - frame.setMaximizable(false); - + UserDefinedColours chooser = new UserDefinedColours( ap, getGroup()); } protected void PIDColour_actionPerformed(ActionEvent e) @@ -400,7 +454,13 @@ frame.setMaximizable(false); protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { - getGroup().cs = new Blosum62ColourScheme(ap.av); + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); + refresh(); } @@ -415,15 +475,29 @@ frame.setMaximizable(false); { SequenceGroup sg = getGroup(); - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(), - sg.getEndRes() ); + if(conservationMenuItem.isSelected()) + { + + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.sequences, 0, + ap.av.alignment.getWidth()); + + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); + ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - c.calculate(); - c.verdict(false, 100); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - sg.cs = ccs; + sg.cs = ccs; + + SliderPanel.setConservationSlider(ap, ccs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else // remove ConservationColouring + { + ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; + sg.cs = ccs.cs; + } refresh(); } @@ -444,60 +518,6 @@ frame.setMaximizable(false); groupName.setText(reply); } - protected void copyGroup_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); - - SequenceI[] s = new Sequence[sg.sequences.size()]; - for (int i=0; i < sg.sequences.size(); i++) - { - s[i] = new Sequence( sg.getSequenceAt(i)); - s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) ); - } - AlignFrame af = new AlignFrame(new Alignment(s)); - int newHeight = s.length * af.viewport.getCharHeight() + 200; - if (newHeight > 500) - newHeight = 500; - Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight); - } - - protected void moveGroup_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); - - SequenceI[] s = new Sequence[sg.sequences.size()]; - - for (int i=0; i < sg.sequences.size(); i++) - s[i] = new Sequence( sg.getSequenceAt(i)); - - AlignFrame af = new AlignFrame(new Alignment(s)); - int newHeight = s.length * af.viewport.getCharHeight() + 200; - if(newHeight>500) - newHeight=500; - Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight); - - - for (int i=0; i < sg.sequences.size(); i++) - ap.av.alignment.deleteSequence(sg.getSequenceAt(i)); - - - ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); - ap.RefreshPanels(); - - - } - - protected void deleteSequences_actionPerformed(ActionEvent e) - { - SequenceGroup sg = ap.av.getRubberbandGroup(); - for (int i=0;i < sg.sequences.size(); i++) - ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i)); - - ap.av.alignment.deleteGroup(sg); - ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); - ap.seqPanel.parent.RefreshPanels(); - - } protected void analyze_actionPerformed(ActionEvent e) { @@ -523,10 +543,11 @@ frame.setMaximizable(false); SequenceGroup getGroup() { - SequenceGroup sg = ap.av.getRubberbandGroup(); + SequenceGroup sg = ap.av.getSelectionGroup(); // this method won't add a new group if it already exists ap.av.alignment.addGroup(sg); + return sg; } @@ -536,7 +557,7 @@ frame.setMaximizable(false); String s = (String)JOptionPane.showInternalInputDialog( ap, "Edit sequence name", - "Edit sequence name", + "Edit sequence name ("+sequence.getName()+")", JOptionPane.PLAIN_MESSAGE, null, null, @@ -545,8 +566,53 @@ frame.setMaximizable(false); if(s!=null) { sequence.setName(s); - ap.RefreshPanels(); + ap.repaint(); + } + + } + + void unGroupMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + ap.repaint(); + } + + void pdbMenuItem_actionPerformed(ActionEvent e) + { + if(sequence.getPDBId()==null) + return; + + try + { + EBIFetchClient ebi = new EBIFetchClient(); + String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null); + + PDBfile pdb = new PDBfile(result); + sequence.setPDBfile(pdb); + + ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true; + ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence; + // ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence(); + + rotCanvas rc = new rotCanvas(pdb); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(rc); + Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400); + } + catch (Exception ex) + { + ex.printStackTrace(); } + } + protected void outline_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE); + if(col!=null) + sg.setOutlineColour(col); } + }