X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=14363e187f0c55eca1a5535e6ce0ba8d0245e1e1;hb=c77ccc33971183dba9cb66b40886a6b61fe8eaa0;hp=26fc93c4a22b1fc8a1daa7d445e84807d12ecf91;hpb=9fff97021c2c637e426f6971d54dcf3fd4191985;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 26fc93c..14363e1 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -24,7 +24,6 @@ import jalview.analysis.*; import jalview.datamodel.*; -import jalview.io.*; import jalview.schemes.*; @@ -63,7 +62,6 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceName = new JMenuItem(); Sequence sequence; JMenuItem unGroupMenuItem = new JMenuItem(); - JMenuItem pdbMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); JMenu colourMenu = new JMenu(); @@ -77,7 +75,7 @@ public class PopupMenu extends JPopupMenu * @param ap DOCUMENT ME! * @param seq DOCUMENT ME! */ - public PopupMenu(AlignmentPanel ap, Sequence seq) + public PopupMenu(final AlignmentPanel ap, Sequence seq) { /////////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -112,11 +110,59 @@ public class PopupMenu extends JPopupMenu e.printStackTrace(); } - if ((seq == null) || (seq.getPDBId() == null)) + + if (seq != null) { - pdbMenuItem.setVisible(false); + JMenuItem menuItem; + if( seq.getDatasetSequence().getPDBId() != null) + { + java.util.Enumeration e = seq.getDatasetSequence().getPDBId(). + elements(); + while (e.hasMoreElements()) + { + final PDBEntry pdb = (PDBEntry) e.nextElement(); + + menuItem = new JMenuItem(); + menuItem.setText("View PDB entry: " + pdb.getId()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas); + } + }); + sequenceMenu.add(menuItem); + } + } + + menuItem = new JMenuItem("Hide Sequences"); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSequences(false); + } + }); + sequenceMenu.add(menuItem); + + if(ap.av.getSelectionGroup() !=null && ap.av.getSelectionGroup().getSize()>1) + { + menuItem = new JMenuItem("Represent Group with " + seq.getName()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSequences(true); + } + }); + sequenceMenu.add(menuItem); + } + + } + + SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null) @@ -172,7 +218,7 @@ public class PopupMenu extends JPopupMenu noColourmenuItem.setSelected(true); } - if (sg.cs instanceof ConservationColourScheme) + if (sg.cs!=null && sg.cs.conservationApplied()) { conservationMenuItem.setSelected(true); } @@ -206,9 +252,12 @@ public class PopupMenu extends JPopupMenu String link = links.elementAt(i).toString(); item = new JMenuItem(link.substring(0, link.indexOf("|"))); + String id = sequence.getName(); + if(id.indexOf("|")>-1) + id = id.substring(id.lastIndexOf("|")+1); final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$")) - + sequence.getName() + + + id + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); @@ -226,6 +275,7 @@ public class PopupMenu extends JPopupMenu } } + /** * DOCUMENT ME! * @@ -244,7 +294,7 @@ public class PopupMenu extends JPopupMenu } }); sequenceMenu.setText("Sequence"); - sequenceName.setText("Edit name"); + sequenceName.setText("Edit Name/Description"); sequenceName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -261,14 +311,7 @@ public class PopupMenu extends JPopupMenu 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() { @@ -325,7 +368,6 @@ public class PopupMenu extends JPopupMenu groupMenu.addSeparator(); groupMenu.add(outline); sequenceMenu.add(sequenceName); - sequenceMenu.add(pdbMenuItem); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); @@ -339,6 +381,28 @@ public class PopupMenu extends JPopupMenu colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); colourMenu.add(userDefinedColour); + + if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours. + getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + JMenuItem item = new JMenuItem(userColours. + nextElement().toString()); + item.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + } + } + + colourMenu.addSeparator(); colourMenu.add(abovePIDColour); colourMenu.add(conservationMenuItem); @@ -423,7 +487,7 @@ public class PopupMenu extends JPopupMenu abovePIDColour_actionPerformed(e); } }); - userDefinedColour.setText("User Defined"); + userDefinedColour.setText("User Defined..."); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -462,16 +526,9 @@ public class PopupMenu extends JPopupMenu */ void refresh() { - SequenceGroup sg = getGroup(); - if(sg!