X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=66b29a0d3de78a9d120fd8878994f9f8de9c6c37;hb=0306c5b7a2aa4cc232ad0590a8ef285022eabd51;hp=398294b7cd9874d59c3d78a31c2adb7de99d81ca;hpb=116786d279dcb83f05afd625ad6e39627a37e1e8;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 398294b..66b29a0 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -12,10 +12,7 @@ import MCview.*; public class PopupMenu extends JPopupMenu { JMenu groupMenu = new JMenu(); - JMenuItem analyze = new JMenuItem(); - JMenu defineMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); - JMenuItem groupAnnotation = new JMenuItem(); protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); @@ -35,13 +32,11 @@ public class PopupMenu extends JPopupMenu AlignmentPanel ap; JMenu sequenceMenu = new JMenu(); JMenuItem sequenceName = new JMenuItem(); - JMenu residueMenu = new JMenu(); - JMenuItem annotateResidue = new JMenuItem(); - Sequence sequence; JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem pdbMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); + JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); public PopupMenu(AlignmentPanel ap, Sequence seq) { @@ -108,25 +103,17 @@ public class PopupMenu extends JPopupMenu conservationMenuItem.setSelected(true); } + if( !ap.av.alignment.getGroups().contains(sg)) + unGroupMenuItem.setVisible(false); - if(seq!=null) - residueMenu.setVisible(false); - else - sequenceMenu.setVisible(false); + if(seq==null) + sequenceMenu.setVisible(false); } private void jbInit() throws Exception { groupMenu.setText("Group"); - analyze.setText("Analyze"); - analyze.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - analyze_actionPerformed(e); - } - }); - defineMenu.setText("Define"); + groupMenu.setText("Define"); groupName.setText("Name"); groupName.addActionListener(new java.awt.event.ActionListener() { @@ -135,15 +122,6 @@ public class PopupMenu extends JPopupMenu groupName_actionPerformed(e); } }); - groupAnnotation.setEnabled(false); - groupAnnotation.setText("Annotation"); - groupAnnotation.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupAnnotation_actionPerformed(e); - } - }); sequenceMenu.setText("Sequence"); sequenceName.setText("Edit name"); sequenceName.addActionListener(new java.awt.event.ActionListener() @@ -153,10 +131,6 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(e); } }); - 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() @@ -182,38 +156,44 @@ public class PopupMenu extends JPopupMenu 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); + add(sequenceMenu); + groupMenu.add(groupName); + groupMenu.addSeparator(); 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(zappoColour); - defineMenu.add(taylorColour); - defineMenu.add(hydrophobicityColour); - defineMenu.add(helixColour); - defineMenu.add(strandColour); - defineMenu.add(turnColour); - defineMenu.add(buriedColour); - defineMenu.add(userDefinedColour); - defineMenu.add(PIDColour); - defineMenu.add(BLOSUM62Colour); - defineMenu.addSeparator(); - defineMenu.add(abovePIDColour); - defineMenu.add(conservationMenuItem); + groupMenu.add(outline); + groupMenu.addSeparator(); + groupMenu.add(noColourmenuItem); + groupMenu.add(clustalColour); + groupMenu.add(BLOSUM62Colour); + groupMenu.add(PIDColour); + + groupMenu.add(zappoColour); + groupMenu.add(taylorColour); + groupMenu.add(hydrophobicityColour); + groupMenu.add(helixColour); + groupMenu.add(strandColour); + groupMenu.add(turnColour); + groupMenu.add(buriedColour); + groupMenu.add(nucleotideMenuItem); + + groupMenu.add(userDefinedColour); + + groupMenu.addSeparator(); + groupMenu.add(abovePIDColour); + groupMenu.add(conservationMenuItem); sequenceMenu.add(sequenceName); sequenceMenu.add(pdbMenuItem); - residueMenu.add(annotateResidue); - noColourmenuItem.setText("None"); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -231,7 +211,7 @@ 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) @@ -239,7 +219,7 @@ 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) @@ -247,7 +227,7 @@ 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) @@ -279,7 +259,7 @@ 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) @@ -287,7 +267,7 @@ 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) @@ -295,7 +275,7 @@ 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) @@ -311,7 +291,7 @@ 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) @@ -319,7 +299,7 @@ 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) @@ -392,6 +372,13 @@ public class PopupMenu extends JPopupMenu refresh(); } + public void nucleotideMenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } + + protected void abovePIDColour_actionPerformed(ActionEvent e) { @@ -424,14 +411,7 @@ public class PopupMenu extends JPopupMenu 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 ("+getGroup().getName()+")", 450,540 ); - frame.setResizable(false); - frame.setIconifiable(false); - frame.setMaximizable(false); - + UserDefinedColours chooser = new UserDefinedColours( ap, getGroup()); } protected void PIDColour_actionPerformed(ActionEvent e) @@ -576,14 +556,10 @@ public class PopupMenu extends JPopupMenu EBIFetchClient ebi = new EBIFetchClient(); String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null); + System.out.println("Got "+ sequence.getPDBId() ); 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); + rotCanvas rc = new rotCanvas(pdb, sequence, ap.av); JInternalFrame frame = new JInternalFrame(); frame.setContentPane(rc); Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400); @@ -600,6 +576,7 @@ public class PopupMenu extends JPopupMenu Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE); if(col!=null) sg.setOutlineColour(col); + ap.repaint(); } }