=null) - { - SuperGroup superG = ap.av.alignment.getSuperGroup(sg); + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); - if (superG != null) - { - superG.setSuperGroupProperties(sg); - } - } ap.seqPanel.repaint(); } @@ -584,6 +641,8 @@ public class PopupMenu extends JPopupMenu protected void abovePIDColour_actionPerformed(ActionEvent e) { SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; if (abovePIDColour.isSelected()) { @@ -593,22 +652,13 @@ public class PopupMenu extends JPopupMenu int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); - if (sg.cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); - } - else if (sg.cs instanceof ScoreColourScheme) - { - ((ScoreColourScheme) sg.cs).setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); - } + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); } else // remove PIDColouring { - ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; - rcs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); - sg.cs = rcs; + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); } refresh(); @@ -621,9 +671,18 @@ public class PopupMenu extends JPopupMenu */ protected void userDefinedColour_actionPerformed(ActionEvent e) { - new UserDefinedColours(ap, getGroup()); - } - + SequenceGroup sg = getGroup(); + + if (e.getActionCommand().equals("User Defined...")) + new UserDefinedColours(ap, sg); + else + { + UserColourScheme udc = (UserColourScheme) UserDefinedColours. + getUserColourSchemes().get(e.getActionCommand()); + + sg.cs = udc; + } + } /** * DOCUMENT ME! * @@ -674,6 +733,8 @@ public class PopupMenu extends JPopupMenu protected void conservationMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; if (conservationMenuItem.isSelected()) { @@ -684,17 +745,14 @@ public class PopupMenu extends JPopupMenu c.calculate(); c.verdict(false, ap.av.ConsPercGaps); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - - sg.cs = ccs; + sg.cs.setConservation(c); - SliderPanel.setConservationSlider(ap, ccs, sg.getName()); + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } else // remove ConservationColouring { - ConservationColourScheme ccs = (ConservationColourScheme) sg.cs; - sg.cs = ccs.cs; + sg.cs.setConservation(null); } refresh(); @@ -769,11 +827,34 @@ public class PopupMenu extends JPopupMenu */ void sequenceName_actionPerformed(ActionEvent e) { - String id = sequence.getName(); - String s = (String) JOptionPane.showInternalInputDialog(ap, - "Edit sequence name", - "Edit sequence name (" + sequence.getName() + ")", - JOptionPane.PLAIN_MESSAGE, null, null, id); + JLabel idlabel = new JLabel( " Sequence Name "); + JLabel desclabel = new JLabel("Sequence Description "); + idlabel.setFont(new Font("Courier", Font.PLAIN, 12)); + desclabel.setFont(new Font("Courier", Font.PLAIN, 12)); + JTextField id = new JTextField(sequence.getName(), 40); + JTextField description = new JTextField(sequence.getDescription(), 40); + JPanel panel = new JPanel(new BorderLayout()); + JPanel panel2 = new JPanel(new BorderLayout()); + panel2.add(idlabel, BorderLayout.WEST); + panel2.add(id, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.NORTH); + panel2 = new JPanel(new BorderLayout()); + panel2.add(desclabel, BorderLayout.WEST); + panel2.add(description, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.SOUTH); + + + int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + panel, "Edit Sequence Name/Description", + JOptionPane.OK_CANCEL_OPTION ); + + + if (reply != JOptionPane.OK_OPTION ) + { + return; + } + + String s = id.getText(); if (s != null) { @@ -786,9 +867,13 @@ public class PopupMenu extends JPopupMenu } s = s.replace(' ', '_'); + sequence.getDatasetSequence().setName(s); sequence.setName(s); ap.repaint(); } + + sequence.getDatasetSequence().setDescription(description.getText()); + sequence.setDescription(description.getText()); } /** @@ -804,37 +889,6 @@ public class PopupMenu extends JPopupMenu refresh(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - 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); - - rotCanvas rc = new rotCanvas(pdb, sequence, ap.av); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(rc); - Desktop.addInternalFrame(frame, - sequence.getName() + " " + sequence.getPDBId(), 400, 400); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } /** * DOCUMENT ME! @@ -905,4 +959,33 @@ public class PopupMenu extends JPopupMenu ex.printStackTrace(); } } + + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if(sg==null || sg.getSize()<1) + { + ap.av.hideSequence(sequence); + return; + } + + int index = 0; + while(index < sg.sequences.size()) + { + if(representGroup && sg.getSequenceAt(index)!=sequence) + { + sequence.addHiddenSequence(sg.getSequenceAt(index)); + ap.av.hideSequence(sg.getSequenceAt(index)); + } + else if(!representGroup) + { + ap.av.hideSequence(sg.getSequenceAt(index)); + } + index ++; + } + + ap.av.setSelectionGroup(null); + refresh(); + } + }